FindVehicle and VehicleFinder: A NER dataset for natural language-based vehicle retrieval and a keyword-based cross-modal vehicle retrieval system

Natural language (NL) based vehicle retrieval is a task aiming to retrieve a vehicle that is most consistent with a given NL query from among all candidate vehicles. Because NL query can be easily obtained, such a task has a promising prospect in building an interactive intelligent traffic system (ITS). Current solutions mainly focus on extracting both text and image features and mapping them to the same latent space to compare the similarity. However, existing methods usually use dependency analysis or semantic role-labelling techniques to find keywords related to vehicle attributes. These techniques may require a lot of pre-processing and post-processing work, and also suffer from extracting the wrong keyword when the NL query is complex. To tackle these problems and simplify, we borrow the idea from named entity recognition (NER) and construct FindVehicle, a NER dataset in the traffic domain. It has 42.3k labelled NL descriptions of vehicle tracks, containing information such as the location, orientation, type and colour of the vehicle. FindVehicle also adopts both overlapping entities and fine-grained entities to meet further requirements. To verify its effectiveness, we propose a baseline NL-based vehicle retrieval model called VehicleFinder. Our experiment shows that by using text encoders pre-trained by FindVehicle, VehicleFinder achieves 87.7\% precision and 89.4\% recall when retrieving a target vehicle by text command on our homemade dataset based on UA-DETRAC. The time cost of VehicleFinder is 279.35 ms on one ARM v8.2 CPU and 93.72 ms on one RTX A4000 GPU, which is much faster than the Transformer-based system. The dataset is open-source via the link https://github.com/GuanRunwei/FindVehicle, and the implementation can be found via the link https://github.com/GuanRunwei/VehicleFinder-CTIM

Preparation and characterization of a novel triple composite scaffold containing silk fibroin, chitosan, extracellular matrix and the mechanism of Akt/FoxO signaling pathway in colonic cancer cells cultured in 3D

This work examined the physical and chemical properties and biocompatibility in vivo and in vitro of a unique triple composite scaffold incorporating silk fibroin, chitosan, and extracellular matrix. The materials were blended, cross-linked, and freeze-dried to create a composite scaffold of silk fibroin/chitosan/colon extracellular matrix (SF/CTS/CEM) with varying CEM contents. The SF/CTS/CEM (1:1:1) scaffold demonstrated the preferable shape, outstanding porosity, favorable connectivity, good moisture absorption, and acceptable and controlled swelling and degradation properties. Additionally, HCT-116 cells cultivated with SF/CTS/CEM (1:1:1) showed excellent proliferation capacity, cell malignancy, and delayed apoptosis, according to the in vitro cytocompatibility examination. We also examined the PI3K/PDK1/Akt/FoxO signaling pathway and discovered that cell culture using a SF/CTS/CEM (1:1:1) scaffold may prevent cell death by phosphorylating Akt and suppressing FoxO expression. Our findings demonstrate the potential of the SF/CTS/CEM (1:1:1) scaffold as an experimental model for colonic cancer cell culture and for replicating the three-dimensional in vivo cell growth environment

Cuproptosis-related risk score predicts prognosis and characterizes the tumor microenvironment in colon adenocarcinoma

IntroductionCuproptosis is a novel copper-dependent regulatory cell death (RCD), which is closely related to the occurrence and development of multiple cancers. However, the potential role of cuproptosis-related genes (CRGs) in the tumor microenvironment (TME) of colon adenocarcinoma (COAD) remains unclear.MethodsTranscriptome, somatic mutation, somatic copy number alteration and the corresponding clinicopathological data of COAD were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO). Difference, survival and correlation analyses were conducted to evaluate the characteristics of CRGs in COAD patients. Consensus unsupervised clustering analysis of CRGs expression profile was used to classify patients into different cuproptosis molecular and gene subtypes. TME characteristics of different molecular subtypes were investigated by using Gene set variation analysis (GSVA) and single sample gene set enrichment analysis (ssGSEA). Next, CRG Risk scoring system was constructed by applying logistic least absolute shrinkage and selection operator (LASSO) cox regression analysis and multivariate cox analysis. Real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) were used to exam the expression of key Risk scoring genes.ResultsOur study indicated that CRGs had relatively common genetic and transcriptional variations in COAD tissues. We identified three cuproptosis molecular subtypes and three gene subtypes based on CRGs expression profile and prognostic differentially expressed genes (DEGs) expression profile, and found that changes in multilayer CRGs were closely related to the clinical characteristics, overall survival (OS), different signaling pathways, and immune cell infiltration of TME. CRG Risk scoring system was constructed according to the expression of 7 key cuproptosis-related risk genes (GLS, NOX1, HOXC6, TNNT1, GLS, HOXC6 and PLA2G12B). RT-qPCR and IHC indicated that the expression of GLS, NOX1, HOXC6, TNNT1 and PLA2G12B were up-regulated in tumor tissues, compared with those in normal tissues, and all of GLS, HOXC6, NOX1 and PLA2G12B were closely related with patient survival. In addition, high CRG risk scores were significantly associated with high microsatellite instability (MSI-H), tumor mutation burden (TMB), cancer stem cell (CSC) indices, stromal and immune scores in TME, drug susceptibility, as well as patient survival. Finally, a highly accurate nomogram was constructed to promote the clinical application of the CRG Risk scoring system.DiscussionOur comprehensive analysis showed that CRGs were greatly associated with TME, clinicopathological characteristics, and prognosis of patient with COAD. These findings may promote our understanding of CRGs in COAD, providing new insights for physicians to predict prognosis and develop more precise and individualized therapy strategies

Restoration of cefixime-induced gut microbiota changes by a prebiotic blend in a mouse model

Recent studies have provided compelling evidence linking the composition of the gut microbiota, host diet, and host physiology. Prebiotics are substrates that are selectively utilized by host microorganisms, conferring health benefits. Prebiotics, such as prebiotic blends (PB), are commonly used worldwide in food processing. Here, microbiome-metabolomics was used to evaluate how PB affect gut microbes and metabolic functions in C57BL/6 J mice administered cefixime. We found favorable effects of PB on obesity outcomes. PB supplementation significantly increased the abundance of Bifidobacterium, Parabacteroides, Alloprevotella, Alistipes, and Dubosiella, and decreased that of Robinsoniella, Blautia, Lachnoclostridium, Coprobacillus, Hungatella, Erysipelatoclostridium, Helicobacter, Clostridium sensu stricto 1, Enterococcus, and Akkermansia compared to that in the cefixime administration (CEF) group. In particular, PB increased the abundance of Parabacteroides goldsteinii and suppressed that of Robinsoniella peoriensis and Akkermansia muciniphila. In addition, it regulated the levels of microbial metabolites such as unsaturated fatty acids and bile acids. Thus, PB can alleviate metabolic disorders induced by antibiotic intervention, indicating a potential dietary strategy for populations with antibiotic-associated diarrhea

A dual emission nanocomposite prepared from copper nanoclusters and carbon dots as a ratiometric fluorescent probe for sulfide and gaseousH(2)S

A dual emission nanocomposite prepared from copper nanoclusters and carbon dots as a ratiometric fluorescent probe for sulfide and gaseousH(2)

The gut microbiota and its products: Establishing causal relationships with obesity related outcomes

Gut microorganisms not only participate in the metabolism of carbohydrate, lipids, protein, and polypeptides in the intestine but also directly affect the metabolic phenotypes of the host. Although many studies have described the apparent effects of gut microbiota on human health, the development of metagenomics and culturomics in the past decade has generated a large amount of evidence suggesting a causal relationship between gut microbiota and obesity. The interaction between the gut microbiota and host is realized by microbial metabolites with multiple biological functions. We concentrated here on several representative beneficial species connected with obesity as well as the mechanisms, with particular emphasis on microbiota-dependent metabolites. Finally, we consider the potential clinical significance of these relationships to fuel the conception and realization of novel therapeutic and preventive strategies

Alginate Oligosaccharide Alleviated Cisplatin-Induced Kidney Oxidative Stress via Lactobacillus Genus-FAHFAs-Nrf2 Axis in Mice

Alginate oligosaccharide is the depolymerized product of alginate, a natural extract of brown algae, which is associated with beneficial health effects. Here, we aimed to investigate the mechanism via which alginate oligosaccharides improve kidney oxidative damage and liver inflammation induced by cisplatin chemotherapy via the gut microbiota. C57BL/6J mice were treated with cisplatin were administered alginate oligosaccharide via gavage for 3 weeks. Compared to that observed in the cisplatin chemotherapy group without intragastric administration of alginate oligosaccharide, liver inflammation improved in the alginate oligosaccharide group, indicated by reduction in lipopolysaccharide and interleukin-1 beta (IL-1 beta) levels. This was accompanied by improvement in the oxidative stress of mice kidneys, indicated by the increase in the levels of superoxide dismutase (SOD), catalase (CAT) and nuclear NF-E2-related factor 2 (Nrf2) in renal tissue, and reduction in the levels of malondialdehyde (MDA) in renal tissue and serum creatinine (Cr) to the levels of the normal control group. Alginate oligosaccharide intervention increased the concentration of fatty acid esters of hydroxy fatty acids (FAHFAs). Alginate oligosaccharide regulated the composition of the intestinal microbial community and promoted Lactobacillus stains, such as Lactobacillus johnsonii and Lactobacillus reuteri. Spearman analysis showed that 5 members of FAHFAs concentrations were positively correlated with Lactobacillus johnsonii and Lactobacillus reuteri abundance. We observed that alginate oligosaccharide increased FAHFAs producing-related bacterial abundance and FAHFAs levels, enhanced the levels of SOD and CAT in kidney tissue, and reduced the levels of MDA via activating Nrf2, thereby ameliorating the renal redox injury caused by cisplatin chemotherapy

Alginate oligosaccharide ameliorates azithromycin-induced gut microbiota disorder via Bacteroides acidifaciens-FAHFAs and Bacteroides-TCA cycle axes

Alginate oligosaccharide is a kind of prebiotic with broad application prospects. However, little attention is paid to the recovery effect of alginate oligosaccharide on disordered intestinal microecology caused by azithromycin. Therefore, we evaluated the regulatory effect of alginate oligosaccharide and its compound on azithromycin-disturbed gut microbiota in mice via microbiome-metabolomics analysis. The gut microbiota analysis revealed that alginate oligosaccharide and its compound significantly increased the richness and diversity of the gut microbiota which were reduced by azithromycin, with an obvious enrichment of beneficial bacteria such as the Akkermansia genus and Bacteroides acidifaciens, and a remarkable decrease of pathogenic bacteria such as the Staphylococcus genus, which indicated its impact on the gut microbiota dysbiosis. Additionally, the effect of the alginate oligosaccharide compound on regulating the gut microbiota disorder is more significant than that of alginate oligosaccharide. The favorable effects of alginate oligosaccharide were confirmed by beneficial alterations in metabolic effector molecules, which indicated that alginate oligosaccharide and its compound improved metabolic homeostasis via the Bacteroides acidifaciens-fatty acid esters of hydroxy fatty acids (FAHFAs) axis and increasing the levels of the intermediate products of the tricarboxylic acid cycle (TCA cycle), such as citric acid, fumaric acid and alpha-ketoglutaric acid. Spearman correlation analysis showed that the contents of these three metabolites were also positively related to Bacteroides acidifaciens and Bacteroides sartorii populations, suggesting the potential regulatory role of the Bacteroides genus in energy balance through the TCA cycle. This study may provide an innovative dietary strategy for the regulation of intestinal microecological disorders caused by antibiotics, and reveal the prospect of alginate oligosaccharide as an intestinal microecological regulator

Table_7_CXCL12, a potential modulator of tumor immune microenvironment (TIME) of bladder cancer: From a comprehensive analysis of TCGA database.docx

BackgroundTumor immune microenvironment (TIME) plays a significant role in the initiation and progression of bladder urothelial carcinoma (BLCA). However, there are only a few researches regarding the association between immune-related genes and tumor-infiltrating immune cells (TICs) in TIME of BLCA.MethodsWe calculated the proportion of immune/stromal component and TICs of 414 BLCA samples and 19 normal samples downloaded from TCGA database with the help of ESTIMATE and CIBERSORT algorithms. Differentially expressed genes (DEGs) were obtained from the comparison between Stromal and Immune Score and further analyzed by GO and KEGG enrichment analysis, as well as PPI network and COX regression analysis. CXCL12 was overlapping among the above analyses. Single gene analysis of CXCL12 was carried out through difference analysis, paired analysis and GSEA. The association between CXCL12 and TICs was assessed by difference analysis and correlation analysis.ResultsImmune and stromal component in TIME of BLCA were associated with patients’ clinicopathological characteristics. 284 DEGs were primarily enriched in immune-associated activities, among which CXCL12 was the most significant gene sharing the leading nodes in PPI network and being closely related with patients’ survival. Single gene analysis and immunohistochemistry revealed that CXCL12 was down-regulated in BLCA samples and significantly related with the clinicopathological characteristics of patients. Further analysis suggested that CXCL12 was involved in the immune-associated activities probably through its close cross-talk with TICs.ConclusionsCXCL12 down-regulation could be a potential biomarker to predict the unbalanced immune status of TIME of BLCA, which might provide an extra insight for the immunotherapy of BLCA.</p

Table_3_CXCL12, a potential modulator of tumor immune microenvironment (TIME) of bladder cancer: From a comprehensive analysis of TCGA database.docx

BackgroundTumor immune microenvironment (TIME) plays a significant role in the initiation and progression of bladder urothelial carcinoma (BLCA). However, there are only a few researches regarding the association between immune-related genes and tumor-infiltrating immune cells (TICs) in TIME of BLCA.MethodsWe calculated the proportion of immune/stromal component and TICs of 414 BLCA samples and 19 normal samples downloaded from TCGA database with the help of ESTIMATE and CIBERSORT algorithms. Differentially expressed genes (DEGs) were obtained from the comparison between Stromal and Immune Score and further analyzed by GO and KEGG enrichment analysis, as well as PPI network and COX regression analysis. CXCL12 was overlapping among the above analyses. Single gene analysis of CXCL12 was carried out through difference analysis, paired analysis and GSEA. The association between CXCL12 and TICs was assessed by difference analysis and correlation analysis.ResultsImmune and stromal component in TIME of BLCA were associated with patients’ clinicopathological characteristics. 284 DEGs were primarily enriched in immune-associated activities, among which CXCL12 was the most significant gene sharing the leading nodes in PPI network and being closely related with patients’ survival. Single gene analysis and immunohistochemistry revealed that CXCL12 was down-regulated in BLCA samples and significantly related with the clinicopathological characteristics of patients. Further analysis suggested that CXCL12 was involved in the immune-associated activities probably through its close cross-talk with TICs.ConclusionsCXCL12 down-regulation could be a potential biomarker to predict the unbalanced immune status of TIME of BLCA, which might provide an extra insight for the immunotherapy of BLCA.</p