Computational framework to support integration of biomolecular and clinical data within a translational approach

Background The use of the knowledge produced by sciences to promote human health is the main goal of translational medicine. To make it feasible we need computational methods to handle the large amount of information that arises from bench to bedside and to deal with its heterogeneity. A computational challenge that must be faced is to promote the integration of clinical, socio-demographic and biological data. In this effort, ontologies play an essential role as a powerful artifact for knowledge representation. Chado is a modular ontology-oriented database model that gained popularity due to its robustness and flexibility as a generic platform to store biological data; however it lacks supporting representation of clinical and socio-demographic information. Results We have implemented an extension of Chado – the Clinical Module - to allow the representation of this kind of information. Our approach consists of a framework for data integration through the use of a common reference ontology. The design of this framework has four levels: data level, to store the data; semantic level, to integrate and standardize the data by the use of ontologies; application level, to manage clinical databases, ontologies and data integration process; and web interface level, to allow interaction between the user and the system. The clinical module was built based on the Entity-Attribute-Value (EAV) model. We also proposed a methodology to migrate data from legacy clinical databases to the integrative framework. A Chado instance was initialized using a relational database management system. The Clinical Module was implemented and the framework was loaded using data from a factual clinical research database. Clinical and demographic data as well as biomaterial data were obtained from patients with tumors of head and neck. We implemented the IPTrans tool that is a complete environment for data migration, which comprises: the construction of a model to describe the legacy clinical data, based on an ontology; the Extraction, Transformation and Load (ETL) process to extract the data from the source clinical database and load it in the Clinical Module of Chado; the development of a web tool and a Bridge Layer to adapt the web tool to Chado, as well as other applications. Conclusions Open-source computational solutions currently available for translational science does not have a model to represent biomolecular information and also are not integrated with the existing bioinformatics tools. On the other hand, existing genomic data models do not represent clinical patient data. A framework was developed to support translational research by integrating biomolecular information coming from different “omics” technologies with patient’s clinical and socio-demographic data. This framework should present some features: flexibility, compression and robustness. The experiments accomplished from a use case demonstrated that the proposed system meets requirements of flexibility and robustness, leading to the desired integration. The Clinical Module can be accessed in http://dcm.ffclrp.usp.br/caib/pg=iptrans webcite.

Computer game-based and traditional learning method: a comparison regarding students’ knowledge retention

Abstract Background Educational computer games are examples of computer-assisted learning objects, representing an educational strategy of growing interest. Given the changes in the digital world over the last decades, students of the current generation expect technology to be used in advancing their learning requiring a need to change traditional passive learning methodologies to an active multisensory experimental learning methodology. The objective of this study was to compare a computer game-based learning method with a traditional learning method, regarding learning gains and knowledge retention, as means of teaching head and neck Anatomy and Physiology to Speech-Language and Hearing pathology undergraduate students. Methods Students were randomized to participate to one of the learning methods and the data analyst was blinded to which method of learning the students had received. Students’ prior knowledge (i.e. before undergoing the learning method), short-term knowledge retention and long-term knowledge retention (i.e. six months after undergoing the learning method) were assessed with a multiple choice questionnaire. Students’ performance was compared considering the three moments of assessment for both for the mean total score and for separated mean scores for Anatomy questions and for Physiology questions. Results Students that received the game-based method performed better in the pos-test assessment only when considering the Anatomy questions section. Students that received the traditional lecture performed better in both post-test and long-term post-test when considering the Anatomy and Physiology questions. Conclusions The game-based learning method is comparable to the traditional learning method in general and in short-term gains, while the traditional lecture still seems to be more effective to improve students’ short and long-term knowledge retention.

CD44/CD24 immunophenotypes on clinicopathologic features of salivary glands malignant neoplasms

Abstract Background Salivary Glands Malignant Neoplasms (SGMNs) account for 3-6% of head and neck cancers and 0.3% of all cancers. Tumor cells that express CD44 and CD24 exhibit a stem-cell-like behavior. CD44 is the binding site for hyaluronic acid, and CD24 is a receptor that interacts with P-selectin to induce metastasis and tumor progression. The present study aims to evaluate the expression of CD44 and CD24 on SGMNs and correlated these data with several clinicopathologic features. Methods Immunohistochemical stains for CD44 and CD24 were performed on tissue microarrays containing SGMN samples from 69 patients. The CD44, CD24 and CD44/CD24 expression phenotypes were correlated to patient clinicopathologic features and outcome. Results CD44 expression was associated with the primary site of neoplasm (p = 0.046). CD24 was associated with clinical stage III/IV (p = 0.008), T stage (p = 0,27) and lymph node (p = 0,001). The CD44/CD24 profiles were associated with the primary site of injury (p = 0.005), lymph node (p = 0.011) and T stage (p = 0.023). Univariate analysis showed a significant relationship between clinical staging and disease- free survival (p = 0.009), and the overall survival presents relation with male gender (p = 0.011) and metastasis (p = 0.027). Conclusion In summary, our investigation confirms that the clinical stage, in accordance with the literature, is the main prognostic factor for SGMN. Additionally, we have presented some evidence that the analysis of isolated CD44 and CD24 immunoexpression or the two combined markers could give prognostic information associated to clinicopathologic features in SGMN. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1284611098470676.

Expression of human protein S100A7 (psoriasin), preparation of antibody and application to human larynx squamous cell carcinoma

Background Up-regulation of S100A7 (Psoriasin), a small calcium-binding protein, is associated with the development of several types of carcinomas, but its function and possibility to serve as a diagnostic or prognostic marker have not been fully defined. In order to prepare antibodies to the protein for immunohistochemical studies we produced the recombinant S100A7 protein in E. coli. mRNA extracted from human tracheal tumor tissue which was amplified by RT-PCR to provide the region coding for the S100A7 gene. The amplified fragment was cloned in the vector pCR2.1-TOPO and sub-cloned in the expression vector pAE. The protein rS100A7 (His-tag) was expressed in E. coli BL21::DE3, purified by affinity chromatography on an Ni-NTA column, recovered in the 2.0 to 3.5 mg/mL range in culture medium, and used to produce a rabbit polyclonal antibody anti-rS100A7 protein. The profile of this polyclonal antibody was evaluated in a tissue microarray. Results The rS100A7 (His-tag) protein was homogeneous by SDS-PAGE and mass spectrometry and was used to produce an anti-recombinant S100A7 (His-tag) rabbit serum (polyclonal antibody anti-rS100A7). The molecular weight of rS100A7 (His-tag) protein determined by linear MALDI-TOF-MS was 12,655.91 Da. The theoretical mass calculated for the nonapeptide attached to the amino terminus is 12,653.26 Da (delta 2.65 Da). Immunostaining with the polyclonal anti-rS100A7 protein generated showed reactivity with little or no background staining in head and neck squamous cell carcinoma cells, detecting S100A7 both in nucleus and cytoplasm. Lower levels of S100A7 were detected in non-neoplastic tissue. Conclusions The polyclonal anti-rS100A7 antibody generated here yielded a good signal-to-noise contrast and should be useful for immunohistochemical detection of S100A7 protein. Its potential use for other epithelial lesions besides human larynx squamous cell carcinoma and non-neoplastic larynx should be explored in future.

Convergence of two major pathophysiologic mechanisms in nasal polyposis: immune response to Staphylococcus aureus and airway remodeling

This review is addressed two pathophysiologic mechanisms implicated in the pathogenesis of nasal polyposis: the unique remodeling process found in nasal polyp tissue and the immune response of patients with nasal polyposis to Staphylococcus aureus. These two theories converge to the same direction in different aspects, including decreased extracellular matrix production, impaired T regulation and favoring of a Th2 immune response. In patients with nasal polyposis, an exaggerated immune response to Staphylococcus aureus may aggravate the airway remodeling process.

Valor da PET/CT na abordagem do câncer de cabeça e pescoço

OBJETIVO: Avaliar a PET/CT na abordagem de pacientes com câncer de cabeça e pescoço. MATERIAIS E MÉTODOS: Estudo retrospectivo de 63 prontuários e exames de PET/CT de pacientes com câncer de cabeça e pescoço. RESULTADOS: Foram encontradas alterações em 76% dos exames. Destes, 7 (11%) foram considerados falso-positivos, com SUV < 5,0. A PET/CT mostrou-se negativa em 15 situações (24%). Dos 14 casos nos quais se utilizou o exame para estadiamento, em 3 (22%) houve aumento no estadiamento. CONCLUSÃO: A PET/CT mostra-se como exame de potencial valor na rotina de avaliação de pacientes com câncer de cabeça e pescoço, entretanto, necessitamos de maior número de casos para definirmos protocolo de uso.

p16 (INK4a) has clinicopathological and prognostic impact on oropharynx and larynx squamous cell carcinoma

CDKN2A encodes proteins such as p16 (INK4a), which negatively regulate the cell-cycle. Molecular genetic studies have revealed that deletions in CDKN2A occur frequently in cancer. Although p16 (INK4a) may be involved in tumor progression, the clinical impact and prognostic implications in head and neck squamous cell carcinoma (HNSCC) are controversial. The objective of this study was to evaluate the frequency of the immunohistochemical expression of p16 (INK4a) in 40 oropharynx and 35 larynx from HNSCC patients treated in a single institution and followed-up at least for 10 years in order to explore potential associations with clinicopathological outcomes and prognostic implications. Forty cases (53.3%) were positive for p16 (INK4a) and this expression was more intense in non-smoking patients (P = 0.050), whose tumors showed negative vascular embolization (P = 0.018), negative lymphatic permeation (P = 0.002), and clear surgical margins (P = 0.050). Importantly, on the basis of negative p16 (INK4a) expression, it was possible to predict a probability of lower survival (P = 0.055) as well as tumors presenting lymph node metastasis (P = 0.050) and capsular rupture (P = 0.0010). Furthermore, increased risk of recurrence was observed in tumors presenting capsular rupture (P = 0.0083). Taken together, the alteration in p16 (INK4a) appears to be a common event in patients with oropharynx and larynx squamous cell carcinoma and the negative expression of this protein correlated with poor prognosis.

Biliary tract schwannoma: A rare cause of obstructive jaundice in a young patient

Schwannoma is a tumor derived from Schwann cells which usually arises in the upper extremities, trunk, head and neck, retroperitoneum, mediastinum, pelvis, and peritoneum. However, it can arise in the gastrointestinal tract, including biliary tract. We present a 24-year-old male patient with obstructive jaundice, whose investigation with computed tomography abdomen showed focal wall thickening in the common hepatic duct, difficult to differentiate with hilar adenocarcinoma. He was diagnosed intraoperatively schwannoma of common bile duct and treated with local resection. The patient recovered well without signs of recurrence of the lesion after 12 mo. We also reviewed the common bile duct schwannoma related in the literature and evaluated the difficulty in pre and intraoperative differential diagnosis with adenocarcinoma hilar. Resection is the treatment of choice for such cases and the tumor did not recur in any of the resected cases. (C) 2012 Baishideng. All rights reserved.

High prevalence of orofacial complaints in patients with fibromyalgia: a case-control study

Objective. The aim of this study was to investigate the orofacial complaints and characteristics of patients with fibromyalgia syndrome (FS) compared with controls. Study Design. We evaluated 25 patients diagnosed with FS compared with 25 gender-and age-matched controls by using a detailed clinical protocol for orofacial pain diagnosis and dental examination. Results. FS patients had a higher frequency of temporomandibular disorders (TMD), masticatory complaints, pain with mandibular movements, and pain upon palpation of the head and neck area. There were no significant differences related to the dental exam. Conclusions. Orofacial complaints including TMD may be present either as symptoms of FS or as a comorbidity associated with this condition. A comprehensive evaluation of patients with FS is necessary to identify the need for specific treatments for orofacial complaints. Future studies, especially those with longitudinal design, should clarify whether a cause-effect relationship exists between orofacial complaints and fibromyalgia. (Oral Surg Oral Med Oral Pathol Oral Radiol 2012;114:e29-e34)

Prevalence of chronic rhinosinusitis in Sao Paulo

Introduction: Studies designed to investigate chronic rhinosinusitis (CRS) epidemiology play an important role to assess population's distribution and risk factors to result in the development and promotion of public health policies. Method: This study design is a survey carried out with a complex two-stage cluster sampling plan. Personal interviews were carried out with 2,003 individuals. The questionnaire included the epidemiological criteria for CRS. Demographic data, history of physician-diagnosed respiratory diseases (asthma, sinusitis, rhinitis), smoking, family income, educational attainment, and household characteristics were also evaluated. Results: The overall response rate was 93.9% of the households. Mean age was 39.8 +/- 21 years; 45.33% were male. The overall prevalence of CRS in the city of Sao Paulo was 5.51%. We found a significant association between diagnosis of CRS and diagnosis of asthma and CRS and diagnosis of rhinitis and a significant association between presence of CRS and belonging to the low-income subgroup. Conclusion: The municipality of Sao Paulo has an urban population of 11 million. According to the present study, the prevalence of CRS is 5.51%, which represents more than 500,000 individuals affected by this condition in the city.

Postural Control in Older Patients with Benign Paroxysmal Positional Vertigo

Objective. To evaluate the effectiveness of a canalith-repositioning procedure in postural control of older patients with idiopathic benign paroxysmal positional vertigo (BPPV). Study Design. Prospective clinical trial. Setting. A tertiary referral center. Methods. A 9-month follow-up survey with a prospective design was conducted among 33 older patients with BPPV. Patients underwent static posturography (Balance Rehabilitation Unit [BRU]) and were administered the Dizziness Handicap Inventory (DHI) before and after the maneuver. After the treatment, they were compared with 33 healthy older subjects. The posturography parameters were the limit of stability (LOS), the center of body-pressure area (COP), and the velocity of oscillation (VOS) under conditions of visual, somatosensory, and visual-vestibular conflict. Results. One canalith-repositioning procedure relieved most patients' complaints (54.5%), and 100% were relieved with 1 to 3 maneuvers. Total DHI score and all subscales improved after treatment (P < .01). The LOS values pretreatment (mean [SD] 134.27 [55.32] cm(2)) and posttreatment (181.03 [47.79] cm(2)) were significantly different (P < .01). Comparative analysis of COP values showed a relevant statistical difference in 8 of 10 postmaneuver conditions (P < .01). The postmaneuver VOS showed a significant difference under 7 conflict conditions. There were no differences between the healthy older subjects and treated patients for all VOS values under all conditions and for COP values under 9 conditions. Conclusion. The canalith-repositioning procedure promotes remission of symptoms, an increase in LOS, and improvement in postural control under conditions of somatosensory and visual conflict and visual-vestibular interaction.

Possible implication of Mdm2 as a prognostic marker in invasive laryngeal carcinoma

Laryngeal squamous cell carcinoma is one of the most common malignant neoplasms of the head and neck. In Brazil, laryngeal tumors represent 2% of all cancers and are associated with approximately 3,000 deaths annually. Human papillomavirus (HPV) has been reported to play an important role in the etiology of laryngeal cancer. The aim of the present study was to evaluate the expression of p53, p27, and Mdm2 in laryngeal carcinomas. Sixty-three larynx biopsies were selected for the study, including 9 in situ laryngeal carcinomas, 27 laryngeal carcinomas without metastasis and 27 laryngeal carcinomas with metastasis. Twenty-seven cervical lymph nodes from patients with metastatic lesions were also evaluated. The expression levels of p53, p27, and Mdm2 were assessed by immunohistochemistry using a computer-assisted system. HPV detection and typing were performed using PCR, and the HPV types that were evaluated included HPV 6, 11, 16, 18, 31 and 33. Out of 63 patients, 53 (84.1%) were positive for beta-globin (internal control), and 10 (15.9%) were beta-globin negative and therefore excluded from the evaluation. Thus, 7 (13.2%) out of 53 patients were HPV positive, and 46 (86.8%) out of 53 patients were HPV negative. Statistically significant differences (p < 0.05) in Mdm2 expression levels were observed in the in situ laryngeal carcinoma samples compared with the laryngeal carcinoma samples with metastasis. No statistically significant differences (p > 0.05) in either p53 or p27 expression levels were detected. These findings suggest that Mdm2 may be associated with the invasiveness and aggressiveness of laryngeal carcinomas.

Tumor microenvironmental genomic alterations in juvenile nasopharyngeal angiofibroma

Background To better characterize the pathophysiology of juvenile nasopharyngeal angiofibroma (JNA), endothelial and stromal cells were evaluated by genomic imbalances in association with transcript expression levels of genes mapped on these altered regions. Methods. High-resolution comparative genomic hybridization (HR-CGH) was used in laser-captured endothelial and stromal cells from 9 JNAs. Ten genes were evaluated by quantitative real-timereverse transcription polymerase chain reaction (qRT-PCR) in 15 cases. Results. Although gains were more frequently detected in endothelial cells, 57% of chromosomal alterations were common by both components. Gene expression analyses revealed a positive correlation between endothelial and stromal components for ASPM, CDH1, CTNNB1, FGF18, and SUPT16H. A significant difference was found for FGF18 and AURKB overexpression in stromal cells and AR down-expression in endothelial cells. Conclusions. A similar pattern of gene expression and chromosomal imbalances in both exponents would suggest a common mechanism of functional regulation. AURKB, FGF18, and SUPT16H were identified as potential molecular markers in JNA. (C) 2011 Wiley Periodicals, Inc. Head Neck 34: 485-492, 2012

At the frontiers of surgery: review

The complete surgical removal of disease is a desirable outcome particularly in oncology. Unfortunately much disease is microscopic and difficult to detect causing a liability to recurrence and worsened overall prognosis with attendant costs in terms of morbidity and mortality. It is hoped that by advances in optical diagnostic technology we could better define our surgical margin and so increase the rate of truly negative margins on the one hand and on the other hand to take out only the necessary amount of tissue and leave more unaffected non-diseased areas so preserving function of vital structures. The task has not been easy but progress is being made as exemplified by the presentations at the 2nd Scientific Meeting of the Head and Neck Optical Diagnostics Society (HNODS) in San Francisco in January 2010. We review the salient advances in the field and propose further directions of investigation.

Validade discriminante do questionário de qualidade de vida da Universidade de Washington no contexto brasileiro

OBJETIVO: Avaliar a validade discriminante do questionário de qualidade de vida da Universidade de Washington para pacientes com câncer de cabeça e pescoço e identificar possíveis fatores sociodemográficos que modifiquem seus resultados. MÉTODOS: Foram entrevistados 47 pacientes com câncer de boca e orofaringe em estágio pré-cirúrgico em um hospital no sul do município de São Paulo em 2007, e 141 pacientes sem câncer, pareados por sexo e idade em uma proporção de três para um, que foram atendidos em ambulatórios do mesmo hospital em 2008. Os resultados obtidos para os dois grupos foram comparados pelo teste t de Student. Para os pacientes sem câncer utilizou-se análise de regressão de Poisson para avaliar possíveis fatores de modificação da qualidade de vida. RESULTADOS: O escore geral de qualidade de vida foi significantemente mais elevado (p < 0,001) para os pacientes sem câncer (91,1) do que para os pacientes com câncer (80,6). Observações análogas foram efetuadas para oito dos doze domínios de qualidade de vida compreendidos no questionário (dor, aparência, deglutição, mastigação, fala, ombros, paladar e ansiedade). Como possíveis fatores de modificação dos escores de qualidade de vida foram identificados renda familiar (com impacto nos domínios de recreação, p = 0,017, e função dos ombros, p = 0,049), escolaridade (em ansiedade, p = 0,003), sexo (em função dos ombros, p = 0,038) e dor de dente (em mastigação, p = 0,015). CONCLUSÕES: O questionário tem validade discriminante, pois seus escores são especificamente mais afetados para pacientes com câncer. Reforça-se a indicação do questionário para monitorar o tratamento e recomenda-se avaliar os fatores que podem causar impacto nesses indicadores.