Integration of dosimetric parameters, clinical factors, and radiomics to predict symptomatic radiation pneumonitis in lung cancer patients undergoing combined immunotherapy and radiotherapy.

PURPOSE: This study aimed to combine clinical/dosimetric factors and handcrafted/deep learning radiomic features to establish a predictive model for symptomatic (grade ≥ 2) radiation pneumonitis (RP) in lung cancer patients who received immunotherapy followed by radiotherapy. MATERIALS AND METHODS: This study retrospectively collected data of 73 lung cancer patients with prior receipt of ICIs who underwent thoracic radiotherapy (TRT). Of these 73 patients, 41 (56.2 %) developed symptomatic grade ≥ 2 RP. RP was defined per multidisciplinary clinician consensus using CTCAE v5.0. Regions of interest (ROIs) (from radiotherapy planning CT images) utilized herein were gross tumor volume (GTV), planning tumor volume (PTV), and PTV-GTV. Clinical/dosimetric (mean lung dose and V5-V30) parameters were collected, and 107 handcrafted radiomic (HCR) features were extracted from each ROI. Deep learning-based radiomic (DLR) features were also extracted based on pre-trained 3D residual network models. HCR models, Fusion HCR model, Fusion HCR + ResNet models, and Fusion HCR + ResNet + Clinical models were built and compared using the receiver operating characteristic (ROC) curve with measurement of the area under the curve (AUC). Five-fold cross-validation was performed to avoid model overfitting. RESULTS: HCR models across various ROIs and the Fusion HCR model showed good predictive ability with AUCs from 0.740 to 0.808 and 0.740-0.802 in the training and testing cohorts, respectively. The addition of DLR features improved the effectiveness of HCR models (AUCs from 0.826 to 0.898 and 0.821-0.898 in both respective cohorts). The best performing prediction model (HCR + ResNet + Clinical) combined HCR & DLR features with 7 clinical/dosimetric characteristics and achieved an average AUC of 0.936 and 0.946 in both respective cohorts. CONCLUSIONS: In patients undergoing combined immunotherapy/RT for lung cancer, integrating clinical/dosimetric factors and handcrafted/deep learning radiomic features can offer a high predictive capacity for RP, and merits further prospective validation.

Biocontrol fungi induced stem-base rot disease resistance of Morinda officinalis How revealed by transcriptome analysis.

Introduction: Morinda officinalis How (MO) is a Rubiaceae plant, and its medicinal part is dried root, which is one of the "Four Southern Medicines" in China. At present, the plant MO breed seedlings mainly by cutting methods. Long-term asexual propagation makes pathogenic fungi accumulate in MO, leading to stem-base rot, which is caused by Fusarium oxysporum (Fon). Methods: In this study, we used Trichoderma harzianum and Pestalotiopsis sp. as biocontrol fungi to investigate their antagonistic ability to Fon through in vitro antagonism and pot experiments, and combined with transcriptome sequencing to explore the mechanism of biocontrol. Results: The results showed that both Trichoderma harzianum and Pestalotiopsis sp. could inhibit the growth of Fon. In addition, Trichoderma harzianum and Pestalotiopsis sp. could also enhance the basic immunity to Fon by increasing the activities of defensive enzymes such as POD and SOD, chlorophyll content, soluble sugar content, and oligosaccharide content of MO. The mechanism of biological control of stem-base rot of MO was discussed by transcriptome technology. MO was treated with two treatments, root irrigation with biocontrol fungi or inoculation with Fon after root irrigation with biocontrol fungi. Transcriptome sequencing revealed that nearly 11,188 differentially expressed genes (DEGs) were involved in the process of inducing MO systemic resistance to Fon by biocontrol fungi. Meanwhile, Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, as well as transcription factor (TFs) prediction showed that there were significant differences in the expression levels of MO roots under different treatments. Also, the genes of the "MAPK signaling pathway" and "plant hormone signaling pathway" were analyzed, in which the ERFs gene of the ethylene signal transduction pathway participated in the metabolism of glycosyl compounds. It is speculated that the ethylene signal may participate in the immune response of the sugar signal to the infection of Fon. After qRT-PCR verification of 10 DEGs related to the ethylene signal transduction pathway, the expression trend is consistent with the results of transcriptome sequencing, which proves the reliability of transcriptome sequencing. Discussion: In conclusion, this study preliminarily identified the molecular mechanism of the biological control of MO stem-base rot and provided a scientific basis for further research on the prevention and control mechanism of MO stem-base rot.

Physiological and transcriptomic analysis reveals the potential mechanism of Morinda officinalis How in response to freezing stress.

BACKGROUND: Morinda officinalis How (MO) is a vine shrub distributed in tropical and subtropical regions, known as one of the "Four Southern Herbal Medicines" in China. The unclear responsive mechanism by which MO adapt to freezing stress limits progress in molecular breeding for MO freezing tolerance. RESULTS: In this study, morphological, physiological and microstructure changes in MO exposed to -2℃ for 0 h, 3 h, 8 h and 24 h were comprehensively characterized. The results showed that freezing stress caused seedling dehydration, palisade cell and spongy mesophyll destruction. A significant increase in the content of proline, soluble protein and soluble sugars, as well as the activity of superoxide dismutase and peroxidase was observed. Subsequently, we analyzed the transcriptomic changes of MO leaves at different times under freezing treatment by RNA-seq. A total of 24,498 unigenes were annotated and 3252 unigenes were identified as differentially expressed genes (DEGs). Most of these DEGs were annotated in starch and sucrose metabolism, plant hormone signal transduction and MAPK signaling pathways. Family Enrichment analysis showed that the glucosyl/glucuronosyl transferases, oxidoreductase, chlorophyll a/b binding protein and calcium binding protein families were significantly enriched. We also characterized 7 types of transcription factors responding to freezing stress, among which the most abundant family was the MYBs, followed by the AP2/ERFs and NACs. Furthermore, 10 DEGs were selected for qRT-PCR analysis, which validated the reliability and accuracy of RNA-seq data. CONCLUSIONS: Our results provide an overall view of the dynamic changes in physiology and insight into the molecular regulation mechanisms of MO in response to freezing stress. This study will lay a foundation for freezing tolerance molecular breeding and improving the quality of MO.

Nomogram for predicting cardiac death and heart transplantation in arrhythmogenic right ventricular cardiomyopathy.

AIMS: In this study, we aimed to develop and validate a competing risk nomogram for predicting cardiac death and heart transplantation (HT) in patients with arrhythmogenic right ventricular cardiomyopathy (ARVC). METHODS: We retrospectively enrolled 149 consecutive patients with ARVC diagnosed at our institution between 2008 and 2022. Cox proportional hazards model was primarily used to identify variables associated with cardiac death and HT. On the basis of these indicators, a competing risk nomogram was developed to predict the 1, 3, and 5 year probabilities of cardiac death and HT. The area under the receiver operating characteristic curve (AUC), Harrell's C-index, and calibration curves were used to evaluate and internally validate the performance of the model. Decision curve analysis was performed to assess the clinical utility of the nomogram. RESULT: Of the 149 patients with ARVC, the mean age was 38.77 ± 15.94 years, and most of the patients were men (67.11%, 100/149). Fourteen patients experienced cardiac death and nine underwent HT, during a median follow-up period of 5.8 years (interquartile range, 0.62-5.56 years). Multivariable COX analysis revealed that extent of TWI in the anterior and inferior leads (P = 0.0057), right atrial diameter on transthoracic echocardiography (P = 0.0498), RVEF (P = 0.1036), and LVEF (P < 0.001) all showed statistical significance. The 1-, 3-, and 5-year cumulative incidence of cardiac death and HT were 3.35%, 8.05%, and 11.4%, respectively. The area under the receiver operating characteristic curve of the nomogram for predicting cardiac death and HT at 1, 3, and 5 years after diagnosis of ARVC were 0.860, 0.935, and 0.956. The value of Harrell's C-index is 0.9273 (95% confidence interval 0.8954-0.9590; P < 0.001), indicating that the model had good discriminative ability in internal validation. Decision curve analysis revealed that our model was clinically useful within the entire range of potential treatment thresholds in most cases. The cumulative incidence of the primary outcomes was significantly different between the three risk groups according to nomogram-derived scores (P < 0.001). CONCLUSIONS: On the basis of a retrospective review of patients with ARVC at a single centre, we developed a novel nomogram for predicting the risk of cardiac death and HT after ARVC diagnosis. This competing risk nomogram based on four readily available clinical parameters (right atrial diameter, right and left ventricular ejection fraction, and T-wave inversion) is a potentially useful tool for individualized prognostic assessment in patients with ARVC.

Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm.

BACKGROUND: Morinda officinalis How (MO) is a perennial herb distributed in tropical and subtropical regions, which known as one of the "Four Southern Herbal Medicines". The extent of genetic variability and the population structure of MO are presently little understood. Here, nine morphological traits, six chemical components and Single nucleotide polymorphism (SNP) markers were used in integrative research of MO germplasm variation among 88 individuals collected from ten populations across four geographical provinces of China. RESULTS: Both phenotype and chemical composition have significant genetic variation, and there is a certain correlation between them such as root diameter and the nystose content, as well as geographical distribution. The principal component analysis (PCA) showed the leaf length, leaf width, nystose, 1F-furanosaccharide nystose, and the section color were the major contributors to diversity. The cluster analysis based on phenotypic and oligosaccharide data distinguished three significant groups, which was consistent with the result of a corresponding analysis with 228,615 SNP markers, and importantly, they all showed a significant correlation with geographical origin. However, there was little similarity between two cluster results. The Shannon's information index (I) varied from 0.17 to 0.53 with a mean of 0.37, suggesting a high level of genetic diversity in MO populations, which mainly existed among individuals within populations, accounting for 99.66% of the total according to the analysis of molecular variance (AMOVA) results. Each population also maintains the connection because of certain gene communication, so that the genetic differentiation between populations was not very significant. The STRUCTURE software was used to analyse the population structure and the result showed that 88 accessions were clustered into three groups, and 67% of them were pure type, which was also confirmed through PCA. CONCLUSIONS: The comprehensive study of phenotypic, chemical and molecular markers will provide valuable information for future breeding plans and understanding the phylogenetic relationship of MO population.

Quality markers for processed products of Morinda officinalis how based on the "oligosaccharides-spectrum-effect".

Morinda officinalis How (MO) possesses prominent tonifying kidney yang and strengthening bone and muscle effects in traditional Chinese medicine (TCM). Due to the complexity of MO components, the chemical mechanism leading to efficacy changes of MO caused by processing remain unclear. This study aimed to investigate and discover quality markers (Q-markers) related to the clinical efficacy of processed MO. The different processed products of MO have different clinical applications, although they originate from the same medicinal herb. The active chemical components from raw and processed MO that protect against reproductive oxidative stress damage were evaluated. The processed products of MO were prepared by different processing methods. The changes in oligosaccharides during processing were characterized by high-performance liquid chromatography with an evaporative light scattering detector (HPLC-ELSD), and the differential components in raw and processed MO were analyzed using SA, HCA, PCA, and OPLS-DA methods. The protective effects of raw and processed MO oligosaccharides (MOOs) against reproductive oxidative stress damage were evaluated based on the spermatic number, spermatic survival rate, abnormal sperm ratio and serum biochemical indicators in cyclophosphamide-induced (CTX-induced) male mice. The results revealed that processed MOOs had better pharmacological effects than raw MOOs. Therefore, gray correlation analysis (GRA) and the technique for order preference by similarity to ideal solution (TOPSIS) methods were used to investigate the spectrum-effect relationships of MOOs. Spectrum-effect relationship analysis revealed that all of the characteristic peaks contributed to the treatment of reproductive oxidative stress damage, and the relative correlation degrees were greater than 0.6. Among them, the peaks 1 F-fructofuranosylnystose, nystose, and 1-kestose and the peaks X2-X5, which were most closely correlated to the treatment of reproductive oxidative stress damage, were identified as inulin-oligosaccharides and inulo-oligosaccharides, respectively. It was proposed that these constituents could be considered Q-markers for processed products of MO. Thus, this study aimed to explore chemical markers that correlate with the clinical efficacy of processed MO.

Effects of dissolved organic carbon on desorption of aged phenanthrene from contaminated soils: A mechanistic study.

Dissolved organic carbon (DOC) has a major influence upon sorption/desorption and transport of hydrophobic organic contaminants (HOCs) in soil environments. However, the molecular mechanisms of DOC sorption and its effects on aged HOC desorption in contaminated soils still remain largely unclear. Here, effects of three different DOC (one from commercial peat and two from biochars produced at 300 °C and 500 °C pyrolysis temperatures, respectively) and oxalate (as a reference) on abiotic desorption behavior of aged phenanthrene from three agricultural soils were investigated. Results showed that desorption of aged phenanthrene from soils was predominantly dependent on soil organic carbon content. The presence of DOC and oxalate resulted in higher desorption of phenanthrene compared to water alone, and the effects were positively related to soil organic carbon content and DOC/oxalate concentration. The facilitating effects of DOC were further increased during the second consecutive desorption, whereas oxalate had no such effect. Ultra-high-resolution Fourier transform-ion cyclotron resonance-mass spectrometry confirmed the molecular fractionation of DOC at the soil-water interface during DOC sorption. Specifically, the DOC molecules with O-rich moieties were preferentially adsorbed, whereas the molecules with phenolic and aromatic structures were selectively retained in the soil solutions through competitive displacement and co-sorption reactions during sorption. The enriched phenyl structures in the retained DOC facilitated its association with phenanthrene in the solutions and thus the release of phenanthrene from the soils. In contrast, oxalate replaced some organic carbon from the soils and thus released the associated phenanthrene into the solutions. Our findings highlight the importance of the molecular composition and structure of DOC for the desorption of phenanthrene in soil-water environments, which may help improve our understanding of the release and transport of organic compounds in the environments.

Molecular understanding of dissolved black carbon sorption in soil-water environment.

Dissolved black carbon (DBC) involves in many biogeochemical processes in both terrestrial and aquatic environments. About 26.5 Tg of charcoal- or black carbon-derived DBC was released into aquatic environments annually, accounting to ∼10% of the global riverine flux of dissolved organic carbon (DOC). Yet the sorption behaviors of DBC and their effects on water quality in soil-water environment are poorly understood. Here we examined the molecular composition variations of DOC induced by the sorption of two biochar-derived DBCs (pyrolyzed at 300 °C and 500 °C) on three contrasting soils. The DBCs were adsorbed mainly through competitive displacement of soil surface functional groups and co-sorption with soil indigenous DOC, which varied with soil properties and the aromaticity of the DBCs. Ultrahigh resolution mass spectrometry analysis indicated that compounds with rich oxygen content or unsaturated structures such as tannins and unsaturated aromatics from both DBC and soil DOC, were preferentially adsorbed on the soils in the presence of DBC. In contrast, compounds with high aromatic structures including condensed aromatics and lignins were concentrated in the aquatic phase. Molecular fractionation also occurred to the heteroatomic compounds during the sorption, and the heteroatomic dissolved organic sulphur in the DBCs was easier to be adsorbed relative to dissolved organic nitrogen. Our results suggest that DBC sorption in soil-water environment could have important implications for water quality by altering DOC molecular composition and decreasing DOC molecular diversity at the soil-water interface. This study provides essential information for understanding the behavior of DBC in the environments.

Synchrotron infrared microspectroscopy reveals the roles of aliphatic and aromatic moieties in sorption of nitroaromatic compounds to soils.

A consensus on the role of organic carbon moieties as the sorptive domains for nonionic organic compounds in soils is lacking due to the extremely complicated compositions of soil matrices. In this study, synchrotron radiation-based infrared microspectroscopy (IMS) was applied to in situ probe the distributions of four nitroaromatic compounds with varying hydrophobicity (namely, 1,3-dinitrobenzene, 1,5-dinitronapthalene, 3-nitrophenanthrene and 6-nitrobenzo[a]pyrene) and their associations with aliphatic and aromatic organic carbon moieties in soils. The technique revealed that both nitro group (NO2) from the nitroaromatic compounds and organic carbon moieties were unevenly distributed in the soils at the micron scale. The spatial distribution of nitro groups was positively correlated with that of aromatic carbon (C=C) (r>0.804, p<0.01), indicating that the aromatic moieties of soil organic carbon play a key role in sorption of nitroaromatic compounds to soils. Neither nitro groups nor aromatic carbon showed a close relationship with aliphatic carbon (CH) in the spatial distribution in the soils. Meanwhile, the nitro groups from 1,3-dinitrobenzene and 1,5-dinitronapthalene exhibited a significant correlation with clay minerals (OH) in their distributions (r>0.629, p<0.01) in the soils and the correlation became insignificant for the other two compounds with high hydrophobicity. This study for the first time provides micron-scale spectroscopic evidence for the roles of organic carbon moieties in the sorption of nonionic organic compounds to soils.

Insights into the attenuated sorption of organic compounds on black carbon aged in soil.

Sorption of organic compounds on fresh black carbons (BCs) can be greatly attenuated in soil over time. We examined herein the changes in surface properties of maize straw-derived BCs (biochars) after aged in a black soil and their effects on the sorptive behaviors of naphthalene, phenanthrene and 1,3-dinitrobenzene. Dissolved fulvic and humic acids extracted from the soil were used to explore the role of dissolved organic carbon (DOC) in the aging of biochars. Chromatography analysis indicated that DOC molecules with relatively large molecular weight were preferentially adsorbed on the biochars during the aging processes. DOC sorption led to blockage of the biochar's micropores according to N2 and CO2 adsorption analyses. Surface chemistry of the biochars was also substantially modified, with more O-rich functional groups on the aged biochars compared to the original biochars, as evidenced by Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and X-ray photoelectron spectroscopy (XPS) analyses. The changes in both the physical and chemical surface properties of biochars by DOC led to significant attenuation of the sorption capacity and nonlinearity of the nonionic organic compounds on the aged biochars. Among the tested organic compounds, phenanthrene was the most attenuated in its sorption by the aging treatments, possibly because of its relatively large molecular size and hydrophobicity. The information can help gain a mechanistic understanding of interactions between BCs and organic compounds in soil environment.

Selected dark sides of biomass-derived biochars as environmental amendments.

With the rapid increase in the application of biochars as amendments, studies are needed to clarify the possible environmental risks derived from biochars to use safely the biomass resources. This work reported selected dark sides of maize straw- and swine manure-derived biochars pyrolyzed at 300 and 500°C. During the pyrolysis processes, total heavy metals in the biochars were enriched greatly accompanying with considerable emission of the heavy metals into atmosphere and the trends became increasingly obvious with pyrolysis temperature. Meanwhile, the biochars showed distinctly decreased available heavy metals compared with raw feedstocks, which could be mainly attributed to the sorption by the inorganics in the biochars. The water- and acid-washing treatments significantly increased the releasing risks of heavy metals from biochars into the environments. Electron paramagnetic resonance analysis indicated that persistent free radicals, emerged strongly in the biochars as a function of the aromatization of biomass feedstocks, were free from the influence of water-, acid-, or organic-washing of the biochars and could remain stable even after aged in soils for 30days. Dissolved biochars, highly produced during pyrolysis processes, showed distinct properties including lower molecular weight distribution while higher aromaticity compared with soil dissolved organic carbon. The results of this study provide important perspectives on the safe usage of biochars as agricultural/environmental amendments.

Determination of fluorotelomer alcohols and their degradation products in biosolids-amended soils and plants using ultra-high performance liquid chromatography tandem mass spectrometry.

Degradation of fluorotelomer alcohols (FTOHs) was recognized as an additional source of perfluorocarboxylic acids (PFCAs). Quantification of FTOHs and their degradation products can help shed light on the sources and fates of PFCAs in the environment. In this study, an analytical method was developed for the determination of 6:2 and 8:2 FTOHs, and their degradation products of poly- and perfluorinated acids, including fluorotelomer saturated and unsaturated carboxylic acids (FTCAs and FTUCAs), secondary polyfluorinated alcohols and PFCAs in biosolids-amended soils and plants using ultra-high performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). The extract efficiencies of different methods including ethyl acetate and methanol (MeOH) for FTOHs and acetonitrile, MeOH, methyl tert-butyl ether (MTBE), NaOH-MeOH and NaOH-MTBE for poly- and perfluorinated acids were tested. The results showed that 6:2 and 8:2 FTOHs and their degradation products could be simultaneously and satisfactorily extracted by MeOH, cleaned up by Envi-Carb graphitized carbon and solid phase extraction, respectively, and determined by UPLC-MS/MS separately. NaOH in the extractant caused the conversion of 6:2 FTCA and 8:2 FTCA into the corresponding FTUCAs. The selected methods have matrix recoveries ranged from 52% to 102%, and detection limits of 0.01-0.46ng/g dry weight for FTOHs and their degradation products in soil and plant. The optimized method was applied successfully to quantify FTOHs and their degradation products in two biosolids-amended soils and plants. The total concentrations of FTOHs in the soils were 44.1±5.8 and 82.6±7.1ng/g, and in plants tissues 3.58±0.25 and 8.33±0.66ng/g. The total concentrations of poly- and perfluorinated acids in the soils were 168.0±13.2 and 349.6±11.2ng/g, and in plants tissues 78.0±6.4 and 75.5±5.3ng/g.

Properties of biomass-derived biochars: Combined effects of operating conditions and biomass types.

Combined effects of operating conditions including heating temperature (200-700 °C), time (1-8h) and rate, and atmosphere (air-flow, air-limited and N2) on the physicochemical properties of biochars with pine sawdust, maize straw and sugarcane bagasse as feedstocks were investigated. The results demonstrated that production temperature and atmosphere acted as the predominant factors that determined the properties of biochars. The X-ray diffraction data confirmed the occurrence of phase transition in the biomass structures at around 400 °C. Heating time and rate showed little effect on the functional group compositions of the biochars within 8h, particularly under N2 atmosphere. In addition, the molecular weights of the biochar-derived dissolved organic carbon tended to increase with increasing temperature. Feedstock type also affected the biochar properties by the compositional differences in mineral salts and cellulose/lignin in the three biomass materials. This work provides important information for optimizing procedures for biochar production with desired properties and high yield.