Publications by authors named "Chao Shen"

Article Synopsis
  • - The study explored how different rates of sewage sludge (0, 30, 75, and 150 tons per hectare) affected bacterial diversity and functions in mudflat soils using advanced sequencing techniques.
  • - Soils treated with sewage sludge, especially the highest rate, showed improved nutrient levels and lower salinity and pH, leading to more diverse and unique bacterial communities compared to untreated soils.
  • - The findings indicate that adding sewage sludge enhances soil health by promoting beneficial bacteria and improving crucial processes like carbon and nitrogen cycling, which is essential for the fertility of mudflat environments.
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Background: The aim of the present study was to investigate the association between monocyte to high-density lipoprotein cholesterol ratio (MHR) and nonalcoholic fatty liver disease (NAFLD) in Chinese population.

Methods: We enrolled 14189 individuals who attended their annual health examinations in the study. We performed the anthropometric and laboratory measurements and diagnosed NAFLD by hepatic ultrasonography without evidence of other etiologies of chronic liver disease.

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Background: Subspine impingement (SSI) has been commonly managed with arthroscopic decompression. However, arthroscopic decompression is a demanding technique, as under- or over-resection of the anterior inferior iliac spine (AIIS) could lead to inferior outcomes. An anterior mini-open approach has also been used in the management of femoroacetabular impingement (FAI), and it could provide adequate visualization of the anterior hip joint without a long learning curve.

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Mitochondria, a kind of subcellular organelle, play crucial roles in cancer cells as an energy source and as a generator of reactive substrates, which concern the generation, proliferation, drug resistance, and other functions of cancer. Therefore, precise delivery of anticancer agents to mitochondria can be a novel strategy for enhanced cancer treatment. Mitochondria have a four-layer structure with a high negative potential, which thereby prevents many molecules from reaching the mitochondria.

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Background: Cervical cancer is one of the most common gynecological cancers worldwide. The tumor microenvironment significantly influences the therapeutic response and clinical outcome. However, the complex tumor microenvironment of cervical cancer and the molecular mechanisms underlying chemotherapy resistance are not well studied.

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Difenoconazole is a typical triazole fungicide that can inhibit demethylation during ergosterol synthesis. Due to its wide use, difenoconazole is frequently detected in surface water, paddy water, agricultural water, and other aquatic environments. Presently, an assessment of the ecological risk posed by difenoconazole in aquatic ecosystems is lacking.

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Accurate quantification of protein-ligand interactions remains a key challenge to structure-based drug design. However, traditional machine learning (ML)-based methods based on handcrafted descriptors, one-dimensional protein sequences, and/or two-dimensional graph representations limit their capability to learn the generalized molecular interactions in 3D space. Here, we proposed a novel deep graph representation learning framework named InteractionGraphNet (IGN) to learn the protein-ligand interactions from the 3D structures of protein-ligand complexes.

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We report a Minisci-type cross-dehydrogenative alkylation in an aerobic atmosphere using abundant and inexpensive cerium chloride as a photocatalyst and air as an oxidant. This photoreaction exhibits excellent tolerance to functional groups and is suitable for both heteroarene and alkane substrates under mild conditions, generating the corresponding products in moderate-to-good yields. Our method provides an alternative approach for the late-stage functionalization of valuable substrates.

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Background: Cerebral small vessel disease is the primary cause of cognitive impairment. Therefore, early recognition is of great significance. Some studies have shown that asymptomatic cerebral small vessel disease (aCSVD) patients have abnormal neurocognitive function, but this is not readily apparent at the initial stage.

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Binding of different ligands to glucocorticoid receptor (GR) may induce different conformational changes and even trigger completely opposite biological functions. To understand the allosteric communication within the GR ligand binding domain, the folding pathway of helix 12 (H12) induced by the binding of the agonist dexamethasone (DEX), antagonist RU486, and modulator AZD9567 are explored by molecular dynamics simulations and Markov state model analysis. The ligands can regulate the volume of the activation function-2 through the residues Phe737 and Gln738.

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De novo drug design is the process of generating novel lead compounds with desirable pharmacological and physiochemical properties. The application of deep learning (DL) in de novo drug design has become a hot topic, and many DL-based approaches have been developed for molecular generation tasks. Generally, these approaches were developed as per four frameworks: recurrent neural networks; encoder-decoder; reinforcement learning; and generative adversarial networks.

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The quantum efficiency of GaN-based micro-light-emitting diodes (micro-LEDs) is of great significance for their luminescence and detection applications. Optimized passivation process can alleviate the trapping of carriers by sidewall defects, such as dangling bonds, and is regarded as an effective way to improve the quantum efficiency of micro-LEDs. In this work, an AlN passivation layer was prepared by atomic layer deposition to improve the electro-optical and photoelectric conversion efficiency in GaN-based micro-LEDs.

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Purpose: To investigate the differences in radiologic parameters between borderline dysplasia hips (BDDH) +/- coxa profunda and normal hips and to evaluate the correlations between these parameters and the prevalence of ischiofemoral impingement (IFI) in borderline dysplasia.

Methods: The imaging of patients with BDDH (18° ≤ lateral center edge angle <25°) treated in our hospital from January 2018 to December 2019 was retrospective reviewed. These patients were divided into BDDH with coxa profunda (acetabular fossa touches the ilioischial line, pBDDH) and without coxa profunda (nBDDH) groups.

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Background: Head and neck squamous cell carcinoma (HNSCC) is an extremely heterogeneous malignant cancer with poor prognosis. Pyroptosis is defined as a novel inflammation-dependent programmed cell death. However, the pyroptosis-associated gene expression in HNSCC and their relationship with prognosis are still indistinct.

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Objective: There is increasing evidence supporting the efficacy of sacubitril/valsartan for treating left heart failure, but few studies have investigated its effects on right ventricular (RV) dysfunction. This study aimed to explore the effects of sacubitril/valsartan on RV dysfunction among patients with heart failure with reduced ejection fraction (HFrEF).

Methods: A total of 93 patients with HFrEF with RV dysfunction who were hospitalized from January 2018 through June 2019 were included in this retrospective observational study.

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Worldwide, countless deaths have been caused by the coronavirus disease 2019. In addition to the virus variants, an increasing number of fatal fungal infections have been reported, which further exacerbates the scenario. Therefore, the development of porous surfaces with both antiviral and antimicrobial capacities is of urgent need.

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Article Synopsis
  • DprE1 is a key enzyme in the cell wall biosynthesis of Mycobacterium, making it a target for new tuberculosis (TB) treatments.
  • The study used advanced molecular modeling techniques to identify two promising compounds, B2 and H3, that can inhibit DprE1 and kill Mycobacterium smegmatis in the lab.
  • Notably, compound H3 was found to effectively inhibit Mycobacterium tuberculosis with minimal harm to mouse cells, highlighting its potential as a new anti-TB drug.
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Article Synopsis
  • Structure-based drug design relies on understanding 3D structures of protein-ligand complexes, but predicting ligand-binding poses remains difficult due to limitations in scoring functions and protein flexibility.
  • This study created XGBoost classifiers to improve accuracy in identifying near-native binding poses using data from the PDBbind database, emphasizing the importance of using Extended Connectivity Interaction Features, Vina energy terms, and docking pose ranks.
  • The research shows that incorporating cross-docked poses in training significantly enhances model performance and provides new datasets and code for future studies in machine learning-based scoring functions for binding pose prediction.
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Nanocatalytic medicine is one of the most recent advances in the development of nanomedicine, which catalyzes intratumoral chemical reactions to produce toxins such as reactive oxygen species for cancer specific treatment by using exogenous-delivered catalysts such as Fenton agents. However, the overexpression of reductive glutathione and Cu-Zn superoxide dismutase in cancer cells will significantly counteract the therapeutic efficacy by reactive oxygen species-mediated oxidative damages. Additionally, the direct delivery of iron-based Fenton agents may arouse undesired detrimental effects such as anaphylactic reactions.

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Foot-and-mouth disease virus (FMDV) infection can be either persistent or acute in susceptible animals. The mechanisms involved in FMDV replication and clearance during persistent infection remain unclear. To identify host factors that are critical for FMDV replication during persistent infection, we used RNA-seq to compare the transcriptomes of infected (BHK-Op) cells and bystander (BHK-VEC) cells, which are exposed to FMDV but not infected.

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Objective: To investigate the effects of lycopene-loaded microemulsion (LME) on the cognitive function and neurogenesis in the dentate gyrus (DG) of the hippocampus and subventricular (SVZ) region of rats with amyloid - (A-) induced Alzheimer's disease (AD) and its mechanism based on the Wnt/-catenin pathway.

Methods: Healthy Wistar rats were divided into four groups: the blank control (CON), AD control, traditional lycopene (LOO), and LME groups. The CON and AD groups were fed with normal saline, while the LOO group was fed with traditional lycopene, and the LME group was fed with lycopene-loaded microemulsion.

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Background: There are no ideal plates or approaches for anatomical restoration and rigid fixation of posterolateral tibial plateau fractures. This study aimed to evaluate the short-term preliminary outcomes of our novel anatomical plate placed via the trans-supra-fibular approach to treat posterolateral tibial plateau fractures.

Methods: From May 2016 to May 2018, 23 consecutive patients with posterolateral tibial quadrant fractures underwent open reduction with internal fixation via the trans-supra-fibular-head approach with our newly developed plate.

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Continuous cell lines are practical models that are widely used in the study of disease mechanisms and particularly cancers. However, the issue of cell line cross-contamination has existed since the 1960s, despite repeated advocation for cell line authentication by many experts. Furthermore, cell line abuse has been underestimated and underreported.

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