Dual-path convolutional neural network using micro-FTIR imaging to predict breast cancer subtypes and biomarkers levels: estrogen receptor, progesterone receptor, HER2 and Ki67

Breast cancer molecular subtypes classification plays an import role to sort patients with divergent prognosis. The biomarkers used are Estrogen Receptor (ER), Progesterone Receptor (PR), HER2, and Ki67. Based on these biomarkers expression levels, subtypes are classified as Luminal A (LA), Luminal B (LB), HER2 subtype, and Triple-Negative Breast Cancer (TNBC). Immunohistochemistry is used to classify subtypes, although interlaboratory and interobserver variations can affect its accuracy, besides being a time-consuming technique. The Fourier transform infrared micro-spectroscopy may be coupled with deep learning for cancer evaluation, where there is still a lack of studies for subtypes and biomarker levels prediction. This study presents a novel 2D deep learning approach to achieve these predictions. Sixty micro-FTIR images of 320x320 pixels were collected from a human breast biopsies microarray. Data were clustered by K-means, preprocessed and 32x32 patches were generated using a fully automated approach. CaReNet-V2, a novel convolutional neural network, was developed to classify breast cancer (CA) vs adjacent tissue (AT) and molecular subtypes, and to predict biomarkers level. The clustering method enabled to remove non-tissue pixels. Test accuracies for CA vs AT and subtype were above 0.84. The model enabled the prediction of ER, PR, and HER2 levels, where borderline values showed lower performance (minimum accuracy of 0.54). Ki67 percentage regression demonstrated a mean error of 3.6%. Thus, CaReNet-V2 is a potential technique for breast cancer biopsies evaluation, standing out as a screening analysis technique and helping to prioritize patients.Comment: 32 pages, 3 figures, 6 table

One-dimensional convolutional neural network model for breast cancer subtypes classification and biochemical content evaluation using micro-FTIR hyperspectral images

Breast cancer treatment still remains a challenge, where molecular subtypes classification plays a crucial role in selecting appropriate and specific therapy. The four subtypes are Luminal A (LA), Luminal B (LB), HER2 subtype, and Triple-Negative Breast Cancer (TNBC). Immunohistochemistry is the gold-standard evaluation, although interobserver variations are reported and molecular signatures identification is time-consuming. Fourier transform infrared micro-spectroscopy with machine learning approaches have been used to evaluate cancer samples, presenting biochemical-related explainability. However, this explainability is harder when using deep learning. This study created a 1D deep learning tool for breast cancer subtype evaluation and biochemical contribution. Sixty hyperspectral images were acquired from a human breast cancer microarray. K-Means clustering was applied to select tissue and paraffin spectra. CaReNet-V1, a novel 1D convolutional neural network, was developed to classify breast cancer (CA) and adjacent tissue (AT), and molecular subtypes. A 1D adaptation of Grad-CAM was applied to assess the biochemical impact to the classifications. CaReNet-V1 effectively classified CA and AT (test accuracy of 0.89), as well as HER2 and TNBC subtypes (0.83 and 0.86), with greater difficulty for LA and LB (0.74 and 0.68). The model enabled the evaluation of the most contributing wavenumbers to the predictions, providing a direct relationship with the biochemical content. Therefore, CaReNet-V1 and hyperspectral images is a potential approach for breast cancer biopsies assessment, providing additional information to the pathology report. Biochemical content impact feature may be used for other studies, such as treatment efficacy evaluation and development new diagnostics and therapeutic methods.Comment: 23 pages, 5 figures, 2 table

Association of Nd:YAG laser and calcium-phosphate desensitizing pastes on dentin permeability and tubule occlusion

Objective: To evaluate the efficacy of Nd:YAG laser associated with calcium-phosphate desensitizing pastes on dentin permeability and tubule occlusion after erosive/abrasive challenges. Methodology: Dentin specimens were exposed to 17% ethylene diamine tetra-acetic acid (EDTA) solution for 5 min and randomly allocated into five groups: G1, control (no treatment); G2, Nd:YAG laser (1 W, 10 Hz, 100 mJ, 85 J/cm2); G3, Laser + TeethmateTM Desensitizer; G4, Laser + Desensibilize Nano P; and G5, Laser+Nupro®. Specimens underwent a 5-day erosion-abrasion cycling. Hydraulic conductance was measured post-EDTA, post-treatment, and post-cycling. Post-treatment and post-cycling permeability (%Lp) was calculated based on post-EDTA measurements, considered 100%. Open dentin tubules (ODT) were calculated at the abovementioned experimental moments using scanning electron microscopy and ImageJ software (n=10). Data were analyzed using two-way repeated measures ANOVA and Tukey’s test (α=0.05). Results: G1 presented the highest %Lp post-treatment of all groups (p<0.05), without significantly differences among them. At post-cycling, %Lp significantly decreased in G1, showed no significant differences from post-treatment in G3 and G4, and increased in G2 and G5, without significant differences from G1 (p>0.05). We found no significant differences in ODT among groups (p>0.05) post-EDTA. At post-treatment, treated groups did not differ from each other, but presented lower ODT than G1 (p<0.001). As for post-cycling, we verified no differences among groups (p>0.05), although ODT was significantly lower for all groups when compared to post-EDTA values (p<0.001). Conclusion: All treatments effectively reduced dentin permeability and promoted tubule occlusion after application

Hematoporfirina e derivados : propriedades ópticas e terapia fotodinâmica de câncer

Orientador: Jorge Humberto NicolaDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb WataghinResumo: No presente trabalho desenvolvemos o estudo, sob o ponto de vista físico, da Terapia fotodinâmica do Câncer (PDT), bem como de substâncias usadas com tal processo. A PDT é uma técnica de uso clínico no tratamento de câncer já consagrada em outros países e ainda não implantada no nosso, que consiste na destruição do tecido maligno via excitação óptica de moléculas de um derivado da hematoporfirina (HpD), previamente injetado no paciente. Na primeira parte do nosso trabalho apresentamos, além de uma revisão bibliográfica, um estudo que situa as fases do processo, separando-as sob o ponto de vista da química, biologia e física, o que inclui a preparação do composto, a ação metabólica do mesmo, bem como o efeito físico propriamente dito da fotorradiação. A parte final do trabalho está dedicada ao estudo das propriedades ópticas da hematoporfirina e de seus derivados, que por sua complexibilidade estrutural apresentam espectros de absorção, fluorescência e Raman, de difícil interpretação, podendo levar até mesmo a erros, como os encontrados na literaturaAbstract: In this work we present a study of Photodynamic Therapy of Cancer (PDT) from the physical point, of view as well as the study of substances used in this process. PDT is a type of cancer treatment, therapy successfully used in other countries, but unknown in our own country. It consists of the destruction of malignous tissues by optical excitation of the molecules of an hematoporphyrin derivative (HpD) previouly injected in the patient. In the first part of this work we present a study with a bibliographical review that establishes the steps of the process, dividing them under the chemical, physical and biological point of view. This includes the compound preparation, its metabolic action and the physical effect of photoradiation. The last part of the work consists of the study of the optical properties of the hematoporphyrin and its derivatives which, due to their complex structures, show absorption, fluorescence and Raman spectra of difficult, interpretation, leading to errors found in other publicationsMestradoFísicaMestre em Físic

Processos para monitoração e otimização da terapia fotodinâmica de tumores

Orientador: Jorge Humberto NicolaTese (doutorado) - Universidade Estadual de Campinas. Instituto de Fisica Gleb W ataghinResumo: A Terapia Fotodinâmica de Câncer, como um processo complexo, permite o desenvolvimento de estudos direcionados à diferentes áreas do conhecimento. No presente trabalho apresentamos inicialmente as bases da terapia ressaltando a sua forte dependência com a espectroscopia óptica. Apresentamos toda a "ferramenta" básica que possibilitou o entendimento dos nossos resultados experimentais em fluorescência e Raman, os quais acrescentam contribuições originais, experimental e teórica, para esta linha de pesquisa. Nosso objetivo principal foi o de utilizar resultados acadêmicos, como os de fluorescência e absorção óptica, para elaborar experimentos fronteiriços com a prática médica. Neste sentido demonstramos a viabilidade de um método capaz de monitorar o processo da terapia "in vivo", bem como mostramos que a eficiência da Terapia Fotodinâmica de câncer pode ser melhorada em condições hiperbáricas de oxigênio adequadasAbstract: Photodynamic Therapy for the treatment of Cancer is a very complex process which leaded us in the study of different areas of knowledge. In this work we discuss all the basic concepts of the Photodinamic Therapy in strong connection to optical spectroscopy. The scientific tools indispensable for understanding of our results in fluorescence and Raman spectra were presented added with original experimental and theoretical contributions. The aim of this thesis was the use of academic results which could be useful in medicine. Therefore we have demonstrated the feasibility of a new method for monitoring the Photodynamic Therapy "in vivo". Besides these results we were able to demonstrate that in Hyperbaric Oxygen atmosphere the PDT process would probably be accelerated.DoutoradoFísicaDoutor em Ciência

Diabetes Monitoring through Urine Analysis Using ATR-FTIR Spectroscopy and Machine Learning

Diabetes mellitus (DM) is a widespread and rapidly growing disease, and it is estimated that it will impact up to 693 million adults by 2045. To cope this challenge, the innovative advances in non-destructive progressive urine glucose-monitoring platforms are important for improving diabetes surveillance technologies. In this study, we aim to better evaluate DM by analyzing 149 urine spectral samples (86 diabetes and 63 healthy control male Wistar rats) utilizing attenuated total reflection–Fourier transform infrared (ATR-FTIR) spectroscopy combined with machine learning (ML) methods, including a 3D discriminant analysis approach—3D–Principal Component Analysis–Linear Discriminant Analysis (3D-PCA-LDA)—in the ‘bio-fingerprint’ region of 1800–900 cm−1. The 3D discriminant analysis technique demonstrated superior performance compared to the conventional PCA-LDA approach with the 3D-PCA-LDA method achieving 100% accuracy, sensitivity, and specificity. Our results show that this study contributes to the existing methodologies on non-destructive diagnostic methods for DM and also highlights the promising potential of ATR-FTIR spectroscopy with an ML-driven 3D-discriminant analysis approach in disease classification and monitoring

Influence of Fixation Products Used in the Histological Processing in the FTIR Spectra of Lung Cells

The aim of the present study is to evaluate the differences on FTIR spectra of the normal lung cell (noncancerous mice lung epithelial cell line e10) due to different fixation protocols for histological processing. The results shown that formalin and methacarn (normally used in fixation) did cause many changes on the FTIR spectra of mice lung cells e10, mainly in the organic compounds (800-1800 cm(-1)) in lipids, DNA, and proteins, and the alcohol 70% fixation protocol caused almost no changes on the FTIR spectra compared to unfixed cells spectra (in PBS). It can be concluded that histological processing with alcohol 70% fixation protocol can be used in the FTIR study of mice lung cell line e10.FAPESP-CEPID [05/51689-2]CNPq-INFO [573916/2008]; CNPq [143166/2009-3

Análise morfológica, através de microscopia eletrônica de varredura, da ação do laser de Er: YAG em superfícies radiculares submetidas à raspagem e aplainamento radicular

The purpose of this study was to morphologically evaluate, by means of scanning electron microscopy, the effects of Er:YAG laser on the treatment of root surfaces submitted to scaling and root planing with conventional periodontal instruments. Eighteen root surfaces (n = 18), which had been previously scaled and planed, were assigned to 3 groups (n = 6). The control Group (G1) received no further treatment; Group 2 (G2) was irradiated with Er:YAG laser (2.94 mum), with 47 mJ/10 Hz, in a focused mode with air/water spray during 15 s and with 0.57 J/cm² of fluency per pulse; Group 3 (G 3) was irradiated with Er:YAG laser (2.94 mum), with 83 mJ/10 Hz, in a focused mode with air/water spray during 15 s and with 1.03 J/cm² of fluency per pulse. We concluded that the parameters adopted for Group 3 removed the smear layer from the root surface, exposing the dentinal tubules. Although no fissures, cracks or carbonized areas were observed, an irregular surface was produced by Er:YAG laser irradiation. Thus, the biocompatibility of the irradiated root surface, within the periodontal healing process, must be assessed.O objetivo do presente estudo foi analisar morfologicamente, através de microscopia eletrônica de varredura, os efeitos do laser de Er:YAG no tratamento de superfícies radiculares submetidas à raspagem e aplainamento radicular com instrumentos manuais. Foram utilizados 18 espécimes (n = 18) de superfícies radiculares que após ser submetidos à raspagem e aplainamento radicular foram divididos em 3 grupos (n = 6). O grupo controle (G1) não sofreu nenhum tratamento; Grupo 2 (G2) foi irradiado com laser de Er:YAG (2,94 mim) 47 mJ/10 Hz, focalizado,com refrigeração à água durante 15 s e fluência de pulso de 0,57 J/cm²; Grupo 3 (G3) foi irradiado com laser de Er:YAG (2,94 mim), 83 mJ/10 Hz, focalizado, com refrigeração à agua durante 15 s e fluência de pulso de 1,03 J/cm². Através da análise dos resultados podemos concluir que o laser de Er:YAG nos parâmetros utilizados no G3 promove a remoção de "smear layer" da superfície radicular e exposição dos túbulos dentinários, porém o laser promove aspecto irregular na superfície, apesar de não demonstrar crateras, fendas, fraturas e carbonização, necessitando de estudos que demonstrem a biocompatibilidade desta superfície no processo de reparo periodontal