Classification ensemble to improve medical named entity recognition

An accurate Named Entity Recognition (NER) is important for knowledge discovery in text mining. This paper proposes an ensemble machine learning approach to recognise Named Entities (NEs) from unstructured and informal medical text. Specifically, Conditional Random Field (CRF) and Maximum Entropy (ME) classifiers are applied individually to the test data set from the i2b2 2010 medication challenge. Each classifier is trained using a different set of features. The first set focuses on the contextual features of the data, while the second concentrates on the linguistic features of each word. The results of the two classifiers are then combined. The proposed approach achieves an f-score of 81.8%, showing a considerable improvement over the results from CRF and ME classifiers individually which achieve f-scores of 76% and 66.3% for the same data set, respectively.

Enhancement of medical named entity recognition using graph-based features

Named Entity Recognition (NER) is a crucial step in text mining. This paper proposes a new graph-based technique for representing unstructured medical text. The new representation is used to extract discriminative features that are able to enhance the NER performance. To evaluate the usefulness of the proposed graph-based technique, the i2b2 medication challenge data set is used. Specifically, the 'treatment' named entities are extracted for evaluation using six different classifiers. The F-measure results of five classifiers are enhanced, with an average improvement of up to 26% in performance.

Evolving Future Internet clean-slate Entity Title Architecture with quality-oriented control-plane extensions

A Internet atual vem sofrendo vários problemas em termos de escalabilidade, desempenho, mobilidade, etc., devido ao vertiginoso incremento no número de usuários e o surgimento de novos serviços com novas demandas, propiciando assim o nascimento da Internet do Futuro. Novas propostas sobre redes orientadas a conteúdo, como a arquitetura Entidade Titulo (ETArch), proveem novos serviços para este tipo de cenários, implementados sobre o paradigma de redes definidas por software. Contudo, o modelo de transporte do ETArch é equivalente ao modelo best-effort da Internet atual, e vem limitando a confiabilidade das suas comunicações. Neste trabalho, ETArch é redesenhado seguindo o paradigma do sobreaprovisionamento de recursos para conseguir uma alocação de recursos avançada integrada com OpenFlow. Como resultado, o framework SMART (Suporte de Sessões Móveis com Alta Demanda de Recursos de Transporte), permite que a rede defina semanticamente os requisitos qualitativos das sessões para assim gerenciar o controle de Qualidade de Serviço visando manter a melhor Qualidade de Experiência possível. A avaliação do planos de dados e de controle teve lugar na plataforma de testes na ilha do projeto OFELIA, mostrando o suporte de aplicações móveis multimídia com alta demanda de recursos de transporte com QoS e QoE garantidos através de um esquema de sinalização restrito em comparação com o ETArch legado

Paranasal sinus infection causing orbital subperiosteal abscess: Surgical management of this devastating entity

Background: Orbital infection is an uncommon devastating infection and is usually a complication of paranasal sinus infection. Without appropriate treatment, orbital infection may lead to serious complications, even death. Prompt treatment is mandatory to avoid visual loss or intracranial complications. The literature shows that initially, intravenous antibiotics should be administered, and after 48 h, if no improvement appears, the affected orbit and the sinuses must be surgically drained. The authors describe two cases of orbital cellulitis with a brief literature review. Case report: The authors describe two cases of orbital abscess caused by paranasal sinus infection. In case 1, the patient presented a decreased visual acuity associated with ophthalmoplegia of the right eye. In case 2, the patient presented a decreased visual acuity. Thus, administration of intravenous antibiotic combined with surgical drainage was performed. After surgical procedure, eye movements were normalized in case 1, and in both patients, the visual acuity returned to normal parameters. Discussion: The authors recommend early surgical drainage with parenteral antibiotic administration and careful postoperative observations by monitoring the signs and symptoms of the orbital complaint. © 2012 Springer-Verlag.

Grade 3 Varicocele in Fertile Men: A Different Entity

Purpose: Although varicocele size has an inverse relationship with baseline semen parameters and a direct relationship with seminal reactive oxygen species in infertile patients, to our knowledge the effect of varicocele grade in fertile men is unknown. We evaluated the impact of varicocele grade on seminal parameters, testicular size and seminal reactive oxygen species in fertile men. Materials and Methods: We prospectively evaluated 194 men from July 2004 to April 2010. Of the men 156 were fertile and classified by presence of varicocele. A total of 38 infertile patients with varicocele as the only identifiable cause of infertility comprised the control group. Physical examination, semen parameters and seminal reactive oxygen species were compared between the groups. Results: Of 156 fertile men 43 (24.3%) had clinical varicocele, which was grade 1 to 3 in 22, 11 and 10, respectively. The remaining 113 men (72.7%) had no varicocele. Infertile men had smaller testes, decreased semen parameters and higher seminal reactive oxygen species than the fertile groups. Testicular size, reactive oxygen species and semen parameters did not differ between fertile men with vs without varicocele. Fertile men with varicocele grade 3 had higher seminal reactive oxygen species than those with lower grade varicocele. As varicocele grade increased, seminal reactive oxygen species increased and sperm concentration decreased. Conclusions: Although fertile men have more efficient defense mechanisms to protect against the consequences of varicocele on testicular function, these mechanisms may not be sufficient in those with varicocele grade 3. Further research is needed to clarify whether they are at increased risk for future infertility.

Confocal microscopy applied to the study of single entity fluorescence and light scattering

A sample scanning confocal optical microscope (SCOM) was designed and constructed in order to perform local measurements of fluorescence, light scattering and Raman scattering. This instrument allows to measure time resolved fluorescence, Raman scattering and light scattering from the same diffraction limited spot. Fluorescence from single molecules and light scattering from metallic nanoparticles can be studied. First, the electric field distribution in the focus of the SCOM was modelled. This enables the design of illumination modes for different purposes, such as the determination of the three-dimensional orientation of single chromophores. Second, a method for the calculation of the de-excitation rates of a chromophore was presented. This permits to compare different detection schemes and experimental geometries in order to optimize the collection of fluorescence photons. Both methods were combined to calculate the SCOM fluorescence signal of a chromophore in a general layered system. The fluorescence excitation and emission of single molecules through a thin gold film was investigated experimentally and modelled. It was demonstrated that, due to the mediation of surface plasmons, single molecule fluorescence near a thin gold film can be excited and detected with an epi-illumination scheme through the film. Single molecule fluorescence as close as 15nm to the gold film was studied in this manner. The fluorescence dynamics (fluorescence blinking and excited state lifetime) of single molecules was studied in the presence and in the absence of a nearby gold film in order to investigate the influence of the metal on the electronic transition rates. The trace-histogram and the autocorrelation methods for the analysis of single molecule fluorescence blinking were presented and compared via the analysis of Monte-Carlo simulated data. The nearby gold influences the total decay rate in agreement to theory. The gold presence produced no influence on the ISC rate from the excited state to the triplet but increased by a factor of 2 the transition rate from the triplet to the singlet ground state. The photoluminescence blinking of Zn0.42Cd0.58Se QDs on glass and ITO substrates was investigated experimentally as a function of the excitation power (P) and modelled via Monte-Carlo simulations. At low P, it was observed that the probability of a certain on- or off-time follows a negative power-law with exponent near to 1.6. As P increased, the on-time fraction reduced on both substrates whereas the off-times did not change. A weak residual memory effect between consecutive on-times and consecutive off-times was observed but not between an on-time and the adjacent off-time. All of this suggests the presence of two independent mechanisms governing the lifetimes of the on- and off-states. The simulated data showed Poisson-distributed off- and on-intensities, demonstrating that the observed non-Poissonian on-intensity distribution of the QDs is not a product of the underlying power-law probability and that the blinking of QDs occurs between a non-emitting off-state and a distribution of emitting on-states with different intensities. All the experimentally observed photo-induced effects could be accounted for by introducing a characteristic lifetime tPI of the on-state in the simulations. The QDs on glass presented a tPI proportional to P-1 suggesting the presence of a one-photon process. Light scattering images and spectra of colloidal and C-shaped gold nano-particles were acquired. The minimum size of a metallic scatterer detectable with the SCOM lies around 20 nm.

Entity extraction e text classification come strumenti per la sentiment analysis di testi giornalistici

In this thesis we are going to talk about technologies which allow us to approach sentiment analysis on newspapers articles. The final goal of this work is to help social scholars to do content analysis on big corpora of texts in a faster way thanks to the support of automatic text classification.

Named Entity Extraction: la piattaforma Gate/Annie

In questo lavoro si introducono i concetti di base di Natural Language Processing, soffermandosi su Information Extraction e analizzandone gli ambiti applicativi, le attività principali e la differenza rispetto a Information Retrieval. Successivamente si analizza il processo di Named Entity Recognition, focalizzando l’attenzione sulle principali problematiche di annotazione di testi e sui metodi per la valutazione della qualità dell’estrazione di entità. Infine si fornisce una panoramica della piattaforma software open-source di language processing GATE/ANNIE, descrivendone l’architettura e i suoi componenti principali, con approfondimenti sugli strumenti che GATE offre per l'approccio rule-based a Named Entity Recognition.

Iatrogenic atrial septal defect, erosion of the septum primum after device closure of a patent foramen ovale as a new medical entity

Iatrogenic atrial septal defects are described in 2 patients. They occurred after implantation of Amplatzer occluders to close a patent foramen ovale. While device erosions to the extra-atrial space have been described, erosion induced atrial septal defects are a new medical entity. They may be fairly common in the situation of an atrial septal aneurysm whipping the rim of the device incessantly. They are clinically silent and benign and require echocardiography for detection. A second device solved the problem in the cases described.

Hemorrhage in vitamin K deficiency--a preventable entity

Der diaplazentare Transport von Vitamin K ist kaum messbar, die Muttermilch ist arm an Vitamin K und die intestinale Flora von Neugeborenen produziert praktisch kein Vitamin K. Deshalb weisen gesunde Neugeborene «physiologischerweise» tiefe Vitamin-K-Spiegel auf, was durch Verminderung der Vitamin-K-abhängigen Gerinnungsfaktoren zu schweren Mangelblutungen führen kann. Die klassische Form der Vitamin-K-Mangelblutung tritt mit einer Inzidenz von bis zu 1.5% bis zum 7. Lebenstag auf, die Spätform wird bis zur 12. Lebenswoche bei bis zu 10 von 100000 Neugeborenen festgestellt. Mit einer adäquaten Vitamin-K-Prophylaxe lassen sich Vitamin-K-Mangelblutungen grösstenteils verhindern. Die heute in der Schweiz empfohlene Prophylaxe von 3 oralen Dosen à 2 mg Konakion® MM in der 4. Lebensstunde, am 4. Lebenstag und in der 4. Lebenswoche ist bezüglich unerwünschter Nebenwirkung äusserst sicher, insbesondere besteht kein erhöhtes Krebsrisiko. Angesichts der dramatischen Folgen der häufig intrakraniell lokalisierten Vitamin-K-Mangelblutungen ist sowohl bei medizinischen Fachpersonen als auch bei den Eltern eine möglichst gute Compliance für diese einfache und sichere Prophylaxe wie auch eine entsprechende Aufklärung anzustreben.

[The "globulomaxillary cyst" a specific entity or a myth?]

The following review investigates the term and concept of the globulomaxillary cyst as a correct clinico-pathological diagnosis to describe a so-called fissural cyst said to be caused by epithelial entrapment between the nasal and maxillary process. After analyzing the available literature it has to be concluded that neither from an embryologic nor from a clinical or pathohistological standpoint the term globulomaxillary cyst represents a real entity by itself. Therefore, globulomaxillary cysts have to be diagnosed alternatively after a thorough clinical, radiological and histological examination as other odontogenic cysts like dentigerous cysts or odontogenic keratocysts, odontogenic tumors like ameloblastoma, central giant cell tumors, solitary bone cysts, etc.

Small omphalocele with umbilical evagination. A distinct entity?

A neonatal case of umbilical evagination of the bladder combined with a small omphalocele is presented. This rare congenital malformation has previously been described in only three cases. Umbilical evagination can be understood as a disturbance of development of both the vitelline and allantoic ducts, resulting in a non-descended but otherwise normal bladder opening to the inferior margin of a small omphalocele. Diagnosis is made by clinical inspection and ultrasound. Since other malformations are not present, this entity may be regarded as a minor form of a lower midline defect with excellent prognosis.

Primary perivascular epithelioid cell tumor of the liver not related to hepatic ligaments: hepatic PEComa as an emerging entity

Primary perivascular epithelioid cell tumor (PEComa) of the liver is a very rare example of an emerging family of hepatic PEC tumors. Only few cases have been described so far. We report the case of a large but benign hepatic PEComa in a 53-year-old man without signs of tuberous sclerosis. In contrast to recently described PEC-derived liver tumors in children and young adults, this neoplasm was not related to the hepatic ligaments but had developed deeply within the liver substance. The neoplastic cells displayed the complete phenotype typical for PEComas, i.e. reactivity for several melanoma markers and for smooth muscle actin. The unique relationship of myoid tumor cells to the adventitia of blood vessels prompted us, in comparison with published findings obtained with angiomyolipomas, to comment on the possible origin of the still enigmatic perivascular epithelioid cells.

Pineal parenchymal tumor of intermediate differentiation: diagnostic pitfalls and discussion of treatment options of a rare tumor entity

Tumors of the pineal region are uncommon, comprising approximately 0.4-1% of all intracranial tumors in adults in European and American series. Histopathologically, they are a very heterogeneous group of tumors. Of genuine pineal tumors, pineal parenchymal tumors of intermediate differentiation (PPTIDs) are the least frequently found type. In this paper, we report on the case of a patient with an unexpected and difficult-to-diagnose PPTID. A 2.2 x 2.2-cm midline mass within the posterior part of the third ventricle with consecutive obstructive hydrocephalus was found in a 44-year-old man presenting with diplopia and gait disturbances. There was no clear connection of the tumor to the pineal gland. Differential diagnosis included all intraventricular and midline tumors, therefore a biopsy was taken. Preliminary histopathological diagnosis was germinoma or primitive neuroectodermal tumor, and the tissue sample was reexamined by a referential neuropathological institute. Final diagnosis was PPTID. The tumor was then resected through a transventricular/transchoroidal approach. Histopathological examination of tumor specimen confirmed the diagnosis of a PPTID. Postoperatively, the patient received gamma-knife radiosurgery. At 1-year follow-up, there are no signs of tumor regrowth. Diagnosis of pineal parenchymal tumors in general and PPTIDs in particular can be troublesome. Their histopathological features are still being defined, as is the biological behavior of the different tumor entities. Thus, treatment options including surgery, radiation therapy, and chemotherapy remain controversial. We recommend surgical removal of PPTID, preferably in toto whenever the size of the tumor permits that kind of excision.

Is Parkinson's disease of early onset a separate disease entity?

Two groups of patients suffering from Parkinson's disease were studied. The first group consisted of 23 patients with an onset age before 40 years; in the second group of 21 patients the onset was after age 50. The clinical findings and the course of the disease were very similar in each group. In spite of a longer disease duration in the patients with early onset of the disease there was no difference in motor impairment; the younger patients did better in mental testing and they were taking less dopaminergic medication. These differences are thought to be due to the age difference rather than to the existence of different disease entities. In the early onset group more familial cases (mostly affecting siblings) were found than in the older ones. The points in favour of there being a hereditary subgroup of early onset Parkinson's disease or of environmental factors causing the disease are reviewed.