High-throughput adaptive sampling for whole-slide histopathology image analysis (HASHI) via convolutional neural networks: Application to invasive breast cancer detection.

Precise detection of invasive cancer on whole-slide images (WSI) is a critical first step in digital pathology tasks of diagnosis and grading. Convolutional neural network (CNN) is the most popular representation learning method for computer vision tasks, which have been successfully applied in digital pathology, including tumor and mitosis detection. However, CNNs are typically only tenable with relatively small image sizes (200 × 200 pixels). Only recently, Fully convolutional networks (FCN) are able to deal with larger image sizes (500 × 500 pixels) for semantic segmentation. Hence, the direct application of CNNs to WSI is not computationally feasible because for a WSI, a CNN would require billions or trillions of parameters. To alleviate this issue, this paper presents a novel method, High-throughput Adaptive Sampling for whole-slide Histopathology Image analysis (HASHI), which involves: i) a new efficient adaptive sampling method based on probability gradient and quasi-Monte Carlo sampling, and, ii) a powerful representation learning classifier based on CNNs. We applied HASHI to automated detection of invasive breast cancer on WSI. HASHI was trained and validated using three different data cohorts involving near 500 cases and then independently tested on 195 studies from The Cancer Genome Atlas. The results show that (1) the adaptive sampling method is an effective strategy to deal with WSI without compromising prediction accuracy by obtaining comparative results of a dense sampling (∼6 million of samples in 24 hours) with far fewer samples (∼2,000 samples in 1 minute), and (2) on an independent test dataset, HASHI is effective and robust to data from multiple sites, scanners, and platforms, achieving an average Dice coefficient of 76%.

Accurate and reproducible invasive breast cancer detection in whole-slide images: A Deep Learning approach for quantifying tumor extent.

With the increasing ability to routinely and rapidly digitize whole slide images with slide scanners, there has been interest in developing computerized image analysis algorithms for automated detection of disease extent from digital pathology images. The manual identification of presence and extent of breast cancer by a pathologist is critical for patient management for tumor staging and assessing treatment response. However, this process is tedious and subject to inter- and intra-reader variability. For computerized methods to be useful as decision support tools, they need to be resilient to data acquired from different sources, different staining and cutting protocols and different scanners. The objective of this study was to evaluate the accuracy and robustness of a deep learning-based method to automatically identify the extent of invasive tumor on digitized images. Here, we present a new method that employs a convolutional neural network for detecting presence of invasive tumor on whole slide images. Our approach involves training the classifier on nearly 400 exemplars from multiple different sites, and scanners, and then independently validating on almost 200 cases from The Cancer Genome Atlas. Our approach yielded a Dice coefficient of 75.86%, a positive predictive value of 71.62% and a negative predictive value of 96.77% in terms of pixel-by-pixel evaluation compared to manually annotated regions of invasive ductal carcinoma.

Toxinas e perfil protéico de amostras de Actinobacillus suis provenientes de plantéis suínos norte-americanos / Toxins and proteic profile of Actinobacillus suis samples from North American hog herds

Actinobacillus suis (A.suis) surgiu como uma grande ameaça aos plantéis suínos norte-americanos. Os sinais clínicos e as lesões são particularmente variáveis e podem lembrar aquelas causadas por outros organismos, como o Actinobacillus pleuropneumoniae (App), podendo ter como causa a similaridade na produção das toxinas ApxI e ApxII. Os objetivos do estudo foram confirmar a produção das toxinas ApxI e ApxII, investigar a produção de toxina geneticamente semelhante à Apx III e analisar as proteínas totais, verificando se existe similaridade entre os isolados provenientes de diferentes plantéis de suínos norte-americanos. Neste estudo, todas as cepas de A. suis foram positivas para os genes codificadores das toxinas ApxI e ApxII, usando o método de reação em cadeia de polimerase - multiplex (PCR-multiplex); e as proteínas totais de 70 amostras de A. suis, oriundos de diferentes plantéis suínos norte-americanos, foram analisadas por meio de eletroforese em gel de poliacrilaminda desnaturante (SDS-PAGE) e foram idênticas. A similaridade eletroforética observada entre as proteínas totais das bactérias analisadas indica a possibilidade de haver uma proteção cruzada a partir de uma provável vacina universal desenvolvida com esses antígenos para A. suis.

Actinobacillus suis (A. suis) has arisen as a great threat to the North American hog herds. The clinical symptoms and lesions are particularly variable and may resemble the same caused by other pathogenic organisms, such as Actinobacillus pleuropneumoniae (App), which can similarly lead to the production of the toxins ApxI and ApxII. This study aimed to confirm the production of the toxins ApxI and ApxII, as well as, to investigate the production of toxins that are genetically similar to ApxIII, and analyze total protein to verify whether there is any similarity among the isolated samples obtained from different North American hog herds. In this study, all the strains of A. suis were positive for the genes that codify the toxins ApxI and ApxII using the multiplex polymerase chain reaction (PCR-multiplex) method; and total protein from 70 samples of A. suis, obtained from different North American hog herds, were analyzed through denaturing polyacrylamide gel electrophoresis (SDS-PAGE), and were identical. The electrophoretic similarity observed among total protein of the analyzed bacteria indicates that there is the possibility of existing a cross protection in case of developing a probable universal vaccine with the antigens of A. suis.

Toxinas e perfil protéico de amostras de Actinobacillus suis provenientes de plantéis suínos norte-americanos

Actinobacillus suis (A. suis) has arisen as a great threat to the North American hog herds. The clinical symptoms and lesions are particularly variable and may resemble the same caused by other pathogenic organisms, such as Actinobacillus pleuropneumoniae (App), which can similarly lead to the production of the toxins ApxI and ApxII. This study aimed to confirm the production of the toxins ApxI and ApxII, as well as, to investigate the production of toxins that are genetically similar to ApxIII, and analyze total protein to verify whether there is any similarity among the isolated samples obtained from different North American hog herds. In this study, all the strains of A. suis were positive for the genes that codify the toxins ApxI and ApxII using the multiplex polymerase chain reaction (PCR-multiplex) method; and total protein from 70 samples of A. suis, obtained from different North American hog herds, were analyzed through denaturing polyacrylamide gel electrophoresis (SDS-PAGE), and were identical. The electrophoretic similarity observed among total protein of the analyzed bacteria indicates that there is the possibility of existing a cross protection in case of developing a probable universal vaccine with the antigens of A. suis.

Actinobacillus suis (A.suis) surgiu como uma grande ameaça aos plantéis suínos norte-americanos. Os sinais clínicos e as lesões são particularmente variáveis e podem lembrar aquelas causadas por outros organismos, como o Actinobacillus pleuropneumoniae (App), podendo ter como causa a similaridade na produção das toxinas ApxI e ApxII. Os objetivos do estudo foram confirmar a produção das toxinas ApxI e ApxII, investigar a produção de toxina geneticamente semelhante à Apx III e analisar as proteínas totais, verificando se existe similaridade entre os isolados provenientes de diferentes plantéis de suínos norte-americanos. Neste estudo, todas as cepas de A. suis foram positivas para os genes codificadores das toxinas ApxI e ApxII, usando o método de reação em cadeia de polimerase - multiplex (PCR-multiplex); e as proteínas totais de 70 amostras de A. suis, oriundos de diferentes plantéis suínos norte-americanos, foram analisadas por meio de eletroforese em gel de poliacrilaminda desnaturante (SDS-PAGE) e foram idênticas. A similaridade eletroforética observada entre as proteínas totais das bactérias analisadas indica a possibilidade de haver uma proteção cruzada a partir de uma provável vacina universal desenvolvida com esses antígenos para A. suis.

Toxinas e perfil protéico de amostras de Actinobacillus suis provenientes de plantéis suínos norte-americanos

Actinobacillus suis (A. suis) has arisen as a great threat to the North American hog herds. The clinical symptoms and lesions are particularly variable and may resemble the same caused by other pathogenic organisms, such as Actinobacillus pleuropneumoniae (App), which can similarly lead to the production of the toxins ApxI and ApxII. This study aimed to confirm the production of the toxins ApxI and ApxII, as well as, to investigate the production of toxins that are genetically similar to ApxIII, and analyze total protein to verify whether there is any similarity among the isolated samples obtained from different North American hog herds. In this study, all the strains of A. suis were positive for the genes that codify the toxins ApxI and ApxII using the multiplex polymerase chain reaction (PCR-multiplex) method; and total protein from 70 samples of A. suis, obtained from different North American hog herds, were analyzed through denaturing polyacrylamide gel electrophoresis (SDS-PAGE), and were identical. The electrophoretic similarity observed among total protein of the analyzed bacteria indicates that there is the possibility of existing a cross protection in case of developing a probable universal vaccine with the antigens of A. suis.

Actinobacillus suis (A.suis) surgiu como uma grande ameaça aos plantéis suínos norte-americanos. Os sinais clínicos e as lesões são particularmente variáveis e podem lembrar aquelas causadas por outros organismos, como o Actinobacillus pleuropneumoniae (App), podendo ter como causa a similaridade na produção das toxinas ApxI e ApxII. Os objetivos do estudo foram confirmar a produção das toxinas ApxI e ApxII, investigar a produção de toxina geneticamente semelhante à Apx III e analisar as proteínas totais, verificando se existe similaridade entre os isolados provenientes de diferentes plantéis de suínos norte-americanos. Neste estudo, todas as cepas de A. suis foram positivas para os genes codificadores das toxinas ApxI e ApxII, usando o método de reação em cadeia de polimerase - multiplex (PCR-multiplex); e as proteínas totais de 70 amostras de A. suis, oriundos de diferentes plantéis suínos norte-americanos, foram analisadas por meio de eletroforese em gel de poliacrilaminda desnaturante (SDS-PAGE) e foram idênticas. A similaridade eletroforética observada entre as proteínas totais das bactérias analisadas indica a possibilidade de haver uma proteção cruzada a partir de uma provável vacina universal desenvolvida com esses antígenos para A. suis.

Toxinas e perfil protéico de amostras de Actinobacillus suis provenientes de plantéis suínos norte-americanos

Actinobacillus suis (A. suis) has arisen as a great threat to the North American hog herds. The clinical symptoms and lesions are particularly variable and may resemble the same caused by other pathogenic organisms, such as Actinobacillus pleuropneumoniae (App), which can similarly lead to the production of the toxins ApxI and ApxII. This study aimed to confirm the production of the toxins ApxI and ApxII, as well as, to investigate the production of toxins that are genetically similar to ApxIII, and analyze total protein to verify whether there is any similarity among the isolated samples obtained from different North American hog herds. In this study, all the strains of A. suis were positive for the genes that codify the toxins ApxI and ApxII using the multiplex polymerase chain reaction (PCR-multiplex) method; and total protein from 70 samples of A. suis, obtained from different North American hog herds, were analyzed through denaturing polyacrylamide gel electrophoresis (SDS-PAGE), and were identical. The electrophoretic similarity observed among total protein of the analyzed bacteria indicates that there is the possibility of existing a cross protection in case of developing a probable universal vaccine with the antigens of A. suis.

Actinobacillus suis (A.suis) surgiu como uma grande ameaça aos plantéis suínos norte-americanos. Os sinais clínicos e as lesões são particularmente variáveis e podem lembrar aquelas causadas por outros organismos, como o Actinobacillus pleuropneumoniae (App), podendo ter como causa a similaridade na produção das toxinas ApxI e ApxII. Os objetivos do estudo foram confirmar a produção das toxinas ApxI e ApxII, investigar a produção de toxina geneticamente semelhante à Apx III e analisar as proteínas totais, verificando se existe similaridade entre os isolados provenientes de diferentes plantéis de suínos norte-americanos. Neste estudo, todas as cepas de A. suis foram positivas para os genes codificadores das toxinas ApxI e ApxII, usando o método de reação em cadeia de polimerase - multiplex (PCR-multiplex); e as proteínas totais de 70 amostras de A. suis, oriundos de diferentes plantéis suínos norte-americanos, foram analisadas por meio de eletroforese em gel de poliacrilaminda desnaturante (SDS-PAGE) e foram idênticas. A similaridade eletroforética observada entre as proteínas totais das bactérias analisadas indica a possibilidade de haver uma proteção cruzada a partir de uma provável vacina universal desenvolvida com esses antígenos para A. suis.