Automatic extraction of definitions

Tese de doutoramento, Informática (Engenharia Informática), Universidade de Lisboa, Faculdade de Ciências, 2014This doctoral research work provides a set of methods and heuristics for building a definition extractor or for fine-tuning an existing one. In order to develop and test the architecture, a generic definitions extractor for the Portuguese language is built. Furthermore, the methods were tested in the construction of an extractor for two languages different from Portuguese, which are English and, less extensively, Dutch. The approach presented in this work makes the proposed extractor completely different in nature in comparison to the other works in the field. It is a matter of fact that most systems that automatically extract definitions have been constructed taking into account a specific corpus on a specific topic, and are based on the manual construction of a set of rules or patterns capable of identifyinf a definition in a text. This research focused on three types of definitions, characterized by the connector between the defined term and its description. The strategy adopted can be seen as a "divide and conquer"approach. Differently from the other works representing the state of the art, specific heuristics were developed in order to deal with different types of definitions, namely copula, verbal and punctuation definitions. We used different methodology for each type of definition, namely we propose to use rule-based methods to extract punctuation definitions, machine learning with sampling algorithms for copula definitions, and machine learning with a method to increase the number of positive examples for verbal definitions. This architecture is justified by the increasing linguistic complexity that characterizes the different types of definitions. Numerous experiments have led to the conclusion that the punctuation definitions are easily described using a set of rules. These rules can be easily adapted to the relevant context and translated into other languages. However, in order to deal with the other two definitions types, the exclusive use of rules is not enough to get good performance and it asks for more advanced methods, in particular a machine learning based approach. Unlike other similar systems, which were built having in mind a specific corpus or a specific domain, the one reported here is meant to obtain good results regardless the domain or context. All the decisions made in the construction of the definition extractor take into consideration this central objective.Este trabalho de doutoramento visa proporcionar um conjunto de métodos e heurísticas para a construção de um extractor de definição ou para melhorar o desempenho de um sistema já existente, quando usado com um corpus específico. A fim de desenvolver e testar a arquitectura, um extractor de definic˛ões genérico para a língua Portuguesa foi construído. Além disso, os métodos foram testados na construção de um extractor para um idioma diferente do Português, nomeadamente Inglês, algumas heurísticas também foram testadas com uma terceira língua, ou seja o Holandês. A abordagem apresentada neste trabalho torna o extractor proposto neste trabalho completamente diferente em comparação com os outros trabalhos na área. É um fato que a maioria dos sistemas de extracção automática de definicões foram construídos tendo em conta um corpus específico com um tema bem determinado e são baseados na construc˛ão manual de um conjunto de regras ou padrões capazes de identificar uma definição num texto dum domínio específico. Esta pesquisa centrou-se em três tipos de definições, caracterizadas pela ligacão entre o termo definido e a sua descrição. A estratégia adoptada pode ser vista como uma abordagem "dividir para conquistar". Diferentemente de outras pesquisa nesta área, foram desenvolvidas heurísticas específicas a fim de lidar com as diferentes tipologias de definições, ou seja, cópula, verbais e definicões de pontuação. No presente trabalho propõe-se utilizar uma metodologia diferente para cada tipo de definição, ou seja, propomos a utilização de métodos baseados em regras para extrair as definições de pontuação, aprendizagem automática, com algoritmos de amostragem para definições cópula e aprendizagem automática com um método para aumentar automáticamente o número de exemplos positivos para a definição verbal. Esta arquitetura é justificada pela complexidade linguística crescente que caracteriza os diferentes tipos de definições. Numerosas experiências levaram à conclusão de que as definições de pontuação são facilmente descritas utilizando um conjunto de regras. Essas regras podem ser facilmente adaptadas ao contexto relevante e traduzido para outras línguas. No entanto, a fim de lidar com os outros dois tipos de definições, o uso exclusivo de regras não é suficiente para obter um bom desempenho e é preciso usar métodos mais avançados, em particular aqueles baseados em aprendizado de máquina. Ao contrário de outros sistemas semelhantes, que foram construídos tendo em mente um corpus ou um domínio específico, o sistema aqui apresentado foi desenvolvido de maneira a obter bons resultados, independentemente do domínio ou da língua. Todas as decisões tomadas na construção do extractor de definição tiveram em consideração este objectivo central.Fundação para a Ciência e a Tecnologia (FCT, SFRH/ BD/36732/2007

peri implantitis and periodontitis use of bacteriological test in dental practice

Peri-implantitis has been defined as an inflamematory condition involving dental implants, surrounding mucosa and bone, which lose supporting bone. Although high success rates for endosseous implants have been reported, failures occur, and some implants are lost or removed. At least 10% of the failures have been suggested to be the result of peri-implantitis. One of the major causes of the peri-implantitis is the bacterial colonization of implant surfaces but additional risk factors such as periodontitis, poor oral hygiene, tobacco consumption, prepost operative therapies and genetic susceptibility should be considered. In the present study a real-time PCR bases assay was designed to detect and quantify red complex species, then used to investigate 307 periodontal pocket samples from 127 periodontitis patients and 180 controls. Results demonstrated a significant higher prevalence of red complex species and increased amount of Porphyromonas gingivalis and Treponema denticolain periodontal pocket of periodontitis. Since a higher risk of peri-implantitis occurs in periodontally affected patients, detection and treatment of bacteria is a fundamental objective to ensure dental implant survival

The diatoms test in veterinary medicine: a pilot study on cetaceans and sea turtles

Fishing activities are considered one of the most relevant threats for cetaceans and sea turtles con- servation since these animals are sometimes found dead entangled in fishing gears. Currently, postmortem diagnosis is based mainly on the presence of nets and lines on the body and the related marks and injuries evident at gross examination. A more detailed and objective evidence is needed to clarify doubts cases and the diatoms technique, used in forensic human medicine, could support drowning diagnosis also in this field. Diatoms\u2019 investigation was implemented to be applied in ma- rine vertebrate on 8 striped (Stenella coeruleoalba) and 1 bottlenose (Tursiops truncatus) dolphins and 5 sea turtles (Caretta caretta) stranded along the Italian coastlines with a likely cause of death hypothized on necropsies carried out by veterinary pathologists. Diatoms were microscopically searched in the bone marrow collected from long bones implementing protocols used in human medicine and their presence was observed in 4 cetaceans and 2 sea turtles. Despite a clear relation between diatoms\u2019 presence and amount and the likely cause of death was not proved due to the poor number of samples, the higher burden of diatoms was found in 3 animals deemed to be death for the interaction with human activity. Despite more studied are necessary to identify the possible relation between the cause of death and diatoms\u2019 findings, the present study implemented this technique to be adapted to marine animals, confirming its possible application also in veterinary forensic medi- cine

Peribiliary glands as a niche of extra-pancreatic precursors yielding insulin-producing cells in experimental and human diabetes

Peribiliary glands (PBGs) are niches in the biliary tree and containing heterogeneous endodermal stem/progenitors cells that can differentiate, in vitro and in vivo, towards pancreatic islets. The aim of this study was to evaluate, in experimental and human diabetes, proliferation of cells in PBGs and differentiation of the biliary tree stem/progenitor cells (BTSCs) towards insulin-producing cells. Diabetes was generated in mice by intraperitoneal injection of a single dose of 200 mg/kg (N=12) or 120 mg/kg (N=12) of streptozotocin. Liver, pancreas and extrahepatic biliary trees were en bloc dissected and examined. Cells in PBGs proliferated in experimental diabetes, and their proliferation was greatest in the PBGs of the hepato-pancreatic ampulla, and inversely correlated with the pancreatic islet area. In rodents, the cell proliferation in PBGs was characterized by the expansion of Sox9-positive stem/progenitor cells that gave rise to insulin-producing cells. Insulin-producing cells were located mostly in PBGs in the portion of the biliary tree closest to the duodenum, and their appearance was associated with up-regulation of MafA and Gli1 gene expression. In patients with type 2 diabetes, PBGs at the level of the hepato-pancreatic ampulla contained cells showing signs of proliferation and pancreatic fate commitment. In vitro, high glucose concentrations induced the differentiation of human BTSCs cultures towards pancreatic beta cell fates. The cells in PBGs respond to diabetes with proliferation and differentiation towards insulin-producing cells indicating that PBG niches may rescue pancreatic islet impairment in diabetes. These findings offer important implications for the patho-physiology and complications of this disease. This article is protected by copyright. All rights reserved

Unexpected and durable response with regorafenib in a metastatic colorectal cancer patient without KDR mutation: A case report

Regorafenib is an oral multikinase inhibitor and is approved as salvage therapy in the standard treatment of advanced colorectal cancer (CRC). Due to its limited efficacy, toxicity profile, and cost, it is necessary to identify those patients who may have the most benefit from regorafenib. In a previous case report, kinase insert domain receptor (KDR) mutation has been associated with exceptional clinical response (CR) in an elderly patient treated with a low dose of regorafenib; thus, it was hypothesized that it could represent a new predictive marker of drug response

Viral hepatitis and iron dysregulation: molecular pathways and the role of lactoferrin

The liver is a frontline immune site specifically designed to check and detect potential pathogens from the bloodstream to maintain a general state of immune hyporesponsiveness. One of the main functions of the liver is the regulation of iron homeostasis. The liver detects changes in systemic iron requirements and can regulate its concentration. Pathological states lead to the dysregulation of iron homeostasis which, in turn, can promote infectious and inflammatory processes. In this context, hepatic viruses deviate hepatocytes' iron metabolism in order to better replicate. Indeed, some viruses are able to alter the expression of iron-related proteins or exploit host receptors to enter inside host cells. Lactoferrin (Lf), a multifunctional iron-binding glycoprotein belonging to the innate immunity, is endowed with potent antiviral activity, mainly related to its ability to block viral entry into host cells by interacting with viral and/or cell surface receptors. Moreover, Lf can act as an iron scavenger by both direct iron-chelation or the modulation of the main iron-related proteins. In this review, the complex interplay between viral hepatitis, iron homeostasis, and inflammation as well as the role of Lf are outlined

Adult human biliary tree stem cells differentiate to β-pancreatic islet cells by treatment with a recombinant human Pdx1 peptide

Generation of β-pancreatic cells represents a major goal in research. The aim of this study was to explore a protein-based strategy to induce differentiation of human biliary tree stem cells (hBTSCs) towards β-pancreatic cells. A plasmid containing the sequence of the human pancreatic and duodenal homeobox 1 (PDX1) has been expressed in E. coli. Epithelial-Cell-Adhesion-Molecule positive hBTSCs or mature human hepatocyte cell line, HepG2, were grown in medium to which Pdx1 peptide was added. Differentiation toward pancreatic islet cells were evaluated by the expression of the β-cell transcription factors, Pdx1 and musculoapo-neurotic fibrosarcoma oncogene homolog A, and of the pancreatic hormones, insulin, glucagon, and somatostatin, investigated by real time polymerase chain reaction, western blot, light microscopy and immunofluorescence. C-peptide secretion in response to high glucose was also measured. Results indicated how purified Pdx1 protein corresponding to the primary structure of the human Pdx1 by mass spectroscopy was efficiently produced in bacteria, and transduced into hBTSCs. Pdx1 exposure triggered the expression of both intermediate and mature stage β-cell differentiation markers only in hBTSCs but not in HepG2 cell line. Furthermore, hBTSCs exposed to Pdx1 showed up-regulation of insulin, glucagon and somatostatin genes and formation of 3-dimensional islet-like structures intensely positive for insulin and glucagon. Finally, Pdx1-induced islet-like structures exhibited glucose-regulated C-peptide secretion. In conclusion, the human Pdx1 is highly effective in triggering hBTSC differentiation toward functional β-pancreatic cells

Unusual Displacement of a Mobilised Dental Bridge during Orotracheal Intubation

Dental trauma during tracheal intubation mostly happens in case of poor dentition, restricted mouth opening, and/or difficult laryngoscopy. 57-year-old man undergoing laparoscopic radiofrequency ablation of unresectable hepatocellular carcinoma had his dental work detached at induction of anesthesia. Oropharyngeal direct view, manual inspection, fibreoptic nosendoscopy, tracheobronchoscopy, and fiberoptic inspection of the esophagus and stomach were unsuccessful in locating the dislodged bridge. While other possible exams were considered, such as lateral and AP x-ray of head and neck, further meticulous manual “sweepings” of the mouth were performed, and by moving the first and second fingers below the soft palate deep towards the posterolateral wall of the pharynx, feeling consistent with a dental prosthesis was detected in the right pharyngeal recess. Only after pulling the palatopharyngeal arch upward was it possible to grasp it and extract it out with the aid of a Magill Catheter Forceps. Even though the preexisting root and bridge deficits were well reported by the consultant dentist, the patient was fully reimbursed. The lack of appropriate documentation of the advanced periodontal disease in the anesthesia records, no mention of potential risks on anesthesia consent, and insufficient protective measures during airway instrumentation reinforced the reimbursement claim

Gabapentin affects the expression of inflammatory mediators on healthy gingival cells

Gabapentin is one of the most used drugs to treat postoperative pain with antihyperalgesic properties and has a unique mechanism of action, which differentiates it from other commonly used drugs. Various studies have shown that the perioperative use of gabapentin reduces postoperative pain. In our study, fragments of gingival tissue of healthy volunteers were collected during operation. Gene expression of 29 genes was investigated in gingival fibroblasts cell culture treated with gabapentin, compared with untreated cells. Of the different chemokines and interleukins studied, only 10 were statistically significant (CCL1, CCR1, CCR4, CCR5, CCR6, ILI1A, ILI1B, IL5, IL6R, TNFSF10). The overexpression of these cytokines, obtained in many studies, leads us to think that gabapentin can interact and cause post-inflammatory gingival hyperplasia, but, probably, in our study the gabapentin has not the same effect, because we used gingival fibroblasts of healthy peopl

oXirisNet Registry: A Prospective, National Registry on the oXiris Membrane.

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