GPTON: Generative Pre-trained Transformers enhanced with Ontology Narration for accurate annotation of biological data.

By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the top five predictions. Manual evaluations confirm GPTON's robustness, highlighting its potential to harness LLMs and structured knowledge to significantly advance biomedical research beyond gene set annotation.

MA-ST3D: Motion Associated Self-Training for Unsupervised Domain Adaptation on 3D Object Detection.

Recently, unsupervised domain adaptation (UDA) for 3D object detectors has increasingly garnered attention as a method to eliminate the prohibitive costs associated with generating extensive 3D annotations, which are crucial for effective model training. Self-training (ST) has emerged as a simple and effective technique for UDA. The major issue involved in ST-UDA for 3D object detection is refining the imprecise predictions caused by domain shift and generating accurate pseudo labels as supervisory signals. This study presents a novel ST-UDA framework to generate high-quality pseudo labels by associating predictions of 3D point cloud sequences during ego-motion according to spatial and temporal consistency, named motion-associated self-training for 3D object detection (MA-ST3D). MA-ST3D maintains a global-local pathway (GLP) architecture to generate high-quality pseudo-labels by leveraging both intra-frame and inter-frame consistencies along the spatial dimension of the LiDAR's ego-motion. It also equips two memory modules for both global and local pathways, called global memory and local memory, to suppress the temporal fluctuation of pseudo-labels during self-training iterations. In addition, a motion-aware loss is introduced to impose discriminated regulations on pseudo labels with different motion statuses, which mitigates the harmful spread of false positive pseudo labels. Finally, our method is evaluated on three representative domain adaptation tasks on authoritative 3D benchmark datasets (i.e. Waymo, Kitti, and nuScenes). MA-ST3D achieved SOTA performance on all evaluated UDA settings and even surpassed the weakly supervised DA methods on the Kitti and NuScenes object detection benchmark.

Excitation-dependent emission and highly efficient near-infrared luminescence in Cs2NaScCl6 double perovskite via Sb3+-Yb3+ alloying for multifunctional photoelectric applications.

A novel Sb3+-Yb3+ co-doped Cs2NaScCl6 double perovskite with multimode luminescence and efficient excitation-dependent emission is proposed. Upon Sb3+-Yb3+ co-substitution in Cs2NaScCl6, NIR emission at 995 nm is greatly enhanced. A new STE emission peaking at 570 nm appears. Its great potential in anti-counterfeiting, LEDs and night vision is successfully demonstrated.

XYLEM NAC DOMAIN 1 (EjXND1) relieves cold-induced lignification by negatively regulating the EjHB1-EjPRX12 module in loquat fruit.

INTRODUCTION: Lignin is a principal constituent of the secondary cell wall, which plays a role in both plant growth and defensing against stress, such as low temperature and pest infestation. Additionally, it also accumulates in fleshy fruits and negatively affects fruit quality. Red-fleshed loquat is temperature sensitive and exhibits cold-induced lignification. A number of technologies have been developed, for example, Low Temperature Conditioning (LTC) treatment, which has been applied in order to relieve the symptom of cold injury. OBJECTIVES: The present study seeks to elucidate the regulatory mechanism underlying cold-induced lignification in loquat fruit. METHODS: The target genes were isolated through the analysis of transcriptome. The gene function was analyzed by transient transgenic method in tobacco leaves and loquat fruit, respectively, as well as stable overexpression in liverwort. The regulatory mechanism study was achieved by in vitro protein-protein interaction assays, dual-luciferase assay, and EMSA. RESULTS: In the present study, the Xylem NAC Domain transcription factor EjXND1 was identified as a repressor of loquat fruit lignification. It was demonstrated that EjXND1 could interact with the characterized lignin activator EjHB1, resulting in a diminution of the activation of EjHB1 on EjPRX12 promoter. Furthermore, two highly methylated regions were identified in the promoter of EjXDN1. One of these regions exhibited a negative correlation between methylation level and EjXND1 expression. Additionally, it was shown that hypermethylation of this region weaken the binding affinity of EjXND1 activators to its promoter. CONCLUSION: The EjXND1 plays a role in modified Low Temperature Conditioning (mLTC) treatment that alleviates cold-induced lignification in red-fleshed loquat fruit by targeting the EjHB1-EjPRX12 module and EjXND1 is regulated by the dynamic of DNA methylation level in the promoter.

The effect of central sleep apnea on sleep architecture in children with obstructive sleep apnea.

OBJECTIVE: This study aimed to investigate how central sleep apnea (CSA) impacts sleep patterns in children with obstructive sleep apnea (OSA). METHODS: Children undergoing polysomnography (PSG) were enrolled and sorted into two groups: those with OSA alone (Group A) and those with both OSA and CSA (CAI <1 nd: children with 10 % CSA or more and less than 50 %, Group B). Statistical analysis was conducted to compare sleep structure and clinical features between Group A and Group B. RESULTS: Group B exhibited significantly higher respiratory events, apnea hypoventilation index, apnea index and oxygen desaturation index (ODI) compared to Group A (p < 0.05). Group B also showed higher total sleep time and arousal index than Group A (P < 0.05). The proportion of time spent in stage N3 was lower in Group B than in Group A (P < 0.05). Moreover, mean heart rate and minimum heart rate were higher in Group B compared to Group A (P < 0.05).Minimum oxygenation levels (including non-rapid eye movement (NREM) stages) were lowe in Group B than in Group A (P < 0.05). Additionally, the prevalence of positional obstructive sleep apnea (P-OSA) was greater in Group B than in Group A (P < 0.05). CONCLUSION: In comparison to those with OSA alone, children with OSA and concurrent CSA exhibited distinct sleep patterns, including reduced N3uration, higher arousal index, longer respiratory events, higher ODI, and lower oxygen saturation, higher heart rate.

The transcription factor EjNAC5 regulates loquat fruit chilling lignification.

Changes in both lignin biosynthesis and DNA methylation have been reported to be associated with chilling stress in plants. When stored at low temperatures, red-fleshed loquat is prone to lignification, with increased lignin content and fruit firmness, which has deleterious effects on taste and eating quality. Here, we found that 5 °C storage mitigated the increasing firmness and lignin content of red-fleshed 'Dahongpao' ('DHP') loquat fruit that occurred during 0 °C storage. EjNAC5 was identified by integrating RNA sequencing with whole-genome bisulfite sequencing analysis of 'DHP' loquat fruit. The transcript levels of EjNAC5 were positively correlated with changes in firmness and negatively correlated with changes in DNA methylation level of a differentially methylated region in the EjNAC5 promoter. In white-fleshed 'Baisha' ('BS') loquat fruit, which do not undergo chilling-induced lignification at 0 °C, the transcripts of EjNAC5 remained low and the methylation level of the differentially methylated region in the EjNAC5 promoter was higher, compared with 'DHP' loquat fruit. Transient overexpression of EjNAC5 in loquat fruit and stable overexpression in Arabidopsis and liverwort led to an increase in lignin content. Furthermore, EjNAC5 interacts with EjERF39 and EjHB1 and activates the transcription of Ej4CL1 and EjPRX12 genes involved in lignin biosynthesis. This regulatory network involves different transcription factors from those involved in the lignification pathway. Our study indicates that EjNAC5 promoter methylation modulates EjNAC5 transcript levels and identifies novel EjNAC5-EjERF39-Ej4CL1 and EjNAC5-EjHB1-EjPRX12 regulatory modules involved in chilling induced-lignification.

Electrochemical Trifluoromethylthiolation/Cyclization of N-Arylacrylamides with AgSCF3: Access to SCF3-Containing Oxindoles.

An environmentally friendly electrochemical strategy for the synthesis of SCF3-containing oxindoles was developed. This electrochemical transformation was accomplished through a cascade trifluoromethylthiolation/cyclization of N-acrylamides with AgSCF3, obviating the requirement for external oxidants. A variety of functional groups were well tolerated in this transformation.

Decreasing light exposure increases the abundance of antibiotic resistance genes in the cecum and feces of laying hens.

The gut microbiome plays a crucial role in maintaining animal health and is influenced by various factors, including light exposure; however, the response in laying hens of the gut microbiome to intermittent light regimes and the related impact on antibiotic resistance genes (ARGs) remain poorly understood. In this study, we divided 20-week-old laying hens into two groups. These groups were exposed to either continuous normal light or intermittent light for 8 weeks. The feces and cecal contents of laying hens were collected for analysis. Metagenomic analysis of both feces and cecal content samples revealed significant shifts in the microbial composition and abundance of ARGs under intermittent light exposure compared to normal light exposure (P < 0.05). Furthermore, metabolomic analysis of the cecal contents revealed substantial alterations in the abundance and composition of ARGs and mobile genetic elements (MGEs) in response to intermittent light exposure (P < 0.05). Network analysis revealed intricate co-occurrence patterns among bacterial communities, metabolites, and ARGs, highlighting correlations between Bacteroidetes species, ARGs, and metabolites. Although certain bacterial species showed differential associations, the dominant bacteria carrying ARGs or MGEs had relatively low numbers, suggesting that other bacterial communities may have had a greater influence on ARG dissemination. Moreover, our observations highlight the crucial role of metabolites as mediators between bacterial communities and ARGs, providing novel insights into the dynamics of antibiotic resistance development. Our findings underscore the impact of intermittent light exposure on ARG proliferation in poultry farming and emphasize interconnections among ARGs, bacterial communities, and metabolic pathways. The results underscore the importance of considering both microbial communities and metabolic processes to understand antibiotic resistance in agricultural settings.

Effect of the immunoregulation activity of a pectin polysaccharide from Saussurea laniceps petals on macrophage polarization.

Saussurea laniceps is a traditional medicinal herb. In our previous study, a pectin polysaccharide, SLP-4, was isolated from the petals of S. laniceps. In this study, the immunomodulatory activity of SLP-4 was studied by analyzing its effects on macrophage (RAW 264.7 cells) polarization. The immunomodulatory activity assays indicated that SLP-4 could significantly enhance the pinocytic and phagocytic capacity and promote the expression and secretion of cytotoxic molecules (nitric oxide, increased by 6.4 times when the SLP-4 concentration was 800 µg/mL) and cytokines (tumor necrosis factor-α and interleukin-6 increased by 7.7 and 11.9 times, respectively) in original macrophage. The possible mechanism could be attributed to the activation of the mitogen-activated protein kinase and nuclear factor-κB signaling pathways through Toll-like receptors 2 and 4. Moreover, SLP-4 significantly induced M1 polarization of original macrophages and transferred macrophages from M2 to M1, but had little effect on the conversion of M1 macrophages into M2 phenotype. Overall, these results demonstrate the potential of SLP-4 as an attractive immunomodulating functional supplement.

Exosomes derived from tendon stem/progenitor cells enhance tendon-bone interface healing after rotator cuff repair in a rat model.

The rate of retear after surgical repair remains high. Mesenchymal stem cells (MSCs) have been extensively employed in regenerative medicine for several decades. However, safety and ethical concerns constrain their clinical application. Tendon Stem/Progenitor Cells (TSPCs)-derived exosomes have emerged as promising cell-free therapeutic agents. Therefore, urgent studies are needed to investigate whether TSPC-Exos could enhance tendon-bone healing and elucidate the underlying mechanisms. In this study, TSPC-Exos were found to promote the proliferation, migration, and expression of fibrogenesis markers in BMSCs. Furthermore, TSPC-Exos demonstrated an ability to suppress the polarization of M1 macrophages while promoting M2 macrophage polarization. In a rat model of rotator cuff repair, TSPC-Exos modulated inflammation and improved the histological structure of the tendon-bone interface, the biomechanical properties of the repaired tendon, and the function of the joint. Mechanistically, TSPC-Exos exhibited high expression of miR-21a-5p, which regulated the expression of PDCD4. The PDCD4/AKT/mTOR axis was implicated in the therapeutic effects of TSPC-Exos on proliferation, migration, and fibrogenesis in BMSCs. This study introduces a novel approach utilizing TSPC-Exos therapy as a promising strategy for cell-free therapies, potentially benefiting patients with rotator cuff tear in the future.

A global view of altered ligand-receptor interactions in bone marrow aging based on single-cell sequencing.

Altered cell-cell communication is a hallmark of aging, but its impact on bone marrow aging remains poorly understood. Based on a common and effective pipeline and single-cell transcriptome sequencing, we detected 384,124 interactions including 2575 ligand-receptor pairs and 16 non-adherent bone marrow cell types in old and young mouse and identified a total of 5560 significantly different interactions, which were then verified by flow cytometry and quantitative real-time PCR. These differential ligand-receptor interactions exhibited enrichment for the senescence-associated secretory phenotypes. Further validation demonstrated supplementing specific extracellular ligands could modify the senescent signs of hematopoietic stem cells derived from old mouse. Our work provides an effective procedure to detect the ligand-receptor interactions based on single-cell sequencing, which contributes to understand mechanisms and provides a potential strategy for intervention of bone marrow aging.

Water training initiates spatially regulated microstructures with competitive mechanics in hydroadaptive polymers.

The strategy using water as a medium for dynamic modulation of competitive plasticity and viscoelasticity provides a unique perspective to attain adaptive materials. We reveal sustainable polymers, herein cellulose phenoxyacetate as a typical example, with unusual water-responsive dual-mechanic functionalities addressed via a chronological water training strategy. The temporal significance of such water-responsive mechanical behaviors becomes apparent considering that a mere 3-minute exposure or a prolonged 3-hour exposure to water induced different types of mechano-responsiveness. This endows the materials with multiple recoverable shape-changes during water and air training, and consequently even underlines the switchability between the pre-loaded stable water shapes (> 20 months) and the sequentially fixed air shapes. Our discovery exploits the competitive mechanics initiated by water training, enabling polymers with spatially regulated microstructures via their inherently distinct mechanical properties. Insights into the molecular changes represents a considerable fundamental innovation, can be broadly applicable to a diverse array of hydroadaptive polymers.

Simple and direct electrochemical detection of rosmarinic acid in food samples based on nanochannel modified carbon electrode.

The detection of rosmarinic acid (Ros A) in food samples holds major significance. Simple and convenient electrochemical detection of Ros A with high performance remains a challenge. In this work, a nanochannel array-modified carbon electrode was constructed using a simple and convenient approach to achieve highly sensitive electrochemical detection of Ros A in food samples. Through simple electrochemical pre-activation of a glassy carbon electrode (GCE), oxygen-containing functional groups were introduced on the electrode surface (p-GCE). Vertically-ordered mesoporous silica film (VMSF) was stably grown on p-GCE through electrochemical-assisted self-assembly (EASA) without the introduction of another adhesive layer (VMSF/p-GCE). Transmission electron microscopy (TEM) characterization demonstrated the highly ordered structure of VMSF with a nanochannel diameter around 2.7 nm. Both p-GCE and the nanochannels significantly enhanced the electrochemical signals of Ros A on the electrode, exhibiting dual signal amplification. VMSF/p-GCE demonstrated sensitive detection of Ros A with a linear range of 500 nM to 1 µM and 1 µM to 35 µM. The detection limit (DL) was 26 nM. Combining the good anti-fouling and anti-interference properties of the nanochannels, VMSF/p-GCE can achieve direct electrochemical detection of Ros A in food samples. The sensor can be easily regenerated for repeated use. The simple fabrication, high detection sensitivity and selectivity of the sensor make it a new strategy for rapid preparation of high-performance electrochemical sensors.

Haplotype-resolved chromosome-level genome assembly of Huyou (Citrus changshanensis).

Huyou (Citrus changshanensis) is a significant citrus species that originated in Zhejiang Province, China, where it is also primarily cultivated. It is valued for its distinctive flavor and notable health benefits, owing to its high content of bioactive compounds like naringin and limonin. However, the absence of a high quality reference genome has limited the exploration of these health-promoting compounds in Huyou and hindered research into the mechanisms behind its medicinal properties. In this study, we present a phased chromosome-level genome assembly of Huyou. By combining PacBio and Hi-C sequencing, we generated a primary genome assembly and two haplotypes, comprising nine pseudo-chromosomes, with sizes of 339.91 Mb, 323.51 Mb, and 311.89 Mb, respectively. By integrating transcriptome data and annotations of homologous species, we identified a total of 29,775 protein-coding genes in the genome of Huyou. Additionally, we detected lots of structural variants between the two haplotypes. This represents the first reference genome of Huyou, providing a valuable resource for future studies on its agricultural characteristics and medicinal applications.

Assessing Antibiotic-Resistant Genes in University Dormitory Washing Machines.

University dormitories represent densely populated environments, and washing machines are potential sites for the spread of bacteria and microbes. However, the extent of antibiotic resistance gene (ARG) variation in washing machines within university dormitories and their potential health risks are largely unknown. To disclose the occurrence of ARGs and antibiotic-resistant bacteria from university dormitories, we collected samples from washing machines in 10 dormitories and used metagenomic sequencing technology to determine microbial and ARG abundance. Our results showed abundant microbial diversity, with Proteobacteria being the dominant microorganism that harbors many ARGs. The majority of the existing ARGs were associated with antibiotic target alteration and efflux, conferring multidrug resistance. We identified tnpA and IS91 as the most abundant mobile genetic elements (MGEs) in washing machines and found that Micavibrio aeruginosavorus, Aquincola tertiaricarbonis, and Mycolicibacterium iranicum had high levels of ARGs. Our study highlights the potential transmission of pathogens from washing machines to humans and the surrounding environment. Pollution in washing machines poses a severe threat to public health and demands attention. Therefore, it is crucial to explore effective methods for reducing the reproduction of multidrug resistance.

Development of prognostic signatures and risk index related to lipid metabolism in ccRCC.

Background: Clear cell renal cell carcinoma (ccRCC) is a metabolic disorder characterized by abnormal lipid accumulation in the cytoplasm. Lipid metabolism-related genes may have important clinical significance for prognosis prediction and individualized treatment. Methods: We collected bulk and single-cell transcriptomic data of ccRCC and normal samples to identify key lipid metabolism-related prognostic signatures. qPCR was used to confirm the expression of signatures in cancer cell lines. Based on the identified signatures, we developed a lipid metabolism risk score (LMRS) as a risk index. We explored the potential application value of prognostic signatures and LMRS in precise treatment from multiple perspectives. Results: Through comprehensive analysis, we identified five lipid metabolism-related prognostic signatures (ACADM, ACAT1, ECHS1, HPGD, DGKZ). We developed a risk index LMRS, which was significantly associated with poor prognosis in patients. There was a significant correlation between LMRS and the infiltration levels of multiple immune cells. Patients with high LMRS may be more likely to respond to immunotherapy. The different LMRS groups were suitable for different anticancer drug treatment regimens. Conclusion: Prognostic signatures and LMRS we developed may be applied to the risk assessment of ccRCC patients, which may have potential guiding significance in the diagnosis and precise treatment of ccRCC patients.

Histone demethylase JMJD2D protects against enteric bacterial infection via up-regulating colonic IL-17F to induce ß-defensin expression.

Histone demethylase JMJD2D (also known as KDM4D) can specifically demethylate H3K9me2/3 to activate its target gene expression. Our previous study has demonstrated that JMJD2D can protect intestine from dextran sulfate sodium (DSS)-induced colitis by activating Hedgehog signaling; however, its involvement in host defense against enteric attaching and effacing bacterial infection remains unclear. The present study was aimed to investigate the role of JMJD2D in host defense against enteric bacteria and its underlying mechanisms. The enteric pathogen Citrobacter rodentium (C. rodentium) model was used to mimic clinical colonic infection. The responses of wild-type and JMJD2D-/- mice to oral infection of C. rodentium were investigated. Bone marrow chimeric mice were infected with C. rodentium. JMJD2D expression was knocked down in CMT93 cells by using small hairpin RNAs, and Western blot and real-time PCR assays were performed in these cells. The relationship between JMJD2D and STAT3 was studied by co-immunoprecipitation and chromatin immunoprecipitation. JMJD2D was significantly up-regulated in colonic epithelial cells of mice in response to Citrobacter rodentium infection. JMJD2D-/- mice displayed an impaired clearance of C. rodentium, more body weight loss, and more severe colonic tissue pathology compared with wild-type mice. JMJD2D-/- mice exhibited an impaired expression of IL-17F in the colonic epithelial cells, which restricts C. rodentium infection by inducing the expression of antimicrobial peptides. Accordingly, JMJD2D-/- mice showed a decreased expression of ß-defensin-1, ß-defensin-3, and ß-defensin-4 in the colonic epithelial cells. Mechanistically, JMJD2D activated STAT3 signaling by inducing STAT3 phosphorylation and cooperated with STAT3 to induce IL-17F expression by interacting with STAT3 and been recruited to the IL-17F promoter to demethylate H3K9me3. Our study demonstrates that JMJD2D contributes to host defense against enteric bacteria through up-regulating IL-17F to induce ß-defensin expression.

Rapid and comprehensive quality evaluation of Huang-qin from different origins by FT-IR and NIR spectroscopy combined with chemometrics.

INTRODUCTION: Quality evaluation of Huang-qin is significant to ensure its clinical efficacy. OBJECTIVE: This study aims to establish an accurate, rapid and comprehensive Huang-qin quality evaluation method to overcome the time-consuming and laborious shortcomings of traditional herbal medicine quality assessment methods. METHODS: The contents of baicalin, baicalein and scutellarin in Huang-qin from five different origins were analyzed by FT-IR and NIR spectra combined with multivariate data technology. The quality of Huang-qin from different origins was evaluated by TOPSIS and consistency analysis based on the content of three active ingredients. The correlation between ecological factors and the accumulation of active ingredients was explored. RESULTS: Satisfactory prediction results of PLS models were obtained. Relatively, the model based on FT-IR combined with the PLS regression method has higher R2 and smaller RMSE than the NIR combined with the PLS method. TOPSIS and consistency analysis results showed that the quality of Huang-qin from different geographical origins was significantly different. The results showed that the quality of Huang-qin produced in Shanxi Province was the best among the five origins studied. The results also found that the quality of Huang-qin in different growing areas of the same origin was not completely consistent. The correlation study showed that altitude, sunshine duration and rainfall were the main factors that caused the quality difference of medicinal materials in different geographical origins. CONCLUSION: This study provides a reference for the rapid quantitative analysis of the active components of herbal medicine and the quality evaluation of them.

DNA methylation controlling abscisic acid catabolism responds to light to mediate strawberry fruit ripening.

Phytohormones, epigenetic regulation and environmental factors regulate fruit ripening but their interplay during strawberry fruit ripening remains to be determined. In this study, bagged strawberry fruit exhibited delayed ripening compared with fruit grown in normal light, correlating with reduced abscisic acid (ABA) accumulation. Transcription of the key ABA catabolism gene, ABA 8'-hydroxylase FaCYP707A4, was induced in bagged fruit. With light exclusion whole genome DNA methylation levels were up-regulated, corresponding to a delayed ripening process, while DNA methylation levels in the promoter of FaCYP707A4 were suppressed, correlating with increases in transcript and decreased ABA content. Experiments indicated FaCRY1, a blue light receptor repressed in bagged fruit and FaAGO4, a key protein involved in RNA-directed DNA methylation, could bind to the promoter of FaCYP707A4. The interaction between FaCRY1 and FaAGO4, and an increased enrichment of FaAGO4 directed to the FaCYP707A4 promoter in fruit grown under light suggests FaCRY1 may influence FaAGO4 to modulate the DNA methylation status of the FaCYP707A4 promoter. Furthermore, transient overexpression of FaCRY1, or an increase in FaCRY1 transcription by blue light treatment, increases the methylation level of the FaCYP707A4 promoter, while transient RNA interference of FaCRY1 displayed opposite phenotypes. These findings reveal a mechanism by which DNA methylation influences ABA catabolism, and participates in light-mediated strawberry ripening.