Identifying subgroups in heart failure patients with multimorbidity by clustering and network analysis.

This study presents a workflow for identifying and characterizing patients with Heart Failure (HF) and multimorbidity utilizing data from Electronic Health Records. Multimorbidity, the co-occurrence of two or more chronic conditions, poses a significant challenge on healthcare systems. Nonetheless, understanding of patients with multimorbidity, including the most common disease interactions, risk factors, and treatment responses, remains limited, particularly for complex and heterogeneous conditions like HF. We conducted a clustering analysis of 3745 HF patients using demographics, comorbidities, laboratory values, and drug prescriptions. Our analysis revealed four distinct clusters with significant differences in multimorbidity profiles showing differential prognostic implications regarding unplanned hospital admissions. These findings underscore the considerable disease heterogeneity within HF patients and emphasize the potential for improved characterization of patient subgroups for clinical risk stratification through the use of EHR data.

Digital media and misinformation: An outlook on multidisciplinary strategies against manipulation.

This review discusses the dynamic mechanisms of misinformation creation and spreading used in social networks. It includes: (1) a conceptualization of misinformation and related terms, such as rumors and disinformation; (2) an analysis of the cognitive vulnerabilities that hinder the correction of the effects of an inaccurate narrative already assimilated; and (3) an interdisciplinary discussion on different strategies for coping with misinformation. The discussion encompasses journalistic, educational, governmental and computational viewpoints on the topic. The review also surveys how digital platforms handle misinformation and gives an outlook on opportunities to address it in light of the presented viewpoints.

Anorectal complications in patients with haematological malignancies.

BACKGROUND: Anorectal complications are common in patients with haematological malignancies. OBJECTIVES: The objectives are to characterize anorectal complications in these patients, identify risk factors and shed light on treatment, morbidity and mortality rates. PATIENTS AND METHODS: A retrospective, observational study that included 83 inpatients with haematological malignancies and proctological symptoms from January 2010 to September 2015 was conducted. Clinical outcomes were obtained through a detailed review of medical records. RESULTS: The median age was 56 years, and 52 (62.7%) patients were men. Fifty-six (67.5%) patients had nonseptic anorectal complications and 27 (32.5%) patients had septic anorectal complications. RISKS FACTORS: Patients with septic anorectal complications were more commonly male, older, and had lower absolute neutrophil counts, but the differences were not statistically significant (P=0.79, 0.67 and 0.89, respectively). In positive blood cultures [23/70 (32.9%)], Enterococcus faecium, Klebsiella pneumonia, and Escherichia coli were the most common isolated agents. TREATMENT: In nonseptic anorectal complications, conservative treatments/minor proctological procedures were adopted, and patients with septic anorectal complications were treated with antibiotics±major proctological procedures and/or surgical drainage/debridement. RESULTS OF TREATMENT: Forty-eight (85.7%) patients in the nonseptic complications group improved compared with 23 (85.2%) patients in the septic complications group. The overall mortality rate was 2.4% (n=2), with one (1.2%) death related to perianal sepsis. CONCLUSION: Enterococcus spp. were more commonly identified in this study and can be increasing in this specific population. In contrast to other reports, we did not identify an association between septic anorectal complications and possible risk factors such as male sex, younger age or a low absolute neutrophil count. Most patients had nonseptic anorectal complications. A major proctological procedure/surgical debridement should always be applied in septic complications, which have better prognoses now than in the past.

Deep neural models for ICD-10 coding of death certificates and autopsy reports in free-text.

We address the assignment of ICD-10 codes for causes of death by analyzing free-text descriptions in death certificates, together with the associated autopsy reports and clinical bulletins, from the Portuguese Ministry of Health. We leverage a deep neural network that combines word embeddings, recurrent units, and neural attention, for the generation of intermediate representations of the textual contents. The neural network also explores the hierarchical nature of the input data, by building representations from the sequences of words within individual fields, which are then combined according to the sequences of fields that compose the inputs. Moreover, we explore innovative mechanisms for initializing the weights of the final nodes of the network, leveraging co-occurrences between classes together with the hierarchical structure of ICD-10. Experimental results attest to the contribution of the different neural network components. Our best model achieves accuracy scores over 89%, 81%, and 76%, respectively for ICD-10 chapters, blocks, and full-codes. Through examples, we also show that our method can produce interpretable results, useful for public health surveillance.

Morphology of the Dentin-resin Interface yielded by Two-step Etch-and-rinse Adhesives with Different Solvents.

AIM: The study aimed to analyze the morphology of the dentin-resin interface yielded by two-step etch-and-rinse adhesive systems with different solvents and compositions. MATERIALS AND METHODS: A total of 32 dentine disks were prepared and randomly assigned to four groups of one-bottle etch-and-rinse adhesive systems containing different solvents: group I, Adper Scotchbond-IXT™ (ethanol/water); group II, XP-Bond™ (tertiary butanol); group III, Prime and Bond NT® (acetone); and group IV, One Coat bond® (5% water). Adhesive systems were applied onto dentin disks, which were then thermal cycled, divided into two hemi-disks (n = 16), and prepared for field-emission scanning electron microscopy to examine the dentin-resin interdiffusion zone. Microphotographs were scanned and data were processed. Data were compared with analysis of variance multivariant test after Kolmogorov-Smirnov and Shapiro-Wilk tests using Statistic Package for the Social Sciences. RESULTS: The adhesive layer thickness average found was group I: 45.9 ± 13.41 urn, group II: 20.6 ± 16.32 urn, group III: 17.7 ± 11.75 urn, and group IV: 50.7 ± 27.81 urn. Significant differences were found between groups I and IV and groups II and III (p < 0.000). Groups I (3.23 ± 0.53 µm) and II (3.13 ± 0.73 µm) yielded significantly thicker hybrid layers than groups III (2.53 ± 0.50 µm) and IV (1.84 ± 0.27 µm) (p < 0.003). Group III presented a less homogeneous hybrid layer, with some gaps. Tag length average was greater in groups II (111.0 ± 36.92 µm) and IV (128.9 ± 78.38 µm) than in groups I (61.5 ± 18.10 µm) and III (68.6 ± 15.84 µm) (p < 0.008). CONCLUSION: Adhesives systems with different solvents led to significant differences in the dentin-resin interface morphology. Solvents role in adhesives bond strength should be considered together with the other adhesive system components. CLINICAL SIGNIFICANCE: The adhesive containing tertiary butanol, in addition, seems to originate a good-quality hybrid layer and long, entangled tags and also appears to have greater ability to originate microtags, which may indicate higher bond strength.

Hepatitis C in a Mobile Low-Threshold Methadone Program.

INTRODUCTION: Data on the epidemiology of hepatitis C among individuals who use drugs in low-threshold settings are lacking, although crucial to assess the burden of disease and aid in the design of treatment strategies. OBJECTIVE: The aim of this study was to characterize the epidemiology and disease related to hepatitis C in a population attending a low-threshold methadone program. MATERIALS AND METHODS: A cross-sectional study in the population attending the Mobile Low-Threshold Methadone Program in Lisbon, Portugal, was carried out. The survey included assessment of risk factors for infection with hepatitis C virus (HCV) and liver disease, HCV serology and RNA detection, HCV genotyping, and liver disease staging. RESULTS: A total of 825 participants were enrolled, 81.3% men, mean age 44.5 years. Injecting drug use (IDU) was reported by 58.4% - among these, 28.2% were people who inject drugs. Excessive drinking and HIV coinfection were reported by 33.4 and 15.9%, respectively. Among participants with active infection, 16.9% were followed up in hospital consultation. The overall seroprevalence for HCV was 67.6% (94.2% in IDU, 30.0% in non-IDU, 97.1% in people who inject drugs, and 75.6% in excessive drinkers). Among seropositives for HCV, active infection was present in 68.4%. Among individuals with active infection, the most common genotypes were 1a (45.3%) and 3a (28.7%), whereas 30% had severe liver fibrosis or cirrhosis. Age 45 years or older, HCV genotype 3, and coinfection with HIV were significant predictors of cirrhosis. CONCLUSION: This population has a high burden of hepatitis C and several characteristics that favor dissemination of infection. Healthcare strategies are urgently needed to address hepatitis C in this setting.

Epidemiology of hepatitis B in Portugal.

The epidemiology of hepatitis B in Portugal is insufficiently characterized. We aimed to review the epidemiology of hepatitis B in Portugal since 1980. A literature review was performed in MEDLINE, Scielo, Web of Science, and the Portuguese Scientific Repository for studies containing 'Hepatitis B' and 'Portugal' published from 1980 to June 2016. The initial search was complemented by abstract books from national gastroenterology and hepatology meetings and reports from the Service for Intervention on Addictive Behaviours and Dependences, the Portuguese Blood Institute, and Directorate-General of Health. Further studies were identified in references of retrieved papers and https://www.google.pt. Ninety references were included. Hepatitis B surface antigen (HBsAg) prevalence was up to 2% in the general population and decreased in the last decades: 1.13-2.0% in studies carried out in 1980-1989 and 0.02-1.45% in studies carried out in 1990-2014. Among pregnant women, HBsAg prevalence was 1.35% in those on primary care, but 6.2% among risk parturients. Among drug abusers, HBsAg prevalence decreased from 10-19.6% in the decades of 1980-1990 to 4.8% in 2014. Higher HBsAg prevalence rates were observed among populations of African or Asian origin. Individuals with hepatitis B were mostly men, mean age 36.9-49 years. The most frequent viral genotype was D. Genotype E is more prevalent in patient cohorts from Central-Southern Portugal (10-62%) than those from Northern Portugal (1-4.1%). The proportion of inactive carriers varied from 24.2 to 73%. The prevalence of cirrhosis varied from 5.8 to 23.7%. Portugal is a low-endemicity country for hepatitis B. Nevertheless, prevalence is high among specific subgroups that may benefit from specifically designed healthcare programs.

Ten years of hospital admissions for liver cirrhosis in Portugal.

BACKGROUND AND AIMS: More data on epidemiology of liver diseases in Europe are needed. We aimed to characterize hospital admissions for liver cirrhosis in Portugal during the past decade. PATIENTS AND METHODS: We analyzed all hospital admissions for cirrhosis in Portugal Mainland between 2003 and 2012 registered in the national Diagnosis-Related Group database. Cirrhosis was classified according to etiology considering alcohol, hepatitis B, and hepatitis C. RESULTS: Between 2003 and 2012, there were 63,910 admissions for cirrhosis in Portugal Mainland; 74.4% involved male patients. Etiologies of admitted cirrhosis were as follows: 76.0% alcoholic, 1.1% hepatitis B, 1.4% hepatitis B plus alcohol, 3.6% hepatitis C, and 4.0% hepatitis C plus alcohol. There was a significant decline (P<0.001) in admissions for alcoholic cirrhosis, whereas hospitalizations for cirrhosis caused by hepatitis C or hepatitis C plus alcohol increased by almost 50% (P<0.001). Patients admitted with alcoholic plus hepatitis B or C cirrhosis were significantly younger than those with either alcoholic or viral cirrhosis (53.1 vs. 59.4 years, respectively, P<0.001). Hospitalization rates for cirrhosis were 124.4/100,000 in men and 32.6/100,000 in women. Hepatocellular carcinoma and fluid retention were more common in viral cirrhosis, whereas encephalopathy and variceal bleeding were more frequent in alcoholic cirrhosis. Hepatorenal syndrome was the strongest predictor of mortality among cirrhosis complications (odds ratio 12.97; 95% confidence interval 11.95-14.09). In-hospital mortality was 15.2%. CONCLUSION: Despite the decline in admissions for alcoholic cirrhosis and the increase in those related to hepatitis C, the observed burden of hospitalized liver cirrhosis in Portugal was essentially attributable to alcoholic liver disease.

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources.

BACKGROUND: Epidemiology is a data-intensive and multi-disciplinary subject, where data integration, curation and sharing are becoming increasingly relevant, given its global context and time constraints. The semantic annotation of epidemiology resources is a cornerstone to effectively support such activities. Although several ontologies cover some of the subdomains of epidemiology, we identified a lack of semantic resources for epidemiology-specific terms. This paper addresses this need by proposing the Epidemiology Ontology (EPO) and by describing its integration with other related ontologies into a semantic enabled platform for sharing epidemiology resources. RESULTS: The EPO follows the OBO Foundry guidelines and uses the Basic Formal Ontology (BFO) as an upper ontology. The first version of EPO models several epidemiology and demography parameters as well as transmission of infection processes, participants and related procedures. It currently has nearly 200 classes and is designed to support the semantic annotation of epidemiology resources and data integration, as well as information retrieval and knowledge discovery activities. CONCLUSIONS: EPO is under active development and is freely available at https://code.google.com/p/epidemiology-ontology/. We believe that the annotation of epidemiology resources with EPO will help researchers to gain a better understanding of global epidemiological events by enhancing data integration and sharing.

Disjunctive shared information between ontology concepts: application to Gene Ontology.

BACKGROUND: The large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities described therein. A common approach, known as semantic similarity, compares ontology concepts through the information content they share in the ontology. However, different disjunctive ancestors in the ontology are frequently neglected, or not properly explored, by semantic similarity measures. RESULTS: This paper proposes a novel method, dubbed DiShIn, that effectively exploits the multiple inheritance relationships present in many biomedical ontologies. DiShIn calculates the shared information content of two ontology concepts, based on the information content of the disjunctive common ancestors of the concepts being compared. DiShIn identifies these disjunctive ancestors through the number of distinct paths from the concepts to their common ancestors. CONCLUSIONS: DiShIn was applied to Gene Ontology and its performance was evaluated against state-of-the-art measures using CESSM, a publicly available evaluation platform of protein similarity measures. By modifying the way traditional semantic similarity measures calculate the shared information content, DiShIn was able to obtain a statistically significant higher correlation between semantic and sequence similarity. Moreover, the incorporation of DiShIn in existing applications that exploit multiple inheritance would reduce their execution time.

An unusual Xanthophyllomyces strain from leaves of Eucalyptus globulus in Chile.

Xanthophyllomyces sp. was isolated as an epiphytic red yeast from leaves of Eucalyptus glo-bulus in Concepción, Chile. Sexual reproduction was by basidiospores produced from one or rarely two metabasidia arising from a yeast cell without preceding paedogamy. The main carotenoid pigment was astaxanthin. This isolate did not cluster with the X. dendrorhous complex (including Phaffia rhodozyma) in ITS and 26S rDNA-based phylogenetic analyses. The phylloplane may be a further habitat for Xanthophyllomyces, in addition to the well-known spring sap-flows of deciduous trees and the recently-characterised ascostromata of Cyttaria hariotii.

GOAnnotator: linking protein GO annotations to evidence text.

BACKGROUND: Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators. RESULTS: In this paper we describe an approach that links uncurated annotations to text extracted from literature. The selection of the text is based on the similarity of the text to the term from the uncurated annotation. Besides substantiating the uncurated annotations, the extracted texts also lead to novel annotations. In addition, the approach uses the GO hierarchy to achieve high precision. Our approach is integrated into GOAnnotator, a tool that assists the curation process for GO annotation of UniProt proteins. CONCLUSION: The GO curators assessed GOAnnotator with a set of 66 distinct UniProt/SwissProt proteins with uncurated annotations. GOAnnotator provided correct evidence text at 93% precision. This high precision results from using the GO hierarchy to only select GO terms similar to GO terms from uncurated annotations in GOA. Our approach is the first one to achieve high precision, which is crucial for the efficient support of GO curators. GOAnnotator was implemented as a web tool that is freely available at http://xldb.di.fc.ul.pt/rebil/tools/goa/.

Finding genomic ontology terms in text using evidence content.

BACKGROUND: The development of text mining systems that annotate biological entities with their properties using scientific literature is an important recent research topic. These systems need first to recognize the biological entities and properties in the text, and then decide which pairs represent valid annotations. METHODS: This document introduces a novel unsupervised method for recognizing biological properties in unstructured text, involving the evidence content of their names. RESULTS: This document shows the results obtained by the application of our method to BioCreative tasks 2.1 and 2.2, where it identified Gene Ontology annotations and their evidence in a set of articles. CONCLUSION: From the performance obtained in BioCreative, we concluded that an automatic annotation system can effectively use our method to identify biological properties in unstructured text.