A large number of putative risk genes for autism spectrum disorder(ASD)have been reported.The functions of most of these susceptibility genes in developing brains remain unknown,and causal relationships between their ...A large number of putative risk genes for autism spectrum disorder(ASD)have been reported.The functions of most of these susceptibility genes in developing brains remain unknown,and causal relationships between their variation and autism traits have not been established.The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes(hcASDs).The results showed that three gene features–gene size,mRNA abundance,and guanine-cytosine content–affect the genome-wide co-expression profiles of hcASDs.To circumvent the interference of these features in gene co-expression analysis,we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes.This method is referred to as"matched-gene co-expression analysis"(MGCA).With MGCA,we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction.The results of analysis of two recently-reported ASD candidate genes,CDH11 and CDH9,suggested the involvement of CDH11,but not CDH9,in ASD.Consistent with this prediction,behavioral studies showed that Cdh11-null mice,but not Cdh9-null mice,have multiple autism-like behavioral alterations.This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.展开更多
Fatty acids （FAs） play crucial rules in signal transduction and plant development, however, the regulation of FA metabolism is still poorly understood. To study the relevant regulatory network, fifty-eight FA biosyn...Fatty acids （FAs） play crucial rules in signal transduction and plant development, however, the regulation of FA metabolism is still poorly understood. To study the relevant regulatory network, fifty-eight FA biosynthesis genes including de novo synthases, desaturases and elongases were selected as ＂guide genes＂ to construct the co-expression network. Calculation of the correlation between all Arabidopsis thaliana （L.） genes with each guide gene by Arabidopsis co-expression dating mining tools （ACT） identifies 797 candidate FA-correlated genes. Gene ontology （GO） analysis of these co-expressed genes showed they are tightly correlated to photosynthesis and carbohydrate metabolism, and function in many processes. Interestingly, 63 transcription factors （TFs） were identified as candidate FA biosynthesis regulators and 8 TF families are enriched. Two TF genes, CRC and AP1, both correlating with 8 FA guide genes, were further characterized. Analyses of the ap1 and crc mutant showed the altered total FA composition of mature seeds. The contents of palmitoleic acid, stearic acid, arachidic acid and eicosadienoic acid are decreased, whereas that of oleic acid is increased in apl and crc seeds, which is consistent with the qRT-PCR analysis revealing the suppressed expression of the corresponding guide genes. In addition, yeast one-hybrid analysis and electrophoretic mobility shift assay （EMSA） revealed that CRC can bind to the promoter regions of KCS7 and KCS15, indicating that CRC may directly regulate FA biosynthesis.展开更多
Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate th...Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate the changes in microRNAs(miRNAs),long intergenic non-coding RNAs(lincRNAs)and mRNAs muscle expression before and after food intake.Results:We measured the miRNA,lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition(AL-T0)and 24 gilts fed ad libitum during either 5 h.(AL-T1,N=12)or 7 h.(AL-T2,N=12)prior to slaughter.The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced,whereas lincRNA and mRNA expression data were already available.In terms of mean and variance,the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs.Food intake induced the differential expression of 149(AL-T0/AL-T1)and 435(AL-T0/AL-T2)mRNAs,6(AL-T0/AL-T1)and 28(AL-T0/AL-T2)miRNAs and none lincRNAs,while the number of differentially dispersed genes was much lower.Among the set of differentially expressed miRNAs,we identified ssc-miR-148a-3p,ssc-miR-22-3p and ssc-miR-1,which play key roles in the regulation of glucose and lipid metabolism.Besides,co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding.One case example was represented by seven miRNAs(ssc-miR-148a-3p,ssc-miR-151-3p,ssc-miR-30a-3p,ssc-miR-30e-3p,ssc-miR-421-5p,ssc-miR-493-5p and ssc-miR-503)which putatively interact with the PDK4 mRNA,one of the master regulators of glucose utilization and fatty acid oxidation.Conclusions:As a whole,our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.展开更多
Six new lanthanide complexes:[Ln(3,4-DEOBA)3(4,4'-DM-2,2'-bipy)]2·2C_(2)H_(5)OH,[Ln=Dy(1),Eu(2),Tb(3),Sm(4),Ho(5),Gd(6);3,4-DEOBA-=3,4-diethoxybenzoate,4,4'-DM-2,2'-bipy=4,4'-dimethyl-2,2'...Six new lanthanide complexes:[Ln(3,4-DEOBA)3(4,4'-DM-2,2'-bipy)]2·2C_(2)H_(5)OH,[Ln=Dy(1),Eu(2),Tb(3),Sm(4),Ho(5),Gd(6);3,4-DEOBA-=3,4-diethoxybenzoate,4,4'-DM-2,2'-bipy=4,4'-dimethyl-2,2'-bipyridine]were successfully synthesized by the volatilization of the solution at room temperature.The crystal structures of six complexes were determined by single-crystal X-ray diffraction technology.The results showed that the complexes all have a binuclear structure,and the structures contain free ethanol molecules.Moreover,the coordination number of the central metal of each structural unit is eight.Adjacent structural units interact with each other through hydrogen bonds and further expand to form 1D chain-like and 2D planar structures.After conducting a systematic study on the luminescence properties of complexes 1-4,their emission and excitation spectra were obtained.Experimental results indicated that the fluorescence lifetimes of complexes 2 and 3 were 0.807 and 0.845 ms,respectively.The emission spectral data of complexes 1-4 were imported into the CIE chromaticity coordinate system,and their corre sponding luminescent regions cover the yellow light,red light,green light,and orange-red light bands,respectively.Within the temperature range of 299.15-1300 K,the thermal decomposition processes of the six complexes were comprehensively analyzed by using TG-DSC/FTIR/MS technology.The hypothesis of the gradual loss of ligand groups during the decomposition process was verified by detecting the escaped gas,3D infrared spectroscopy,and ion fragment information detected by mass spectrometry.The specific decomposition path is as follows:firstly,free ethanol molecules and neutral ligands are removed,and finally,acidic ligands are released;the final product is the corresponding metal oxide.CCDC:2430420,1;2430422,2;2430419,3;2430424,4;2430421,5;2430423,6.展开更多
Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macro...Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.展开更多
BACKGROUND Gastric cancer(GC)is one of the most common malignant tumors of the digestive system worldwide,the prognosis of patients with advanced GC remains poor.AIM To evaluate the combined expression characteristics...BACKGROUND Gastric cancer(GC)is one of the most common malignant tumors of the digestive system worldwide,the prognosis of patients with advanced GC remains poor.AIM To evaluate the combined expression characteristics of cancer stem cell markers CD24 and CD133 in GC pathological tissues,and to explore their association with patients’clinicopathological parameters and postoperative survival outcomes.METHODS A total of 304 GC patients who underwent surgical treatment in our hospital from January 2018 to January 2020 were retrospectively included.Immunohistochemistry was used to detect the protein expression of CD24 and CD133 in tumor tissues,adjacent tissues,and normal gastric mucosa tissues.Based on staining intensity and the proportion of positive cells,expression levels were classified into low and high expression,while clinicopathological parameters were recorded.χ2 test was used to evaluate the correlation between expression and categorical variables,Spearman rank correlation analysis was performed to assess the correlation between the expression intensities of the two markers,and multivariate regression models were applied to identify independent risk factors influencing co-expression.Kaplan-Meier survival curves and Log-rank test were used to compare survival differences among groups with different expression patterns.RESULTS Among the 304 patients,155 cases(50.99%)were CD24 positive,including 91 low-expression and 64 highexpression;133 cases(43.75%)were CD133 positive,including 81 low-expression and 52 high-expression.There were 74 cases(24.34%)with double positivity and 81 cases(26.64%)with double negativity.Compared with tumor tissues,the positive rates of CD24 and CD133 in normal gastric tissues and adjacent tissues were significantly lower(P<0.05).Univariate analysis showed that co-expression of CD24 and CD133 in GC tissues was significantly correlated with tumor size,Lauren classification,T stage,N stage,and vascular invasion(P<0.05),but not with patient age,gender,tumor site,World Health Organization histological classification,or M stage(P>0.05).Further multivariate regression analysis suggested that tumor size,T stage,N stage,and vascular invasion were independent risk factors promoting CD24 and CD133 double positivity.Spearman rank correlation analysis indicated a moderate positive correlation between their expression intensities(r=0.420,P<0.001).During follow-up,29 of 304 patients were lost(loss rate 9.54%);146 deaths occurred.According to expression combination,there were 89 cases of CD24 single positivity(39 deaths),68 cases of CD133 single positivity(31 deaths),81 cases of double negativity(25 deaths),and 66 cases of double positivity(51 deaths).Log-rank test showed significant differences in overall survival among the four groups(χ2=20.89,P<0.001),with CD24+/CD133+group showing the worst prognosis.CONCLUSION CD24 and CD133 exhibit high positive detection rates in GC tissues,and their co-positivity is closely associated with tumor stage progression and significantly indicates unfavorable survival outcomes.The co-expression of CD24/CD133 may reflect higher aggressiveness and metastatic potential of GC,serving as a potential prognostic marker and a direction for targeted therapeutic strategies.However,as this is a single-center retrospective study with limitations such as patient loss to follow-up and sample size,further prospective,multicenter,and mechanistic studies are required to validate its clinical applicability and biological role.展开更多
Background:Receptor-interacting protein kinases(RIPKs)regulate cell death,inflammation,and immune responses,yet their roles in cancer are not fully understood.This study investigates the expression,genomic alterations...Background:Receptor-interacting protein kinases(RIPKs)regulate cell death,inflammation,and immune responses,yet their roles in cancer are not fully understood.This study investigates the expression,genomic alterations,and functional implications of RIPK family members across various cancers.Methods:We collected multi-omics data from The Cancer Genome Atlas and other public databases,including gene expression,copy number variation(CNV),mutation,methylation,tumor mutation burden(TMB),and microsatellite instability(MSI).Differential expression and survival analyses were performed using DESeq2 and Cox proportional hazards models.CNV and mutation data were analyzed with GISTIC2 and Mutect2,and methylation data with the ChAMP package.Correlations with TMB and MSI were assessed using Pearson coefficients,and gene set enrichment analysis was conducted with the MSigDB Hallmark gene sets.Results:RIPK family members show significant differential expression in various cancers,with RIPK1 and RIPK4 frequently altered.Survival analysis reveals heterogeneous impacts on overall survival.CNV and mutation analyses identify high alteration frequencies for RIPK2 and RIPK7,affecting gene expression.RIPK1 and RIPK7 are hypermethylated in several cancers,inversely correlating with RIPK3 expression.RIPK1,RIPK2,RIPK5,RIPK6,and RIPK7 correlate positively with TMB,while RIPK3 shows negative correlations in some cancers.MSI analysis indicates associations with DNA mismatch repair.G ene set enrichment analysis highlights immune-related pathway enrichment for RIPK1,RIPK2,RIPK3,and RIPK6,and cell proliferation and DNA repair pathways for RIPK4 and RIPK5.RIPK family members showed heterogeneous alterations across cancers:for example,RIPK7 was mutated in up to~15%of u terine c orpus e ndometrial c arcinoma and l ung s quamous c ell c arcinoma cases,and RIPK1 and RIPK7 exhibited frequent promoter hypermethylation in multiple tumor types.Several genes displayed context-dependent associations with overall survival and with TMB/MSI.Conclusion:This pan-cancer analysis of the RIPK family reveals their diverse roles and potential as biomarkers and therapeutic targets.The findings emphasize the importance of RIPK genes in tumorigenesis and suggest context-dependent functions across cancer types.Further studies are needed to explore their mechanisms in cancer development and clinical applications.展开更多
The sulfation and decomposition process has proven effective in selectively extracting lithium from lepidolite.It is essential to clarify the thermochemical behavior and kinetic parameters of decomposition reactions.A...The sulfation and decomposition process has proven effective in selectively extracting lithium from lepidolite.It is essential to clarify the thermochemical behavior and kinetic parameters of decomposition reactions.Accordingly,comprehensive kinetic study by employing thermalgravimetric analysis at various heating rates was presented in this paper.Two main weight loss regions were observed during heating.The initial region corresponded to the dehydration of crystal water,whereas the subsequent region with overlapping peaks involved complex decomposition reactions.The overlapping peaks were separated into two individual reaction peaks and the activation energy of each peak was calculated using isoconversional kinetics methods.The activation energy of peak 1 exhibited a continual increase as the reaction conversion progressed,while that of peak 2 steadily decreased.The optimal kinetic models,identified as belonging to the random nucleation and subsequent growth category,provided valuable insights into the mechanism of the decomposition reactions.Furthermore,the adjustment factor was introduced to reconstruct the kinetic mechanism models,and the reconstructed models described the kinetic mechanism model more accurately for the decomposition reactions.This study enhanced the understanding of the thermochemical behavior and kinetic parameters of the lepidolite sulfation product decomposition reactions,further providing theoretical basis for promoting the selective extraction of lithium.展开更多
Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is s...Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).展开更多
AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression lev...AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.展开更多
AIM:To present an overview of the research on global glaucoma treatment in the last decade in terms of publication year,journals,countries/regions,organizations,references,and keywords,to investigate the current resea...AIM:To present an overview of the research on global glaucoma treatment in the last decade in terms of publication year,journals,countries/regions,organizations,references,and keywords,to investigate the current research international trends and hot topics in this area.METHODS:Bibliometric analysis was conducted on 9128 articles in the Web of Science Core Collection(WoSCC;Clarivate)database.Quantitative and qualitative analysis was employed using VOSviewer(v1.6.18),Pajek(v1.0.0.0),and CiteSpace(v6.1.R2)software.RESULTS:The 9128 papers relating to glaucoma treatment were published from April 2013 to April 2023,of which 7482 articles(82%)were original research articles and 1464(18%)were review articles.The United States(2867)and Johns Hopkins University(166)were the most productive country and institution,respectively,but the University College London had the highest h-index(54).The Journal of Glaucoma was the most productive and Ophthalmology had the highest h-index compared with other journals.The Keywords of interest included treatment surgery,cyclophotocoagulation,minimally invasive glaucoma surgery(MIGS),trabeculectomy,baerveldt,epidemiology,medication adherence,nanoparticle,optical coherence tomography(OCT),gene therapy,and artificial intelligence(AI).Glaucoma surgery appeared as a current research hotspot through the analysis of keywords.CONCLUSION:This study provides insights into the research trends and potential research hotspots in the treatment of glaucoma.This will help researchers to evaluate research policies and to promote international cooperation.展开更多
This paper investigates the reliability of internal marine combustion engines using an integrated approach that combines Fault Tree Analysis(FTA)and Bayesian Networks(BN).FTA provides a structured,top-down method for ...This paper investigates the reliability of internal marine combustion engines using an integrated approach that combines Fault Tree Analysis(FTA)and Bayesian Networks(BN).FTA provides a structured,top-down method for identifying critical failure modes and their root causes,while BN introduces flexibility in probabilistic reasoning,enabling dynamic updates based on new evidence.This dual methodology overcomes the limitations of static FTA models,offering a comprehensive framework for system reliability analysis.Critical failures,including External Leakage(ELU),Failure to Start(FTS),and Overheating(OHE),were identified as key risks.By incorporating redundancy into high-risk components such as pumps and batteries,the likelihood of these failures was significantly reduced.For instance,redundant pumps reduced the probability of ELU by 31.88%,while additional batteries decreased the occurrence of FTS by 36.45%.The results underscore the practical benefits of combining FTA and BN for enhancing system reliability,particularly in maritime applications where operational safety and efficiency are critical.This research provides valuable insights for maintenance planning and highlights the importance of redundancy in critical systems,especially as the industry transitions toward more autonomous vessels.展开更多
Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair perip...Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021.展开更多
To ensure the safe transportation of radioactive materials,numerous countries have established specific standards.For the transfer of fissile materials,it is imperative that the material within the packaging remains i...To ensure the safe transportation of radioactive materials,numerous countries have established specific standards.For the transfer of fissile materials,it is imperative that the material within the packaging remains in a subcritical state during routine,normal,and accidental transport conditions.In the event of an accident,the rods within the storage tank may become rearranged,introducing uncertainty that must be accounted for to ensure that criticality analysis results are conservative.Historically,this uncertainty was addressed overly conservatively due to limited research on non-uniform arrangement scenarios,which proved unsuitable for criticality safety analysis of spent fuel packages.This paper introduced three distinct methods to non-uniformly rearrange fuel rods—Uniform Arrangement by Blocks,Layer-by-Layer Determination,and Birdcage Deformation—and meticulously evaluates the influences of rod rearrangement on the effective multiplication factor of neutrons,k eff,utilizing the Monte Carlo method.Ultimately,this study presents a holistic method capable of encompassing the entire spectrum of potential effects stemming from the rearrangement of fuel rods during rods mispositioning accident.By augmenting the safety margin,this approach proves to be adeptly suited for the criticality safety analysis of nuclear fuel transport containers.展开更多
Industrial waste salts are commonly used to make value-added snow-melting agents to ensure traffic safety in northern China during winter and spring after snowfall.However,heavy metals in industrial waste salts may po...Industrial waste salts are commonly used to make value-added snow-melting agents to ensure traffic safety in northern China during winter and spring after snowfall.However,heavy metals in industrial waste salts may pose certain environmental risks.Snow-melting agents and snow samples were collected and analyzed from highways,arterial roads,footbridges,and other locations in Beijing after the snowstorm in December 2023.It was found that the main component of snow-melting agents was sodium chloride with high concentrations of Cu,Mn,and Zn,which are not regulated in the current policies,despite the recent promotion of environmentally friendly snow-melting agents.The Pb,Zn and Cr contents of some snow samples exceeded the limitation value of surface water quality standards,potentially affecting the soil and water environment near roadsides,although the snow-melting agents comply with relevant standards,which indicates the policy gap in the management of recycled industrial salts.We reviewed and analyzed the relevant standards for snow-melting agents and industrial waste salts proposed nationally and internationally over the past 30 years.Through comparative analysis,we proposed relevant policy recommendations to the existing quality standards of snow-melting agents and the management regulations of industrial waste salts,and the formulation of corresponding usage strategies,aimed at reducing the potential environmental release of heavy metals from the use of snow-melting agents,thereby promoting more sustainable green urban development and environmentally sound waste management.展开更多
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict t...Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.展开更多
Background:Epidemiological studies have confirmed that longer exposure to insecticides like cypermethrin(CYP)significantly increases the risk of male reproductive toxicity.Crocus sativus L.has been recognized due to i...Background:Epidemiological studies have confirmed that longer exposure to insecticides like cypermethrin(CYP)significantly increases the risk of male reproductive toxicity.Crocus sativus L.has been recognized due to its therapeutic properties,but its exact role and molecular mechanisms in treatment of reproductive dysfunction remain unclear.Methods:During this study,36 rats were randomly divided into six groups(n=6):control,CYP-induced(60 mg/kg),standard(leuprolide 3 mg/kg)and three treatment groups receiving aqueous,ethanolic,and oil extracts(50 mg/kg or 20 mL/kg)for post-toxicity induction.Results:The finding represented that exposure of CYP significantly increased oxidative stress,disrupted testicular architecture,and markedly reduced testosterone levels(P<0.05).Importantly,Crocus sativus L.treatment alleviated these changes by increasing the expression of Nrf2(nuclear factor erythroid 2-related factor 2),restoring the activity of antioxidant enzymes,and enhancing testicular histomorphology.Surprisingly,molecular docking established a high binding affinity of Crocus sativus L.phytoconstituents such as gallic acid,cinnamic acid and quercetin to the Nrf2-Keap1 complex.It is worth noting that,Crocus sativus L.exhibited a high level of protection against reproductive toxicity caused by CYP in male rats,which was mediated by the activation of Nrf2 pathway,reduction of oxidative damage,and favorable ADMET characteristics.Conclusion:Notably,this research provides a more valid,safe,and effective method of developing new drugs for reproductive disorders,however,further investigation is needed to support the research findings and implement it in clinical practice.展开更多
Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughp...Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle.展开更多
Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different c...Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.展开更多
Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in ...Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties.Here,a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis(WGCNA)and other in silico prediction tools to identify modules(denoting cluster of genes with related expression pattern)of co-expressed genes,modular genes which are conserved differentially expressed genes(DEGs)across independent RNA-Seq studies,and the molecular pathways of the conserved modular DEGs.WGCNA identified 16 modules of co-expressed genes.Twenty-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq studies.Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways and 15 Gene Ontology(GO)terms,including the substrate-specific transmembrane transporter and the small molecule metabolic process.Further,the well-studied transcription factors(OsWOX11 and OsbHLH120),protein kinase(OsCDPK20 and OsMPK17),and miRNAs(OSA-MIR397A and OSA-MIR397B)were predicted to target some of the identified conserved modular DEGs.Out of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive genes.Findings from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice.展开更多
基金This work was supported by the National Natural Science Foundation of China(31871501 and ISF-32061143016)the Hussman Foundation(HIAS15006)the Simons Foundation(296143).
文摘A large number of putative risk genes for autism spectrum disorder(ASD)have been reported.The functions of most of these susceptibility genes in developing brains remain unknown,and causal relationships between their variation and autism traits have not been established.The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes(hcASDs).The results showed that three gene features–gene size,mRNA abundance,and guanine-cytosine content–affect the genome-wide co-expression profiles of hcASDs.To circumvent the interference of these features in gene co-expression analysis,we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes.This method is referred to as"matched-gene co-expression analysis"(MGCA).With MGCA,we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction.The results of analysis of two recently-reported ASD candidate genes,CDH11 and CDH9,suggested the involvement of CDH11,but not CDH9,in ASD.Consistent with this prediction,behavioral studies showed that Cdh11-null mice,but not Cdh9-null mice,have multiple autism-like behavioral alterations.This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.
基金supported by the National High-tech R&D Program (863 Program, 2007AA02Z128)
文摘Fatty acids （FAs） play crucial rules in signal transduction and plant development, however, the regulation of FA metabolism is still poorly understood. To study the relevant regulatory network, fifty-eight FA biosynthesis genes including de novo synthases, desaturases and elongases were selected as ＂guide genes＂ to construct the co-expression network. Calculation of the correlation between all Arabidopsis thaliana （L.） genes with each guide gene by Arabidopsis co-expression dating mining tools （ACT） identifies 797 candidate FA-correlated genes. Gene ontology （GO） analysis of these co-expressed genes showed they are tightly correlated to photosynthesis and carbohydrate metabolism, and function in many processes. Interestingly, 63 transcription factors （TFs） were identified as candidate FA biosynthesis regulators and 8 TF families are enriched. Two TF genes, CRC and AP1, both correlating with 8 FA guide genes, were further characterized. Analyses of the ap1 and crc mutant showed the altered total FA composition of mature seeds. The contents of palmitoleic acid, stearic acid, arachidic acid and eicosadienoic acid are decreased, whereas that of oleic acid is increased in apl and crc seeds, which is consistent with the qRT-PCR analysis revealing the suppressed expression of the corresponding guide genes. In addition, yeast one-hybrid analysis and electrophoretic mobility shift assay （EMSA） revealed that CRC can bind to the promoter regions of KCS7 and KCS15, indicating that CRC may directly regulate FA biosynthesis.
基金The research presented in this publication was funded by grants AGL2013–48742-C2–1-R and AGL2013–48742-C2–2-R awarded by the Spanish Ministry of Economy and Competitivity.We also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016–2019(SEV-2015-0533)grant awarded to the Centre for Research in Agricultural Genomics(CRAG).E.Mármol-Sánchez was funded with a PhD fellowship FPU15/01733 awarded by the Spanish Ministry of Education and Culture(MECD).Y.Ramayo-Caldas is financially supported by the European Union H2020 Research and Innovation programme under Marie Skłodowska-Curie grant(P-Sphere)agreement N°6655919.T.F.Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education,Ministry of Education of the Federal Government of Brazil.Thanks also to the CERCA Programme of the Generalitat de Catalunya.
文摘Background:The role of non-coding RNAs in the porcine muscle metabolism is poorly understood,with few studies investigating their expression patterns in response to nutrient supply.Therefore,we aimed to investigate the changes in microRNAs(miRNAs),long intergenic non-coding RNAs(lincRNAs)and mRNAs muscle expression before and after food intake.Results:We measured the miRNA,lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition(AL-T0)and 24 gilts fed ad libitum during either 5 h.(AL-T1,N=12)or 7 h.(AL-T2,N=12)prior to slaughter.The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced,whereas lincRNA and mRNA expression data were already available.In terms of mean and variance,the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs.Food intake induced the differential expression of 149(AL-T0/AL-T1)and 435(AL-T0/AL-T2)mRNAs,6(AL-T0/AL-T1)and 28(AL-T0/AL-T2)miRNAs and none lincRNAs,while the number of differentially dispersed genes was much lower.Among the set of differentially expressed miRNAs,we identified ssc-miR-148a-3p,ssc-miR-22-3p and ssc-miR-1,which play key roles in the regulation of glucose and lipid metabolism.Besides,co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding.One case example was represented by seven miRNAs(ssc-miR-148a-3p,ssc-miR-151-3p,ssc-miR-30a-3p,ssc-miR-30e-3p,ssc-miR-421-5p,ssc-miR-493-5p and ssc-miR-503)which putatively interact with the PDK4 mRNA,one of the master regulators of glucose utilization and fatty acid oxidation.Conclusions:As a whole,our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.
文摘Six new lanthanide complexes:[Ln(3,4-DEOBA)3(4,4'-DM-2,2'-bipy)]2·2C_(2)H_(5)OH,[Ln=Dy(1),Eu(2),Tb(3),Sm(4),Ho(5),Gd(6);3,4-DEOBA-=3,4-diethoxybenzoate,4,4'-DM-2,2'-bipy=4,4'-dimethyl-2,2'-bipyridine]were successfully synthesized by the volatilization of the solution at room temperature.The crystal structures of six complexes were determined by single-crystal X-ray diffraction technology.The results showed that the complexes all have a binuclear structure,and the structures contain free ethanol molecules.Moreover,the coordination number of the central metal of each structural unit is eight.Adjacent structural units interact with each other through hydrogen bonds and further expand to form 1D chain-like and 2D planar structures.After conducting a systematic study on the luminescence properties of complexes 1-4,their emission and excitation spectra were obtained.Experimental results indicated that the fluorescence lifetimes of complexes 2 and 3 were 0.807 and 0.845 ms,respectively.The emission spectral data of complexes 1-4 were imported into the CIE chromaticity coordinate system,and their corre sponding luminescent regions cover the yellow light,red light,green light,and orange-red light bands,respectively.Within the temperature range of 299.15-1300 K,the thermal decomposition processes of the six complexes were comprehensively analyzed by using TG-DSC/FTIR/MS technology.The hypothesis of the gradual loss of ligand groups during the decomposition process was verified by detecting the escaped gas,3D infrared spectroscopy,and ion fragment information detected by mass spectrometry.The specific decomposition path is as follows:firstly,free ethanol molecules and neutral ligands are removed,and finally,acidic ligands are released;the final product is the corresponding metal oxide.CCDC:2430420,1;2430422,2;2430419,3;2430424,4;2430421,5;2430423,6.
基金supported by Qingdao Key Medical and Health Discipline ProjectThe Intramural Research Program of the Affiliated Hospital of Qingdao University,No. 4910Qingdao West Coast New Area Science and Technology Project,No. 2020-55 (all to SW)。
文摘Border-associated macrophages are located at the interface between the brain and the periphery, including the perivascular spaces, choroid plexus, and meninges. Until recently, the functions of border-associated macrophages have been poorly understood and largely overlooked. However, a recent study reported that border-associated macrophages participate in stroke-induced inflammation, although many details and the underlying mechanisms remain unclear. In this study, we performed a comprehensive single-cell analysis of mouse border-associated macrophages using sequencing data obtained from the Gene Expression Omnibus(GEO) database(GSE174574 and GSE225948). Differentially expressed genes were identified, and enrichment analysis was performed to identify the transcription profile of border-associated macrophages. CellChat analysis was conducted to determine the cell communication network of border-associated macrophages. Transcription factors were predicted using the ‘pySCENIC' tool. We found that, in response to hypoxia, borderassociated macrophages underwent dynamic transcriptional changes and participated in the regulation of inflammatory-related pathways. Notably, the tumor necrosis factor pathway was activated by border-associated macrophages following ischemic stroke. The pySCENIC analysis indicated that the activity of signal transducer and activator of transcription 3(Stat3) was obviously upregulated in stroke, suggesting that Stat3 inhibition may be a promising strategy for treating border-associated macrophages-induced neuroinflammation. Finally, we constructed an animal model to investigate the effects of border-associated macrophages depletion following a stroke. Treatment with liposomes containing clodronate significantly reduced infarct volume in the animals and improved neurological scores compared with untreated animals. Taken together, our results demonstrate comprehensive changes in border-associated macrophages following a stroke, providing a theoretical basis for targeting border-associated macrophages-induced neuroinflammation in stroke treatment.
基金National Natural Science Foundation of China,No.82003223and China Postdoctoral Science Foundation,No.2020M671398.
文摘BACKGROUND Gastric cancer(GC)is one of the most common malignant tumors of the digestive system worldwide,the prognosis of patients with advanced GC remains poor.AIM To evaluate the combined expression characteristics of cancer stem cell markers CD24 and CD133 in GC pathological tissues,and to explore their association with patients’clinicopathological parameters and postoperative survival outcomes.METHODS A total of 304 GC patients who underwent surgical treatment in our hospital from January 2018 to January 2020 were retrospectively included.Immunohistochemistry was used to detect the protein expression of CD24 and CD133 in tumor tissues,adjacent tissues,and normal gastric mucosa tissues.Based on staining intensity and the proportion of positive cells,expression levels were classified into low and high expression,while clinicopathological parameters were recorded.χ2 test was used to evaluate the correlation between expression and categorical variables,Spearman rank correlation analysis was performed to assess the correlation between the expression intensities of the two markers,and multivariate regression models were applied to identify independent risk factors influencing co-expression.Kaplan-Meier survival curves and Log-rank test were used to compare survival differences among groups with different expression patterns.RESULTS Among the 304 patients,155 cases(50.99%)were CD24 positive,including 91 low-expression and 64 highexpression;133 cases(43.75%)were CD133 positive,including 81 low-expression and 52 high-expression.There were 74 cases(24.34%)with double positivity and 81 cases(26.64%)with double negativity.Compared with tumor tissues,the positive rates of CD24 and CD133 in normal gastric tissues and adjacent tissues were significantly lower(P<0.05).Univariate analysis showed that co-expression of CD24 and CD133 in GC tissues was significantly correlated with tumor size,Lauren classification,T stage,N stage,and vascular invasion(P<0.05),but not with patient age,gender,tumor site,World Health Organization histological classification,or M stage(P>0.05).Further multivariate regression analysis suggested that tumor size,T stage,N stage,and vascular invasion were independent risk factors promoting CD24 and CD133 double positivity.Spearman rank correlation analysis indicated a moderate positive correlation between their expression intensities(r=0.420,P<0.001).During follow-up,29 of 304 patients were lost(loss rate 9.54%);146 deaths occurred.According to expression combination,there were 89 cases of CD24 single positivity(39 deaths),68 cases of CD133 single positivity(31 deaths),81 cases of double negativity(25 deaths),and 66 cases of double positivity(51 deaths).Log-rank test showed significant differences in overall survival among the four groups(χ2=20.89,P<0.001),with CD24+/CD133+group showing the worst prognosis.CONCLUSION CD24 and CD133 exhibit high positive detection rates in GC tissues,and their co-positivity is closely associated with tumor stage progression and significantly indicates unfavorable survival outcomes.The co-expression of CD24/CD133 may reflect higher aggressiveness and metastatic potential of GC,serving as a potential prognostic marker and a direction for targeted therapeutic strategies.However,as this is a single-center retrospective study with limitations such as patient loss to follow-up and sample size,further prospective,multicenter,and mechanistic studies are required to validate its clinical applicability and biological role.
基金supported by grants from the Tianjin Health Technology Project(Grant no.2022QN106).
文摘Background:Receptor-interacting protein kinases(RIPKs)regulate cell death,inflammation,and immune responses,yet their roles in cancer are not fully understood.This study investigates the expression,genomic alterations,and functional implications of RIPK family members across various cancers.Methods:We collected multi-omics data from The Cancer Genome Atlas and other public databases,including gene expression,copy number variation(CNV),mutation,methylation,tumor mutation burden(TMB),and microsatellite instability(MSI).Differential expression and survival analyses were performed using DESeq2 and Cox proportional hazards models.CNV and mutation data were analyzed with GISTIC2 and Mutect2,and methylation data with the ChAMP package.Correlations with TMB and MSI were assessed using Pearson coefficients,and gene set enrichment analysis was conducted with the MSigDB Hallmark gene sets.Results:RIPK family members show significant differential expression in various cancers,with RIPK1 and RIPK4 frequently altered.Survival analysis reveals heterogeneous impacts on overall survival.CNV and mutation analyses identify high alteration frequencies for RIPK2 and RIPK7,affecting gene expression.RIPK1 and RIPK7 are hypermethylated in several cancers,inversely correlating with RIPK3 expression.RIPK1,RIPK2,RIPK5,RIPK6,and RIPK7 correlate positively with TMB,while RIPK3 shows negative correlations in some cancers.MSI analysis indicates associations with DNA mismatch repair.G ene set enrichment analysis highlights immune-related pathway enrichment for RIPK1,RIPK2,RIPK3,and RIPK6,and cell proliferation and DNA repair pathways for RIPK4 and RIPK5.RIPK family members showed heterogeneous alterations across cancers:for example,RIPK7 was mutated in up to~15%of u terine c orpus e ndometrial c arcinoma and l ung s quamous c ell c arcinoma cases,and RIPK1 and RIPK7 exhibited frequent promoter hypermethylation in multiple tumor types.Several genes displayed context-dependent associations with overall survival and with TMB/MSI.Conclusion:This pan-cancer analysis of the RIPK family reveals their diverse roles and potential as biomarkers and therapeutic targets.The findings emphasize the importance of RIPK genes in tumorigenesis and suggest context-dependent functions across cancer types.Further studies are needed to explore their mechanisms in cancer development and clinical applications.
基金financially supported by the National Natural Science Foundation of China(Nos.52034002 and U2202254)the Fundamental Research Funds for the Central Universities,China(No.FRF-TT-19-001)。
文摘The sulfation and decomposition process has proven effective in selectively extracting lithium from lepidolite.It is essential to clarify the thermochemical behavior and kinetic parameters of decomposition reactions.Accordingly,comprehensive kinetic study by employing thermalgravimetric analysis at various heating rates was presented in this paper.Two main weight loss regions were observed during heating.The initial region corresponded to the dehydration of crystal water,whereas the subsequent region with overlapping peaks involved complex decomposition reactions.The overlapping peaks were separated into two individual reaction peaks and the activation energy of each peak was calculated using isoconversional kinetics methods.The activation energy of peak 1 exhibited a continual increase as the reaction conversion progressed,while that of peak 2 steadily decreased.The optimal kinetic models,identified as belonging to the random nucleation and subsequent growth category,provided valuable insights into the mechanism of the decomposition reactions.Furthermore,the adjustment factor was introduced to reconstruct the kinetic mechanism models,and the reconstructed models described the kinetic mechanism model more accurately for the decomposition reactions.This study enhanced the understanding of the thermochemical behavior and kinetic parameters of the lepidolite sulfation product decomposition reactions,further providing theoretical basis for promoting the selective extraction of lithium.
基金supported by the Notional Natural Science Foundation of China,No.81960417 (to JX)Guangxi Key Research and Development Program,No.GuiKeA B20159027 (to JX)the Natural Science Foundation of Guangxi Zhuang Autonomous Region,No.2022GXNSFBA035545 (to YG)。
文摘Immune changes and inflammatory responses have been identified as central events in the pathological process of spinal co rd injury.They can greatly affect nerve regeneration and functional recovery.However,there is still limited understanding of the peripheral immune inflammato ry response in spinal cord inju ry.In this study.we obtained microRNA expression profiles from the peripheral blood of patients with spinal co rd injury using high-throughput sequencing.We also obtained the mRNA expression profile of spinal cord injury patients from the Gene Expression Omnibus(GEO)database(GSE151371).We identified 54 differentially expressed microRNAs and 1656 diffe rentially expressed genes using bioinformatics approaches.Functional enrichment analysis revealed that various common immune and inflammation-related signaling pathways,such as neutrophil extracellular trap formation pathway,T cell receptor signaling pathway,and nuclear factor-κB signal pathway,we re abnormally activated or inhibited in spinal cord inju ry patient samples.We applied an integrated strategy that combines weighted gene co-expression network analysis,LASSO logistic regression,and SVM-RFE algorithm and identified three biomarke rs associated with spinal cord injury:ANO10,BST1,and ZFP36L2.We verified the expression levels and diagnostic perfo rmance of these three genes in the original training dataset and clinical samples through the receiver operating characteristic curve.Quantitative polymerase chain reaction results showed that ANO20 and BST1 mRNA levels were increased and ZFP36L2 mRNA was decreased in the peripheral blood of spinal cord injury patients.We also constructed a small RNA-mRNA interaction network using Cytoscape.Additionally,we evaluated the proportion of 22 types of immune cells in the peripheral blood of spinal co rd injury patients using the CIBERSORT tool.The proportions of naive B cells,plasma cells,monocytes,and neutrophils were increased while the proportions of memory B cells,CD8^(+)T cells,resting natural killer cells,resting dendritic cells,and eosinophils were markedly decreased in spinal cord injury patients increased compared with healthy subjects,and ANO10,BST1 and ZFP26L2we re closely related to the proportion of certain immune cell types.The findings from this study provide new directions for the development of treatment strategies related to immune inflammation in spinal co rd inju ry and suggest that ANO10,BST2,and ZFP36L2 are potential biomarkers for spinal cord injury.The study was registe red in the Chinese Clinical Trial Registry(registration No.ChiCTR2200066985,December 12,2022).
基金Supported by the National Natural Science Foundation of China(No.81271019No.61463046)Gansu Province Science Foundation for Youths(No.145RJYA282)
文摘AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma.
基金Suppotred by Tianjin Key Medical Discipline Construction Project(No.TJYXZDXK-3-004A-2).
文摘AIM:To present an overview of the research on global glaucoma treatment in the last decade in terms of publication year,journals,countries/regions,organizations,references,and keywords,to investigate the current research international trends and hot topics in this area.METHODS:Bibliometric analysis was conducted on 9128 articles in the Web of Science Core Collection(WoSCC;Clarivate)database.Quantitative and qualitative analysis was employed using VOSviewer(v1.6.18),Pajek(v1.0.0.0),and CiteSpace(v6.1.R2)software.RESULTS:The 9128 papers relating to glaucoma treatment were published from April 2013 to April 2023,of which 7482 articles(82%)were original research articles and 1464(18%)were review articles.The United States(2867)and Johns Hopkins University(166)were the most productive country and institution,respectively,but the University College London had the highest h-index(54).The Journal of Glaucoma was the most productive and Ophthalmology had the highest h-index compared with other journals.The Keywords of interest included treatment surgery,cyclophotocoagulation,minimally invasive glaucoma surgery(MIGS),trabeculectomy,baerveldt,epidemiology,medication adherence,nanoparticle,optical coherence tomography(OCT),gene therapy,and artificial intelligence(AI).Glaucoma surgery appeared as a current research hotspot through the analysis of keywords.CONCLUSION:This study provides insights into the research trends and potential research hotspots in the treatment of glaucoma.This will help researchers to evaluate research policies and to promote international cooperation.
基金supported by Istanbul Technical University(Project No.45698)supported through the“Young Researchers’Career Development Project-training of doctoral students”of the Croatian Science Foundation.
文摘This paper investigates the reliability of internal marine combustion engines using an integrated approach that combines Fault Tree Analysis(FTA)and Bayesian Networks(BN).FTA provides a structured,top-down method for identifying critical failure modes and their root causes,while BN introduces flexibility in probabilistic reasoning,enabling dynamic updates based on new evidence.This dual methodology overcomes the limitations of static FTA models,offering a comprehensive framework for system reliability analysis.Critical failures,including External Leakage(ELU),Failure to Start(FTS),and Overheating(OHE),were identified as key risks.By incorporating redundancy into high-risk components such as pumps and batteries,the likelihood of these failures was significantly reduced.For instance,redundant pumps reduced the probability of ELU by 31.88%,while additional batteries decreased the occurrence of FTS by 36.45%.The results underscore the practical benefits of combining FTA and BN for enhancing system reliability,particularly in maritime applications where operational safety and efficiency are critical.This research provides valuable insights for maintenance planning and highlights the importance of redundancy in critical systems,especially as the industry transitions toward more autonomous vessels.
基金supported by the National Major Project of Research and Development of China,No.2017YFA0104701(to BY)the National Natural Science Foundation of China,No.32000725(to QQC)+1 种基金the Natural Science Foundation of Jiangsu Province of China,No.BK20200973(to QQC)the Jiangsu Provincial University Innovation Training Key Project of China,No.202010304021Z(to ML)。
文摘Peripheral nerve injury repair requires a certain degree of cooperation between axon regeneration and Wallerian degeneration.Therefore,investigating how axon regeneration and degeneration work together to repair peripheral nerve injury may uncover the molecular mechanisms and signal cascades underlying peripheral nerve repair and provide potential strategies for improving the low axon regeneration capacity of the central nervous system.In this study,we applied weighted gene co-expression network analysis to identify differentially expressed genes in proximal and distal sciatic nerve segments from rats with sciatic nerve injury.We identified 31 and 15 co-expression modules from the proximal and distal sciatic nerve segments,respectively.Functional enrichment analysis revealed that the differentially expressed genes in proximal modules promoted regeneration,while the differentially expressed genes in distal modules promoted neurodegeneration.Next,we constructed hub gene networks for selected modules and identified a key hub gene,Kif22,which was up-regulated in both nerve segments.In vitro experiments confirmed that Kif22 knockdown inhibited proliferation and migration of Schwann cells by modulating the activity of the extracellular signal-regulated kinase signaling pathway.Collectively,our findings provide a comparative framework of gene modules that are co-expressed in injured proximal and distal sciatic nerve segments,and identify Kif22 as a potential therapeutic target for promoting peripheral nerve injury repair via Schwann cell proliferation and migration.All animal experiments were approved by the Institutional Animal Ethics Committee of Nantong University,China(approval No.S20210322-008)on March 22,2021.
文摘To ensure the safe transportation of radioactive materials,numerous countries have established specific standards.For the transfer of fissile materials,it is imperative that the material within the packaging remains in a subcritical state during routine,normal,and accidental transport conditions.In the event of an accident,the rods within the storage tank may become rearranged,introducing uncertainty that must be accounted for to ensure that criticality analysis results are conservative.Historically,this uncertainty was addressed overly conservatively due to limited research on non-uniform arrangement scenarios,which proved unsuitable for criticality safety analysis of spent fuel packages.This paper introduced three distinct methods to non-uniformly rearrange fuel rods—Uniform Arrangement by Blocks,Layer-by-Layer Determination,and Birdcage Deformation—and meticulously evaluates the influences of rod rearrangement on the effective multiplication factor of neutrons,k eff,utilizing the Monte Carlo method.Ultimately,this study presents a holistic method capable of encompassing the entire spectrum of potential effects stemming from the rearrangement of fuel rods during rods mispositioning accident.By augmenting the safety margin,this approach proves to be adeptly suited for the criticality safety analysis of nuclear fuel transport containers.
基金supported by the National Natural Science Foundation of China(No.22176200)the Industrial Innovation Entrepreneurial Team Project of Ordos 2021.
文摘Industrial waste salts are commonly used to make value-added snow-melting agents to ensure traffic safety in northern China during winter and spring after snowfall.However,heavy metals in industrial waste salts may pose certain environmental risks.Snow-melting agents and snow samples were collected and analyzed from highways,arterial roads,footbridges,and other locations in Beijing after the snowstorm in December 2023.It was found that the main component of snow-melting agents was sodium chloride with high concentrations of Cu,Mn,and Zn,which are not regulated in the current policies,despite the recent promotion of environmentally friendly snow-melting agents.The Pb,Zn and Cr contents of some snow samples exceeded the limitation value of surface water quality standards,potentially affecting the soil and water environment near roadsides,although the snow-melting agents comply with relevant standards,which indicates the policy gap in the management of recycled industrial salts.We reviewed and analyzed the relevant standards for snow-melting agents and industrial waste salts proposed nationally and internationally over the past 30 years.Through comparative analysis,we proposed relevant policy recommendations to the existing quality standards of snow-melting agents and the management regulations of industrial waste salts,and the formulation of corresponding usage strategies,aimed at reducing the potential environmental release of heavy metals from the use of snow-melting agents,thereby promoting more sustainable green urban development and environmentally sound waste management.
文摘Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer.
文摘Background:Epidemiological studies have confirmed that longer exposure to insecticides like cypermethrin(CYP)significantly increases the risk of male reproductive toxicity.Crocus sativus L.has been recognized due to its therapeutic properties,but its exact role and molecular mechanisms in treatment of reproductive dysfunction remain unclear.Methods:During this study,36 rats were randomly divided into six groups(n=6):control,CYP-induced(60 mg/kg),standard(leuprolide 3 mg/kg)and three treatment groups receiving aqueous,ethanolic,and oil extracts(50 mg/kg or 20 mL/kg)for post-toxicity induction.Results:The finding represented that exposure of CYP significantly increased oxidative stress,disrupted testicular architecture,and markedly reduced testosterone levels(P<0.05).Importantly,Crocus sativus L.treatment alleviated these changes by increasing the expression of Nrf2(nuclear factor erythroid 2-related factor 2),restoring the activity of antioxidant enzymes,and enhancing testicular histomorphology.Surprisingly,molecular docking established a high binding affinity of Crocus sativus L.phytoconstituents such as gallic acid,cinnamic acid and quercetin to the Nrf2-Keap1 complex.It is worth noting that,Crocus sativus L.exhibited a high level of protection against reproductive toxicity caused by CYP in male rats,which was mediated by the activation of Nrf2 pathway,reduction of oxidative damage,and favorable ADMET characteristics.Conclusion:Notably,this research provides a more valid,safe,and effective method of developing new drugs for reproductive disorders,however,further investigation is needed to support the research findings and implement it in clinical practice.
基金Fund supported by the National Natural Science Foundation of China(81460598 and 81660644)the Natural Science Foundation of Jiangsu Province(BK20170267)Guangxi Special Fund for the First-Class Discipline Construction Project(05019038).
文摘Objective Alzheimer's disease(AD)is the most common cause of dementia.The pathophysiology of the disease mostly remains unearthed,thereby challenging drug development for AD.This study aims to screen high throughput gene expression data using weighted co-expression network analysis(WGCNA)to explore the potential therapeutic targets.Methods The dataset of GSE36980 was obtained from the Gene Expression Omnibus(GEO)database.Normalization,quality control,filtration,and soft-threshold calculation were carried out before clustering the co-expressed genes into different modules.Furthermore,the correlation coefiidents between the modules and clinical traits were computed to identify the key modules.Gene ontology and pathway enrichment analyses were performed on the key module genes.The STRING database was used to construct the protein-protein interaction(PPI)networks,which were further analyzed by Cytoscape app(MCODE).Finally,validation of hub genes was conducted by external GEO datasets of GSE 1297 and GSE 28146.Results Co-expressed genes were clustered into 27 modules,among which 6 modules were identified as the key module relating to AD occurrence.These key modules are primarily involved in chemical synaptic transmission(G0:0007268),the tricarboxylic acid(TCA)cycle and respiratory electron transport(R-HSA-1428517).WDR47,OXCT1,C3orfl4,ATP6V1A,SLC25A14,NAPB were found as the hub genes and their expression were validated by external datasets.Conclusions Through modules co-expression network analyses and PPI network analyses,we identified the hub genes of AD,including WDR47,0XCT1,C3orfl4i ATP6V1A,SLC25A14 and NAPB.Among them,three hub genes(ATP6V1A,SLC25A14,OXCT1)might contribute to AD pathogenesis through pathway of TCA cycle.
基金supported by the National Natural Science Foundation of China under Grants No.61720106004 and No.61872405the Key R&D Project of Sichuan Province,China under Grants No.20ZDYF2772 and No.2020YFS0243.
文摘Cardiomyopathies represent the most common clinical and genetic heterogeneous group of diseases that affect the heart function.Though progress has been made to elucidate the process,molecular mechanisms of different classes of cardiomyopathies remain elusive.This paper aims to describe the similarities and differences in molecular features of dilated cardiomyopathy(DCM)and ischemic cardiomyopathy(ICM).We firstly detected the co-expressed modules using the weighted gene co-expression network analysis(WGCNA).Significant modules associated with DCM/ICM were identified by the Pearson correlation coefficient(PCC)between the modules and the phenotype of DCM/ICM.The differentially expressed genes in the modules were selected to perform functional enrichment.The potential transcription factors(TFs)prediction was conducted for transcription regulation of hub genes.Apoptosis and cardiac conduction were perturbed in DCM and ICM,respectively.TFs demonstrated that the biomarkers and the transcription regulations in DCM and ICM were different,which helps make more accurate discrimination between them at molecular levels.In conclusion,comprehensive analyses of the molecular features may advance our understanding of DCM and ICM causes and progression.Thus,this understanding may promote the development of innovative diagnoses and treatments.
基金financially supported by the Chinese Academy of Agricultural Sciences-Agricultural Science and Technology Innovation Programthe Shenzhen Science and Technology Program (Grant No. JCYJ20200109150650397)
文摘Zinc(Zn)malnutrition is a major public health issue.Genetic biofortification of Zn in rice grain can alleviate global Zn malnutrition.Therefore,elucidating the genetic mechanisms regulating Zn deprivation response in rice is essential to identify elite genes useful for breeding high grain Zn rice varieties.Here,a meta-analysis of previous RNA-Seq studies involving Zn deficient conditions was conducted using the weighted gene co-expression network analysis(WGCNA)and other in silico prediction tools to identify modules(denoting cluster of genes with related expression pattern)of co-expressed genes,modular genes which are conserved differentially expressed genes(DEGs)across independent RNA-Seq studies,and the molecular pathways of the conserved modular DEGs.WGCNA identified 16 modules of co-expressed genes.Twenty-eight and five modular DEGs were conserved in leaf and crown,and root tissues across two independent RNA-Seq studies.Functional enrichment analysis showed that 24 of the 28 conserved modular DEGs from leaf and crown tissues significantly up-regulated 2 Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways and 15 Gene Ontology(GO)terms,including the substrate-specific transmembrane transporter and the small molecule metabolic process.Further,the well-studied transcription factors(OsWOX11 and OsbHLH120),protein kinase(OsCDPK20 and OsMPK17),and miRNAs(OSA-MIR397A and OSA-MIR397B)were predicted to target some of the identified conserved modular DEGs.Out of the 24 conserved and up-regulated modular DEGs,19 were yet to be experimentally validated as Zn deficiency responsive genes.Findings from this study provide a comprehensive insight on the molecular mechanisms of Zn deficiency response and may facilitate gene and pathway prioritization for improving Zn use efficiency and Zn biofortification in rice.
