A RT-FDTD method of analyzing wireless propagation characteristics in underground mine

Efficient communication is crucial in reducing injuries and fatalities in coal mine accidents, necessitating the study of simulation methods for mine communication. When transceiver antennas are positioned close to the same side of the tunnel, the simulation results from the Ray Tracing (RT) method exhibit significant errors. Additionally, the Finite-Difference Time-Domain (FDTD) method demands substantial computational resources. In response to these challenges, we propose a RT-FDTD method, guided by the law of conservation of energy. This approach involves dividing the mine tunnel into a cuboidal region, using the RT method to calculate the electric field strength on the cuboid's surface, and then employing this as the excitation source for the FDTD method. Subsequently, the FDTD method is used to calculate the electric field strength within the cuboid. Experimental results demonstrate that the RT-FDTD method effectively mitigates the limitations of the RT and FDTD methods, enhancing both the efficiency and accuracy of simulations in underground mine.

Effects of Long-Term Cryopreservation on the Transcriptomes of Giant Grouper Sperm

The giant grouper fish (Epinephelus lanceolatus), one of the largest and rarest groupers, is a fast-growing economic fish. Grouper sperm is often used for cross-breeding with other fish and therefore sperm cryopreservation is important. However, freezing damage cannot be avoided. Herein, we performed a transcriptome analysis to compare fresh and frozen sperm of the giant grouper with frozen storage times of 0, 23, 49, and 61 months. In total, 1911 differentially expressed genes (DEGs), including 91 in El-0-vs-El-23 (40 upregulated and 51 downregulated), 251 in El-0-vs-El-49 (152 upregulated and 69 downregulated), and 1569 in El-0-vs-El-61 (984 upregulated and 585 downregulated), were obtained in the giant grouper sperm. DEGs were significantly increased at 61 months of cryopreservation (p < 0.05). GO and KEGG enrichment analyses of the DEGs revealed significant enrichment in the pilus assembly, metabolic process, MAPK signaling pathway, apoptosis, and P53 signaling pathway. Time-series expression profiling of the DEGs showed that consistently upregulated modules were also significantly enriched in signaling pathways associated with apoptosis. Four genes, scarb1, odf3, exoc8, and atp5f1d, were associated with mitochondria and flagella in a weighted correlation network analysis. These genes may play an important role in the response to sperm freezing. The experimental results show that long-term cryopreservation results in freezing damage to the giant grouper sperm. This study provides rich data for studies of the mechanism underlying frozen fish sperm damage as well as a technical reference and evaluation index for the long-term cryopreservation of fish sperm.

Rauwolfia polysaccharide can inhibit the progress of ulcerative colitis through NOS2-mediated JAK2/STAT3 pathway

BACKGROUND

Ulcerative colitis (UC) is an inflammatory disease of the digestive tract. Rauwolfia polysaccharide (Rau) has therapeutic effects on colitis in mice, but its mechanism of action needs to be further clarified. In the study, we explored the effect of Rau on the UC cell model induced by Lipopolysaccharide (LPS).

METHODS

We constructed a UC cell model by stimulating HT-29 cells with LPS. Dextran sodium sulfate (DSS) was used to induce mice to construct an animal model of UC. Subsequently, we performed Rau administration on the UC cell model. Then, the therapeutic effect of Rau on UC cell model and was validated through methods such as Cell Counting Kit-8 (CCK8), Muse, Quantitative real‑time polymerase chain reaction (RT-qPCR), Western blotting, and Enzyme-linked immunosorbent assay (ELISA).

RESULTS

The results showed that Rau can promote the proliferation and inhibit the apoptosis of the HT-29 cells-induced by LPS. Moreover, we observed that Rau can inhibit the expression of NOS2/JAK2/STAT3 in LPS-induced HT-29 cells. To further explore the role of NOS2 in UC progression, we used siRNA technology to knock down NOS2 and search for its mechanism in UC. The results illustrated that NOS2 knockdown can promote proliferation and inhibit the apoptosis of LPS-induced HT-29 cells by JAK2/STAT3 pathway. In addition, in vitro and in vivo experiments, we observed that the activation of the JAK2/STAT3 pathway can inhibit the effect of Rau on DSS-induced UC model.

CONCLUSION

In short, Rauwolfia polysaccharide can inhibit the progress of ulcerative colitis through NOS2-mediated JAK2/STAT3 pathway. This study provides a theoretical clue for the treatment of UC by Rau.

Doping Ferrocene-Based Conjugated Microporous Polymers with 7,7,8,8-Tetracyanoquinodimethane for Efficient Photocatalytic CO2 Reduction

The design and synthesis of organic photocatalysts remain a great challenge due to their strict structural constraints. However, this could be mitigated by achieving structural flexibility by constructing permanent porosity into the materials. Conjugated microporous polymers (CMPs) are an emerging class of porous materials with an amorphous, three-dimensional network structure, which makes it possible to integrate the elaborate functional groups to enhance photocatalytic performance. Here, we report the synthesis of a novel CMP, named TAPFc-TFPPy-CMP, constructed by 1,1'3,3'-tetra(4-aminophenyl)ferrocene (TAPFc) and 1,3,6,8-tetrakis(4-formylphenyl)pyrene (TFPPy) monomers. The integration of the p-type dopant 7,7,8,8-tetracyanoquinodimethane (TCNQ) into the TAPFc-TFPPy-CMP improved the light adsorption performance, leading to a decrease in the optical bandgap from 2.00 to 1.43 eV. The doped CMP (TCNQ@TAPFc-TFPPy-CMP) exhibited promising catalytic activity in photocatalytic CO2 reduction under visible light, yielding 546.8 μmol g-1 h-1 of CO with a selectivity of 96% and 5.2 μmol g-1 h-1 of CH4. This represented an 80% increase in the CO yield compared to the maternal TAPFc-TFPPy-CMP. The steady-state photoluminescence (PL) and fluorescence lifetime (FL) measurements reveal faster carrier separation and transport after the doping. This study provides guidance for the development of organic photocatalysts for the utilization of renewable energy.

Handling the Challenges of Small-Scale Labeled Data and Class Imbalances in Classifying the N and K Statuses of Rubber Leaves Using Hyperspectroscopy Techniques

The nutritional status of rubber trees (Hevea brasiliensis) is inseparable from the production of natural rubber. Nitrogen (N) and potassium (K) levels in rubber leaves are 2 crucial criteria that reflect the nutritional status of the rubber tree. Advanced hyperspectral technology can evaluate N and K statuses in leaves rapidly. However, high bias and uncertain results will be generated when using a small size and imbalance dataset to train a spectral estimaion model. A typical solution of laborious long-term nutrient stress and high-intensive data collection deviates from rapid and flexible advantages of hyperspectral tech. Therefore, a less intensive and streamlined method, remining information from hyperspectral image data, was assessed. From this new perspective, a semisupervised learning (SSL) method and resampling techniques were employed for generating pseudo-labeling data and class rebalancing. Subsequently, a 5-classification spectral model of the N and K statuses of rubber leaves was established. The SSL model based on random forest classifiers and mean sampling techniques yielded optimal classification results both on imbalance/balance dataset (weighted average precision 67.8/78.6%, macro averaged precision 61.2/74.4%, and weighted recall 65.7/78.5% for the N status). All data and code could be viewed on the:Github https://github.com/WeehowTang/SSL-rebalancingtest. Ultimately, we proposed an efficient way to rapidly and accurately monitor the N and K levels in rubber leaves, especially in the scenario of small annotation and imbalance categories ratios.

Research on energy-saving control of agricultural hybrid tractors integrating working condition prediction

To address the issues of tractors using too much fuel and not being energy efficient, a predictive control strategy based on Pontryagin's minimum principle integrating working condition prediction is proposed for agricultural hybrid tractors. The Dongfanghong 1804 tractor is being used for research. Firstly, the main parameters of the hybrid drive system are determined and modeled. Secondly, based on the adaptive cubic exponential forecasting method, the working condition information for a period of time in the future is predicted through historical working condition information. Furthermore, combining the predicted working conditions information, the goal is to minimize the total energy consumption cost of the entire machine. Motor power and diesel engine power are control variables. The battery state of charge is a state variable. Subsequently, a predictive control strategy based on Pontryagin's minimum principle integrating working condition prediction is proposed. Finally, the simulation test is carried out based on the MATLAB simulation platform. Research indicates: under plowing conditions, compared with the power following control strategy, the proposed predictive control strategy can effectively manage the performance of the diesel engine and motor, ensuring they operate at their most efficient level. The total energy consumption costs of the power following control and predictive control strategies are 37.17 China Yuan (CNY) and 33.67 CNY, respectively. The cost of energy used is decreased by 9. 42%, which helps make tractor field plowing more efficient and economical.

Complex hybrid weighted pruning method for accelerating convolutional neural networks

The increasing interest in filter pruning of convolutional neural networks stems from its inherent ability to effectively compress and accelerate these networks. Currently, filter pruning is mainly divided into two schools: norm-based and relation-based. These methods aim to selectively remove the least important filters according to predefined rules. However, the limitations of these methods lie in the inadequate consideration of filter diversity and the impact of batch normalization (BN) layers on the input of the next layer, which may lead to performance degradation. To address the above limitations of norm-based and similarity-based methods, this study conducts empirical analyses to reveal their drawbacks and subsequently introduces a groundbreaking complex hybrid weighted pruning method. By evaluating the correlations and norms between individual filters, as well as the parameters of the BN layer, our method effectively identifies and prunes the most redundant filters in a robust manner, thereby avoiding significant decreases in network performance. We conducted comprehensive and direct pruning experiments on different depths of ResNet using publicly available image classification datasets, ImageNet and CIFAR-10. The results demonstrate the significant efficacy of our approach. In particular, when applied to the ResNet-50 on the ImageNet dataset, achieves a significant reduction of 53.5% in floating-point operations, with a performance loss of only 0.6%.

Influence of cancer-directed surgery on the prognosis of liver metastases from gastric cancer

There are controversial about the application of cancer-directed surgery (CDS) in patients with liver metastases from gastric cancer, with improved responses to chemotherapy and targeted treatments, the role of CDS in metastatic gastric cancer to the liver needs to be revisited. This study aimed to evaluate the effect of CDS on patients with liver metastases from gastric cancer. Data for patients with liver metastases from gastric cancer were extracted from the population-based Surveillance, Epidemiology, and End Results (SEER) database. A total of 958 individuals were enrolled, 285 in the CDS group and 673 in the non-cancer guided surgery (Non-CDS) group. Following propensity score matching (PSM) analysis at 1:1 in the two groups,285 were included in the survival analysis for each group. Kaplan-Meier values and Cox proportional risk models were used to estimate the effect of CDS on patients' prognoses. Compared with the Non-CDS group, the CDS group significantly prolonged the median overall survival from 4 months (95% confidence interval [CI] 3-5) to 11 months (95% CI 8-12), p value < 0.001. Overall survival (OS) at 1 year was higher in the CDS group than in the Non-CDS group, at 44% (95 CI 38-50) and 25% (95 CI 20-30), respectively. OS at 3 years was also higher in the CDS group than in the Non-CDS group, at 24% (95 CI 19-29) and 6% (95 CI 3-9), respectively. Multivariate analysis showed that Non-CDS (hazard ratio[HR] = 2.26, 95% CI 1.88-2.72, p value < 0.001) was an adverse independent prognostic factor for patients. This study concludes that CDS prolonged survival in patients with gastric cancer with liver metastases. Due to the lack of information on the quality of life, biomarkers, targeted therapies, and immunotherapy in the SEER database, the observed improved survival rates following CDS of hepatic metastasis from gastric cancer requires prospective studies that take these factors into account to properly address the survival advantages and impact on quality of life of such a method.

Maternal fiber-rich diet promotes early-life intestinal development in offspring through milk-derived extracellular vesicles carrying miR-146a-5p

BACKGROUNDS

The intestinal development in early life is profoundly influenced by multiple biological components of breast milk, in which milk-derived extracellular vesicles (mEVs) contain a large amount of vertically transmitted signal from the mother. However, little is known about how maternal fiber-rich diet regulates offspring intestinal development by influencing the mEVs.

RESULTS

In this study, we found that maternal resistant starch (RS) consumption during late gestation and lactation improved the growth and intestinal health of offspring. The mEVs in breast milk are the primary factor driving these beneficial effects, especially enhancing intestinal cell proliferation and migration. To be specific, administration of mEVs after maternal RS intake enhanced intestinal cell proliferation and migration in vivo (performed in mice model and indicated by intestinal histological observation, EdU assay, and the quantification of cyclin proteins) and in vitro (indicated by CCK8, MTT, EdU, and wound healing experiments). Noteworthily, miR-146a-5p was found to be highly expressed in the mEVs from maternal RS group, which also promotes intestinal cell proliferation in cells and mice models. Mechanically, miR-146a-5p target to silence the expression of ubiquitin ligase 3 gene NEDD4L, thereby inhibiting DVL2 ubiquitination, activating the Wnt pathway, and promoting intestinal development.

CONCLUSION

These findings demonstrated the beneficial role of mEVs in the connection between maternal fiber rich diet and offspring intestinal growth. In addition, we identified a novel miRNA-146a-5p-NEDD4L-β-catenin/Wnt signaling axis in regulating early intestinal development. This work provided a new perspective for studying the influence of maternal diet on offspring development.

XAV939 Improves the Prognosis of Myocardial Infarction by Blocking the Wnt/β-Catenin Signalling Pathway

Myocardial infarction (MI) is closely related to the Wnt signalling pathway, but the role of XAV939 (a Wnt/β-catenin signalling pathway blocker) in MI has not been elucidated. The purpose of this study was to explore the role of XAV939 in mouse hearts and to provide a new and feasible treatment for improving the prognosis of MI. C57BL/6 (male, 8 weeks old, 20-25 g) mice were selected for our study. The MI model was made by ligating the left anterior descending coronary artery. On day 28 after the operation, cardiac function was examined by echocardiography. Infarct size, fibrosis, and angiogenesis were individually measured by TTC assays, Masson's trichrome staining, and CD31 analysis, respectively. Apoptosis was examined by TdT-mediated dUTP nick-end labelling (TUNEL) staining. The expression of Wnt, β-catenin, caspase 3, Bax, and Bcl-2 was determined by western blotting. XAV939 successfully blocked Wnt/β-catenin signalling pathway activation in cardiomyocytes after MI by promoting the degradation of β-catenin. XAV939 suppressed fibrosis and apoptosis, promoted angiogenesis, reduced myocardial infarct size and improved cardiac function after MI. XAV939 can reduce myocardial infarct size and improve cardiac function by blocking the Wnt/β-catenin signalling pathway, which may provide a new strategy for improving the prognosis of MI.

Chemical Constituents and Bioactivities of the Plant-Derived Fungus Aspergillus fumigatus

A new bergamotane sesquiterpenoid, named xylariterpenoid H (1), along with fourteen known compounds (2-15), were isolated from the crude extract of Aspergillus fumigatus, an endophytic fungus isolated from Delphinium grandiflorum L. Their structures were elucidated mainly by extensive analyses of NMR and MS spectroscopic data. In addition, the screening results of antibacterial and cytotoxic activities of compounds 1-15 showed that compound 4 displayed antibacterial activities against Staphylococcus aureus and MRSA (methicillin-resistant S. aureus) with an MIC value of 3.12 µg/mL.

Polysaccharide from Artocarpus heterophyllus Lam. (Jackfruit) Pulp Ameliorates Dextran Sodium Sulfate-Induced Enteritis in Rats

A polysaccharide from Artocarpus heterophyllus Lam. (jackfruit) pulp (JFP-Ps) is known for its excellent bioactivities. However, its impact on small intestinal barrier function is still largely unexplored. The study aimed to examine the protection effect of JFP-Ps against dextran sodium sulfate-induced enteritis and its underlying mechanism. This research revealed that JFP-Ps mitigated small intestinal tissue damage by reducing the expression of pro-inflammatory cytokines and promoting the expression of the anti-inflammatory cytokine interleukin-10 in the small intestine. JFP-Ps diminished oxidative stress by bolstering the activity of antioxidant enzymes and reducing the concentration of malondialdehyde in the small intestine. In addition, JFP-Ps may restore the mechanical barrier and inhibit intestinal structure damage by augmenting the expression of short-chain fatty acids (SCFAs) receptors (GPR41/43) and up-regulating the expression of tight junction proteins (occludin). In conclusion, JFP-Ps may positively influence intestinal health by relieving oxidative stress in the small intestine, improving mechanical barrier function, activating the SCFA-GPR41/GPR43 axis, and inhibiting TLR4/MAPK pathway activation. The results augment our comprehension of the bioactivities of JFP-Ps, corroborating its great potential as a functional food.

Effect of Cyclosporine A on Th1/Th2 Cytokine Production by Decidual Stromal Cells Mediated by Trophoblast-derived Galectin-9

This study aimed to investigate the effect of cyclosporine A (CsA) on secretion of Th1 and Th2 cytokines by decidual stromal cells (DSCs) mediated by galectin (Gal)-9.HTR8/SVneo cells and primary trophoblasts were used for in vitro studies. Gal-9 expression was measured using quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay, CsA was used to regulate Gal-9 expression in trophoblasts. DSCs were treated with trophoblast supernatant and changes in Th1 and Th2 cytokine levels were analyzed. Changes in DSC levels of the T-cell immunoglobulin mucin receptor 3 (TIM-3) levels in DSCs after treatment with Gal-9 were assessed. Western blotting and ERK and AKT inhibitors were used to assess the involvement of the corresponding signaling pathways. Gal-9 was expressed by both primary trophoblasts and HTR8/SVneo cells. CsA treatment increased Gal-9 secretion by trophoblasts, which in turn increased IL-6 (Th2 cytokine) and decreased TNF-α and IFN-γ (Th1 cytokines) secretion in DSCs. Upon downregulation of trophoblast Gal-9 secretion, DSCs secreted lower levels of Th2 cytokines and higher levels of Th1 cytokines, and the effect was reversed by addition of CsA. TIM-3 expression changed in parallel with Gal-9 secretion. CsA treatment upregulated expression of Gal-9 in trophoblasts, promoted secretion of Th2 cytokines, and inhibited secretion of Th1 cytokines via ERK signaling.

Identification and virtual screening of novel salty peptides from hydrolysate of tilapia by-product by batch molecular docking

Introduction

Tilapia produces a large number of by-products during processing, which contain potentially flavorful peptides.

Methods

The application of PyRx software enabled batch molecular docking andscreening of 16 potential salty peptides from 189 peptides identified in the enzymaticdigestion of tilapia by-products.

Results

According to sensory analysis, all 16 peptides werepredominantly salty with a threshold of 0.256 - 0.379 mmol/L with some sournessand astringency, among which HLDDALR had the highest salty intensity, followedby VIEPLDIGDDKVR, FPGIPDHL, and DFKSPDDPSRH. I addition, moleculardocking results showed these four core peptides with high salt intensity bound to thesalt receptor TRPV1 mainly via van der Waals interactions, hydrogen bonds, andhydrophobic forces; Arg491, Tyr487, VAL441, and Asp708 were the key sites for thebinding of salty peptides to TRPV1. Therefore, the application of batch moleculardocking using PyRx is effective and economical for the virtual screening of saltypeptides.

Two-stage multi-task deep learning framework for simultaneous pelvic bone segmentation and landmark detection from CT images

PURPOSE

Pelvic bone segmentation and landmark definition from computed tomography (CT) images are prerequisite steps for the preoperative planning of total hip arthroplasty. In clinical applications, the diseased pelvic anatomy usually degrades the accuracies of bone segmentation and landmark detection, leading to improper surgery planning and potential operative complications.

METHODS

This work proposes a two-stage multi-task algorithm to improve the accuracy of pelvic bone segmentation and landmark detection, especially for the diseased cases. The two-stage framework uses a coarse-to-fine strategy which first conducts global-scale bone segmentation and landmark detection and then focuses on the important local region to further refine the accuracy. For the global stage, a dual-task network is designed to share the common features between the segmentation and detection tasks, so that the two tasks mutually reinforce each other's performance. For the local-scale segmentation, an edge-enhanced dual-task network is designed for simultaneous bone segmentation and edge detection, leading to the more accurate delineation of the acetabulum boundary.

RESULTS

This method was evaluated via threefold cross-validation based on 81 CT images (including 31 diseased and 50 healthy cases). The first stage achieved DSC scores of 0.94, 0.97, and 0.97 for the sacrum, left and right hips, respectively, and an average distance error of 3.24 mm for the bone landmarks. The second stage further improved the DSC of the acetabulum by 5.42%, and this accuracy outperforms the state-of-the-arts (SOTA) methods by 0.63%. Our method also accurately segmented the diseased acetabulum boundaries. The entire workflow took ~ 10 s, which was only half of the U-Net run time.

CONCLUSION

Using the multi-task networks and the coarse-to-fine strategy, this method achieved more accurate bone segmentation and landmark detection than the SOTA method, especially for diseased hip images. Our work contributes to accurate and rapid design of acetabular cup prostheses.

Changes in Phenolic Compounds and Antioxidant Capacity of Artocarpus heterophyllus Lam. (Jackfruit) Pulp during In Vitro Gastrointestinal Digestion

An in vitro gastrointestinal digestion model was applied to investigate the effect of digestion on the phenolic compounds and antioxidant capacity of Artocarpus heterophyllus Lam. (jackfruit) pulp. The total phenol content (TPC) was determined using Folin-Ciocalteu method, and the antioxidant activities were evaluated by DPPH and ABTS assays. Phenolic compounds were analyzed using ultra-performance liquid chromatography coupled with electrospray ionization, followed by quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS/MS). The results showed that TPC was significantly higher after gastric digestion. Thirty phenolic compounds (hydroxybenzoic acids and derivatives, hydroxycinnamic acids and derivatives, and flavonoids) were identified. The antioxidant activities of the digested samples varied with the TPC, and there was a correlation between antioxidant activity and TPC. The present study implies that gastrointestinal digestion may improve TPC and increase the amount of free phenolic compounds, mainly related to changes in pH value and digestive enzymes.

Six Undescribed Capnosane-Type Macrocyclic Diterpenoids from South China Sea Soft Coral Sarcophyton crassocaule: Structural Determination and Biological Evaluation

Six undescribed capnosane-type macrocyclic diterpenes sarcocrassolins A-F (1-6) and one related known analog pavidolide D (7) were isolated from Sarcophyton crassocaule, a soft coral collected off the Nansha Islands, in the South China Sea. Their complete structures, relative configurations and absolute configurations were established through comprehensive spectroscopic analysis, quantum mechanical nuclear magnetic resonance (QM-NMR) and single-crystal X-ray diffraction. Sarcocrassolins D (4) and E (5) showed inhibitory activity against lipopolysaccharide (LPS)-stimulated inflammatory responses in RAW264.7 cells with IC50 values of 76.8 ± 8.0 μM and 93.0 ± 3.8 μM, respectively.

Supramolecular Peptide Amphiphile Nanospheres Reprogram Tumor-associated Macrophage to Reshape the Immune Microenvironment for Enhanced Breast Cancer Immunotherapy

Tumor immunotherapy has become a research hotspot in cancer treatment, with macrophages playing a crucial role in tumor development. However, the tumor microenvironment restricts macrophage functionality, limiting their therapeutic potential. Therefore, modulating macrophage function and polarization is essential for enhancing tumor immunotherapy outcomes. Here, a supramolecular peptide amphiphile drug-delivery system (SPADS) is utilized to reprogram macrophages and reshape the tumor immune microenvironment (TIM) for immune-based therapies. The approach involved designing highly specific SPADS that selectively targets surface receptors of M2-type macrophages (M2-Mφ). These targeted peptides induced M2-Mφ repolarization into M1-type macrophages by dual inhibition of endoplasmic reticulum and oxidative stresses, resulting in improved macrophagic antitumor activity and immunoregulatory function. Additionally, TIM reshaping disrupted the immune evasion mechanisms employed by tumor cells, leading to increased infiltration, and activation of immune cells. Furthermore, the synergistic effect of macrophage reshaping and anti-PD-1 antibody (aPD-1) therapy significantly improved the immune system's ability to recognize and eliminate tumor cells, thereby enhancing tumor immunotherapy efficacy. SPADS utilization also induced lung metastasis suppression. Overall, this study demonstrates the potential of SPADS to drive macrophage reprogramming and reshape TIM, providing new insights, and directions for developing more effective immunotherapeutic approaches in cancer treatment.

Comprehensive integrated analysis of MR and DCE-MR radiomics models for prognostic prediction in nasopharyngeal carcinoma

Although prognostic prediction of nasopharyngeal carcinoma (NPC) remains a pivotal research area, the role of dynamic contrast-enhanced magnetic resonance (DCE-MR) has been less explored. This study aimed to investigate the role of DCR-MR in predicting progression-free survival (PFS) in patients with NPC using magnetic resonance (MR)- and DCE-MR-based radiomic models. A total of 434 patients with two MR scanning sequences were included. The MR- and DCE-MR-based radiomics models were developed based on 289 patients with only MR scanning sequences and 145 patients with four additional pharmacokinetic parameters (volume fraction of extravascular extracellular space (ve), volume fraction of plasma space (vp), volume transfer constant (Ktrans), and reverse reflux rate constant (kep) of DCE-MR. A combined model integrating MR and DCE-MR was constructed. Utilizing methods such as correlation analysis, least absolute shrinkage and selection operator regression, and multivariate Cox proportional hazards regression, we built the radiomics models. Finally, we calculated the net reclassification index and C-index to evaluate and compare the prognostic performance of the radiomics models. Kaplan-Meier survival curve analysis was performed to investigate the model's ability to stratify risk in patients with NPC. The integration of MR and DCE-MR radiomic features significantly enhanced prognostic prediction performance compared to MR- and DCE-MR-based models, evidenced by a test set C-index of 0.808 vs 0.729 and 0.731, respectively. The combined radiomics model improved net reclassification by 22.9%-52.6% and could significantly stratify the risk levels of patients with NPC (p = 0.036). Furthermore, the MR-based radiomic feature maps achieved similar results to the DCE-MR pharmacokinetic parameters in terms of reflecting the underlying angiogenesis information in NPC. Compared to conventional MR-based radiomics models, the combined radiomics model integrating MR and DCE-MR showed promising results in delivering more accurate prognostic predictions and provided more clinical benefits in quantifying and monitoring phenotypic changes associated with NPC prognosis.

In Silico Analysis and Immune Response of YaeT Protein Against Riemerella anatipestifer in Ducks

Riemerella anatipestifer (RA) is one of the most harmful bacterial pathogens in waterfowl and causes enormous economic loss worldwide. Due to weak cross-immunity protection against different serotypes of RA, inactivated and attenuated vaccines are only effective for RA of specific serotypes. In this paper, outer membrane protein YaeT in RA was analyzed through bioinformatics, in vivo, and in vitro assays. Homology, physicochemical and structural properties, transmembrane domains, and B-cell binding epitopes were investigated. The recombinant outer membrane protein YaeT was then inoculated into Cherry Valley ducks to analyze its immune protection against RA. Results showed that the protein was conservative in different RA strains and had sufficient B-cell binding epitopes. The immunized duck serum contains high-affinity antibodies that could activate complement and promote the opsonophagocytosis of RA by phagocytes. After RA challenge, the survival rate of the YaeT protein-immunized ducks was 80%.

Autonomous detection of myocarditis based on the fusion of improved quantum genetic algorithm and adaptive differential evolution optimization back propagation neural network

Myocarditis is cardiac damage caused by a viral infection. Its result often leads to a variety of arrhythmias. However, rapid and reliable identification of myocarditis has a great impact on early diagnosis, expedited treatment, and improved patient survival rates. Therefore, a novel strategy for the autonomous detection of myocarditis is suggested in this work. First, the improved quantum genetic algorithm (IQGA) is proposed to extract the optimal features of ECG beat and heart rate variability (HRV) from raw ECG signals. Second, the backpropagation neural network (BPNN) is optimized using the adaptive differential evolution (ADE) algorithm to classify various ECG signal types with high accuracy. This study examines analogies among five different ECG signal types: normal, abnormal, myocarditis, myocardial infarction (MI), and prior myocardial infarction (PMI). Additionally, the study uses binary and multiclass classification to group myocarditis with other cardiovascular disorders in order to assess how well the algorithm performs in categorization. The experimental results demonstrate that the combination of IQGA and ADE-BPNN can effectively increase the precision and accuracy of myocarditis autonomous diagnosis. In addition, HRV assesses the method's robustness, and the classification tool can detect viruses in myocarditis patients one week before symptoms worsen. The model can be utilized in intensive care units or wearable monitoring devices and has strong performance in the detection of myocarditis.

Koninginins X-Z, Three New Polyketides from Trichoderma koningiopsis SC-5

Koninginins X-Z (1-3), three novel polyketides, were isolated from the solid fermentation of the endophytic fungus Trichoderma koningiopsis SC-5. Their structures, including the absolute configurations, were comprehensively characterized by a combination of NMR spectroscopic methods, HRESIMS, 13C NMR, DFT GIAO 13C NMR, and electronic circular dichroism calculations as well as single crystal X-ray diffraction. In addition, all the compounds were evaluated for antifungal activity against Candida albicans.

Distinguishing infectivity in patients with pulmonary tuberculosis using deep learning

Introduction

This study aimed to develop and assess a deep-learning model based on CT images for distinguishing infectivity in patients with pulmonary tuberculosis (PTB).

Methods

We labeled all 925 patients from four centers with weak and strong infectivity based on multiple sputum smears within a month for our deep-learning model named TBINet's training. We compared TBINet's performance in identifying infectious patients to that of the conventional 3D ResNet model. For model explainability, we used gradient-weighted class activation mapping (Grad-CAM) technology to identify the site of lesion activation in the CT images.

Results

The TBINet model demonstrated superior performance with an area under the curve (AUC) of 0.819 and 0.753 on the validation and external test sets, respectively, compared to existing deep learning methods. Furthermore, using Grad-CAM, we observed that CT images with higher levels of consolidation, voids, upper lobe involvement, and enlarged lymph nodes were more likely to come from patients with highly infectious forms of PTB.

Conclusion

Our study proves the feasibility of using CT images to identify the infectivity of PTB patients based on the deep learning method.

Integrating genome-wide association study into genomic selection for the prediction of agronomic traits in rice (Oryza sativa L.)

Accurately identifying varieties with targeted agronomic traits was thought to contribute to genetic selection and accelerate rice breeding progress. Genomic selection (GS) is a promising technique that uses markers covering the whole genome to predict the genomic-estimated breeding values (GEBV), with the ability to select before phenotypes are measured. To choose the appropriate GS models for breeding work, we analyzed the predictability of nine agronomic traits measured from a population of 459 diverse rice varieties. By the comparison of eight representative GS models, we found that the prediction accuracies ranged from 0.407 to 0.896, with reproducing kernel Hilbert space (RKHS) having the highest predictive ability in most traits. Further results demonstrated the predictivity of GS is altered by several factors. Moreover, we assessed the method of integrating genome-wide association study (GWAS) into various GS models. The predictabilities of GS combined peak-associated markers generated from six different GWAS models were significantly different; a recommendation of Mixed Linear Model (MLM)-RKHS was given for the GWAS-GS-integrated prediction. Finally, based on the above result, we experimented with applying the P-values obtained from optimal GWAS models into ridge regression best linear unbiased prediction (rrBLUP), which benefited the low predictive traits in rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01423-y.

Mitogenomic Phylogeny of Tonnoidea Suter, 1913 (1825) (Gastropoda: Caenogastropoda)

The Tonnoidea Suter, 1913 (1825) is a moderately diverse group of large predatory gastropods, the systematics of which remain unclear. In the present study, the complete mitochondrial genomes of nine Tonnoidean species were sequenced. All newly sequenced mitogenomes contain 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes, showing similar patterns in genome size, gene order and nucleotide composition. The ratio of nonsynonymous to synonymous of PCGs indicated that NADH complex genes of Tonnoideans were experiencing a more relaxed purifying selection compared with the COX genes. The reconstructed phylogeny based on the combined amino acid sequences of 13 protein-coding genes and the nucleotide sequences of two rRNA genes supported that Ficidae Meek, 1864 (1840) is a sister to Tonnoidea. The monophylies of all Tonnoidean families were recovered and the internal phylogenetic relationships were consistent with the current classification. The phylogeny also revealed that Tutufa rebuta (Linnaeus, 1758) is composed of at least two different species, indicating that the species diversity within Bursidae Thiele, 1925 might be underestimated. The present study contributes to the understanding of the Tonnoidean systematics, and it could provide important information for the revision of Tonnoidean systematics in the future.

Neglected Adult Tinea Capitis in South China: A Retrospective Study in Nanchang, Jiangxi Province, from 2007 to 2021

Tinea capitis (TC) in adults is much less frequently diagnosed in comparison to TC in children. In this study, we explored retrospectively adult TC in a specialized dermatology hospital, located in South China, during the years 2007-2021. Among 1037 TC cases, 168 (16.2%) patients were older than 18 years. The majority of adults with TC, 77.38% (130/168), were older than 40, with a peak in the age of 51-60 years (40/168, 23.81%). Before presenting at our hospital, many of patients did not got proper treatment due to misdiagnosis or simply did not consulted an appropriate clinic. 60.71% (102/168) of the patients reported symptoms lasting for more than 1 year and 29.76% (50/168) reported chronic scalp problems of at least 10 years. And 27.38% (46/168) of the patients had an immunocompromised status, including long-term use of corticosteroids shampoo, type 2 diabetes mellitus (DM), psoriasis vulgaris, rheumatoid arthritis, systemic lupus erythematosus or bullous pemphigoid. As for clinical presentation, 87.5% (147/168) of the cases presented as black dot type of TC and anthropophilic dermatophytes were the predominant etiology, with Trichophyton violaceum (126), T. tonsurans (15), T. rubrum (8) and T. shoenleinii (6). Grey patch type of TC (3.57%, 6/168) was seldom in Jiangxi Province and zoophilic/geophilic dermatophytes were rare. Our study indicates that anthropophilic Trichophyton species can cause long-lasting TC in adults. Not in all cases, the manifestation had symptom clearly indicating a dermatophyte-related TC. Thus, patients with long-lasting scalp inflammation, also older ones, should be examined for the presence of dermatophyte-related TC.

Rapid Detection of blaKPC in Carbapenem-Resistant Enterobacterales Based on CRISPR/Cas13a

Klebsiella pneumoniae carbapenemase (KPC) is a crucial enzyme that causes carbapenem resistance in Enterobacterales, and infections by these "superbugs" are extremely challenging to treat. Therefore, there is a pressing need for a rapid and accurate KPC detection test to control the prevalence of carbapenem-resistant Enterobacterales (CREs). In this study, we established a novel method for detection of blaKPC, the gene responsible for encoding KPC, based on a recombinase polymerase amplification (RPA) and a CRISPR/Cas13a reaction coupled to fluorophore activation (termed RPA-Cas13a assay). We carefully selected a pair of optimal amplification primers for blaKPC and achieved a lower limit of detection of approximately 2.5 copies/μL by repeatedly amplifying a recombinant plasmid containing blaKPC. The RPA-Cas13a assay demonstrated a sensitivity of 96.5% and specificity of 100% when tested on 57 blaKPC-positive CRE strains, which were confirmed by DNA sequencing. Moreover, in 311 sputum samples, the theoretical antibiotic resistance characteristics of blaKPC-positive strains obtained by the RPA-Cas13a assay were highly consistent with the results of antibiotic susceptibility test (Kappa = 0.978 > 0.81, P < 0.01). In conclusion, the RPA-Cas13a system is a simple and one-hour efficient technology for the detection of a potentially fatal antibiotic resistance gene.

Genome-wide analysis of the U-box E3 ubiquitin ligase family role in drought tolerance in sesame (Sesamum indicum L.)

Plant U-box (PUB) proteins belong to a class of ubiquitin ligases essential in various biological processes. Sesame (Sesamum indicum L.) is an important and worldwide cultivated oilseed crop. However few studies have been conducted to explore the role of PUBs in drought tolerance in sesame. This study identified a total of 56 members of the sesame PUB family (SiPUB) genes distributed unevenly across all 13 chromosomes. Based on phylogenetic analysis, all 56 SiPUB genes were classified into six groups with various structures and motifs. Cis-acting element analysis suggested that the SiPUB genes are involved in response to various stresses including drought. Based on RNA-seq analysis and quantitative real-time PCR, we identified nine SiPUB genes with significantly different expression profiles under drought stress. The expression patterns of six SiPUB genes in root, leaf and stem tissues corroborated the reliability of the RNA-seq datasets. These findings underscore the importance of SiPUB genes in enhancing drought tolerance in sesame plants. Our study provides novel insights into the evolutionary patterns and variations of PUB genes in sesame and lays the foundation for comprehending the functional characteristics of SiPUB genes under drought-induced stress conditions.

Construction and Evaluation of Alginate Dialdehyde Grafted RGD Derivatives/Polyvinyl Alcohol/Cellulose Nanocrystals IPN Composite Hydrogels

To enhance the mechanical strength and cell adhesion of alginate hydrogel, making it satisfy the requirements of an ideal tissue engineering scaffold, the grafting of Arg-Gly-Asp (RGD) polypeptide sequence onto the alginate molecular chain was conducted by oxidation of sodium periodate and subsequent reduction amination of 2-methylpyridine borane complex (2-PBC) to synthesize alginate dialdehyde grafted RGD derivatives (ADA-RGD) with good cellular affinity. The interpenetrating network (IPN) composite hydrogels of alginate/polyvinyl alcohol/cellulose nanocrystals (ALG/PVA/CNCs) were fabricated through a physical mixture of ion cross-linking of sodium alginate (SA) with hydroxyapatite/D-glucono-δ-lactone (HAP/GDL), and physical cross-linking of polyvinyl alcohol (PVA) by a freezing/thawing method, using cellulose nanocrystals (CNCs) as the reinforcement agent. The effects of the addition of CNCs and different contents of PVA on the morphology, thermal stability, mechanical properties, swelling, biodegradability, and cell compatibility of the IPN composite hydrogels were investigated, and the effect of RGD grafting on the biological properties of the IPN composite hydrogels was also studied. The resultant IPN ALG/PVA/CNCs composite hydrogels exhibited good pore structure and regular 3D morphology, whose pore size and porosity could be regulated by adjusting PVA content and the addition of CNCs. By increasing the PVA content, the number of physical cross-linking points in PVA increased, resulting in greater stress support for the IPN composite hydrogels of ALG/PVA/CNCs and consequently improving their mechanical characteristics. The creation of the IPN ALG/PVA/CNCs composite hydrogels' physical cross-linking network through intramolecular or intermolecular hydrogen bonding led to improved thermal resistance and reduced swelling and biodegradation rate. Conversely, the ADA-RGD/PVA/CNCs IPN composite hydrogels exhibited a quicker degradation rate, attributed to the elimination of ADA-RGD by alkali. The results of the in vitro cytocompatibility showed that ALG/0.5PVA/0.3%CNCs and ADA-RGD/PVA/0.3%CNCs composite hydrogels showed better proliferative activity in comparison with other composite hydrogels, while ALG/PVA/0.3%CNCs and ADA-RGD/PVA/0.3%CNCs composite hydrogels displayed obvious proliferation effects, indicating that PVA, CNCs, and ADA-RGD with good biocompatibility were conducive to cell proliferation and differentiation for the IPN composite hydrogels.

Prevalence and factors associated with pentavalent vaccination: a cross-sectional study in Southern China

BACKGROUND

Immunization is one of the most far-reaching and cost-effective strategies for promoting good health and saving lives. A complex immunization schedule, however, may be burdensome to parents and lead to reduced vaccine compliance and completion. Thus, it is critical to develop combination vaccines to reduce the number of injections and simplify the immunization schedule. This study aimed to investigate the current status of the pentavalent diphtheria-tetanus-acellular pertussis inactivated poliomyelitis and Haemophilus influenzae type B conjugate (DTaP-IPV/Hib) vaccination in Southern China as well as explore the factors in the general population associated with uptake and the differences between urban and rural populations.

METHODS

A cross-sectional study was conducted with recently enrolled kindergarten students in Hainan Province between December 2022 and January 2023. The study employed a stratified multistage cluster random sampling method. Information regarding the demographic characteristics and factors that influence decisions were collected from the caregivers of children via an online questionnaire. Multivariate logistic regression was used to determine the factors associated with the status of DTap-IPV/Hib vaccinations.

RESULTS

Of the 4818 valid responses, 95.3% of children were aged 3-4 years, and 2856 (59.3%) held rural hukou. Coverage rates of the DTaP-IPV/Hib vaccine, from 1 to 4 doses, were 24.4%, 20.7%, 18.5%, and 16.0%, respectively. Caregivers who are concerned about vaccine efficacy [adjusted odds ratio (aOR) = 1.53, 95% confidence interval (CI): 1.30-1.79], the manufacturer (aOR = 2.05, 95% CI: 1.69-2.49), and a simple immunization schedule (aOR = 1.26, 95% CI: 1.04-1.54) are factors associated with a higher likelihood of vaccinating children against DTaP-IPV/Hib. In addition, caregivers in urban areas showed more concern about the vaccine price (P = 0.010) and immunization schedule (P = 0.022) in regard to vaccinating children.

CONCLUSIONS

The DTaP-IPV/Hib vaccine coverage rate in Hainan Province remains low. Factors such as lower socioeconomic status, cultural beliefs, concerns about vaccine safety, and cost may hinder caregivers from vaccinating their children. Further measures, such as health education campaigns to raise knowledge and awareness, and encouragement of domestic vaccine innovation, which would reduce out-of-pocket costs, could be implemented to improve the coverage of DTap-IPV/Hib vaccination.

The Complete Mitochondrial Genomes of Two Rock Scallops (Bivalvia: Spondylidae) Indicate Extensive Gene Rearrangements and Adaptive Evolution Compared with Pectinidae

Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the present study, the complete mitochondrial genomes of Spondylus versicolor and S. spinosus were sequenced and compared with those of pectinids. The mtDNA of S. versicolor and S. spinosus show similar patterns with respect to genome size, AT content, AT skew, GC skew, and codon usage, and their mitogenomic sizes are longer than most pectinid species. The mtDNA of S. spinosus is 27,566 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, while an additional tRNA-Met was found in the mtDNA of S. versicolor, which is 28,600 bp in length. The monophylies of Spondylidae and Pectinidae were well supported, but the internal relationships within Pectinidae remain unresolved due to the paraphyly of the genus Mimachlamy and the controversial position of the tribe Aequipectinini. The gene orders of S. versicolor and S. spinosus are almost identical but differ greatly from species of the Pectinidae, indicating extensive gene rearrangements compared with Pectinidae. Positive selection analysis revealed evidence of adaptive evolution in the branch of Spondylidae. The present study could provide important information with which to understand the evolutionary progress of the diverse and economically significant marine bivalve Pectinoidea.

Correcting batch effects in large-scale multiomics studies using a reference-material-based ratio method

BACKGROUND

Batch effects are notoriously common technical variations in multiomics data and may result in misleading outcomes if uncorrected or over-corrected. A plethora of batch-effect correction algorithms are proposed to facilitate data integration. However, their respective advantages and limitations are not adequately assessed in terms of omics types, the performance metrics, and the application scenarios.

RESULTS

As part of the Quartet Project for quality control and data integration of multiomics profiling, we comprehensively assess the performance of seven batch effect correction algorithms based on different performance metrics of clinical relevance, i.e., the accuracy of identifying differentially expressed features, the robustness of predictive models, and the ability of accurately clustering cross-batch samples into their own donors. The ratio-based method, i.e., by scaling absolute feature values of study samples relative to those of concurrently profiled reference material(s), is found to be much more effective and broadly applicable than others, especially when batch effects are completely confounded with biological factors of study interests. We further provide practical guidelines for implementing the ratio based approach in increasingly large-scale multiomics studies.

CONCLUSIONS

Multiomics measurements are prone to batch effects, which can be effectively corrected using ratio-based scaling of the multiomics data. Our study lays the foundation for eliminating batch effects at a ratio scale.

Treatment of berberine alleviates diabetic nephropathy by reducing iron overload and inhibiting oxidative stress

Diabetic nephropathy (DN) has become one of the major fatal factors in diabetic patients. The aim of this study was to elucidate the function and mechanism by which berberine exerts renoprotective effects in DN. In this work, we first demonstrated that urinary iron concentration, serum ferritin and hepcidin levels were increased and total antioxidant capacity was significantly decreased in DN rats, while these changes could be partially reversed by berberine treatment. Berberine treatment also alleviated DN-induced changes in the expression of proteins involved in iron transport or iron uptake. In addition, berberine treatment also partially blocked the expression of renal fibrosis markers induced by DN, including MMP2, MMP9, TIMP3, β-arrestin-1, and TGF-β1. In conclusion, the results of this study suggest that berberine may exert renoprotective effects by ameliorating iron overload and oxidative stress and reducing DN.

Investigation of SNP markers for the melatonin production trait in the Hu sheep with bulked segregant analysis

BACKGROUND

As an important reproductive hormone, melatonin plays an important role in regulating the reproductive activities of sheep and other mammals. Hu sheep is a breed favoring for meat, with prolific traits. In order to explore the relationship between melatonin and reproductive function of Hu sheep, 7,694,759 SNPs were screened out through the whole genome sequencing analysis from high and low melatonin production Hu sheep.

RESULTS

A total of 68,673 SNPs, involving in 1126 genes, were identified by ED association analysis. Correlation analysis of SNPs of AANAT/ASMT gene and MTNR1A/MTNR1B gene were carried out. The melatonin level of CG genotype 7,981,372 of AANAT, GA genotype 7,981,866 of ASMT and GG genotype 17,355,171 of MTNR1A were higher than the average melatonin level of 1.64 ng/mL. High melatonin Hu sheep appear to have better multiple reproductive performance.

CONCLUSIONS

By using different methods, three SNPs which are associated with high melatonin production trait have been identified in Hu sheep. These 3 SNPs are located in melatonin synthetase AANAT/ASMT and receptor MTNR1A, respectively. Considering the positive association between melatonin production and reproductive performance in ruminants, these three SNPs can be served as the potential molecular markers for breading Hu sheep with the desirable reproductive traits.

Human embryonic stem cells secrete macrophage migration inhibitory factor: A novel finding

Macrophage migration inhibitory factor (MIF) is expressed in a variety of cells and participates in important biological mechanisms. However, few studies have reported whether MIF is expressed in human Embryonic stem cells (ESCs) and its effect on human ESCs. Two human ESCs cell lines, H1 and H9 were used. The expression of MIF and its receptors CD74, CD44, CXCR2, CXCR4 and CXCR7 were detected by an immunofluorescence assay, RT-qPCR and western blotting, respectively. The autocrine level of MIF was measured via enzyme-linked immunosorbent assay. The interaction between MIF and its main receptor was investigated by co-immunoprecipitation and confocal immunofluorescence microscopy. Finally, the effect of MIF on the proliferation and survival of human ESCs was preliminarily explored by incubating cells with exogenous MIF, MIF competitive ligand CXCL12 and MIF classic inhibitor ISO-1. We reported that MIF was highly expressed in H1 and H9 human ESCs. MIF was positively expressed in the cytoplasm, cell membrane and culture medium. Several surprising results emerge. The autosecreted concentration of MIF was 22 ng/mL, which was significantly higher than 2 ng/mL-6 ng/mL in normal human serum, and this was independent of cell culture time and cell number. Human ESCs mainly expressed the MIF receptors CXCR2 and CXCR7 rather than the classical receptor CD74. The protein receptor that interacts with MIF on human embryonic stem cells is CXCR7, and no evidence of interaction with CXCR2 was found. We found no evidence that MIF supports the proliferation and survival of human embryonic stem cells. In conclusion, we first found that MIF was highly expressed in human ESCs and at the same time highly expressed in associated receptors, suggesting that MIF mainly acts in an autocrine form in human ESCs.

Dietary Taurine Intake Affects the Growth Performance, Lipid Composition, and Antioxidant Defense of Juvenile Ivory Shell (Babylonia areolata)

In this study, an eight-week feeding trial was performed to investigate the effects of different taurine supplementation levels (0.0% as control, 1.0%, 1.5%, 2.0%, 2.5%, and 3.0%) on the growth performance, lipid composition, and antioxidant ability in juvenile ivory shells Babylonia areolata. The results showed that taurine supplementation significantly improved the specific growth rates (SGRs) and survival rates of ivory shell (except the survival rate in the 3.0% taurine diet group) (p < 0.05). The SGRs showed an increasing and then decreasing tendency with increasing dietary taurine supplementation, and the highest value was observed in the 2.0% taurine diet (2.60%/d). The taurine content in the muscle of ivory shells fed taurine-supplemented diets significantly increased when compared to the control group (p < 0.05). The profiles of C22:2n6 in the muscle of ivory shells fed taurine-supplemented diets were significantly higher than in the control group (p < 0.05), and the highest values were observed in the 2.0% taurine supplementation group. The high-density lipoprotein cholesterol (HDL-C) content in the hepatopancreas showed an increasing and then decreasing tendency with increasing dietary taurine supplementation, while the low-density lipoprotein cholesterol (LDL-C) concentration showed a decreasing tendency. Furthermore, the activities of pepsin and lipase in both the intestine and hepatopancreas significantly increased at moderate taurine supplementation levels compared to the control group (p < 0.05). Accordingly, obvious increases in the histological parameters in the intestine of ivory shells fed taurine-supplemented diets were also found. As for the antioxidant ability, the activities of the total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) showed an increasing and then decreasing tendency with increasing dietary taurine supplementation, and the highest values were observed in the 1.0% and 1.0-2.0% taurine supplementation groups, respectively; the malondialdehyde (MDA) contents significantly decreased with increasing dietary taurine supplementation (p < 0.05). The taurine intake affected the expression of four appetite-related genes in the hepatopancreas, in which orexin and NPY showed an increasing and then decreasing tendency, while leptin and cholecyatoklnin decreased with increasing dietary taurine supplementation. In conclusion, moderate taurine supplementation in an artificial diet (about 1.5-2.0%) could improve the growth performance and antioxidant ability and change the lipid composition of juvenile ivory shells.

Genome-Wide Identification and Characterization Analysis of WUSCHEL-Related Homeobox Family in Melon (Cucumis melo L.)

WUSCHEL-related homeobox (WOX) proteins are very important in controlling plant development and stress responses. However, the WOX family members and their role in response to abiotic stresses are largely unknown in melon (Cucumis melo L.). In this study, 11 WOX (CmWOX) transcript factors with conserved WUS and homeobox motif were identified and characterized, and subdivided into modern clade, ancient clade and intermediate clade based on bioinformatic and phylogenetic analysis. Evolutionary analysis revealed that the CmWOX family showed protein variations in Arabidopsis, tomato, cucumber, melon and rice. Alignment of protein sequences uncovered that all CmWOXs had the typical homeodomain, which consisted of conserved amino acids. Cis-element analysis showed that CmWOX genes may response to abiotic stress. RNA-seq and qRT-PCR results further revealed that the expression of partially CmWOX genes are associated with cold and drought. CmWOX13a and CmWOX13b were constitutively expressed under abiotic stresses, CmWOX4 may play a role in abiotic processes during plant development. Taken together, this study offers new perspectives on the CmWOX family's interaction and provides the framework for research on the molecular functions of CmWOX genes.

Using A Protoplast Transformation System to Enable Functional Studies in Mangifera indica L

Mangoes (Mangifera indica L.) are an important kind of perennial fruit tree, but their biochemical testing method and transformation technology were insufficient and had not been rigorously explored. The protoplast technology is an excellent method for creating a rapid and effective tool for transient expression and transformation assays, particularly in plants that lack an Agrobacterium-mediated plant transformation system. This study optimized the conditions of the protoplast isolation and transformation system, which can provide a lot of help in the gene expression regulation study of mango. The most beneficial protoplast isolation conditions were 150 mg/mL of cellulase R-10 and 180 mg/mL of macerozyme R-10 in the digestion solution at pH 5.6 and 12 h of digestion time. The 0.16 M and 0.08 M mannitol in wash solution (WI) and suspension for counting (MMG), respectively, were optimal for the protoplast isolation yield. The isolated leaf protoplasts (~5.4 × 105 cells/10 mL) were transfected for 30 min mediated by 40% calcium-chloride-based polyethylene glycol (PEG)-4000-CaCl2, from which 84.38% of the protoplasts were transformed. About 0.08 M and 0.12 M of mannitol concentration in MMG and transfection solutions, respectively, were optimal for protoplast viability. Under the florescence signal, GFP was seen in the transformed protoplasts. This showed that the target gene was successfully induced into the protoplast and that it can be transcribed and translated. Experimental results in this paper show that our high-efficiency protoplast isolation and PEG-mediated transformation protocols can provide excellent new methods for creating a rapid and effective tool for the molecular mechanism study of mangoes.

Taming transposable elements in livestock and poultry: a review of their roles and applications

Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.

Effect of Nanoparticles on Rheological Properties of Water-Based Drilling Fluid

Nano-water-based drilling fluids (NWBDFs) are prepared using nano-copper oxide (CuO) and multiwalled carbon nanotubes (MWCNTs) as modification materials. The effects of the temperature and concentration of the nanoparticles (NPs) on the rheological properties are studied using a rotational rheometer and viscometer. Also, the influence of two NPs on the filtration properties is studied using a low-pressure and low-temperature filtration apparatus, as well as a scanning electron microscope (SEM). It is found that MWCNTs with a concentration of 0.05 w/v% have the most obvious influence on the NWBDFs, which improve the stability of the gel structure against temperature and also decrease the filtration rate. Finally, a theoretical model predicating the yield point (YP) and the plastic viscosity (PV) as a function of the temperature considering the influence of the NPs is developed based on DLVO theory.

Rapid and sensitive determination of Se and heavy metals in foods using electrothermal vaporization inductively coupled plasma mass spectrometry with a novel transportation system

Rapid, sensitive and simultaneous determination of trace multi-elements in various plant food samples such as grain, oilseed, vegetable and tea is always a challenge thus far. In this work, a rapid determination method for Se, Cd, As and Pb in food samples by inductively coupled plasma mass spectrometry (ICP-MS) using slurry sampling electrothermal vaporization (SS-ETV) was developed. To improve the analytical sensitivity and precision as well as eliminate the memory effect, a gas turbulator line and signal delay device (SDD) were for the first time designed for the graphite furnace (GF) ETV coupled with ICP-MS. The signal acquisition parameters of ICP-MS, ashing and vaporization conditions, and the flow rates of carrier gas and gas turbulator were investigated for Se, Cd, As and Pb in food samples. Under the optimized conditions, the limits of determination (LODs) for Se, Cd, As and Pb were 0.5 ng g^-1, 0.3 ng g^-1, 0.3 ng g^-1 and 0.6 ng g^-1, respectively; the limits of quantification (LOQs) for Se, Cd, As and Pb were 1.7 ng g^-1, 1.0 ng g^-1, 1.0 ng g^-1 and 1.9 ng g^-1, respectively; linearity (R²) in the range of 1 to 4,000 ng g^-1 was >0.999 using the standard addition method. This method was used to analyze 5 CRMs including rice, tea and soybeans, and the concentrations detected by this method were within the range of the certified values. The recoveries of Se, Cd, As and Pb in plant food matrices including grain, oilseed, celery, spinach, carrot and tea samples were 86-118% compared to the microwave digestion ICP-MS method; and the relative standard deviations (RSDs) were 1.2-8.9% for real food sample analysis, proving a good precision and accuracy for the simultaneous determination of multi-elements. The analysis time was less than 3 min, slurry preparation time < 5 min without sample digestion process. The proposed direct slurry sampling ICP-MS method is thus suitable for rapid and sensitive determination of Se, Cd, As and Pb in food samples with advantages such as simplicity, green and safety, as well as with a promising application potential in detecting more elements to protect food safety and human health.

Spatiotemporal variations and impact factors of nutrients in the Sanya Bay, northern South China Sea

Nutrients play a fundamental role in maintaining coastal ecosystem stability. Based on two cruise observations in the winter of 2020 and the summer of 2021, the spatiotemporal variations of dissolved inorganic nitrogen (DIN) and orthophosphate (PO₄^3-) and their influencing factors in Sanya Bay were analyzed. Results show that the mean DIN concentrations in the bay are 2.36 μmol/L in winter and 1.73 μmol/L in summer, and the mean PO₄^3- concentrations are 0.08 μmol/L in winter and 0.04 μmol/L in summer. The nutrient concentrations and composition are significantly affected by the Sanya River. The surface DIN concentrations at the Sanya River estuary are 15.80 and 5.25 times than those inside the bay in winter and summer, respectively. Meanwhile, a high proportion of NO₃^- (74%) and a low proportion of NH₄⁺ (20%) in DIN appear near the river estuary, while a low proportion of NO₃^- (37%) and a high proportion of NH₄⁺ (53%) occur away from the estuary. In addition, the thermocline promotes the accumulation of NH₄⁺ at the bottom layer in summer. The high proportion of NO₃^- is likely not favorable for the survival of coral reefs in eastern bay. Compared with the previous nutrient concentrations, the DIN concentration in the bay has a decrease after 2014, which might benefit from the implementation of the environmental protection policy by government.

Metal-free highly chemo-selective bisphosphorylation and deoxyphosphorylation of carboxylic acids

Carboxylic acids are readily available in both the natural and synthetic world. Their direct utilization for preparing organophosphorus compounds would greatly benefit the development of organophosphorus chemistry. In this manuscript, we describe a novel and practical phosphorylating reaction under transition metal-free reaction conditions that can selectively convert carboxylic acids into the P-C-O-P motif-containing compounds through bisphosphorylation, and the benzyl phosphorus compounds through deoxyphosphorylation. This strategy provides a new route for carboxylic acid conversion as the alkyl source, enabling highly efficient and practical synthesis of the corresponding value-added organophosphorus compounds with high chemo-selectivity and wide substrate scope, including the late modification of complex APIs (active pharmaceutical ingredients). Moreover, this reaction also indicates a new strategy for converting carboxylic acids into alkenes by coupling this work and the subsequent WHE reaction with ketones and aldehydes. We anticipate that this new mode of transforming carboxylic acids will find wide application in chemical synthesis.

Modification of biochar by phosphoric acid via wet pyrolysis and using it for adsorption of methylene blue

Algae biochar (ABC), coconut shell biochar (CSBC), and coconut coat biochar (CCBC) were prepared by wet pyrolysis in a phosphoric acid solvent under normal pressure. Materials were characterized for their micromorphology, specific surface area, and surface functional groups by scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) nitrogen adsorption-desorption spectrum technique and Fourier transform infrared diffraction (FT-IR). The evaluation of the liquid-phase adsorption performance using methylene blue (MB) as a pigment model, and the effects of temperature, pH, adsorbent dosage, and pollutant concentration of the MB adsorption onto modified biochars were fully investigated. The adsorption mechanism was proposed based on the adsorption kinetics curve and adsorption isotherm. The synthetic biochar showed great adsorption properties toward cationic dyes rather than anionic dyes. Specifically, the adsorption abilities for algal biochar, coconut shell biochar, and coconut coat biochar were determined to be 97.5%, 95.4% and 21.2%, respectively. The isothermal adsorption of MB by the three kinds of biochar conformed to the Langmuir equation, and the adsorption process fitted to the quasi-second-order kinetic equation, which suggested that ABC and CSBC effectively adsorbed MB dye molecules through hydrogen bonding, π-π stacking, and electrostatic interactions.

Gut microbiome combined with metabolomics reveals biomarkers and pathways in central precocious puberty

BACKGROUND

Central precocious puberty (CPP) is a common disease in prepubertal children and results mainly from disorders in the endocrine system. Emerging evidence has highlighted the involvement of gut microbes in hormone secretion, but their roles and downstream metabolic pathways in CPP remain unknown.

METHODS

To explore the gut microbes and metabolism alterations in CPP, we performed the 16S rRNA sequencing and untargeted metabolomics profiling for 91 CPP patients and 59 healthy controls. Bioinformatics and statistical analyses, including the comparisons of alpha and beta diversity, abundances of microbes, were undertaken on the 16S rRNA gene sequences and metabolism profiling. Classifiers were constructed based on the microorganisms and metabolites. Functional and pathway enrichment analyses were performed for identification of the altered microorganisms and metabolites in CPP.

RESULTS

We integrated a multi-omics approach to investigate the alterations and functional characteristics of gut microbes and metabolites in CPP patients. The fecal microbiome profiles and fecal and blood metabolite profiles for 91 CPP patients and 59 healthy controls were generated and compared. We identified the altered microorganisms and metabolites during the development of CPP and constructed a machine learning-based classifier for distinguishing CPP. The Area Under Curves (AUCs) of the classifies were ranged from 0.832 to 1.00. In addition, functional analysis of the gut microbiota revealed that the nitric oxide synthesis was closely associated with the progression of CPP. Finally, we investigated the metabolic potential of gut microbes and discovered the genus Streptococcus could be a candidate molecular marker for CPP treatment.

CONCLUSIONS

Overall, we utilized multi-omics data from microorganisms and metabolites to build a classifier for discriminating CPP patients from the common populations and recognized potential therapeutic molecular markers for CPP through comprehensive analyses.

Double sodium channel mutation, I265T/L1014F, is possibly related to pyrethroid-resistant in Thrips palmi

Thrips palmi Karny (Thysanoptera: Thripidae) can harm a variety of agricultural crops and transmit plant viruses, causing heavy economic losses. In the Hainan province of China, pyrethroids were sprayed widely to control T. palmi, which leaded to resistance to pyrethroids in T. palmi. The bioassay has shown that the resistance ratio of T. palmi to pyrethroids increases annually. Resistance ratio to λ-cyhalothrin has increased from 10.711 to 23.321 and to cypermethrin has increased from 5.507 to 23.051 for 3 years, 2020-2022. The double mutation (I265T/L1014F) was identified from the field strain for the first time, which were located in the domains I and II of the voltage-gated sodium channel of T. palmi, respectively. The double mutation is probably the reason for the higher resistance of T. palmi in Hainan. The frequencies of the double mutation were 53.33% in HN2020, 70.00% in HN2021, and 96.67% in HN2022. Results indicated that T. palmi had developed different degrees of resistance to pyrethroids in Hainan. This study provides theoretical guidance for the use of insecticides in the field control of thrips.

MiR-532-3p inhibited the methylation of SOCS2 to suppress the progression of PC by targeting DNMT3A

Pancreatic cancer (PC) is one of the deadliest malignancies, with poor diagnosis and prognosis. miR-532-3p has been reported to be a tumor suppressor in various cancers, whereas the mechanism of miR-532-3p in the progression of PC remains poorly understood. In this study, it was found that miR-532-3p and SOCS2 were down-regulated, whereas DNMT3A was up-regulated in PC. Knockdown of DNMT3A or overexpression of miR-532-3p suppressed PC cell proliferation, invasion, and migration, as well as tumor formation in nude mice. DNMT3A induced the methylation of SOCS2 promoter. SOCS2 knockdown reversed the inhibiting effect of DNMT3A silencing on PC cell growth. miR-532-3p directly bound to DNMT3A and negatively regulated its expression while up-regulating SOCS2 levels. DNMT3A overexpression reversed the inhibiting effect of miR-532-3p overexpression on PC cell growth. In conclusion, the overexpression of miR-532-3p could suppress proliferation, invasion, and migration of PC cells, as well as tumor formation in nude mice through inhibiting the methylation of SOCS2 by targeting DNMT3A.

Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus

Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.

Control of Aedes mosquito populations using recombinant microalgae expressing short hairpin RNAs and their effect on plankton

New biocontrol strategies are urgently needed to combat vector-borne infectious diseases. This study presents a low-cost method to produce a potential mosquito insecticide that utilizes the microalgae released into suburban water sources to control mosquito populations. Chlorella microalgae are ubiquitous in local waters, which were chosen as the host for genetic transfection. This species facilitated the recombinant algae to adapt to the prevailing environmental conditions with rapid growth and high relative abundance. The procedure involved microalgae RNAi-based insecticides developed using short hairpin RNAs targeting the Aedes aegypti chitin synthase A (chsa) gene in Chlorella. These insecticides effectively silenced the chsa gene, inhibiting Aedes metamorphosis in the laboratory and simulated-field trials. This study explored the impact of recombinant microalgae on the phytoplankton and zooplankton in suburban waters. High-throughput sequencing revealed that rapid reproduction of recombinant Chlorella indirectly caused the disappearance of some phytoplankton and reduced the protozoan species. This study demonstrated that a recombinant microalgae-based insecticide could effectively reduce the population of Aedes mosquitoes in the laboratory and simulated field trials. However, the impact of this technology on the environment and ecology requires further investigation.