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Macrophages have strong plasticity and heterogeneity, and can undergo functional transformation in response to different signal stimuli, such as classical activation of M1 type (M1 type polarization) and selective activation of M2 type (M2 type polarization). The pathways of macrophage M1/M2 polarization are quite extensive, involving nuclear factor-κB (NF-κB)/mitogen-activated protein kinase (MAPK) signaling pathway, interleukin-4 (IL-4)/signal transduction and activator of transcription 6 (STAT6) signaling pathway, Notch signaling pathway, Wnt/β-catenin signaling pathway, etc. At the same time, M1/M2 polarization of macrophages is also regulated by exosomes, metabolites, non-coding RNA, electrical stimulation, probiotics, etc., and its imbalance is closely related to the occurrence and development of different types of liver disease. In this paper, the mechanism of its polarization was reviewed, and it was found that M1 polarization of macrophages played a promoting role in the process of liver tissue injury, inflammation and fibrosis, while M2 polarization of macrophages played the opposite role. Among them, hepatocellular carcinoma, as the advanced stage of chronic liver disease, was characterized by increased M2 polarization and impaired M1 polarization of macrophages. Therefore, this paper pays attention to the role of M1/M2 polarization of macrophages in different types of liver diseases, in order to better establish the targeted therapy of macrophage subsets.

Background/Objectives: Understanding the relationship between DNA sequences and gene expression levels is of significant biological importance. Recent advancements have demonstrated the ability of deep learning to predict gene expression levels directly from genomic data. However, traditional methods are limited by basic word encoding techniques, which fail to capture the inherent features and patterns of DNA sequences. Methods: We introduce TExCNN, a novel framework that integrates the pre-trained models DNABERT and DNABERT-2 to generate word embeddings for DNA sequences. We partitioned the DNA sequences into manageable segments and computed their respective embeddings using the pre-trained models. These embeddings were then utilized as inputs to our deep learning framework, which was based on convolutional neural network. Results: TExCNN outperformed current state-of-the-art models, achieving an average R2 score of 0.622, compared to the 0.596 score achieved by the DeepLncLoc model, which is based on the Word2Vec model and a text convolutional neural network. Furthermore, when the sequence length was extended from 10,500 bp to 50,000 bp, TExCNN achieved an even higher average R2 score of 0.639. The prediction accuracy improved further when additional biological features were incorporated. Conclusions: Our experimental results demonstrate that the use of pre-trained models for word embedding generation significantly improves the accuracy of predicting gene expression. The proposed TExCNN pipeline performes optimally with longer DNA sequences and is adaptable for both cell-type-independent and cell-type-dependent predictions. [ABSTRACT FROM AUTHOR]

To provide a more comprehensive understanding of the efficacy and safety profile of cabozantinib versus placebo in malignant tumors, we conducted a systematic review and meta-analysis. This involved analyzing a collection of published randomized controlled trials to assess the outcomes. We used RevMan5.3 software to evaluate the outcomes of the collected studies. The primary outcome we focused on was progression-free survival (PFS), and the secondary outcomes included overall survival (OS) and disease control rate (DCR). Our findings revealed that compared to placebo, cabozantinib significantly extended the PFS of patients [hazard ratios (HR) 0.37, 95% confidence intervals (CI): 0.32, 0.43, p < 0.00001]. Additionally, cabozantinib improved the OS of patients [HR 0.78, 95%CI: 0.68, 0.91, p = 0.002]. While it is important to note that cabozantinib was associated with a higher likelihood of causing digestive, cutaneous, and cardiovascular related adverse events [relative risk (RR) 4.40, 95% CI: 3.10, 6.25, p < 0.00001]. Based on our analysis, cabozantinib significantly prolonged the PFS and OS of patients with malignant tumors (p < 0.01). We recommend the use of cabozantinib in treating advanced malignant tumors. However, it is important to continuously monitor and manage the drug-related adverse events. PROSPERO (No. CRD42023449261). [ABSTRACT FROM AUTHOR]

Recurrence and distant metastasis after paclitaxel (PTX)‐based chemotherapy in ovarian cancer (OC) patients remains a clinical obstacle. Flavokawain A (FKA) is a novel chalcone from kava plant that can induce G2/M arrest and inhibit invasion and metastasis in different tumor cells. In this study, we examined the effects and the molecular mechanism of sodium aescinate (Aes)‐stabilized nanoparticles FKA‐A NPs in enhancing the efficacy of PTX‐A NPs in vitro and in vivo. We showed that FKA‐A NPs combined with PTX‐A NPs notably inhibited the proliferation and migration and reduced the expression of EMT‐related markers in OCs. YAP nuclear translocation and its downstream signaling pathway were remarkably activated after PTX‐A NPs treatment in OCs. FKA‐A NPs obviously inhibited YAP nuclear translocation and reduced the transcriptional activity of YAP target genes. Simultaneously, FKA‐A NPs dose and time dependently inhibited Skp2 expression in A2780 and Skov3 cells. In contrast, overexpression of Skp2 significantly attenuated the inhibition of FKA‐A NPs on YAP nuclear translocation. In OC homograft mice, treatment with FKA‐A NPs and PTX‐A NPs significantly suppressed the growth of homograft tumor compared with PTX‐A NPs but did not decrease mice's body weight. In summary, we demonstrate that FKA‐A NPs enhance the efficacy of PTX‐A NPs against OCs in vitro and in vivo via reducing Skp2 expression, thus suppressing YAP nuclear translocation and activity of its target genes. [ABSTRACT FROM AUTHOR]

Organization preference knowledge is critical to enhancing the intelligence and efficiency of the multi-platform aircraft mission system (MPAMS), particularly the collaboration tactics of task behaviors, platform types, and mount resources. However, it is challenging to extract such knowledge concisely, which is buried in massive historical data. Therefore, this paper proposes an innovative data-driven approach via frequent closed itemset mining (FCIM) algorithm to discover valuable MPAMS organizational knowledge. The proposed approach addresses the limitations of poor effectiveness and low mining efficiency for the previously discovered knowledge. To ensure the knowledge effectiveness, this paper designs a multi-layer knowledge discovery framework from the system-of-systems perspective, allowing to discover more systematic knowledge than traditional frameworks considering an isolated layer. Additionally, the MPAMS's contextual capability reflecting the decision motivation is integrated into the knowledge representation, making the knowledge more intelligible to decision-makers. Further, to ensure mining efficiency, the knowledge mining process is accelerated by designing an itemset storage structure and three pruning strategies for FCIM. The simulation of 1100 air-to-sea assault scenarios has provided abundant knowledge with high interpretability. The performance superiority of the proposed approach is thoroughly verified by comparative experiments. The approach provides guidance and insights for future MPAMS development and organization optimization. [ABSTRACT FROM AUTHOR]

The radiation-induced inflammatory response is involved in radiation damage to the cochlea and causes sensorineural hearing loss (SNHL). NF-κB, as the master switch of the inflammatory response, regulates the expression of many inflammation-related genes and thus the inflammatory response. Therefore, in this study we used a mouse model to determine whether radiation-induced NF-κB activation is involved in damage to the cochlea and to investigate the underlying mechanism. Eventually, we found that NF-κB was activated after radiation of the cochleae and the activation reached a maximum at 2–6 h after radiation. And morphological analysis showed severe damage to the cochleae after radiation, but this damage was significantly ameliorated by JSH-23 (an inhibitor of NF-κB) pretreatment. Along with these morphological changes, the expression levels of proinflammatory molecules (including proinflammatory cytokines IL-6, TNF-α, COX-2 and inflammation-related proteins VCAM-1, MIP-1β) in the cochlear tissues were significantly increased after radiation, but were significantly decreased by JSH-23 pretreatment compared to radiation alone. Therefore, these results indicated that radiation-induced NF-κB activation was involved in damage to the cochleae and resultant SNHL via its promotion of the inflammatory response mediated by overexpression of some proinflammatory molecules in cochlear tissues, and inhibition of radiation-induced NF-κB was conducive to preventing such damage. [ABSTRACT FROM AUTHOR]

With the rapid increase of renewable energy sources, the variability and uncertainty in power systems are significantly increased, and the power system operation is facing more and more challenges. In the traditional dynamic economic dispatch (DED) of transmission systems, the frequency and voltage regulation effects are not actively utilized. In addition, the transmission systems and distribution systems are optimized separately; the transmission–distribution coordination effect is not considered. In this article, a new DED is proposed. The optimal scheduling results are obtained by making a balance between operating cost and reliability cost. Both the automatic regulation effect and transmission–distribution coordination effect are explored and exploited in terms of the equivalent reserve, which can reduce the reserve provided by generating units, and can further enhance the security and economics of power system operation. The validity and effectiveness of the proposed model are illustrated by case studies. [ABSTRACT FROM AUTHOR]

Based on the hybrid coordinate ocean model (HYCOM) reanalysis data, the dynamical and thermal response of Zhejiang coastal waters to 12 typhoons from 2011 to 2015 was studied, and the relationship between the oceanic response and typhoon characteristics was analyzed. The HYCOM reanalysis data were validated by satellite-observed sea surface temperature data. Results show that all the 12 typhoons caused near-inertial waves, sea surface cooling and seafloor warming, but significant differences existed among them. Based on statistics, it was found that the domain-averaged near-inertial kinetic energy and seafloor warming are significantly correlated with the typhoon's maximum wind speed, both of which show a positive relationship. The domain-averaged seafloor warming also decreases with the typhoon's translation speed. Moreover, there exists a positive correlation between the domain-averaged sea surface cooling and seafloor warming. The different mechanisms that caused the seafloor warming for the 12 typhoons were also investigated in this study. [ABSTRACT FROM AUTHOR]

Abstract Background H. pylori (Helicobacter pylori) is the major causative agent of chronic active gastritis. The population of H. pylori shows a high genomic variability among isolates. And the polymorphism of repeat-units of genomics had participated the important process of evolution. Its long term colonization of the stomach caused different clinical outcomes, which may relate to the high degree of genetic variation of H. pylori. A variety of molecular typing tools have been developed to access genetic relatedness in H. pylori isolates. However, there is still no standard genotyping system of this bacterium. The MLVA (Multi-locus of variable number of tandem repeat analysis) method is useful for performing phylogenetic analysis and is widely used in bacteria genotyping; however, there's little application in H. pylori analysis. This article is the first application of the MLVA method to investigate H. pylori from different districts and ethnic groups of China. Results MLVA of 12 VNTR loci with high discrimination power based on 30 candidates were performed on a collection of 202 strains of H. pylori which originated from five regions of China and Japan. Phylogenetic tree was constructed using MLVA profiles. 12 VNTR loci presented with high various polymorphisms, and the results demonstrated very close relationships between genotypes and ethnic groups. Conclusions This study used MLVA methodology providing a new perspective on the ethnic groups and distribution characteristics of H. pylori.

Engineering vehicles are widely used under various harsh working conditions. For many components in them, service loadings they suffered are usually random and nonstationary due to their remarkable characteristic called cyclic operation. To deal with that, section method can be applied. However, this method will neglect those transition cycles caused by switching load section, which can contribute a lot to fatigue. In order to consider those transition cycles, this paper applied the model called "Switching Markov Chain of Turning Points" (SMCTP). Then the expected rain-flow matrix is compared with the overall rain-flow matrix conducted by section method. The comparison result shows that SMCTP can perform well in processing nonstationary loadings. As a result, the Switching Markov Chain method (SMC) was proved to be effective in stochastically characterizing the nonstationary switching loadings of engineering vehicles. [ABSTRACT FROM AUTHOR]

Extensive neck lymph node metastasis (LNM) is an important clinical feature of hypopharyngeal squamous cell carcinoma (HSCC). Stathmin1 (STMN1) is closely associated with LNM in numerous human cancers. In the present study, the association between STMN1 and neck LNM in HSCC and the underlying molecular mechanisms were explored. First, postoperative samples of HSCC were screened and the association between STMN1 and neck LNM in HSCC was analyzed. Then, cell functional experiments were performed to assess the potential of STMN1 to promote invasion and migration. Subsequently, the potential target genes and pathways of STMN1 were predicted using bioinformatics analysis. Finally, the obtained target genes and pathways of STMN1 were validated by reverse transcription-quantitative PCR (RT-qPCR) and western blot analyses to confirm the potential mechanisms by which STMN1 promotes LNM in HSCC. As a result, a total of 117 postoperative samples of HSCC were screened, and STMN1 was proven to be associated with neck LNM in HSCC. Further, cell functional experiments established that high expression of STMN1 could actually promote FaDu cell invasion and metastasis. Bioinformatics analysis revealed that high expression of STMN1 was associated with the activation of hypoxia inducible factor-1alpha (HIF-1α) pathway and increased expression of metastasis-associated protein 1 (MTA1). Finally, RT-qPCR and western blot analyses confirmed that STMN1 promotes the expression levels of HIF-1α/vascular endothelial growth factor (VEGF)-A and MTA1 in FaDu cell lines. In conclusion, it was found that high expression of STMN1 promoted neck LNM in HSCC and the potential mechanisms may be via regulation of the HIF-1α/VEGF-A axis and MTA1 expression. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) are emerging as important regulators in various biological processes. However, to date, no systematic characterization of lncRNAs has been reported in the silkworm Bombyx mori. In the present study, we generated eighteen RNA-seq datasets with relatively high depth. Using an in-house designed lncRNA identification pipeline, 11,810 lncRNAs were identified for 5,556 loci. Among these lncRNAs, 474 transcripts were intronic lncRNAs (ilncRNAs), 6,250 transcripts were intergenic lncRNAs (lincRNAs), and 5,086 were natural antisense lncRNAs (lncNATs). Compared with protein-coding mRNAs, silkworm lncRNAs are shorter in terms of full length but longer in terms of exon and intron length. In addition, lncRNAs exhibit a lower level of sequence conservation, more repeat sequences overlapped and higher tissue specificity than protein-coding mRNAs in the silkworm. We found that 69 lncRNA transcripts from 33 gene loci may function as miRNA precursors, and 104 lncRNA transcripts from 72 gene loci may act as competing endogenous RNAs (ceRNAs). In total, 49.47% of all gene loci (2,749/5,556) for which lncRNAs were identified showed sex-biased expression. Co-expression network analysis resulted in 19 modules, 12 of which revealed relatively high tissue specificity. The highlighted darkgoldenrod module was specifically associated with middle and posterior silk glands, and the hub lncRNAs within this module were co-expressed with proteins involved in translation, translocation, and secretory processes, suggesting that these hub lncRNAs may function as regulators of the biosynthesis, translocation, and secretion of silk proteins. This study presents the first comprehensive genome-wide analysis of silkworm lncRNAs and provides an invaluable resource for genetic, evolutionary, and genomic studies of B. mori. [ABSTRACT FROM AUTHOR]

Silk proteins are synthesized in the middle and posterior silk glands of silkworms, then transit into the anterior of the silk gland, where the silk fibers are produced, stored and processed. The mechanism of formation and spinning of the silk fibers has not been fully elucidated, and transcriptome analyses specific to the anterior silk gland have not been reported. In the present study, we explored gene expression profiles in five regions of silk gland samples using the RNA-Seq method. As a result, there were 959,979,570 raw reads obtained, of which 583,068,172 reads were mapped to the silkworm genome. A total of 7419 genes were found to be expressed in terms of reads per kilobase of exon model per million mapped reads ≥ 5 in at least one sample. The gene numbers and expression levels of the expressed genes differed between these regions. The differentially expressed genes were analyzed, and 282 genes were detected as up-regulated in the anterior silk gland, compared with the other parts. Functions of these genes were addressed using the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases, and seven key pathways were enriched. It suggested that the ion transportation, energy metabolism, protease inhibitors and cuticle proteins played essential roles in the process of silk formation and spinning in the anterior silk gland. In addition, 210 genes were found differently expressed between males and females, which should help to elucidate the mechanism of the quality difference in silk fibers from male and female silkworms. [ABSTRACT FROM AUTHOR]

The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG) and posterior silk gland (PSG). Three sericin genes (sericin 1, sericin 2, and sericin 3) were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25) were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs) and 361 insertion-deletions (INDELs) were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research. [ABSTRACT FROM AUTHOR]

In the silkworm Bombyx mori, pigment mutants with diverse body colors have been maintained throughout domestication for about 5000 years. The silkworm larval body color is formed through the mutual interaction of melanin, ommochromes, pteridines and uric acid. These pigments/compounds are synthesized by the cooperative action of various genes and enzymes. Previous reports showed that melanin, ommochrome and pteridine are increased in silkworm quail (q) mutants. To understand the pigment increase and alterations in pigment synthesis in q mutant, transcriptome profiles of the silkworm integument were investigated at 16 h after head capsule slippage in the fourth molt in q mutants and wild-type (Dazao). Compared to the wild-type, 1161 genes were differentially expressed in the q mutant. Of these modulated genes, 62.4% (725 genes) were upregulated and 37.6% (436 genes) were downregulated in the q mutant. The molecular function of differently expressed genes was analyzed by Blast2GO. The results showed that upregulated genes were mainly involved in protein binding, small molecule binding, transferase activity, nucleic acid binding, specific DNA-binding transcription factor activity and chromatin binding, while exclusively down-expressed genes functioned in oxidoreductase activity, cofactor binding, tetrapyrrole binding, peroxidase activity and pigment binding. We focused on genes related to melanin, pteridine and ommochrome biosynthesis; transport of uric acid; and juvenile hormone metabolism because of their importance in integument coloration during molting. This study identified differently expressed genes implicated in silkworm integument formation and pigmentation using silkworm q mutant. The results estimated the number and types of genes that drive new integument formation. [ABSTRACT FROM AUTHOR]