Improving the performance of deep learning models in predicting and classifying gamma passing rates with discriminative features and a class balancing technique: a retrospective cohort study.

BACKGROUND: The purpose of this study was to improve the deep learning (DL) model performance in predicting and classifying IMRT gamma passing rate (GPR) by using input features related to machine parameters and a class balancing technique. METHODS: A total of 2348 fields from 204 IMRT plans for patients with nasopharyngeal carcinoma were retrospectively collected to form a dataset. Input feature maps, including fluence, leaf gap, leaf speed of both banks, and corresponding errors, were constructed from the dynamic log files. The SHAP framework was employed to compute the impact of each feature on the model output for recursive feature elimination. A series of UNet++ based models were trained on the obtained eight feature sets with three fine-tuning methods including the standard mean squared error (MSE) loss, a re-sampling technique, and a proposed weighted MSE loss (WMSE). Differences in mean absolute error, area under the receiver operating characteristic curve (AUC), sensitivity, and specificity were compared between the different models. RESULTS: The models trained with feature sets including leaf speed and leaf gap features predicted GPR for failed fields more accurately than the other models (F(7, 147) = 5.378, p < 0.001). The WMSE loss had the highest accuracy in predicting GPR for failed fields among the three fine-tuning methods (F(2, 42) = 14.149, p < 0.001), while an opposite trend was observed in predicting GPR for passed fields (F(2, 730) = 9.907, p < 0.001). The WMSE_FS5 model achieved a superior AUC (0.92) and more balanced sensitivity (0.77) and specificity (0.89) compared to the other models. CONCLUSIONS: Machine parameters can provide discriminative input features for GPR prediction in DL. The novel weighted loss function demonstrates the ability to balance the prediction and classification accuracy between the passed and failed fields. The proposed approach is able to improve the DL model performance in predicting and classifying GPR, and can potentially be integrated into the plan optimization process to generate higher deliverability plans. TRIAL REGISTRATION: This clinical trial was registered in the Chinese Clinical Trial Registry on March 26th, 2020 (registration number: ChiCTR2000031276). https://clinicaltrials.gov/ct2/show/ChiCTR2000031276.

Hydrodynamic analysis and manipulation control on a streamlined I-AUV.

Hydrodynamics analysis and control are very significant for the seabed operations, particularly for the intelligent manipulation process of streamlined intervention autonomous underwater vehicles (I-AUVs). The computation fluid dynamics simulations and verification were conducted in the consideration with water channel domain, mesh insensitivity, support straight bar connector, free surface and other boundary conditions. The variation trend of hydrodynamic coefficients in the process of manipulation is obtained, by simulations of streamlined I-AUV manipulation under dynamic manipulation state. To further realize underwater floating manipulation, a novel controller with an integral termed nonlinear sliding mode surface and disturbance observer has been developed. The disturbance observer can make quantity analysis on the interaction forces between I-AUV and the environment from hydrodynamic analysis. Simulations and experiments have verified the controller performance.

Global Distribution of Mercury in Foliage Predicted by Machine Learning.

Foliar assimilation of elemental mercury (Hg0) from the atmosphere plays a critical role in the global Hg biogeochemical cycle, leading to atmospheric Hg removal and soil Hg insertion. Recent studies have estimated global foliar Hg assimilation; however, large uncertainties remained due to coarse accounting of observed foliar Hg concentrations, posing a substantial challenge in constraining the global Hg budget. Here, we integrated a comprehensive observation database of foliar Hg concentrations and machine learning algorithms to predict the first spatial distribution of foliar Hg concentrations on a global scale, contributing to the first estimate of global Hg pools in foliage. The global average of foliar Hg concentrations was estimated to be 24.0 ng g-1 (7.5-56.5 ng g-1), and the global total in foliar Hg pools reached 4561.3 Mg (1455.2-9062.8 Mg). The spatial distribution showed the hotspots in tropical regions, including the Amazon, Central Africa, and Southeast Asia. A range of 2268.5-2727.0 Mg yr-1 was estimated for annual foliar Hg assimilation accounting for the perennial continuous assimilation by evergreen vegetation foliage. The first spatial maps of foliar Hg concentrations and Hg pools may aid in understanding the global biogeochemical cycling of Hg, especially in the context of climate change and global vegetation greening.

One-Pot Fabrication of Supramolecular Synthetic Protein Hydrogel with Tissue-like Integrated Dynamic Features.

Protein-incorporated soft networks have received remarkable attention during the past several years. They possess desirable properties similar to native tissues and organs and exhibit unique advantages in applications. However, fabrication of protein-based hydrogels usually suffers from complex protein mutation and modification or chemical synthesis, which limited the scale and yield of production. Meanwhile, the lack of rationally designed noncovalent interactions in networks may result in a deficiency of the dynamic features of materials. Therefore, a highly efficient method is needed to include supramolecular interactions into protein hydrogel to generate a highly dynamic hydrogel possessing integrated tissue-like properties. Here, we report the design and construction of native protein-based supramolecular synthetic protein hydrogels through a simple and efficient one-pot polymerization of acrylamide and ligand monomers in the presence of a ligand-binding protein. The supramolecular interactions in the network yield integrated dynamic properties, including remarkable stretchability over 10,000% of their original length, ultrafast self-healing abilities within 3-4 s, tissue-like fast stress relaxation, satisfactory ability of adhesion to different living and nonliving substrates, injectability, and high biocompatibility. Furthermore, this material demonstrated potential as a biosensor to monitor small finger movements. This strategy provides a new avenue for fabricating synthetic protein hydrogels with integrated features.

miR-612 Enhances RSL3-Induced Ferroptosis of Hepatocellular Carcinoma Cells via Mevalonate Pathway.

Background: MicroRNA-612 (miR-612) has been proven to suppress the formation of invadopodia and inhibit hepatocellular carcinoma (HCC) metastasis by hydroxyacyl-CoA dehydrogenase alpha subunit (HADHA)-mediated lipid reprogramming. However, its biological roles in HCC cell ferroptosis remain unclear. Methods and Results: In this study, we found that HCC cells with high metastatic potential were more resistant to ferroptosis, indicating that ferroptosis is related to HCC metastasis. The levels of lipid reactive oxygen species (ROS) were found to be much lower in HCC cells with high metastatic potential by flow cytometry (FCM). We used HCC cells with miR-612 overexpression/knockout and HADHA overexpression/knockdown to test cell viability after stimulation with RSL3. HCC cells overexpressing miR-612 were more sensitive to ferroptosis, and miR-612 could increase lipid ROS levels. Furthermore, colony formation assays and Transwell assays showed that miR-612 could inhibit the proliferation and metastasis of HCC cells by promoting ferroptosis. We next confirmed that miR-612 influenced HCC cell ferroptosis by regulating HADHA. HADHA could upregulate the expression of key enzymes in the mevalonate (MVA) pathway. HADHA overexpression upregulated the expression of CoQ10 and decreased polyunsaturated fatty acid (PUFA) levels and lipid peroxide abundance. miR-612 also suppressed HCC cell proliferation and metastasis by enhancing RSL3- and lovastatin-induced ferroptosis in vivo. Conclusion: Overall, miR-612 promotes ferroptosis in HCC cells and affects HCC proliferation and metastasis by downregulating CoQ10 and increasing cellular PUFA levels and lipid peroxides via the HADHA-mediated MVA pathway.

Transcriptome analysis showed that tomato-rootstock enhanced salt tolerance of grafted seedlings was accompanied by multiple metabolic processes and gene differences.

Introduction: Grafting is a commonly used cultural practice to counteract salt stress and is especially important for vegetable production. However, it is not clear which metabolic processes and genes are involved in the response of tomato rootstocks to salt stress. Methods: To elucidate the regulatory mechanism through which grafting enhances salt tolerance, we first evaluated the salt damage index, electrolyte permeability and Na+ accumulation in tomato (Solanum lycopersicum L.) leaves of grafted seedlings (GSs) and nongrafted seedlings (NGSs) subjected to 175 mmol·L- 1 NaCl for 0-96 h, covering the front, middle and rear ranges. Results: Compared with the NGS, the GSs were more salt tolerant, and the Na+ content in the leaves decreased significantly. Through transcriptome sequencing data analysis of 36 samples, we found that GSs exhibited more stable gene expression patterns, with a lower number of DEGs. WRKY and PosF21 transcription factors were significantly upregulated in the GSs compared to the NGSs. Moreover, the GSs presented more amino acids, a higher photosynthetic index and a higher content of growth-promoting hormones. The main differences between GSs and NGSs were in the expression levels of genes involved in the BR signaling pathway, with significant upregulation of XTHs. The above results show that the metabolic pathways of "photosynthetic antenna protein", "amino acid biosynthesis" and "plant hormone signal transduction" participate in the salt tolerance response of grafted seedlings at different stages of salt stress, maintaining the stability of the photosynthetic system and increasing the contents of amino acids and growth-promoting hormones (especially BRs). In this process, the transcription factors WRKYs, PosF21 and XTHs might play an important role at the molecular level. Discussion: The results of this study demonstrates that grafting on salt tolerant rootstocks can bring different metabolic processes and transcription levels changes to scion leaves, thereby the scion leaves show stronger salt tolerance. This information provides new insight into the mechanism underlying tolerance to salt stress regulation and provides useful molecular biological basis for improving plant salt resistance.

Rapid quantitative detection of Klebsiella pneumoniae in infants with severe infection disease by point-of-care immunochromatographic technique based on nanofluorescent microspheres.

Background: Klebsiella pneumoniae (KP, K. pneumoniae) is one of the most important nosocomial pathogens that cause severe respiratory infections. As evolutionary high-toxic strains with drug resistance genes increase year by year, the infections caused by it are often accompanied by high mortality, which may be fatal to infants and can cause invasive infections in healthy adults. At present, the traditional clinical methods for detecting K. pneumoniae are cumbersome and time-consuming, and the accuracy and sensitivity are not high. In this study, nanofluorescent microsphere (nFM)-based immunochromatographic test strip (ICTS) quantitative testing platform were developed for point-of-care testing (POCT) method of K. pneumoniae. Methods: 19 clinical samples of infants were collected, the genus-specific gene of mdh was screened from K. pneumoniae. Polymerase chain reaction (PCR) combined with nFM-ICTS based on magnetic purification assay (PCR-ICTS) and strand exchange amplification (SEA) combined with nFM-ICTS based on magnetic purification assay (SEA-ICTS) were developed for the quantitative detection of K. pneumoniae. The sensitivity and specificity of SEA-ICTS and PCR-ICTS were demonstrated by the existing used classical microbiological methods, the real-time fluorescent quantitative PCR (RTFQ-PCR) and PCR assay based on agarose gel electrophoresis (PCR-GE). Results: Under optimum working conditions, the detection limits of PCR-GE, RTFQ-PCR, PCR-ICTS and SEA-ICTS are 7.7 × 10-3, 2.5 × 10-6, 7.7 × 10-6, 2.82 × 10-7 ng/µL, respectively. The SEA-ICTS and PCR-ICTS assays can quickly identify K. pneumoniae, and could specifically distinguish K. pneumoniae samples from non-K. pneumoniae samples. Experiments have shown a diagnostic agreement of 100% between immunochromatographic test strip methods and the traditional clinical methods on the detection of clinical samples. During the purification process, the Silicon coated magnetic nanoparticles (Si-MNPs) were used to removed false positive results effectively from the products, which showed of great screening ability. The SEA-ICTS method was developed based on PCR-ICTS, which is a more rapid (20 min), low-costed method compared with PCR-ICTS assay for the detection of K. pneumoniae in infants. Only need a cheap thermostatic water bath and takes a short detection time, this new method can potentially serve as an efficient point-of-care testing method for on-site detection of pathogens and disease outbreaks without fluorescent polymerase chain reaction instruments and professional technicians operation.

Microwave-ultra-fast recovery of valuable metals from spent lithium-ion batteries by deep eutectic solvents.

The large-scale use of electric vehicles produced massive discarded lithium-ion batteries, containing many recyclable valuable metals and toxic and harmful substances. Biodegradable and recyclable deep eutectic solvent (DES) is considered a green recycling technology for spent LIBs. Herein, we proposed a microwave-enhanced approach to shorten the leaching time in the urea/lactic acid: choline chloride: ethylene glycol DES system. The dipole moments induced by urea or lactic acid on LiCoO2 surface increased over two orders of magnitude under the high electric field. Because of this, over 90 % of Li and Co can be fast leached at 4 min and 160 W in the urea/lactic acid: choline chloride: ethylene glycol DES system. Meanwhile, we established two models to explain the leaching mechanism of metal ions from their leaching kinetics and micro-level behavior, and named them dot-etching and layer-peeling processes, respectively. By further analyzing, we found that the dot-etching can be attributed to the synergistic effect of reduction and coordination, which caused the surface of leaching residues porous. The layer-peeling process depends on neutralization, and the leaching residues had a smooth surface in this process. This work highlights the effect of microwave-enhanced strategy and DES surface chemistry on spent electrode materials recovery.

Native Mass Spectrometry Coupled to Spectroscopic Methods to Investigate the Effect of Soybean Isoflavones on Structural Stability and Aggregation of Zinc Deficient and Metal-Free Superoxide Dismutase.

The deficiency or wrong combination of metal ions in Cu, Zn-superoxide dismutase (SOD1), is regarded as one of the main factors causing the aggregation of SOD1 and then inducing amyotrophic lateral sclerosis (ALS). A ligands-targets screening process based on native electrospray ionization ion mobility mass spectrometry (ESI-IMS-MS) was established in this study. Four glycosides including daidzin, sophoricoside, glycitin, and genistin were screened out from seven soybean isoflavone compounds and were found to interact with zinc-deficient or metal-free SOD1. The structure and conformation stability of metal-free and zinc-deficient SOD1 and their complexes with the four glycosides was investigated by collision-induced dissociation (CID) and collision-induced unfolding (CIU). The four glycosides could strongly bind to the metal-free and copper recombined SOD1 and enhance the folding stability of these proteins. Additionally, the ThT fluorescence assay showed that these glycosides could inhibit the toxic aggregation of the zinc-deficient or metal-free SOD1. The competitive interaction experiments together with molecular docking indicate that glycitin, which showed the best stabilizing effects, binds with SOD1 between ß-sheet 6 and loop IV. In short, this study provides good insight into the relationship between inhibitors and different SOD1s.

An anticoagulant/hemostatic indwelling needle for oral glucose tolerance test.

Indwelling needles are widely used in the clinic for their advantages of reducing the pain and discomfort caused by repeated venipuncture. Achieving anticoagulation and hemostasis with one single indwelling needle is highly desired from perspective of implantation patency and the prevention of needle-withdrawal-induced uncontrolled bleeding. Herein, we develop a sophisticated indwelling needle with an anticoagulant/hemostatic dual function by anchoring an anticoagulant heparin coating and a hemostatic hydrogel coating on the inner surface and the outer surface of the indwelling needle, respectively. The results of in vitro tests and continuous blood collections from the rabbit ear vein indicate that the anticoagulant coating can resist the adhesion of proteins and blood cells, and its anticoagulant effect can maintain the patency of the indwelling needle for 3 hours after implantation. Meanwhile, the xerogel-hydrogel transition of the hemostatic coating upon contacting blood promotes the aggregation of blood cells, thus sealing the puncture site to achieve complete hemostasis after needle removal. Importantly, this anticoagulant/hemostatic indwelling needle can replace traditional repeated puncture, and can be used to monitor blood glucose concentration changes in diabetic rats through continuous blood collection, portending its promising application in the oral glucose tolerance test.