The International LAM Registry: A Component of an Innovative Web-Based Clinician, Researcher, and Patient-Driven Rare Disease Research Platform

Background: A relative friability to capture a sufficiently large patient population in any one geographic location has traditionally limited research into rare diseases. Methods and Results: Clinicians interested in the rare disease lymphangioleiomyomatosis (LAM) have worked with the LAM Treatment Alliance, the MIT Media Lab, and Clozure Associates to cooperate in the design of a state-of-the-art data coordination platform that can be used for clinical trials and other research focused on the global LAM patient population. This platform is a component of a set of web-based resources, including a patient self-report data portal, aimed at accelerating research in rare diseases in a rigorous fashion. Conclusions: Collaboration between clinicians, researchers, advocacy groups, and patients can create essential community resource infrastructure to accelerate rare disease research. The International LAM Registry is an example of such an effort.

Use of Medical Subject Headings (MeSH) in Portuguese for categorizing web-based healthcare content

Introduction: Internet users are increasingly using the worldwide web to search for information relating to their health. This situation makes it necessary to create specialized tools capable of supporting users in their searches. Objective: To apply and compare strategies that were developed to investigate the use of the Portuguese version of Medical Subject Headings (MeSH) for constructing an automated classifier for Brazilian Portuguese-language web-based content within or outside of the field of healthcare, focusing on the lay public. Methods: 3658 Brazilian web pages were used to train the classifier and 606 Brazilian web pages were used to validate it. The strategies proposed were constructed using content-based vector methods for text classification, such that Naive Bayes was used for the task of classifying vector patterns with characteristics obtained through the proposed strategies. Results: A strategy named InDeCS was developed specifically to adapt MeSH for the problem that was put forward. This approach achieved better accuracy for this pattern classification task (0.94 sensitivity, specificity and area under the ROC curve). Conclusions: Because of the significant results achieved by InDeCS, this tool has been successfully applied to the Brazilian healthcare search portal known as Busca Saude. Furthermore, it could be shown that MeSH presents important results when used for the task of classifying web-based content focusing on the lay public. It was also possible to show from this study that MeSH was able to map out mutable non-deterministic characteristics of the web. (c) 2010 Elsevier Inc. All rights reserved.

Oral Health Promotion Through an Online Training Program for Medical Students

The objective of this study was to compare the impact on knowledge and counseling skills of face-to-face and Internet-based oral health training programs on medical students. Participants consisted of 148 (82 percent) of the 180 invited students attending their fifth academic year at the Faculty of Medicine, University of Sao Paulo, Brasil, in 2007. The interventions took place during a three-month training period in the clinical Center for Health Promotion, which comprised part of a clerkship in Internal Medicine. The students were divided into four groups: 1) Control Group (Control), with basic intervention; 2) Brochure Group (Br), with basic intervention plus complete brochure with oral health themes; 3) Cybertutor Group (Cy), with basic intervention plus access to an Internet-based training program about oral health themes; and 4) Cybertutor + Contact Group (Cy+C), the same as Cy plus brief proactive contact with a tutor. The impact of these interventions on student knowledge was measured with pre- and post assessments, and student skills in asking and counseling about oral health were assessed with an objective structured clinical examination (OSCE). Multivariate logistic regression models were applied to identify the odds ratios of scoring above Control's medians on the final assessment and the OSCE. In the results, Cy+C performed significantly better than Control on both the final assessment (OR 9.4; 95% CI 2.7-32.8) and the OSCE (OR 5.6; 95% CI 1.9-16.3) and outperformed all the other groups. The Cy+C group showed the most significant increase in knowledge and the best skills in asking and counseling about oral health.

ProbFAST: Probabilistic Functional Analysis System Tool

Background: The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results: We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions: ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.

A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling

Background: High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent powerful techniques that provide global transcription profiles of different cell types through sequencing of short fragments of transcripts, denominated sequence tags. These techniques have improved our understanding about the relationships between these expression profiles and cellular phenotypes. Despite this, more reliable datasets are still necessary. In this work, we present a web-based tool named S3T: Score System for Sequence Tags, to index sequenced tags in accordance with their reliability. This is made through a series of evaluations based on a defined rule set. S3T allows the identification/selection of tags, considered more reliable for further gene expression analysis. Results: This methodology was applied to a public SAGE dataset. In order to compare data before and after filtering, a hierarchical clustering analysis was performed in samples from the same type of tissue, in distinct biological conditions, using these two datasets. Our results provide evidences suggesting that it is possible to find more congruous clusters after using S3T scoring system. Conclusion: These results substantiate the proposed application to generate more reliable data. This is a significant contribution for determination of global gene expression profiles. The library analysis with S3T is freely available at http://gdm.fmrp.usp.br/s3t/.S3T source code and datasets can also be downloaded from the aforementioned website.

Insulin and leptin relations in obesity: a multimedia approach

Obesity has been recognized as a worldwide public health problem. It significantly increases the chances of developing several diseases, including Type II diabetes. The roles of insulin and leptin in obesity involve reactions that can be better understood when they are presented step by step. The aim of this work was to design software with data from some of the most recent publications on obesity, especially those concerning the roles of insulin and leptin in this metabolic disturbance. The most notable characteristic of this software is the use of animations representing the cellular response together with the presentation of recently discovered mechanisms on the participation of insulin and leptin in processes leading to obesity. The software was field tested in the Biochemistry of Nutrition web-based course. After using the software and discussing its contents in chatrooms, students were asked to answer an evaluation survey about the whole activity and the usefulness of the software within the learning process. The teaching assistants (TA) evaluated the software as a tool to help in the teaching process. The students' and TAs' satisfaction was very evident and encouraged us to move forward with the software development and to improve the use of this kind of educational tool in biochemistry classes.

Accuracy of store-and-forward diagnosis in leproy

Telemedicine might increase the speed of diagnosis for leprosy and reduce the development of disabilities. We compared the accuracy of diagnosis made by telemedicine with that made by in-person examination. The cases were patients with suspected leprosy at eight public health clinics in outlying areas of the city of Sao Paulo. The case history and clinical examination data, and at least two clinical images for each patient, were stored in a web-based system developed for teledermatology. After the examination in the public clinic, patients then attended a teaching hospital for an in-person examination. The benchmark was the clinical examination of two dermatologists at the university hospital. From August 2005 to April 2006, 142 suspected cases of leprosy were forwarded to the website by the doctors at the clinics. Of these, 36 cases were excluded. There was overall agreement in the diagnosis of leprosy in 74% of the 106 remaining cases. The sensitivity was 78% and the specificity was 31%. Although the specificity was low, the study suggests that telemedicine may be a useful low-cost method for obtaining second opinions in programmes to control leprosy.

Factors affecting management decisions in rectal cancer in clinical practice: results from a national survey

Management of rectal cancer has become increasingly complex and a multidisciplinary approach is considered of key importance for improving outcomes. A national survey among specialists involved in this multidisciplinary setting was performed. A web-based survey containing 11 questions regarding rectal cancer management was sent to surgeons and medical oncologists registered by their corresponding societies as members. Statistical analysis was performed using the chi-square and Fisher`s exact tests for all categorical variables according to response to individual questions. Multivariate analysis was performed using Cox`s logistic regression. Overall, 418 email recipients responded the survey. Local staging was performed without either magnetic resonance imaging or endorectal ultrasound by 64% of responders. Seventy-two percent considered that final management decision should be made after neoadjuvant chemoradiation therapy. Additionally, 46% considered that an alternative procedure (local excision or observation) was appropriate in a patient with a complete clinical response. Colorectal surgeons were more frequently in favor of longer intervals after completion of chemoradiation therapy (P = 0.001) and of alternative management procedures after a complete clinical response (P = 0.02). After multivariate analysis, the choice of a watch and wait approach after a complete clinical response following neoadjuvant chemoradiation therapy was significantly more frequent among surgeons (OR 3.5, 95% CI 1.8-7.1). Surgeons seem to be more in favor of tailoring management of rectal cancer according to tumor response after neoadjuvant chemoradiation therapy, with longer intervals after chemoradiation therapy, decisions about treatment strategy being made after chemoradiation therapy instead of before, and the use of alternative surgical procedures after a complete clinical response following neoadjuvant therapy.

PK/DB: database for pharmacokinetic properties and predictive in silico ADME models

The study of pharmacokinetic properties (PK) is of great importance in drug discovery and development. In the present work, PK/DB (a new freely available database for PK) was designed with the aim of creating robust databases for pharmacokinetic studies and in silico absorption, distribution, metabolism and excretion (ADME) prediction. Comprehensive, web-based and easy to access, PK/DB manages 1203 compounds which represent 2973 pharmacokinetic measurements, including five models for in silico ADME prediction (human intestinal absorption, human oral bioavailability, plasma protein binding, bloodbrain barrier and water solubility).

Remote Spectroscopy in the Visible Using Fibers on the Optical Internet Network

The work presented here demonstrates the feasibility of using the single-mode fibers of an optical Internet network to deliver visible light between separate laboratories as a way to perform remote spectroscopy in the visible for teaching purposes. The coupling of a broadband light source into the single-mode fiber (SMF) and the characterization of optical losses as a function of the wavelength are discussed. Sample spectra were measured with a portable spectrometer controlled by an acquisition program developed with the LabVIEW software that allows the data to be collected and analyzed.