Integrated proteogenomic approach identifying a protein signature of COPD and a new splice variant of SORBS1.

Translation of genomic alterations to protein changes in chronic obstructive pulmonary disease (COPD) is largely unexplored. Using integrated proteomic and RNA sequencing analysis of COPD and control lung tissues, we identified a protein signature in COPD characterised by extracellular matrix changes and a potential regulatory role for SUMO2. Furthermore, we identified 61 differentially expressed novel, non-reference, peptides in COPD compared with control lungs. This included two peptides encoding for a new splice variant of SORBS1, of which the transcript usage was higher in COPD compared with control lungs. These explorative findings and integrative proteogenomic approach open new avenues to further unravel the pathology of COPD.

Deep learning for sex determination: Analyzing over 200,000 panoramic radiographs.

The objective of this study is to assess the performance of an innovative AI-powered tool for sex determination using panoramic radiographs (PR) and to explore factors affecting the performance of the convolutional neural network (CNN). The study involved 207,946 panoramic dental X-rays and their corresponding reports from 15 clinical centers in São Paulo, Brazil. The PRs were acquired with four different devices, and 58% of the patients were female. Data preprocessing included anonymizing the exams, extracting pertinent information from the reports, such as sex, age, type of dentition, and number of missing teeth, and organizing the data into a PostgreSQL database. Two neural network architectures, a standard CNN and a ResNet, were utilized for sex classification, with both undergoing hyperparameter tuning and cross-validation to ensure optimal performance. The CNN model achieved 95.02% accuracy in sex estimation, with image resolution being a significant influencing factor. The ResNet model attained over 86% accuracy in subjects older than 6 years and over 96% in those over 16 years. The algorithm performed better on female images, and the area under the curve (AUC) exceeded 96% for most age groups, except the youngest. Accuracy values were also assessed for different dentition types (deciduous, mixed, and permanent) and missing teeth. This study demonstrates the effectiveness of an AI-driven tool for sex determination using PR and emphasizes the role of image resolution, age, and sex in determining the algorithm's performance.

Contrast phase recognition in liver computer tomography using deep learning.

Hepatocellular carcinoma (HCC) has become the 4th leading cause of cancer-related deaths, with high social, economical and health implications. Imaging techniques such as multiphase computed tomography (CT) have been successfully used for diagnosis of liver tumors such as HCC in a feasible and accurate way and its interpretation relies mainly on comparing the appearance of the lesions in the different contrast phases of the exam. Recently, some researchers have been dedicated to the development of tools based on machine learning (ML) algorithms, especially by deep learning techniques, to improve the diagnosis of liver lesions in imaging exams. However, the lack of standardization in the naming of the CT contrast phases in the DICOM metadata is a problem for real-life deployment of machine learning tools. Therefore, it is important to correctly identify the exam phase based only on the image and not on the exam metadata, which is unreliable. Motivated by this problem, we successfully created an annotation platform and implemented a convolutional neural network (CNN) to automatically identify the CT scan phases in the HCFMUSP database in the city of São Paulo, Brazil. We improved this algorithm with hyperparameter tuning and evaluated it with cross validation methods. Comparing its predictions with the radiologists annotation, it achieved an accuracy of 94.6%, 98% and 100% in the testing dataset for the slice, volume and exam evaluation, respectively.