[Role of Ferroptosis in Non-small Cell Lung Cancer and Progress 
of Traditional Chinese Medicine Intervention].

Non-small cell lung cancer (NSCLC) is one of the malignant tumors with high morbidity and mortality worldwide. Ferroptosis is a new type of programmed cell death caused by abnormal accumulation of iron-dependent reactive oxygen species (ROS) leading to lipid peroxidation. It involves the balance between iron metabolism, lipid metabolism, oxygen free radical reaction and lipid peroxidation. Recent studies have found that ferroptosis is closely related to the occurrence and development of NSCLC. Due to the emergence of chemotherapy resistance and radiotherapy resistance in the treatment of NSCLC, there is an urgent need to develop new effective drugs and treatment strategies. Traditional Chinese medicine has unique advantages in the prevention and treatment of NSCLC due to its multi-targets and minimal side effects. In this review, we summarize the mechanism of ferroptosis in NSCLC, and discuss the research status of active ingredients of traditional Chinese medicine, single-herb traditional Chinese medicine and Chinese herbal compounds in the intervention of NSCLC through ferroptosis, in order to provide a new theoretical basis for the research of ferroptosis pathway and the prevention and treatment of NSCLC by targeted ferroptosis of traditional Chinese medicine.
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Positive effect of deep diaphragmatic breathing training on gastroesophageal reflux-induced chronic cough: a clinical randomized controlled study.

BACKGROUND AND OBJECTIVE: To explore the efficacy of deep diaphragmatic breathing training (DEP) in patients with gastroesophageal reflux-induced chronic cough (GERC). METHODS: A randomized controlled study was conducted involving 60 GERC patients who were divided into the intervention group and the control group (each with 30 patients). Both groups received routine medication treatment for GERC, while the intervention group received DEP training additionally. Both groups were evaluated by cough symptom scores, Hull airway reflux questionnaire (HARQ), gastroesophageal reflux diagnostic questionnaire (GerdQ), generalized anxiety disorder scale-7 (GAD-7), patient health questionnaire-9 (PHQ-9), Pittsburgh sleep quality index (PSQI), the Leicester cough questionnaire (LCQ), as well as capsaicin cough sensitivity testing, B-ultrasound and surface electromyography (sEMG) of the diaphragmatic muscles before and after treatment. The cough resolution rate and changes of the above indictors was compared between the two groups after eight weeks of treatment. RESULTS: After eight weeks of treatment, cough symptoms improved in both groups, but the cough resolution rate in the intervention group of 94% was significantly higher than that in the control group of 77% (χ2 = 6.402, P = 0.041). The intervention group showed significant improvements to the control group in GerdQ (6.13(0.35) VS 6.57(0.77)), GAD-7 (0(0;1) VS 1(0;3)), PSQI (2(1;3) VS 4(3;6)), LCQ (17.19(1.56) VS 15.88(1.92)) and PHQ-9 (0(0;0) VS 0(0;3)) after treatment. Compared to control group, sEMG activity of the diaphragmatic muscle was significantly increased in the intervention group after treatment, measured during DEP (79.00(2.49) VS 74.65 (1.93)) and quiet breathing (72.73 (1.96) VS 67.15 (2.48)). CONCLUSION: DEP training can improve cough symptoms as an adjunctive treatment in GERC patients. TRIAL REGISTRATION: The protocol was registered in February 2, 2022 via the Chinese Clinical Trials Register ( http://www.chictr.org.cn/ ) [ChiCTR2200056246].

Research Progress on Quality Detection of Livestock and Poultry Meat Based on Machine Vision, Hyperspectral and Multi-Source Information Fusion Technologies.

Presently, the traditional methods employed for detecting livestock and poultry meat predominantly involve sensory evaluation conducted by humans, chemical index detection, and microbial detection. While these methods demonstrate commendable accuracy in detection, their application becomes more challenging when applied to large-scale production by enterprises. Compared with traditional detection methods, machine vision and hyperspectral technology can realize real-time online detection of large throughput because of their advantages of high efficiency, accuracy, and non-contact measurement, so they have been widely concerned by researchers. Based on this, in order to further enhance the accuracy of online quality detection for livestock and poultry meat, this article presents a comprehensive overview of methods based on machine vision, hyperspectral, and multi-sensor information fusion technologies. This review encompasses an examination of the current research status and the latest advancements in these methodologies while also deliberating on potential future development trends. The ultimate objective is to provide pertinent information and serve as a valuable research resource for the non-destructive online quality detection of livestock and poultry meat.

A comparison between a gastroesophageal reflux disease questionnaire-based algorithm and multichannel intraluminal impedance-pH monitoring for the treatment of gastroesophageal reflux-induced chronic cough.

BACKGROUND: Empiric therapy with multichannel intraluminal impedance-pH monitoring (MII-pH) has been used for the initial treatment of gastroesophageal reflux-induced chronic cough (GERC). However, an algorithm based on the gastroesophageal reflux disease questionnaire (GerdQ) has the potential to achieve a simple, structured, and effective treatment approach for patients with GERC. OBJECTIVES: This study compared the efficacy of anti-reflux therapy based on GerdQ (new structured pathway, NSP) with medical treatment after MII-pH examination (ordinary clinical pathway, OCP) in the management of GERC. DESIGN: For the NSP, we adapted the GerdQ score to establish the basis for a treatment algorithm. For the OCP, treatment was determined using the MII-pH examination results. METHODS: The non-inferiority (NI) hypothesis was used to evaluate NSP versus OCP. RESULTS: Overall, the NSP and OCP-based therapeutic algorithms have similar efficacy for GERC [NI analysis: 95% confidence interval (CI), -4.97 to 17.73, p = 0.009; superiority analysis: p = 0.420]. Moreover, the cough symptom scores and cough threshold improved faster in the NSP group than in the OCP group at week 8 (p < 0.05). In the subgroup analyses using the GerdQ and GerdQ impact scale (GIS) scores, patients with low-likelihood GERC (GerdQ < 8) were more likely to benefit from OCP (NI analysis: 95% CI, -19.73 to 18.02, p = 0.213). On the other hand, in patients with high-likelihood and low-reflux impact GERC patients (GerdQ > 8 and GIS < 4), the NSP arm was not inferior to the standard treatment of OCP (NI analysis: 95% CI, -8.85 to 28.21%, p = 0.04; superiority analysis: p = 0.339), indicating that GerdQ- and GIS-guided diagnosis and management of patients with GERC could be an alternative to MII-pH management, especially in settings with reduced medical resources. CONCLUSIONS: The use of the GerdQ algorithm should be considered when handling patients with GERC in the primary care setting. TRIAL REGISTRATION: This research was registered in the Chinese Clinical Trials Registry (ChiCTR-ODT-12001899).

Post-reflux swallow-induced peristaltic wave index: a new parameter for the identification of non-acid gastroesophageal reflux-related chronic cough.

BACKGROUND: The current available diagnostic criteria for gastroesophageal reflux-related chronic cough (GERC) dominated by non-acid reflux is imperfect. The post-reflux swallow-induced peristaltic wave index (PSPWI) is a parameter reflecting esophageal clearance function. OBJECTIVES: This study aims to investigate its diagnostic value for non-acid GERC. DESIGN: This study sought to compare the diagnostic value of PSPWI in different types of GERC, particularly non-acid GERC, and explore the clinical significance of PSPWI in the diagnosis of non-acid GERC through diagnostic experiments. METHODS: A retrospective analysis was performed based on 223 patients with suspected GERC who underwent multichannel intraluminal impedance-pH monitoring (MII-pH) in the outpatient clinic of our department from August 2016 to June 2021. Their clinical information, laboratory test results, and treatment responses were assessed and the underlying etiologies of chronic cough were categorized. The predictive value of the PSPWI in diagnosing different types of GERC, especially non-acid GERC, was analyzed and compared. RESULTS: A total of 195 patients with chronic cough who met the inclusion criteria underwent MII-pH monitoring. 143 patients had a definitive diagnosis of GERC, including 98 with acid GERC and 45 with non-acid GERC. The diagnostic value of PSPWI alone was moderate for GERC with an area under the working curve (AUC) 0.760, but poor for non-acid GERC with an AUC of 0.569. However, PSPWI < 39.8% combining with acid exposure time (AET) ⩽ 6.2% demonstrated a moderate diagnostic value for non-acid GERC, with an AUC of 0.722. When PSPWI < 39.8% combined with a non-acid reflux ratio >68.75%, the diagnostic value for non-acid GERC was improved (AUCROC = 0.80 versus AUCROC = 0.722, p < 0.05), which was significantly superior to non-acid symptom index (AUCROC = 0.804 versus AUCROC = 0.550, p < 0.05) and non-acid symptom association probability (AUCROC = 0.804 versus AUCROC = 0.571, p < 0.05). CONCLUSION: PSPWI < 39.8% and AET ⩽ 6.2% have demonstrated good diagnostic value for non-acid GERC. The diagnostic value was further improved when combined with non-acid reflux ratio >68.75%.

State-of-the-art review of soil erosion control by MICP and EICP techniques: Problems, applications, and prospects.

In recent years, the application of microbially induced calcite precipitation (MICP) and enzyme-induced carbonate precipitation (EICP) techniques have been extensively studied to mitigate soil erosion, yielding substantial achievements in this regard. This paper presents a comprehensive review of the recent progress in erosion control by MICP and EICP techniques. To further discuss the effectiveness of erosion mitigation in-depth, the estimation methods and characterization of erosion resistance were initially compiled. Moreover, factors affecting the erosion resistance of MICP/EICP-treated soil were expounded, spanning from soil properties to treatment protocols and environmental conditions. The development of optimization and upscaling in erosion mitigation via MICP/EICP was also included in this review. In addition, this review discussed the limitations and correspondingly proposed prospective applications of erosion control via the MICP/EICP approach. The current review presents up-to-date information on the research activities for improving erosion resistance by MICP/EICP, aiming at providing insights for interdisciplinary researchers and guidance for promoting this method to further applications in erosion mitigation.

Effect of tixagevimab/cilgavimab for pre-exposure prophylaxis during the China Omicron outbreak.

OBJECTIVES: By the end of 2022, China had made a pivotal decision to optimize the COVID-19 policy. The dominant Omicron variant in China at that time was highly transmissible. In this study, we aimed to evaluate the real-world safety and efficacy of tixagevimab and cilgavimab against this background in China. METHODS: Participants were enrolled if they were over 12 years old and were planning to receive tixagevimab or cilgavimab. All participants received intramuscular administration of tixagevimab (150 mg) and cilgavimab (150 mg). Data were collected on demographics, underlying illness, prior infection, vaccination, adverse events, and COVID-19 outcomes (e.g., infection rate, hospitalization rate, and severe disease). RESULTS: During the study period, 168 (37.9%) of 443 who received tixagevimab/cilgavimab were diagnosed with SARS-CoV-2 infection. All infected patients had mild COVID-19. Two patients (0.5%) were hospitalized for COVID-19, but none of them were admitted to the ICU. None of the patients died during this study. 4 (0.9%) reported mild local adverse events, and no severe systemic adverse reactions were reported. CONCLUSION: Tixagevimab/cilgavimab may have protected high-risk populations against infection with the Omicron variant, hospitalization and severe disease during the China COVID-19 pandemic.

Research Progress on Low Damage Grasping of Fruit, Vegetable and Meat Raw Materials.

The sorting and processing of food raw materials is an important step in the food production process, and the quality of the sorting operation can directly or indirectly affect the quality of the product. In order to improve production efficiency and reduce damage to food raw materials, some food production enterprises currently use robots for sorting operations of food raw materials. In the process of robot grasping, some food raw materials such as fruits, vegetables and meat have a soft appearance, complex and changeable shape, and are easily damaged by the robot gripper. Therefore, higher requirements have been put forward for robot grippers, and the research and development of robot grippers that can reduce damage to food raw materials and ensure stable grasping has been a major focus. In addition, in order to grasp food raw materials with various shapes and sizes with low damage, a variety of sensors and control strategies are required. Based on this, this paper summarizes the low damage grasp principle and characteristics of electric grippers, pneumatic grippers, vacuum grippers and magnetic grippers used in automated sorting production lines of fruit, vegetable and meat products, as well as gripper design methods to reduce grasp damage. Then, a grasping control strategy based on visual sensors and tactile sensors was introduced. Finally, the challenges and potential future trends faced by food robot grippers were summarized.

Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus (Rhamnaceae).

Rhamnus cathartica and Frangula alnus are economically valuable medicinal plants from the Rhamnaceae family. However, their chloroplast genome structure, phylogenetic position, relationships, and evolution remain poorly understood. Herein, the complete chloroplast genome resources of R. cathartica and F. alnus have been added. The first comparative analysis of the Rhamnus and Frangula species based on complete chloroplast genomes was provided. The chloroplast genomes of R. cathartica and F. alnus exhibited a quadripartite structure, with total lengths of 161,149 bp and 161,255 bp, respectively. The lack of the infA and psbL genes does not negatively impact the normal functioning of Rhamnus and Frangula species. The rpl20 and rpl33 genes are undergoing rapid evolution. Rhamnus and Frangula species prefer amino acids with A/U-terminal codons. There were between 100 and 126 simple sequence repeats and between 38 and 100 long repeats. Several highly divergent intergenic regions (trnK-UUU-trnQ-UUG, atpH-atpI, trnY-GUA-trnE-UUC, trnG-GCC-trnfM-CAU, trnT-UGU-trnF-GAA, rpl20-rps12, and rpl22-rps19) and highly divergent genes (ycf3, ndhA, rpl32, and ycf1) were identified, which could serve as potential phylogenetic markers due to their variability. We reconstructed the phylogenetic relationships among Rhamnus species and F. alnus using complete chloroplast genomes. There is no significant correlation between the medicinal value of the species analyzed and their phylogenetic relationships. These results provide valuable insights for understanding the phylogenetic relationship and evolution of Rhamnus and Frangula species. These findings could serve as a foundation for future studies on the Rhamnaceae. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01331-7.

Psychological morbidity and chronic cough: which is predominant? A comparison of clinical characteristics.

Background: The clinical characteristics of chronic cough with pre-existing psychological co-morbidity (PCC) and chronic cough with secondary anxiety and depression (SCC) were compared to provide a basis for diagnosing and treating psychological co-morbidities in people with chronic cough. Methods: A prospective study was conducted to analyze the general clinical data between the PCC, SCC, and the chronic cough without anxiety and depression (CC) groups. A total of 203 patients with chronic cough were enrolled in the study. The final diagnosis was made in all cases using a combination of psychosomatic and respiratory diagnoses. The three groups' general clinical data, capsaicin cough sensitivity, cough symptom score, Leicester cough questionnaire (LCQ), and psychosomatic scale scores were compared among the three groups. The diagnostic value of the patient health questionnaire (PHQ)-9 and general anxiety disorder (GAD)-7 in patients with PCC and the follow-up information were analyzed. Results: Compared with the SCC group, the duration of cough in the PCC group was shorter (H = -3.54, p = 0.001), the night cough symptoms were milder (H = -4.60, p < 0.001), the total LCQ score was lower (H = -2.97, p = 0.009), and the PHQ-9 (H = 2.90, p = 0.011) and GAD-7 scores (H = 2.71, p = 0.002) were higher. When using PHQ-9 and GAD-7 scores for the combined prediction and diagnosis of PCC, the area under the curve (AUC) was 0.88, and the sensitivity and specificity were 90.0% and 73.85%, respectively. After 8 weeks of psychosomatic treatment, cough symptoms improved in the PCC group, but the psychological improvement was not significant. The psychological status of the SCC group improved after cough symptoms were ameliorated by etiologic or empirical treatment. Conclusion: The clinical characteristics of patients with PCC and SCC are different. The evaluation of psychosomatic scales is of value to distinguish between the two groups. Chronic cough patients with psychological co-morbidity benefit from the combined diagnosis of psychosomatic medicine in a timely fashion. PCC requires more attention in psychological therapy, but for SCC, targeting etiological treatment of the cough is preferred. Trial registration: The protocol was registered in the Chinese Clinical Trials Register (http://www.chictr.org.cn/) [ChiCTR2000037429].

Designing Versatile Superhydrophilic Structures via an Alginate-Based Hydrophilic Plasticene.

The rational design of superhydrophilic materials with a controllable structure is a critical component in various applications, including solar steam generation, liquid spontaneous transport, etc. The arbitrary manipulation of the 2D, 3D, and hierarchical structures of superhydrophilic substrates is highly desirable for smart liquid manipulation in both research and application fields. To design versatile superhydrophilic interfaces with various structures, here we introduce a hydrophilic plasticene that possesses high flexibility, deformability, water absorption, and crosslinking capabilities. Through a pattern-pressing process with a specific template, 2D prior fast spreading of liquids at speeds up to 600 mm/s was achieved on the superhydrophilic surface with designed channels. Additionally, 3D superhydrophilic structures can be facilely designed by combining the hydrophilic plasticene with a 3D-printed template. The assembly of 3D superhydrophilic microstructure arrays were explored, providing a promising route to facilitate the continuous and spontaneous liquid transport. The further modification of superhydrophilic 3D structures with pyrrole can promote the applications of solar steam generation. The optimal evaporation rate of an as-prepared superhydrophilic evaporator reached ~1.60 kg·m-2·h-1 with a conversion efficiency of approximately 92.96%. Overall, we envision that the hydrophilic plasticene should satisfy a wide range of requirements for superhydrophilic structures and update our understanding of superhydrophilic materials in both fabrication and application.

Unidirectional Moisture Delivery via a Janus Photothermal Interface for Indoor Dehumidification: A Smart Roof.

Rational control of the humidity in specific environments plays an important role in green building, equipment protection, etc. A smart apparatus that can actively expel inner moisture and largely prevent outer liquid penetration can be highly desirable. Through the integration of the Janus interface with unidirectional liquid manipulation and the solar evaporating layer, here, a Janus solar dehumidifying interface (JSDI) is designed for the switchable moisture management of an indoor environment. By covering with the JSDI roof, the continuous elimination of inner water is achieved via outward condensate delivery and solar evaporation on sunny days. On rainy days, JSDI with a hydrophobic lower surface can largely hamper inward liquid leakage and then spontaneously drain the accumulated water via a siphoning structure. The real-world water evaporation rate via the JSDI is ≈0.38 kg m-2 h-1 on an autumn day, showing a promising function of in situ moisture expelling. In addition, the JSDI is made of natural materials that are easy to scale up with a cost of four dollars per square meter. It is envisioned that the JSDI may meet the wide requirements of indoor dehumidification and update the understanding of the integration of Janus interfaces and solar steam generation.

Modifying the Molecular Structure of Carbon Nanotubes through Gas-Phase Reactants.

Current approaches to carbon nanotube (CNT) synthesis are limited in their ability to control the placement of atoms on the surface of nanotubes. Some of this limitation stems from a lack of understanding of the chemical bond-building mechanisms at play in CNT growth. Here, we provide experimental evidence that supports an alkyne polymerization pathway in which short-chained alkynes directly incorporate into the CNT lattice during growth, partially retaining their side groups and influencing CNT morphology. Using acetylene, methyl acetylene, and vinyl acetylene as feedstock gases, unique morphological differences were observed. Interwall spacing, a highly conserved value in natural graphitic materials, varied to accommodate side groups, increasing systematically from acetylene to methyl acetylene to vinyl acetylene. Furthermore, attenuated total reflectance Fourier-transfer infrared spectroscopy (ATR-FTIR) illustrated the existence of intact methyl groups in the multiwalled CNTs derived from methyl acetylene. Finally, the nanoscale alignment of the CNTs grown in vertically aligned forests differed systematically. Methyl acetylene induced the most tortuous growth while CNTs from acetylene and vinyl-acetylene were more aligned, presumably due to the presence of polymerizable unsaturated bonds in the structure. These results demonstrate that feedstock hydrocarbons can alter the atomic-scale structure of CNTs, which in turn can affect properties on larger scales. This information could be leveraged to create more chemically and structurally complex CNT structures, enable more sustainable chemical pathways by avoiding the need for solvents and postreaction modifications, and potentially unlock experimental routes to a host of higher-order carbonaceous nanomaterials.

Mean Nocturnal Baseline Impedance (MNBI) Provides Evidence for Standardized Management Algorithms of Nonacid Gastroesophageal Reflux-Induced Chronic Cough.

Background: The clinical management of nonacid gastroesophageal reflux-induced chronic cough (GERC) is challenging, and patient response to standard antireflux therapy (omeprazole 20 mg twice daily plus mosapride 10 mg thrice daily) is suboptimal. This study aimed to identify predictors of standard antireflux therapy efficacy and provide evidence for standardized management algorithms of nonacid GERC. Methods: A total of 115 nonacid GERC patients who underwent multichannel intraluminal impedance-pH monitoring (MII-pH) were enrolled between March 2017 and March 2021. Retrospective analysis of general information and MII-pH indications were used to establish a regression analysis model for multiple factors affecting standard antireflux therapy efficacy. Results: 90 patients met the inclusion criteria, and the overall response rate to standard antireflux therapy was 55.5% (50/90). The mean nocturnal baseline impedance (MNBI) (1817.75 ± 259.26 vs. 2369.93 ± 326.35, P = 0.030) and proximal MNBI (1833.39 ± 92.16 vs. 2742.57 ± 204.64, P ≤ 0.001) of responders were lower than those of nonresponders. Weakly acid reflux (56.00 (31.70, 86.00) vs. 14.00 (14.00, 44.20), P = 0.022), nonacid reflux (61.35 (15.90.86.50) vs. 21.60 (0.00, 52.50), P = 0.008), and proximal extent (19.00 (5.04, 24.00) vs. 5.50 (2.56, 11.13), P = 0.011) were markedly higher in responders than nonresponders. Proximal MNBI (OR = 0.997, P = 0.042, and optimal cutoff = 2140 Ω) and weakly acid reflux (OR = 1.051, P = 0.029, and optimal cutoff = 45) were independent predictors of standard antireflux therapy efficacy. The combination predictive value did not show better results than either individual predictor. Conclusions: Proximal MNBI < 2140 Ω may be used to screen patients with nonacid GERC suitable for standard antireflux therapy and in standardized management algorithms for nonacid GERC. In the absence of MNBI, weakly acid reflux > 45 can be used as an auxiliary indicator.

Comparative chloroplast genome analyses of diverse Phoebe (Lauraceae) species endemic to China provide insight into their phylogeographical origin.

The genus Phoebe (Lauraceae) includes about 90 evergreen tree species that are an ideal source of timber. Habitat destruction and deforestation have resulted in most of them being endemic to China. The accurate identification of endangered Phoebe species in China is necessary for their conservation. Chloroplast genome sequences can play an important role in species identification. In this study, comparative chloroplast genome analyses were conducted on diverse Phoebe species that are primarily distributed in China. Despite the conserved nature of chloroplast genomes, we detected some highly divergent intergenic regions (petA-psbE, ndhF-rpl32, and psbM-trnD-GUC) as well as three highly divergent genes (rbcL, ycf1, and ycf2) that have potential applications in phylogenetics and evolutionary analysis. The phylogenetic analysis indicated that various Phoebe species in China were divided into three clades. The complete chloroplast genome was better suited for phylogenetic analysis of Phoebe species. In addition, based on the phylogeographical analysis of Phoebe species in China, we inferred that the Phoebe species in China first originated in Yunnan and then spread to other southern areas of the Yangtze River. The results of this research will add to existing case studies on the phylogenetic analysis of Phoebe species and have the potential to contribute to the conservation of Phoebe species that are in danger of extinction.

Entanglement of Signal Paths via Noisy Superconducting Quantum Devices.

Quantum routers will provide for important functionality in emerging quantum networks, and the deployment of quantum routing in real networks will initially be realized on low-complexity (few-qubit) noisy quantum devices. A true working quantum router will represent a new application for quantum entanglement-the coherent superposition of multiple communication paths traversed by the same quantum signal. Most end-user benefits of this application are yet to be discovered, but a few important use-cases are now known. In this work, we investigate the deployment of quantum routing on low-complexity superconducting quantum devices. In such devices, we verify the quantum nature of the routing process as well as the preservation of the routed quantum signal. We also implement quantum random access memory, a key application of quantum routing, on these same devices. Our experiments then embed a five-qubit quantum error-correcting code within the router, outlining the pathway for error-corrected quantum routing. We detail the importance of the qubit-coupling map for a superconducting quantum device that hopes to act as a quantum router, and experimentally verify that optimizing the number of controlled-X gates decreases hardware errors that impact routing performance. Our results indicate that near-term realization of quantum routing using noisy superconducting quantum devices within real-world quantum networks is possible.

DeepPRObind: Modular Deep Learner that Accurately Predicts Structure and Disorder-Annotated Protein Binding Residues.

Current sequence-based predictors of protein-binding residues (PBRs) belong to two distinct categories: structure-trained vs. intrinsic disorder-trained. Since disordered PBRs differ from structured PBRs in several ways, including ability to bind multiple partners by folding into different conformations and enrichment in different amino acids, the structure-trained and disorder-trained predictors were shown to provide inaccurate results for the other annotation type. A simple consensus-based solution that combines structure- and disorder-trained methods provides limited levels of predictive performance and generates relatively many cross-predictions, where residues that interact with other ligand types are predicted as PBRs. We address this unsolved problem by designing a novel and fast deep-learner, DeepPRObind, that relies on carefully designed modular convolutional architecture and uses innovative aggregate input features. Comparative empirical tests on a low-similarity test dataset reveal that DeepPRObind generates accurate predictions of structured and disordered PBRs and low amounts of cross-predictions, outperforming a comprehensive collection of 12 predictors of PBRs. Given the relatively low runtime of DeepPRObind (40 seconds per protein), we further validate its results based on an analysis of putative PBRs in the yeast proteome, confirming that interactions in disordered regions are enriched among hub proteins. We release DeepPRObind as a convenient web server at https://www.csuligroup.com/DeepPRObind/.

A Deep Learning Framework for Predicting Protein Functions With Co-Occurrence of GO Terms.

The understanding of protein functions is critical to many biological problems such as the development of new drugs and new crops. To reduce the huge gap between the increase of protein sequences and annotations of protein functions, many methods have been proposed to deal with this problem. These methods use Gene Ontology (GO) to classify the functions of proteins and consider one GO term as a class label. However, they ignore the co-occurrence of GO terms that is helpful for protein function prediction. We propose a new deep learning model, named DeepPFP-CO, which uses Graph Convolutional Network (GCN) to explore and capture the co-occurrence of GO terms to improve the protein function prediction performance. In this way, we can further deduce the protein functions by fusing the predicted propensity of the center function and its co-occurrence functions. We use Fmax and AUPR to evaluate the performance of DeepPFP-CO and compare DeepPFP-CO with state-of-the-art methods such as DeepGOPlus and DeepGOA. The computational results show that DeepPFP-CO outperforms DeepGOPlus and other methods. Moreover, we further analyze our model at the protein level. The results have demonstrated that DeepPFP-CO improves the performance of protein function prediction. DeepPFP-CO is available at https://csuligroup.com/DeepPFP/.

Study on the mechanism of Fufang E'jiao Jiang on precancerous lesions of gastric cancer based on network pharmacology and metabolomics.

ETHNOPHARMACOLOGICAL RELEVANCE: Fufang E'jiao Jiang (FEJ) is a prominent traditional Chinese medicine prescription, which consists of Asini Corii Colla (Donkey-hide gelatin prepared by stewing and concentrating from the hide of Equus asinus Linnaeus., ACC), Codonopsis Radix (the dried roots of Codonopsis pilosula (Franch.) Nannf., CR), Ginseng Radix et Rhizoma Rubra (the steamed and dried root of Panax ginseng C.A. Mey., GRR), Crataegi Fructus (the mature fruits of Crataegus pinnatifida Bunge., CF), and Rehmanniae Radix Praeparata (the steamed and sun dried tuber of Rehmannia glutinosa (Gaertn.) Libosch. ex Fisch. & C.A. Mey., RRP). It is a popularly used prescription for "nourishing Qi and nourishing blood". AIM OF THE STUDY: To explore the potential mechanism of FEJ on precancerous lesion of gastric cancer in rats by combining network pharmacology and metabolomics. METHODS: Traditional Chinese Medicine Systems Pharmacology and Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine were used to identify the ingredients and potential targets of FEJ. GeneCards database was used to define PLGC-associated targets. We built a herb-component-disease-target network and analyzed the protein-protein interaction network. Underlying mechanisms were identified using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, 40% ethanol, N-methyl-N'-nitro-N-nitroguanidine and irregular eating were used to establish PLGC rats model. We also evaluated the efficacy of FEJ on MNNG-induced PLGC rats by body weight, histopathology, blood routine and cytokine levels, while the predicted pathway was determined by the Western blot. Ultra-performance liquid chromatography-tandem mass spectrometry-based serum non-targeted metabolomics was used to select potential biomarkers and relevant pathways for FEJ in the treatment of PLGC. RESULTS: Network pharmacology showed that FEJ exhibited anti-PLGC effects through regulating ALB, TNF, VEGFA, TP53, AKT1 and other targets, and the potential pathways mainly involved cancer-related, TNF, PI3K-AKT, HIF-1, and other signaling pathways. Animal experiments illustrated that FEJ could suppress inflammation, regulate gastrointestinal hormones, and inhibit the expression of PI3K/AKT/HIF-1α pathway-related proteins. Based on serum non-targeted metabolomics analysis, 12 differential metabolites responding to FEJ treatment were identified, and metabolic pathway analysis showed that the role of FEJ was concentrated in 6 metabolic pathways. CONCLUSION: Based on network pharmacology, animal experiments and metabolomics, we found that FEJ might ameliorate gastric mucosal injury in PLGC rats by regulating gastrointestinal hormones and inhibiting inflammation, and its mechanism of action is related to the inhibition of excessive activation of PI3K/AKT/HIF-1α signaling pathway and regulation of disorders of body energy metabolism. This comprehensive strategy also provided a reasonable way for unveiling the pharmacodynamic mechanisms of multi-components, multi-targets, and multi-pathways in Traditional Chinese Medicine.

A probe-based nanometric morphology measurement system using intermittent-contact mode.

In the present study, a homemade probe-based nanometric morphology measurement system is proposed, which can be easily integrated with other probes, such as a diamond probe and an electrochemical electrode. In this system, an intermittent-contact mode is adopted, which is based on a set of micro-force servo modules. The micro-force serve module is mainly composed of a piezoelectric ceramic transducer, a capacitive displacement sensor, an excitation piezoelectric ceramic ring, and a four-beam spring. The four-beam spring integrated with a diamond probe is driven by the excitation piezoelectric ceramic ring. The mechanical structure and the control system of the measurement system are also designed. The vibration amplitude and the resolution of a normal load are calibrated during the engagement process under open-loop control. Moreover, the optimal values for parameters P, I, and D are obtained for the closed-loop measurement. The performance of the developed system is verified by measuring a standard sample. The measured depths agree well with the results obtained by commercial atomic force microscopy. The developed system can be used to measure nanostructures with high precision.