Radiogenomics of lower-grade gliomas: machine learning-based MRI texture analysis for predicting 1p/19q codeletion status.

OBJECTIVE: To evaluate the potential value of the machine learning (ML)-based MRI texture analysis for predicting 1p/19q codeletion status of lower-grade gliomas (LGG), using various state-of-the-art ML algorithms. MATERIALS AND METHODS: For this retrospective study, 107 patients with LGG were included from a public database. Texture features were extracted from conventional T2-weighted and contrast-enhanced T1-weighted MRI images, using LIFEx software. Training and unseen validation splits were created using stratified 10-fold cross-validation technique along with minority over-sampling. Dimension reduction was done using collinearity analysis and feature selection (ReliefF). Classifications were done using adaptive boosting, k-nearest neighbours, naive Bayes, neural network, random forest, stochastic gradient descent, and support vector machine. Friedman test and pairwise post hoc analyses were used for comparison of classification performances based on the area under the curve (AUC). RESULTS: Overall, the predictive performance of the ML algorithms were statistically significantly different, χ2(6) = 26.7, p < 0.001. There was no statistically significant difference among the performance of the neural network, naive Bayes, support vector machine, random forest, and stochastic gradient descent, adjusted p > 0.05. The mean AUC and accuracy values of these five algorithms ranged from 0.769 to 0.869 and from 80.1 to 84%, respectively. The neural network had the highest mean rank with mean AUC and accuracy values of 0.869 and 83.8%, respectively. CONCLUSIONS: The ML-based MRI texture analysis might be a promising non-invasive technique for predicting the 1p/19q codeletion status of LGGs. Using this technique along with various ML algorithms, more than four-fifths of the LGGs can be correctly classified. KEY POINTS: • More than four-fifths of the lower-grade gliomas can be correctly classified with machine learning-based MRI texture analysis. Satisfying classification outcomes are not limited to a single algorithm. • A few-slice-based volumetric segmentation technique would be a valid approach, providing satisfactory predictive textural information and avoiding excessive segmentation duration in clinical practice. • Feature selection is sensitive to different patient data set samples so that each sampling leads to the selection of different feature subsets, which needs to be considered in future works.

Radiomics of Renal Masses: Systematic Review of Reproducibility and Validation Strategies.

OBJECTIVE. The purpose of this study was to systematically review the radiomics literature on renal mass characterization in terms of reproducibility and validation strategies. MATERIALS AND METHODS. With use of PubMed and Google Scholar, a systematic literature search was performed to identify original research papers assessing the value of radiomics in characterization of renal masses. The data items were extracted on the basis of three main categories: baseline study characteristics, radiomic feature reproducibility strategies, and statistical model validation strategies. RESULTS. After screening and application of the eligibility criteria, a total of 41 papers were included in the study. Almost one-half of the papers (19 [46%]) presented at least one reproducibility analysis. Segmentation variability (18 [44%]) was the main theme of the analyses, outnumbering image acquisition or processing (3 [7%]). No single paper considered slice selection bias. The most commonly used statistical tool for analysis was intraclass correlation coefficient (14 of 19 [74%]), with no consensus on the threshold or cutoff values. Approximately one-half of the papers (22 [54%]) used at least one validation method, with a predominance of internal validation techniques (20 [49%]). The most frequently used internal validation technique was k-fold cross-validation (12 [29%]). Independent or external validation was used in only three papers (7%). CONCLUSION. Workflow characteristics described in the radiomics literature about renal mass characterization are heterogeneous. To bring radiomics from a mere research area to clinical use, the field needs many more papers that consider the reproducibility of radiomic features and include independent or external validation in their workflow.

Influence of segmentation margin on machine learning-based high-dimensional quantitative CT texture analysis: a reproducibility study on renal clear cell carcinomas.

OBJECTIVE: To determine the possible influence of segmentation margin on each step (feature reproducibility, selection, and classification) of the machine learning (ML)-based high-dimensional quantitative computed tomography (CT) texture analysis (qCT-TA) of renal clear cell carcinomas (RcCCs). MATERIALS AND METHODS: For this retrospective study, 47 patients with RcCC were included from a public database. Two segmentations were obtained by two radiologists for each tumour: (i) contour-focused and (ii) margin shrinkage of 2 mm. Texture features were extracted from original, filtered, and transformed CT images. Feature selection was done using a correlation-based algorithm. The ML classifier was k-nearest neighbours. Classifications were performed with and without using synthetic minority over-sampling technique. Reference standard was nuclear grade (low versus high). Intraclass correlation coefficient (ICC), Pearson's correlation coefficient, Wilcoxon signed-ranks test, and McNemar's test were used in the analysis. RESULTS: The segmentation with margin shrinkage of 2 mm (772 of 828; 93.2%) yielded more texture features with excellent reproducibility (ICC ≥ 0.9) than contour-focused segmentation (714 of 828; 86.2%), p < 0.0001. The feature selection algorithms resulted in different feature subsets for two segmentation datasets with only one common feature. All ML-based models based on contour-focused segmentation (area under the curve [AUC] range, 0.865-0.984) performed better than those with margin shrinkage of 2 mm (AUC range, 0.745-0.887), p < 0.05. CONCLUSIONS: Each step of the ML-based high-dimensional qCT-TA was susceptible to a slight change of 2 mm in segmentation margin. Despite yielding fewer features with excellent reproducibility, use of the contour-focused segmentation provided better classification performance for distinguishing nuclear grade. KEY POINTS: • Each step of a machine learning (ML)-based high-dimensional quantitative computed tomography texture analysis (qCT-TA) is sensitive to even a slight change of 2 mm in segmentation margin. • Despite yielding fewer texture features with excellent reproducibility, performing the segmentation focusing on the outermost boundary of the tumours provides better classification performance in ML-based qCT-TA of renal clear cell carcinomas for distinguishing nuclear grade. • Findings of an ML-based high-dimensional qCT-TA may not be reproducible in clinical practice even using the same feature selection algorithm and ML classifier unless the possible influence of the segmentation margin is considered.

Radiogenomics in Clear Cell Renal Cell Carcinoma: Machine Learning-Based High-Dimensional Quantitative CT Texture Analysis in Predicting PBRM1 Mutation Status.

OBJECTIVE: The purpose of this study is to evaluate the potential value of machine learning (ML)-based high-dimensional quantitative CT texture analysis in predicting the mutation status of the gene encoding the protein polybromo-1 (PBRM1) in patients with clear cell renal cell carcinoma (RCC). MATERIALS AND METHODS: In this retrospective study, 45 patients with clear cell RCC (29 without the PBRM1 mutation and 16 with the PBRM1 mutation) were identified in The Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma database. To create stable ML models and balanced classes, the data were augmented to a total of 161 labeled segmentations (87 without the PBRM1 mutation and 74 with the PBRM1 mutation) by obtaining three to five different samples per patient. Texture features were extracted from corticomedullary phase contrast-enhanced CT images with the use of an open-source software package for the extraction of radiomic data from medical images. Reproducibility analysis (intraclass correlation) was performed by two radiologists. Attribute selection and model optimization were done using a wrapper-based classifier-specific algorithm with nested cross-validation. ML classifiers were an artificial neural network (ANN) algorithm and a random forest (RF) algorithm. The models were validated using 10-fold cross-validation. The reference standard was the PBRM1 mutation status. The main performance metric was the AUC value. RESULTS: Of 828 extracted texture features, 759 had excellent reproducibility. Using 10 selected features, the ANN algorithm correctly classified 88.2% (142 of 161) of the clear cell RCCs in terms of PBRM1 mutation status (AUC value, 0.925). Using five selected features, the RF algorithm correctly classified 95.0% (153 of 161) of the clear cell RCCs (AUC value, 0.987). Overall, the RF algorithm performed better than the ANN algorithm (z score = -2.677; p = 0.007). CONCLUSION: ML-based high-dimensional quantitative CT texture analysis might be a feasible and potential method for predicting PBRM1 mutation status in patients with clear cell RCC.

Unenhanced CT Texture Analysis of Clear Cell Renal Cell Carcinomas: A Machine Learning-Based Study for Predicting Histopathologic Nuclear Grade.

OBJECTIVE. The purpose of this study is to investigate the predictive performance of machine learning (ML)-based unenhanced CT texture analysis in distinguishing low (grades I and II) and high (grades III and IV) nuclear grade clear cell renal cell carcinomas (RCCs). MATERIALS AND METHODS. For this retrospective study, 81 patients with clear cell RCC (56 high and 25 low nuclear grade) were included from a public database. Using 2D manual segmentation, 744 texture features were extracted from unenhanced CT images. Dimension reduction was done in three consecutive steps: reproducibility analysis by two radiologists, collinearity analysis, and feature selection. Models were created using artificial neural network (ANN) and binary logistic regression, with and without synthetic minority oversampling technique (SMOTE), and were validated using 10-fold cross-validation. The reference standard was histopathologic nuclear grade (low vs high). RESULTS. Dimension reduction steps yielded five texture features for the ANN and six for the logistic regression algorithm. None of clinical variables was selected. ANN alone and ANN with SMOTE correctly classified 81.5% and 70.5%, respectively, of clear cell RCCs, with AUC values of 0.714 and 0.702, respectively. The logistic regression algorithm alone and with SMOTE correctly classified 75.3% and 62.5%, respectively, of the tumors, with AUC values of 0.656 and 0.666, respectively. The ANN performed better than the logistic regression (p < 0.05). No statistically significant difference was present between the model performances created with and without SMOTE (p > 0.05). CONCLUSION. ML-based unenhanced CT texture analysis using ANN can be a promising noninvasive method in predicting the nuclear grade of clear cell RCCs.

Reliability of Single-Slice-Based 2D CT Texture Analysis of Renal Masses: Influence of Intra- and Interobserver Manual Segmentation Variability on Radiomic Feature Reproducibility.

OBJECTIVE. The objective of our study was to investigate the potential influence of intra- and interobserver manual segmentation variability on the reliability of single-slice-based 2D CT texture analysis of renal masses. MATERIALS AND METHODS. For this retrospective study, 30 patients with clear cell renal cell carcinoma were included from a public database. For intra- and interobserver analyses, three radiologists with varying degrees of experience segmented the tumors from unenhanced CT and corticomedullary phase contrast-enhanced CT (CECT) in different sessions. Each radiologist was blind to the image slices selected by other radiologists and him- or herself in the previous session. A total of 744 texture features were extracted from original, filtered, and transformed images. The intraclass correlation coefficient was used for reliability analysis. RESULTS. In the intraobserver analysis, the rates of features with good to excellent reliability were 84.4-92.2% for unenhanced CT and 85.5-93.1% for CECT. Considering the mean rates of unenhanced CT and CECT, having high experience resulted in better reliability rates in terms of the intraobserver analysis. In the interobserver analysis, the rates were 76.7% for unenhanced CT and 84.9% for CECT. The gray-level cooccurrence matrix and first-order feature groups yielded higher good to excellent reliability rates on both unenhanced CT and CECT. Filtered and transformed images resulted in more features with good to excellent reliability than the original images did on both unenhanced CT and CECT. CONCLUSION. Single-slice-based 2D CT texture analysis of renal masses is sensitive to intra- and interobserver manual segmentation variability. Therefore, it may lead to nonreproducible results in radiomic analysis unless a reliability analysis is considered in the workflow.

Effects of different expansion appliances and surgical incisions on maxillary expansion: A finite element analysis.

PURPOSE: This study aims to assess the impact of different surgical techniques and three expansion appliances on maxillary expansion in adults using finite element analysis (FEA), with a focus on maxillary displacement and stress on surrounding structures. METHODS: Seven different FEA models were created to compare different surgical techniques and three different expansion appliances. Model I represented a bone-supported appliance without surgical assistance. Model II, Model III, and Model IV were surgically assisted rapid palatal expansion (SARPE) models without pterygomaxillary suture disjunction (PMD). Model V, Model VI, and Model VII were SARPE models with PMD. RESULTS: The largest displacement at the anterior nasal spine (ANS) was recorded for Model II (2.95 mm). For the posterior nasal spine (PNS), the highest displacement was observed in Models V, VI, VII (2.50 mm), with the lowest in Model III (0.79 mm). Stress analysis revealed the highest stress in Model I, with models featuring PMD displaying nearly zero stress at all anatomical points, highlighting distinct expansion patterns and stress distributions between models with and without PMD. CONCLUSION: SARPE models with PMD demonstrated a parallel expansion of the maxilla with minimal stress, while the miniscrew assisted rapid maxillary expansion (MARPE) model displayed transverse rotation. SARPE models without PMD exhibited a V-shaped expansion pattern. SARPE models with PMD represent an optimal approach for achieving uniform expansion and minimizing stress, with stress levels nearly negligible at all anatomical points in models with PMD.

Studying the stability of polymer nanoparticles by size exclusion chromatography of radioactive polymers.

The properties of nanomedicines will influence how they can deliver drugs to patients reproducibly and effectively. For conventional pharmaceutical products, Chemistry, Manufacturing and Control (CMC) documents require monitoring stability and storage conditions. For nanomedicines, studying these important considerations is hindered by a lack of appropriate methods. In this paper, we show how combining radiolabelling with size exclusion chromatography, using a method called SERP (for Size Exclusion of Radioactive Polymers), can inform on the in vitro degradation of polymer nanoparticles. Using nanoparticles composed of biodegradable poly(lactic acid) (PLA) and poly(lactic-co-glycolic acid) (PLGA), we show that SERP is more sensitive than dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA) to detect degradation. We also demonstrate that the properties of the polymer composition and the nature of the aqueous buffer affect nanoparticle degradation. Importantly, we show that minute changes in stability that cannot be detected by DLS and NTA impact the pharmacokinetic of nanoparticles injected in vivo. We believe that SERP might prove a valuable method to document and understand the pharmaceutical quality of polymer nanoparticles.

Color changes of nanocomposites used for clear aligner attachments: an in vitro study.

PURPOSE: The purpose of this study was to compare the color changes of two different nanocomposites used for two different designs of clear aligner attachments. METHODS: In all, 120 human premolars were embedded in 12 upper dental models with 10 premolars in each model. Models were scanned and attachments were digitally designed. Conventional attachments (CA) were prepared for the first six models and optimized multiplane attachments (OA) were prepared for the other six models with packable composite (PC) on the right quadrant and flowable composite (FC) on the left quadrant of each model. The models were subjected to 2000 thermal cycles at 5 °C/55 °C and then consecutively immersed in the five different staining solutions each for 48 h to simulate external discoloration. Color measurements were taken with a spectrophotometer. Color changes (∆E*ab) of the attachments before and after immersion were compared with the Commission Internationale de l'Éclairage L*a*b* (CIELAB) color space approach. RESULTS: When ∆E*ab values were examined, no significant difference was observed between the groups according to the attachment type (P > 0.05). After the coloration process, the flowable composite group showed less coloration than the packable composite group for both attachment designs (P < 0.05). Color difference values after the staining procedure were significantly higher in the CA-PC and OA-PC groups compared to the CA-FC and OA-FC groups (P < 0.05). CONCLUSION: Color change of the packable nanocomposite was more pronounced than that of the flowable nanocomposite for both attachment designs. Therefore, clear aligner attachments created using flowable nanocomposite can be recommended, especially in the anterior region where esthetics are important for the patient.

Radiomics with artificial intelligence: a practical guide for beginners.

Radiomics is a relatively new word for the field of radiology, meaning the extraction of a high number of quantitative features from medical images. Artificial intelligence (AI) is broadly a set of advanced computational algorithms that basically learn the patterns in the data provided to make predictions on unseen data sets. Radiomics can be coupled with AI because of its better capability of handling a massive amount of data compared with the traditional statistical methods. Together, the primary purpose of these fields is to extract and analyze as much and meaningful hidden quantitative data as possible to be used in decision support. Nowadays, both radiomics and AI have been getting attention for their remarkable success in various radiological tasks, which has been met with anxiety by most of the radiologists due to the fear of replacement by intelligent machines. Considering ever-developing advances in computational power and availability of large data sets, the marriage of humans and machines in future clinical practice seems inevitable. Therefore, regardless of their feelings, the radiologists should be familiar with these concepts. Our goal in this paper was three-fold: first, to familiarize radiologists with the radiomics and AI; second, to encourage the radiologists to get involved in these ever-developing fields; and, third, to provide a set of recommendations for good practice in design and assessment of future works.