An Efficient Sulfadiazine Selection Scheme for Stable Transformation in the Model Liverwort Marchantia polymorpha.

Plant macroevolutionary studies leverage the phylogenetic position of non-flowering model systems like the liverwort Marchantia polymorpha to investigate the origin and evolution of key plant processes. To date, most molecular genetic studies in Marchantia rely on hygromycin and/or chlorsulfuron herbicide resistance markers for the selection of stable transformants. Here, we use a sulfonamide-resistant dihydropteroate synthase (DHPS) gene to enable sulfadiazine-based transformation selection in M. polymorpha. We demonstrate the reliability of sulfadiazine selection on its own and in combination with existing hygromycin and chlorsulfuron selection schemes through transgene stacking experiments. The utility of this system is further demonstrated through confocal microscopy of a triple transgenic line carrying fluorescent proteins labelling the plasma membrane, cortical microtubules, and the nucleus. Collectively, our findings and resources broaden the capacity to genetically manipulate the increasingly popular model liverwort M. polymorpha.

Temporal Machine Learning Analysis of Prior Mammograms for Breast Cancer Risk Prediction.

The identification of women at risk for sporadic breast cancer remains a clinical challenge. We hypothesize that the temporal analysis of annual screening mammograms, using a long short-term memory (LSTM) network, could accurately identify women at risk of future breast cancer. Women with an imaging abnormality, which had been biopsy-confirmed to be cancer or benign, who also had antecedent imaging available were included in this case-control study. Sequences of antecedent mammograms were retrospectively collected under HIPAA-approved guidelines. Radiomic and deep-learning-based features were extracted on regions of interest placed posterior to the nipple in antecedent images. These features were input to LSTM recurrent networks to classify whether the future lesion would be malignant or benign. Classification performance was assessed using all available antecedent time-points and using a single antecedent time-point in the task of lesion classification. Classifiers incorporating multiple time-points with LSTM, based either on deep-learning-extracted features or on radiomic features, tended to perform statistically better than chance, whereas those using only a single time-point failed to show improved performance compared to chance, as judged by area under the receiver operating characteristic curves (AUC: 0.63 ± 0.05, 0.65 ± 0.05, 0.52 ± 0.06 and 0.54 ± 0.06, respectively). Lastly, similar classification performance was observed when using features extracted from the affected versus the contralateral breast in predicting future unilateral malignancy (AUC: 0.63 ± 0.05 vs. 0.59 ± 0.06 for deep-learning-extracted features; 0.65 ± 0.05 vs. 0.62 ± 0.06 for radiomic features). The results of this study suggest that the incorporation of temporal information into radiomic analyses may improve the overall classification performance through LSTM, as demonstrated by the improved discrimination of future lesions as malignant or benign. Further, our data suggest that a potential field effect, changes in the breast extending beyond the lesion itself, is present in both the affected and contralateral breasts in antecedent imaging, and, thus, the evaluation of either breast might inform on the future risk of breast cancer.

Prognostic value of pre-treatment CT texture analysis in combination with change in size of the primary tumor in response to induction chemotherapy for HPV-positive oropharyngeal squamous cell carcinoma.

BACKGROUND: To determine the additive value of quantitative radiomic texture features in predicting progression in human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC) based on pre-treatment CT. METHODS: Retrospective analysis of a single-center cohort of adult patients enrolled in a response-adapted radiation volume de-escalation trial treated with induction chemotherapy. Texture analysis of HPV-positive OPSCC was performed via primary tumor site contouring on pre-treatment contrast-enhanced CT scans. Percent change in size of the tumor in response to induction chemotherapy based on RECIST 1.1 criteria and progression free survival were clinically determined for this cohort. Receiver operating characteristic (ROC) analysis was performed to compare the accuracy of percent change in tumor size after induction chemotherapy with a combination of change in tumor size and radiomic texture features for predicting tumor progression. RESULTS: Radiomic texture analysis of the primary tumors in 38 patients with OPSCC depicted on pre-treatment neck CT scans using skewness and entropy in combination with percent change in tumor size after induction chemotherapy yielded a statistically significant increase in accuracy for predicting tumor progression over change in tumor size alone, with an area under the curve of 0.80 versus 0.56 (one-tailed P=0.0087). CONCLUSIONS: This pilot study suggests that disease progression in patients with HPV-positive OPSCC is more accurately predicted using a combination of texture features on pre-treatment CT scans, along with change in tumor size compared to change in tumor size alone and could therefore serve as a radiomic texture signature.

Radiomics robustness assessment and classification evaluation: A two-stage method demonstrated on multivendor FFDM.

PURPOSE: Radiomic texture analysis is typically performed on images acquired under specific, homogeneous imaging conditions. These controlled conditions may not be representative of the range of imaging conditions implemented clinically. We aim to develop a two-stage method of radiomic texture analysis that incorporates the reproducibility of individual texture features across imaging conditions to guide the development of texture signatures which are robust across mammography unit vendors. METHODS: Full-field digital mammograms were retrospectively collected for women who underwent screening mammography on both a Hologic Lorad Selenia and GE Senographe 2000D system. Radiomic features were calculated on manually placed regions of interest in each image. In stage one (robustness assessment), we identified a set of nonredundant features that were reproducible across the two different vendors. This was achieved through hierarchical clustering and application of robustness metrics. In stage two (classification evaluation), we performed stepwise feature selection and leave-one-out quadratic discriminant analysis (QDA) to construct radiomic signatures. We refer to this two-state method as robustness assessment, classification evaluation (RACE). These radiomic signatures were used to classify the risk of breast cancer through receiver operator characteristic (ROC) analysis, using the area under the ROC curve as a figure of merit in the task of distinguishing between women with and without high-risk factors present. Generalizability was investigated by comparing the classification performance of a feature set on the images from which they were selected (intravendor) to the classification performance on images from the vendor on which it was not selected (intervendor). Intervendor and intravendor performances were also compared to the performance obtained by implementing ComBat, a feature-level harmonization method and to the performance by implementing ComBat followed by RACE. RESULTS: Generalizability, defined as the difference between intervendor and intravendor classification performance, was shown to monotonically decrease as the number of clusters used in stage one increased (Mann-Kendall P < 0.001). Intravendor performance was not shown to be statistically different from ComBat harmonization while intervendor performance was significantly higher than ComBat. No significant difference was observed between either of the single methods and the use of ComBat followed by RACE. CONCLUSIONS: A two-stage method for robust radiomic signature construction is proposed and demonstrated in the task of breast cancer risk assessment. The proposed method was used to assess generalizability of radiomic texture signatures at varying levels of feature robustness criteria. The results suggest that generalizability of feature sets monotonically decreases as reproducibility of features decreases. This trend suggests that considerations of feature robustness in feature selection methodology could improve classifier generalizability in multifarious full-field digital mammography datasets collected on various vendor units. Additionally, harmonization methods such as ComBat may hold utility in classification schemes and should continue to be investigated.

Variation in algorithm implementation across radiomics software.

Given the increased need for consistent quantitative image analysis, variations in radiomics feature calculations due to differences in radiomics software were investigated. Two in-house radiomics packages and two freely available radiomics packages, MaZda and IBEX, were utilized. Forty 256 × 256 - pixel regions of interest (ROIs) from 40 digital mammograms were studied along with 39 manually delineated ROIs from the head and neck (HN) computed tomography (CT) scans of 39 patients. Each package was used to calculate first-order histogram and second-order gray-level co-occurrence matrix (GLCM) features. Friedman tests determined differences in feature values across packages, whereas intraclass-correlation coefficients (ICC) quantified agreement. All first-order features computed from both mammography and HN cases (except skewness in mammography) showed significant differences across all packages due to systematic biases introduced by each package; however, based on ICC values, all but one first-order feature calculated on mammography ROIs and all but two first-order features calculated on HN CT ROIs showed excellent agreement, indicating the observed differences were small relative to the feature values but the bias was systematic. All second-order features computed from the two databases both differed significantly and showed poor agreement among packages, due largely to discrepancies in package-specific default GLCM parameters. Additional differences in radiomics features were traced to variations in image preprocessing, algorithm implementation, and naming conventions. Large variations in features among software packages indicate that increased efforts to standardize radiomics processes must be conducted.