Diogo Patrão

Hospital Israelita Albert Einstein | IIEPAE · Big Data

TNM is a classification system for assessment of progression stage of malignant tumors. The physician, upon patient examination, classifies a tumor using three variables: T, N and M. Definitions of values for T, N and M depend on the tumor topography (or body part), specified as ICD-O codes. These values are then used to infer the Clinical Stage (C...

Clinical trials are studies designed to assess whether a new intervention is better than the current alternatives. However, most of them fail to recruit participants on schedule. It is hard to use Electronic Health Record (EHR) data to find eligible patients, therefore studies rely on manual assessment, which is time consuming, inefficient and requ...

This work develops an automated classifier of pathology reports which infers the topography and the morphology classes of a tumor using codes from the International Classification of Diseases for Oncology (ICD-O). Data from 94,980 patients of the A.C. Camargo Cancer Center was used for training and validation of Naive Bayes classifiers, evaluated b...

The computer-assisted search for knowledge in the medical field has become increasingly frequent. Scientific progress in subjects such as ontology and artificial intelligence allowed researchers to develop methods for capturing, using and sharing specific knowledge. The Li-Fraumeni Syndrome (LFS) is a syndrome that causes multiple primary tumors in...

TUSS is a Brazilian health procedure standard used by the supplementary health providers. Currently, there is no available mapping between TUSS and other standards. In this paper, we analyze performance of two term weighting algorithms when classifying TUSS procedure description. The TF-IDF classified 99% of chapters, 89% of groups, and 33% of subg...

Pathology reports are a main source of information regarding cancer diagnosis and are commonly written following semi-structured templates that include tumour localisation and behaviour. In this work, we evaluated the efficiency of support vector machines (SVMs) to classify pathology reports written in Portuguese into the International Classificati...

Pathology reports are a main source of information regarding cancer diagnosis and are commonly written following semi-structured templates that include tumour localisation and behaviour. In this work, we evaluated the efficiency of support vector machines (SVMs) to classify pathology reports written in Portuguese into the International Classificati...

Background The development of high performance studies evaluating gene expression generated strong demand for biorepositories linked to clinical databases. Juvenile autoimmune diseases provides a unique opportunity to study genetic factors involved in breaking tolerance with minimal influence of environmental factors and represent privileged models...

This work aims at developing an automated classifier of pathology reports, which should be able to infer the localization (topography) and the histological type (morphology) of a tumor in the International Classification of Diseases for Oncology (ICD-O). We used data provided by the A.C. Camargo Cancer Center located in São Paulo for training and v...

Relevant biomedical research relies on finding enough subjects matching inclusion criteria. Researchers struggle to find eligible patients due to: information scattered in many different databases, incompatible data representation, and the technical knowledge required to work directly with databases. We identified the required features of a clinica...

This article discusses the importance of biobanking to health research advancement in developing countries by analyzing the impact of the establishment of a tumor bank at the A C Camargo Hospital, a cancer care and research center located in Sao Paulo, Brazil. For the past 13 years, the human biological samples provided by the tumor bank have been...

In breast cancer patients, primary chemotherapy is associated with the same survival benefits as adjuvant chemotherapy. Residual tumors represent a clinical challenge, as they may be resistant to additional cycles of the same drugs. Our aim was to identify differential transcripts expressed in residual tumors, after neoadjuvant chemotherapy, that m...

Wilms tumor (WT), a tumor composed of three histological components - blastema (BL), epithelia and stroma - is considered an appropriate model system to study the biological relationship between differentiation and tumorigenesis. To investigate molecular associations between nephrogenesis and WT, the gene expression pattern of individual cellular c...

In women with breast cancer submitted to neoadjuvant chemotherapy based in doxorubicin, tumor expression of groups of three genes (PRSS11, MTSS1, CLPTM1 and PRSS11, MTSS1, SMYD2) have classified them as responsive or resistant. We have investigated whether expression of these trios of genes could predict mammary carcinoma response in dogs and wheth...

One goal of gene expression profiling is to identify signature genes that robustly distinguish different types or grades of tumors. Several tumor classifiers based on expression profiling have been proposed using microarray technique. Due to important differences in the probabilistic models of microarray and SAGE technologies, it is important to de...

Clinical stage (CS) is an established indicator of breast cancer outcome. In the present study, a cDNA microarray platform containing 692 genes was used to identify molecular differences between CSII and CSIII disease. Tumor samples were collected from patients with CSII or CSIII breast cancer, and normal breast tissue was collected from women with...

The members of the DnaJ/Hsp40 proteins are highly conserved through evolution, expressed in several tissues and act as co-chaperone regulating protein folding, transport, translational initiation and gene expression. Recently, using cDNA microarray we identified differences in the expression of the JDP1 (DNAJC12) gene, a member of the DnaJ/Hsp40 fa...

One of the goals of gene expression experiments is the identification of differentially expressed genes among populations that could be used as markers. For this purpose, we implemented a model-free Bayesian approach in a user-friendly and freely available web-based tool called BayBoots. In spite of a common misunderstanding that Bayesian and model...

This study was designed to identify genes that could predict response to doxorubicin-based primary chemotherapy in breast cancer patients. Biopsy samples were obtained before primary treatment with doxorubicin and cyclophosphamide. RNA was extracted and amplified and gene expression was analyzed using cDNA microarrays. Response to chemotherapy was...

An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE), "Digital Northern" or Massively Parallel Signature Sequencing (MPSS), is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of...

Results for all evidence measures. This file allows the user to interactively define significance cutoffs for ranked tags. The ranks are based on evidence measures against "no differential expression" hypothesis, i.e., evidences closer to 0 (zero) denote higher confidence in differential expression and closer to 1 (one) denote no evidence of differ...

Brazil is considered to have an immature national innovation system. One significant situation that contributes to it is that Brazil concentrates its research efforts and inventiveness in academic environments, while the private sector has very little access to this activity. Measures are being taken to correct this situation. Nevertheless, scienti...