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.

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.

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.

Primary tuberculosis of the TMJ: presentation of a case and literature review

Tuberculosis (TB) is a frequent health problem. The prevalence of extrapulmonary TB has increased in the last couple of years. Head and neck tuberculosis forms nearly 10% of all extrapulmonary manifestations of the disease. TB of the temporomandibular joint (TMJ) is rare; only a few cases have been reported. The clinical appearance of TB infection of the TMJ has been described as unspecific, resembling arthritis, osteomyelitis, cancer or any kind of chronic joint diseases. This article describes a 22-year-old woman with pain and left preauricular swelling. Magnetic resonance imaging and computed tomography showed an expansive process with destruction of the left condyle and condylar fossa. A fine needle aspiration examination of the swelling showed non-specific granulomatous inflammation. In the following days, a preauricular fistula developed, of which a swab and biopsy specimens were taken. Histological and microbiological examinations revealed an infection with Mycobacterium tuberculosis. The initial antituberculosis treatment consisted of a combination of four antibiotics and could be reduced to two antibiotics in the course of treatment. The treatment was completed successfully after 9 months.

Ear canal cholesteatoma: meta-analysis of clinical characteristics with update on classification, staging and treatment

We present an update on clinical evaluation, staging, classification and treatment of canal cholesteatoma, including a meta-analysis of clinical data of the last 30 years.

Reduced endurance of the cervical flexor muscles in patients with concurrent temporomandibular disorders and neck disability

Subjects with temporomandibular disorders (TMDs) have been found to have clinical signs and symptoms of cervical dysfunction. Although many studies have investigated the relationship between the cervical spine and TMD, no study has evaluated the endurance capacity of the cervical muscles in patients with TMD. Thus the objective of this study was to determine whether patients with TMD had a reduced endurance of the cervical flexor muscles at any level of muscular contraction when compared with healthy subjects. One hundred and forty-nine participants provided data for this study (49 subjects were healthy, 54 had myogenous TMD, and 46 had mixed TMD). There was a significant difference in holding time at 25% MVC between subjects with mixed TMD when compared to subjects with myogenous TMD and healthy subjects. This implies that subjects with mixed TMD had less endurance capacity at a lower level of contraction (25% MVC) than healthy subjects and subjects with myogenous TMD. No significant associations between neck disability, jaw disability, clinical variables and neck flexor endurance test were found.

Do Central Hypersensitivity and Altered Pain Modulation Predict the Course of Chronic Low Back and Neck Pain?

OBJECTIVES:: Widespread central hypersensitivity and altered conditioned pain modulation (CPM) have been documented in chronic pain conditions. Information on their prognostic values is limited. This study tested the hypothesis that widespread central hypersensitivity (WCH) and altered CPM, assessed during the chronic phase of low back and neck pain, predict poor outcome. METHODS:: A total of 169 consecutive patients with chronic low back or neck pain, referred to the pain clinic during 1 year, were analyzed. Pressure pain tolerance threshold at the second toe and tolerance time during cold pressor test at the hand assessed WCH. CPM was measured by the change in pressure pain tolerance threshold (test stimulus) after cold pressor test (conditioning stimulus). A structured telephone interview was performed 12 to 15 months after testing to record outcome parameters. Linear regression models were used, with average and maximum pain intensity of the last 24 hours at follow-up as endpoints. Multivariable analyses included sex, age, catastrophizing scale, Beck Depression Inventory, pain duration, intake of opioids, and type of pain syndrome. RESULTS:: Statistically significant reductions from baseline to follow-up were observed in pain intensity (P<0.001). No evidence for an association between the measures of WCH or CPM and intensity of chronic pain at follow-up was found. DISCUSSION:: A major predictive value of the measures that we used is unlikely. Future studies adopting other assessment modalities and possibly standardized treatments are needed to further elucidate the prognostic value of WCH and altered CPM in chronic pain.

Functional results and quality of life after retrosigmoid vestibular neurectomy in patients with Menière's disease

Severe Ménière's disease (MD) may be debilitating and compromising, despite intensive medical treatment. Vestibular neurectomy (VN) is considered an effective surgical treatment for disabling MD. Our aim was to analyse the medium- to long-term outcome after retrosigmoid VN with special regard to vertigo, quality of life (American Academy of Otolaryngology-Head and Neck Surgery criteria), and pure tone average (PTA).

Diagnosis and treatment of recurrent laryngeal cancer following initial nonsurgical therapy

Surgery is the preferred modality for curative treatment of recurrent laryngeal cancer after failure of nonsurgical treatments. Patients with initial early-stage cancer experiencing recurrence following radiotherapy often have more advanced-stage tumors by the time the recurrence is recognized. About one third of such recurrent cancers are suitable for conservation surgery. Endoscopic resection with the CO(2) laser or open partial laryngectomy (partial vertical, supracricoid, or supraglottic laryngectomies) have been used. The outcomes of conservation surgery appear better than those after total laryngectomy, because of selection bias. Transoral laser surgery is currently used more frequently than open partial laryngectomy for treatment of early-stage recurrence, with outcomes equivalent to open surgery but with less associated morbidity. Laser surgery has also been employed for selective cases of advanced recurrent disease, but patient selection and expertise are required for application of this modality to rT3 tumors. In general, conservation laryngeal surgery is a safe and effective treatment for localized recurrences after radiotherapy for early-stage glottic cancer. Recurrent advanced-stage cancers should generally be treated by total laryngectomy.

Radionecrosis or tumor recurrence after radiation of laryngeal and hypopharyngeal carcinomas

OBJECTIVE: To analyze the incidence and diagnostic difficulties of radionecrosis vs tumor recurrence of laryngeal and hypopharyngeal carcinomas. STUDY DESIGN AND SETTING: Retrospective study on 341 patients treated by radiation alone or radiochemotherapy. The clinicopathologic findings, work-up, treatment, and follow-up of 20 patients with symptoms suggestive but negative for tumor recurrence on initial imaging studies and endoscopy were analyzed. RESULTS: The incidence of chondroradionecrosis in 341 irradiated patients was 5%. Ten of 20 patients initially negative for tumor recurrence were treated by total laryngectomy; in all laryngectomy specimens, chondroradionecrosis was present, in six specimens associated with tumor recurrence. Ten patients were treated by tracheotomy and tumor recurrence was detected in one patient during follow-up. CONCLUSION: Chondroradionecrosis is a relatively rare treatment complication. Typical imaging findings suggestive of radionecrosis are often missing. Tumor recurrence may be present beneath an intact mucosa and missed by endoscopy.