Utility of Machine Learning and Radiomics Based on Cavity for Predicting the Therapeutic Response of MDR-TB.

Background: Sputum culture result at the sixth month is essential for predicting therapeutic response to longer multidrug-resistant tuberculosis (MDR-TB) regimens. This study aimed to construct a predictive model using cavity-based radiomics to predict sputum status at the sixth month for MDR-TB patients treated with longer regimens. Methods: This retrospective study recruited 315 MDR-TB patients treated with longer regimens from two centers (250 patients from center 1 and 65 patients from center 2), who were divided into persistently positive and conversion to negative sputum culture groups according to sputum results. Radiomics features were extracted based on the cavity, and a radiomics model was selected and established using a random forest classifier. The clinical characteristics and primary CT signs with significant differences were integrated to build a clinical model. A combined model was generated using the radiomics and clinical model. ROC curves, F1-score and DCA curves were used to assess the predictive performance of the models. Results: Twenty-eight radiomics features were selected to build a radiomics model for predicting the sputum status. The radiomics model achieved good performance, with AUCs of 0.892 and 0.839 in the training and testing cohort, respectively, which was similar to the performance of the combined model (0.913 and 0.815) and much higher than that of the clinical model (0.688 and 0.525) in the two cohorts. Conclusion: The cavity-based radiomics model has the potential to predict sputum culture status for MDR-TB patients receiving longer regimens, which could guide follow-up treatment effectively.

A histone deacetylase inhibitor enhances rice immunity by derepressing the expression of defense-related genes.

Histone deacetylase (HDAC) inhibitors (HDACis) have been widely used in plants to investigate the role of histone acetylation, particularly the function of HDACs, in the regulation of development and stress response. However, how histone acetylation is involved in rice (Oryza sativa L.) disease resistance has hardly been studied. In this paper, four HDACis including Sodium butyrate (NaBT), Suberoylanilide Hydroxamic Acid (SAHA), LBH-589 and Trichostatin A (TSA) were used to treat rice seedlings at different concentrations before inoculation of Magnaporthe oryzae. We found that only 10mM NaBT treatment can significantly enhanced rice blast resistance. However, treatment of the four HDACis all increased global histone acetylation but at different sites, suggesting that the inhibition selectivity of these HDACis is different. Notably, the global H3K9ac level was dramatically elevated after both NaBT and LBH589 treatment although LBH589 could not enhance rice blast resistance. This indicates that the HDACs they inhibit target different genes. In accordance with the phenotype, transcriptomic analysis showed that many defense-related genes were up-regulated by NaBT treatment. Up-regulation of the four genes bsr-d1, PR10B, OsNAC4, OsKS4 were confirmed by RT-qPCR. ChIP-qPCR results revealed that H3K9ac level on these genes was increased after NaBT treatment, suggesting that these defense-related genes were repressed by HDACs. In addition, by promoter motif analysis of the genes that induced by both NaBT treatment and rice blast infection, we found that the motifs bound by ERF and AHL transcription factors (TFs) were the most abundant, which demonstrates that ERF and AHL proteins may act as the candidate TFs that recruit HDACs to defense-related genes to repress their expression when plants are not infected by rice blast.

Differentiating malignant pleural mesothelioma and metastatic pleural disease based on a machine learning model with primary CT signs: A multicentre study.

Rationale and Objectives: It is still a challenge to make confirming diagnosis of malignant pleural mesothelioma (MPM), especially differentiating from metastatic pleural disease (MPD). The aim of this study was to develop a model to distinguish MPM with MPD based on primary CT signs. Materials and methods: We retrospectively recruited 150 MPM patients and 147 MPD patients from two centers and assigned them to training (115 MPM patients and 113 MPD patients) and testing (35 MPM patients and 34 MPD patients) cohorts. The images were analyzed for pleural thickening, hydrothorax, lymphadenopathy, thoracic volume and calcified pleural plaque (CPP). The selected clinical characteristics and primary CT signs comprised the model by multivariate logistic regression in the training cohort. Then the model was tested on the external testing cohort. ROC curve and F1 score were used to validate the capability of the model in both two cohorts. Results: There were significant differences between two groups: (1) carcinoembryonic antigen (CEA); (2) nodular and mass pleural thickening; (3) the enhancement of pleura; (4) focal, diffuse and circumferential pleural thickening; (5) the thickest pleura; (6) thickening of diaphragmatic pleura; (7) multiple nodules and effusion of interlobar pleura; (8) hilar LN and ring enhancement of LN; (9) punctate and stipe CPP. The AUC and F1 score of the model were 0.970 and 0.857 in the training cohort, 0.955 and 0.818 in the testing cohort. Conclusion: The model holds promise for use as a diagnostic tool to distinguish MPM from MPD.

Osteobiography of a seventh-century potter at the Oupan kiln, China by osteological and multi-isotope approach.

In recent years, the reconstruction of individual life history by the multi-isotope analysis of different skeletal elements has become an active topic in bioarchaeological field. However, most studies focus on the persons with high social status and none cares for craftsmen with low social status. In this study, we undertook a comprehensive analysis on a human skeleton buried in the Oupan kiln, Anhui, China to recover his osteobiography. The archaeological context and dating result (534-644 cal. AD) indicate that he might be a potter at the kiln during the Sui and early Tang Dynasty, characteristic of low social hierarchy. The osteological investigation suggests that he had abnormal vertebrae related to long-term physical labor. In general, the isotopic data demonstrate that he mainly consumed C3(wheat, beans)/C4(millets)-based terrestrial foods. The isotopic (C, N) profiles of dentin sections and isotopic data (C, O) of bone apatite and teeth enamel indicate that he had experienced dramatic dietary changes and/or several migrations throughout the childhood and adulthood. His turbulent life trajectory was highly relevant to his identity and low social status. Our study provides a pilot insight into the life history of craftsmen who was generally overlooked in archaeological, historic and anthropological research.