Dependency parsing is often used as a component in many text analysis pipelines. However, performance, especially in specialized domains, suffers from the presence of complex terminology. Our hypothesis is that including named entity annotations can improve the speed and quality of dependency parses. As part of BLAH5, we built a web service delivering improved dependency parses by taking into account named entity annotations obtained by third party services. Our evaluation shows improved results and better speed.
Natural Language Processing

Purpose: In the present study, meningococcal serogroup B outer membrane vesicles (OMVs) were associated with bilayer fragments of a cationic lipid, dioctadecyldimethylammonium (DDA-BF), used as adjuvant, in an antigenic preparation tested in adult female outbred mice. This adjuvant was compared to the traditional adjuvant aluminum hydroxide. Materials and Methods: The potential in generating humoral response was evaluated by enzyme-linked immunosorbent assay (ELISA). Individual serum was collected and immunoglobulin G (IgG), IgG1, IgG2a, and IgG2b were quantified. Analyses were carried out 15 and 60 days after immunization. Antibodies avidity index were also analyzed by ELISA. Immunoblot and dot-ELISA were carried out to evaluate specific reaction for homologous strains and cross-reactive antigens present in other meningococcal strains isolated in 2011–2012 year, in Brazil. Delayed type hypersensitivity was used as indicative of cellular immunity and compared between two experimental groups, 24 hours after homologous strain challenge. Results: The OMVs of Neisseria meningitidis, and N. lactamica (related species) were characterized by electrophoretic separation of proteins in 13% polyacrylamide gel. The strains presented antigens in the range of 8 to 130 kDa, showing a heterogeneous protein migration pattern. In the group immunized with OMVs/DDA-BF, we found no significant production of total IgG 15 days after the first immunization. On the other hand, 60 days after first immunization both adjuvants act benefiting total IgG production similarly. The antibodies of the IgG isotype produced by animals immunized after one or two doses after first immunization, showed intermediate and high avidity, independent on the adjuvant used. In both experimental groups the swelling of the footpads was significantly higher than those of the controls, suggesting that only one dose was enough to stimulate the generation of cellular immunity. Conclusion The use of this cationic adjuvant for N. meningitidis OMVs preparation revealed good potential for future new antigen preparation for N. meningitidis vaccine.

Automatic document classification for highly interrelated classes is a demanding task that becomes more challenging when there is little labeled data for training. Such is the case of the coronavirus disease 2019 (COVID-19) Clinical repository—a repository of classified and translated academic articles related to COVID-19 and relevant to the clinical practice—where a 3-way classification scheme is being applied to COVID-19 literature. During the 7th Biomedical Linked Annotation Hackathon (BLAH7) hackathon, we performed experiments to explore the use of named-entity-recognition (NER) to improve the classification. We processed the literature with OntoGene’s Biomedical Entity Recogniser (OGER) and used the resulting identified Named Entities (NE) and their links to major biological databases as extra input features for the classifier. We compared the results with a baseline model without the OGER extracted features. In these proof-of-concept experiments, we observed a clear gain on COVID-19 literature classification. In particular, NE’s origin was useful to classify document types and NE’s type for clinical specialties. Due to the limitations of the small dataset, we can only conclude that our results suggests that NER would benefit this classification task. In order to accurately estimate this benefit, further experiments with a larger dataset would be needed.

No abstract available.
Data Mining

Managing liver cirrhosis in clinical practice is still a challenging problem as its progression is associated with serious complications, such as variceal bleeding that may increase mortality. Portal hypertension (PH) is the main key for the development of liver cirrhosis complications. Portal pressure above 10 mmHg, termed as clinically significant portal hypertension, is associated with formation of varices; meanwhile, portal pressure above 12 mmHg is associated with variceal bleeding. Hepatic vein pressure gradient measurement and esophagogastroduodenoscopy remain the gold standard for assessing portal pressure and detecting varices. Recently, non-invasive methods have been studied for evaluation of portal pressure and varices detection in liver cirrhotic patients. Various guidelines have been published for clinicians’ guidance in the management of esophagogastric varices which aims to prevent development of varices, acute variceal bleeding, and variceal rebleeding. This writing provides a comprehensive review on development of PH and varices in liver cirrhosis patients and its management based on current international guidelines and real experience in Indonesia.

Lichen planus (LP) is a relatively common mucocutaneous disease with autoimmune etiology. Considering its malignancy potential, it is important to define the correct diagnosis, treatment, and clinical follow-up for patients with LP so that the disease is not diagnosed late, thus hindering the chances of curing the disease. This study aims to describe a clinical case of oral squamous cell carcinoma, potentially originated from LP. The patient is undergoing clinical and histopathological follow-up. A 64-year-old Caucasian male patient presented with a proliferative verrucous lesion on the tongue and sought treatment at the School of Dentistry, University of Passo Fundo (UPF), Passo Fundo, Brazil. He claimed the lesion had been present since 1988, and had been initially diagnoses as “oral lichen planus.” The physical exam presented three diagnostic hypotheses: plaque-like oral LP, verrucous carcinoma, and squamous cell carcinoma. After incisional biopsy and histopathological analysis, squamous cell carcinoma was diagnosed, probably originating from oral LP. The case study shows that malignancy from oral LP is possible, which justifies periodic clinical and histopathological follow-up, as well as the elimination of risk factors for carcinoma in patients with oral LP.
Biopsy ; Brazil ; Carcinoma, Squamous Cell* ; Carcinoma, Verrucous ; Dentistry ; Diagnosis ; Epithelial Cells* ; Follow-Up Studies ; Humans ; Lichen Planus ; Lichen Planus, Oral* ; Lichens ; Male ; Middle Aged ; Mouth Neoplasms ; Risk Factors ; Tongue

INTRODUCTIONSince the first human cases of H5N1 avian influenza virus infection were detected in Indonesia in 2005, the Sulianti Saroso Infectious Diseases Hospital in Jakarta has managed 27 confirmed cases from September 2005 to December 2007.

MATERIALS AND METHODSWe reviewed the clinical and epidemiological data of these patients.

RESULTSClinical and radiological features were not specific. Most patients were young and had indirect contact with infected poultry. The majority of cases presented to the Infectious Diseases hospital late when the patients already had features of the systemic inflammatory response syndrome (SIRS). The mortality was high at 77%.

CONCLUSIONThere is clearly an urgent need for better field diagnostics and therapeutics for the management of this emerging pathogen.

Adolescent ; Adult ; Animals ; Birds ; Child ; Child, Preschool ; Female ; Humans ; Indonesia ; epidemiology ; Infant ; Infant, Newborn ; Influenza A Virus, H5N1 Subtype ; isolation & purification ; Influenza in Birds ; diagnosis ; epidemiology ; Male ; Retrospective Studies ; Risk Factors