Detecting coupling pattern between elements in a complex system is a basic task in data-driven analysis. The trajectory for each specific element is a cooperative result of its intrinsic dynamic, its couplings with ot...Detecting coupling pattern between elements in a complex system is a basic task in data-driven analysis. The trajectory for each specific element is a cooperative result of its intrinsic dynamic, its couplings with other elements, and the environment. It is subsequently composed of many components, only some of which take part in the couplings. In this paper we present a framework to detect the component correlation pattern. Firstly, the interested trajectories are decomposed into components by using decomposing methods such as the Fourier expansion and the Wavelet transformation. Secondly, the cross-correlations between the components are calculated, resulting into a component cross-correlation matrix(network).Finally, the dominant structure in the network is identified to characterize the coupling pattern in the system. Several deterministic dynamical models turn out to be characterized with rich structures such as the clustering of the components. The pattern of correlation between respiratory(RESP) and ECG signals is composed of five sub-clusters that are mainly formed by the components in ECG signal. Interestingly, only 7 components from RESP(scattered in four sub-clusters) take part in the realization of coupling between the two signals.展开更多
Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important informatio...Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid （AsA）, which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato （Solanum lycopersicum L.） fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty- four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.展开更多
This article discusses the covariance correlation tensor (CCT) in quantum network theory for four Bell bases in detail. Furthermore, it gives the expression of the density operator in terms of CCT for a quantum networ...This article discusses the covariance correlation tensor (CCT) in quantum network theory for four Bell bases in detail. Furthermore, it gives the expression of the density operator in terms of CCT for a quantum network of three nodes, thus gives the criterion of entanglement for this case, i.e. the conditions of complete separability and partial separability for a given quantum state of three bodies. Finally it discusses the general case for the quantum network of nodes.展开更多
Background:One-third of veterans returning from the 1990–1991 Gulf War reported a myriad of symptoms including cognitive dysfunction,skin rashes,musculoskeletal discomfort,and fatigue.This symptom cluster is now refe...Background:One-third of veterans returning from the 1990–1991 Gulf War reported a myriad of symptoms including cognitive dysfunction,skin rashes,musculoskeletal discomfort,and fatigue.This symptom cluster is now referred to as Gulf War Illness(GWI).As the underlying mechanisms of GWI have yet to be fully elucidated,diagnosis and treatment are based on symptomatic presentation.One confounding factor tied to the illness is the high presence of post-traumatic stress disorder(PTSD).Previous research efforts have demonstrated that both GWI and PTSD are associated with immunological dysfunction.As such,this research endeavor aimed to provide insight into the complex relationship between GWI symptoms,cytokine presence,and immune cell populations to pinpoint the impact of PTSD on these measures in GWI.Methods:Symptom measures were gathered through the Multidimensional fatigue inventory(MFI)and 36-item short form health survey(SF-36)scales and biological measures were obtained through cytokine&cytometry analysis.Subgrouping was conducted using Davidson Trauma Scale scores and the Structured Clinical Interview for Diagnostic and statistical manual of mental disorders(DSM)-5,into GWI with high probability of PTSD symptoms(GWIH)and GWI with low probability of PTSD symptoms(GWIL).Data was analyzed using analysis of variance(ANOVA)statistical analysis along with correlation graph analysis.We mapped correlations between immune cells and cytokine signaling measures,hormones and GWI symptom measures to identify patterns in regulation between the GWIH,GWIL,and healthy control groups.Results:GWI with comorbid PTSD symptoms resulted in poorer health outcomes compared with both healthy control(HC)and the GWIL subgroup.Significant differences were found in basophil levels of GWI compared with HC at peak exercise regardless of PTSD symptom comorbidity(ANOVA F=4.7,P=0.01)indicating its potential usage as a biomarker for general GWI from control.While the unique identification of GWI with PTSD symptoms was less clear,the GWIL subgroup was found to be delineated from both GWIH and HC on measures of IL-15 across an exercise challenge(ANOVA F>3.75,P<0.03).Additional differences in natural killer(NK)cell numbers and function highlight IL-15 as a potential biomarker of GWI in the absence of PTSD symptoms.Conclusions:We conclude that disentangling GWI and PTSD by defining trauma-based subgroups may aid in the identification of unique GWI biosignatures that can help to improve diagnosis and target treatment of GWI more effectively.展开更多
Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in ...Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in apple plants.The present study exhibits a detailed overview of the phylogeny and structure of 29 defensins(MdDEF)in apple.Expression analysis revealed that MdDEF genes were spatiotemporally diverse across apple tissues.Five MdDEF genes were found to be significantly up-regulated following a challenge with Cytospora mali.The transgenic overexpression of five defensin genes in apple calli enhanced resistance to C.mali.Among them,MdDEF30 was strongly induced and conferred the highest resistance level in vivo.Meanwhile,antifungal activity assays in vitro demonstrated that a recombinant protein produced from MdDEF30could inhibit the growth of C.mali.Notably,MdDEF30 promoted the accumulation of reactive oxygen species(ROS)and activated defense-related genes such as PR4,PR10,CML13,and MPK3.Co-expression regulatory network analysis showed that MdWRKY75 may regulate the expression of MdDEF30.Further yeast onehybrid(Y1H),luciferase,and chromatin Immunoprecipitation quantitative polymerase chain reaction(ChIPqPCR)assays verified that MdWRKY75 could directly bind to the promoter of MdDEF30.Importantly,pathogen inoculation assays confirmed that MdWRKY75 positively regulates resistance by transcriptionally activating MdDEF30.Overall,these results demonstrated that MdDEF30 promotes resistance to C.mali in apple plants and that MdWRKY75 regulates MdDEF30 expression during the induction of resistance,thereby clarifying biochemical mechanisms of resistance to C.mali in apple trees.展开更多
BACKGROUND Voltage-gated sodium channels(VGSCs,or Navs)are highly expressed in various tumors and play a critical role in tumor metastasis and invasion.AIM To identify Nav1.6-associated cancer genes through bioinforma...BACKGROUND Voltage-gated sodium channels(VGSCs,or Navs)are highly expressed in various tumors and play a critical role in tumor metastasis and invasion.AIM To identify Nav1.6-associated cancer genes through bioinformatics analysis and experimental validation,with the goal of determining the role of Nav1.6 in colorectal cancer(CRC)metastasis.METHODS The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)data were analyzed using weighted correlation network analysis(WGCNA)and Venn analysis to identify Nav1.6-associated genes in CRC.siRNA,real-time PCR,and western blotting were employed to validate the Nav1.6-associated cancer genes and signaling pathways identified in CRC.Cell counting kit-8 and Transwell migration assays were used to assess the proliferation and migration of CRC cells.RESULTS The analysis of TCGA and GEO datasets,along with WGCNA,identified 575 differentially expressed genes associated with SCN8A(Nav1.6)in CRC,which were particularly enriched in MAPK signaling pathways.Tissue microarray analysis of surgical samples revealed elevated Nav1.6 levels in CRC tissues,which were predominantly in the cytoplasm and nucleus rather than in the membrane.Cytoplasmic Nav1.6 expression increased with T stage increases,consistent with the TCGA findings.SCN8A knockdown in colon tumor cells significantly reduced cell proliferation and invasion and downregulated key proteins in the RAF-MAPK pathway.CONCLUSION These findings suggest that Nav1.6 promotes CRC cell proliferation and invasion which is related to the MAPK signaling pathway.展开更多
This article discusses the separability of the pure states and mixed states of the quantum network of two nodes by means of the criterion of no entanglement in terms of the covariance correlation tensor in quantum net...This article discusses the separability of the pure states and mixed states of the quantum network of two nodes by means of the criterion of no entanglement in terms of the covariance correlation tensor in quantum network theory, i.e. for a composite system consisting of two nodes. The covariance correlation tensor is equal to zero for all possible and .展开更多
BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut mic...BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut microbiome.There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis.AIM To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA patients.METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA.Analytical techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway analysis.RESULTS Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(S.gallolyticus),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA patients.Mediterraneibacter gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA groups.Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);S.gallolyticus was a major contributor.Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,whereas TA patients exhibited co-occurrence of CRC-associated bacteria.Furthermore,the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients.CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development,providing insights concerning the roles of microbial species,functional pathways,and microbial interactions in colorectal carcinogenesis.展开更多
Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the cont...Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the contents of malondialdehyde(MDA),soluble sugar(SS),and proline(Pro)and the transcriptome of oat leaves under 0,12,24,36,and 48 h of drought treatment,revealing that the content of MDA increased with drought duration,whereas the contents of SS and Pro reached their maximum at 24 h of treatment,with a total between 0 h of treatment and the other groups.Differentially expressed genes(DEGs)presented significant enrichment in the phenylpropanoid biosynthetic pathway,flavonoid biosynthetic pathway,galactose metabolism,and glutathione metabolism.The biological changes caused by drought stress resulted in the obvious activation of antioxidase genes.The sugar and flavonoid biosynthetic genes were studied based on the detailed temporal patterns of expression of four major metabolic pathways.Additionally,14 candidate hub genes,such as the genes that encoded galactinol synthase,serine/threonineprotein kinase,and 1-aminocyclopropane-1-carboxylate oxidase,were identified by virtue of weighted gene co-expression network analysis.Differential transcription factor(TF)analysis showed that NAM,ATAF1/2,CUC2(NAC),Heat Shock(HS),Trihelix,TEOSINTE BRANCHED1/CYCLOIDEA/PCF(TCP),and other 11 TF families were closely related to drought stress.These findings help us understand the early responses of oat to drought stress from new perspectives and can guide further research.展开更多
The roles of lnc RNAs in the infection of enteroviruses have been barely demonstrated. In this study, we used coxsackievirus B3(CVB3), a typical enterovirus, as a model to investigate the expression profiles and funct...The roles of lnc RNAs in the infection of enteroviruses have been barely demonstrated. In this study, we used coxsackievirus B3(CVB3), a typical enterovirus, as a model to investigate the expression profiles and functional roles of lnc RNAs in enterovirus infection. We profiled lnc RNAs and m RNA expression in CVB3-infected He La cells by lnc RNA-m RNA integrated microarrays. As a result, 700 differentially expressed lnc RNAs(431 up-regulated and 269 down-regulated) and665 differentially expressed m RNAs(299 up-regulated and 366 down-regulated) were identified in CVB3 infection. Then we performed lnc RNA-m RNA integrated pathway analysis to identify potential functional impacts of the differentially expressed m RNAs, in which lnc RNA-m RNA correlation network was built. According to lnc RNA-m RNA correlation, we found that XLOC-001188, an lnc RNA down-regulated in CVB3 infection, was negatively correlated with NFAT5 m RNA,an anti-CVB3 gene reported previously. This interaction was supported by q PCR detection following si RNA-mediated knockdown of XLOC-001188, which showed an increase of NFAT5 m RNA and a reduction of CVB3 genomic RNA. In addition, we observed that four most significantly altered lnc RNAs, SNHG11, RP11-145 F16.2, RP11-1023 L17.1 and RP11-1021 N1.2 share several common correlated genes critical for CVB3 infection, such as BRE and IRF2 BP1. In all, our studies reveal the alteration of lnc RNA expression in CVB3 infection and its potential influence on CVB3 replication,providing useful information for future studies of enterovirus infection.展开更多
Environment perception is one of the most critical technology of intelligent transportation systems(ITS).Motion interaction between multiple vehicles in ITS makes it important to perform multi-object tracking(MOT).How...Environment perception is one of the most critical technology of intelligent transportation systems(ITS).Motion interaction between multiple vehicles in ITS makes it important to perform multi-object tracking(MOT).However,most existing MOT algorithms follow the tracking-by-detection framework,which separates detection and tracking into two independent segments and limit the global efciency.Recently,a few algorithms have combined feature extraction into one network;however,the tracking portion continues to rely on data association,and requires com‑plex post-processing for life cycle management.Those methods do not combine detection and tracking efciently.This paper presents a novel network to realize joint multi-object detection and tracking in an end-to-end manner for ITS,named as global correlation network(GCNet).Unlike most object detection methods,GCNet introduces a global correlation layer for regression of absolute size and coordinates of bounding boxes,instead of ofsetting predictions.The pipeline of detection and tracking in GCNet is conceptually simple,and does not require compli‑cated tracking strategies such as non-maximum suppression and data association.GCNet was evaluated on a multivehicle tracking dataset,UA-DETRAC,demonstrating promising performance compared to state-of-the-art detectors and trackers.展开更多
The treatment of PML/RARA+acute promyelocytic leukemia(APL)with all-trans-retinoic acid and arsenic trioxide(ATRA/ATO)has been recognized as a model for translational medicine research.Though an altered microenvironme...The treatment of PML/RARA+acute promyelocytic leukemia(APL)with all-trans-retinoic acid and arsenic trioxide(ATRA/ATO)has been recognized as a model for translational medicine research.Though an altered microenvironment is a general cancer hallmark,how APL blasts shape their plasma composition is poorly understood.Here,we reported a cross-sectional correlation network to interpret multilayered datasets on clinical parameters,proteomes,and metabolomes of paired plasma samples from patients with APL before or after ATRA/ATO induction therapy.Our study revealed the two prominent features of the APL plasma,suggesting a possible involvement of APL blasts in modulating plasma composition.One was characterized by altered secretory protein and metabolite profiles correlating with heightened proliferation and energy consumption in APL blasts,and the other featured APL plasma-enriched proteins or enzymes catalyzing plasma-altered metabolites that were potential trans-regulatory targets of PML/RARA.Furthermore,results indicated heightened interferon-gamma signaling characterizing a tumor-suppressing function of the immune system at the first hematological complete remission stage,which likely resulted from therapy-induced cell death or senescence and ensuing supraphysiological levels of intracellular proteins.Overall,our work sheds new light on the pathophysiology and treatment of APL and provides an information-rich reference data cohort for the exploratory and translational study of leukemia microenvironment.展开更多
Fermented foods are a potential source to produce novel dipeptidyl peptidase-IV inhibitory peptides(D4IPs).In this study,the fermented mandarin fish(Chouguiyu)was used to screen D4IPs and their formation mechanism was...Fermented foods are a potential source to produce novel dipeptidyl peptidase-IV inhibitory peptides(D4IPs).In this study,the fermented mandarin fish(Chouguiyu)was used to screen D4IPs and their formation mechanism was studied by metagenomics and peptidomics.A total of 400 D4IPs with DPP-IV inhibition structure and high hydrophobicity were identified.The correlation network map showed that Lactococcus,Bacillus,Lysobacter,Pelagivirga,Kocuria,Escherichia,Streptococcus,and Peptostreptococcus were significantly correlated with the most D4IPs.Four stable D4IPs,including KAGARALTDAETAT,GEKVDFDDIQK,VVDADEMYLKGK,and GQKDSYVGDEAQ were respectively from the precursor proteins parvalbumin,troponin,myosin,and actin,and were mainly formed by the hydrolysis of subtilisin(EC 3.4.21.62),aspartic proteinase(EC 3.4.23.1),thermolysin(EC 3.4.24.27),oligopeptidase B(EC 3.4.21.83),and proteinase P1(EC 3.4.21.96)from Bacillus,Kocuria,Lysobacter,Lactococcus,and Peptostreptococcus.The inhibition mainly resulted from the hydrogen bond and salt bridge between D4IPs and DPP-IV enzyme.This study provides important information on the proteases and related microbial strains to directionally prepare D4IPs in Chouguiyu.展开更多
Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from She...Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from Shenzhen and Taiyuan for 24 h.To detect overall protein expression,the Q Exactive mass spectrometer was used.Gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and Perseus software were used to screen DEPs.Results Overall,67 DEPs were screened in the Shenzhen sample-treated group,of which 46 were upregulated and 21 were downregulated.In total,252 DEPs were screened in the Taiyuan sampletreated group,of which 134 were upregulated and 118 were downregulated.KEGG analysis demonstrated that DEPs were mainly enriched in ubiquitin-mediated proteolysis and HIF-1 signal pathways in Shenzhen PM2.5 samples-treated group.The GO analysis demonstrated that Shenzhen sample-induced DEPs were mainly involved in the biological process for absorption of various metal ions and cell components.The Taiyuan PM2.5-induced DEPs were mainly involved in biological processes of protein aggregation regulation and molecular function of oxidase activity.Additionally,three important DEPs,including ANXA2,DIABLO,and AIMP1,were screened.Conclusion Our findings provide a valuable basis for further evaluation of PM2.5-associated carcinogenesis.展开更多
Stomach adenocarcinoma (STAD) is the fifth most prevalent cancer and the third leading cause of cancer-related death in the world and is more common in Asia than in most Western countries. There is an urgent need to i...Stomach adenocarcinoma (STAD) is the fifth most prevalent cancer and the third leading cause of cancer-related death in the world and is more common in Asia than in most Western countries. There is an urgent need to identify potential novel oncogenes and tumor suppressor genes, and biomarkers for STAD. 6652 differentially expressed genes were identified between STAD and normal samples based on the transcriptome data analysis of the TCGA and GEO databases. 13 key modules were identified in STAD by WGCNA analysis. 293 potential STAD associated genes were identified from intersection by Venn Diagram. The 293 intersected genes were enriched in cell cortex and infection by GO and KEGG analysis. 10 hub genes were identified from PPI and Cytoscape analyses of the intersected genes. KLF4/CGN low and SHH/LIF high expression were associated with short overall survival of Asian STAD patients. Bioinformatics analysis revealed potential novel tumor suppressors (KLF4/CGN), oncogenes (SHH/LIF) and biomarkers for diagnosis, therapy and prognosis of STAD, specifically for Asian patients.展开更多
The Kunlunshan Mountain Ms8.1 earthquake, occurred in Nov.14, 2001, is the first event with magnitude more than 8 in the China earthquake monitoring history, specifically at the beginning of digital techniques in prec...The Kunlunshan Mountain Ms8.1 earthquake, occurred in Nov.14, 2001, is the first event with magnitude more than 8 in the China earthquake monitoring history, specifically at the beginning of digital techniques in precursor monitoring networks. Any investigation of recorded data on this earthquake is very important for testing the operation of the digital monitoring networks and understanding the preparation, occurrence, and adjustment of stress/strain of strong continental earthquakes. In this paper we investigated the coseismic response changes of well water level of groundwater and volume strain meter of bore hole in digital earthquake monitoring network of Capital area and its vicinity, due to the Nov.14, 2001 Ms8.1 Kunlun Mountain earthquake. The responding time, shapes or manners, amplitudes, and lasting time of well water level and strain-meters to seismic wave are studied in comparison. Then we discussed the possibility that the response changes of groundwater to strong distant earthquakes can be understood as one kind of observing evidence of stress/strain changes induced by distant earthquake.展开更多
From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we sho...From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we show that there is a one to one correspondence between four Bell bases and four oriented links of the linkage in knot theory.展开更多
Maize is an essential source of nutrition for humans and animals and is rich in various metabolites that determine its quality.Different maize varieties show significant differences in metabolite content.Two kinds of ...Maize is an essential source of nutrition for humans and animals and is rich in various metabolites that determine its quality.Different maize varieties show significant differences in metabolite content.Two kinds of waxy maize parental materials,S181 and 49B,created by the Chongqing Academy of Agricultural Sciences,are widely grown in China.S181 shows higher starch and sugar contents than 49B.This study generated metabolic profiles to assess the differences between the two varieties.A total of 674 metabolites that were significantly differentially expressed between the two varieties were identified by gas chromatography and untargeted metabolomics technology.These metabolites were associated with 21 categories,including antioxidant metabolites.Moreover,6415 differentially expressed genes(DEGs)were identified by RNA-seq.Interestingly,these DEGs comprised starch and sugar synthesis pathway genes and 72 different transcription factor families.Among these,six families that were reported to play an essential role in plant antioxidant action accounted for 39.2%of the transcription factor families.Using the Kyoto Encyclopedia of Genes and Genomes(KEGG)classification,the DEGs were mainly involved in amino acid biosynthesis,glycolysis/glucose metabolism,and the synthetic and metabolic pathways of antioxidant active substances.Furthermore,the correlation analysis of transcriptome and metabolomics identified five key transcription factors(ZmbHLH172,ZmNAC44,ZmNAC-like18,ZmS1FA2,ZmERF172),one ubiquitin ligase gene(ZmE25A)and one sucrose synthase gene(ZmSS1).They likely contribute to the quality traits of waxy corn through involvement in the metabolic regulatory network of antioxidant substances.Thus,our results provide new insights into maize quality-related antioxidant metabolite networks and have potential applications for waxy corn breeding.展开更多
Ready-to-eat jellyfish production is restricted by the high aluminum residue and unable use of thermal sterilization.In this study,the combined dealumination and sterilization by slightly acidic electrolyzed water(SAE...Ready-to-eat jellyfish production is restricted by the high aluminum residue and unable use of thermal sterilization.In this study,the combined dealumination and sterilization by slightly acidic electrolyzed water(SAEW)were used to produce ready-to-eat jellyfish.The optimal aluminum removal amount reaching 120.17 mg/kg was obtained after response surface analysis.Structure observation through optical microscope after Masson staining and scanning electron microscope showed that the microstructure of jellyfish was not destroyed after SAEW treatment.The increase of total plate count(TPC)and pH value during storage was significantly inhibited by SAEW,while the other properties did not changed significantly.Staphylococcus,especially Staphylococcus epidermidis was dominant in the ready-to-eat jellyfish and many spoilage bacteria were inhibited by SAEW.The correlation network maps showed that Pseudomonas and Shewanella contributed most to the increase of TPC and pH value in the control group,while the correlated microbial genera mainly changed to Acinetobacter,Cutibacterium,and Pseudomonas after SAEW treatment,resulting in the decrease of hardness and chewiness of ready-to-eat jellyfish during storage.The inhibited Pseudomonas contributed most to the decrease of TPC and pH value after SAEW treatment.This study provides a novel technology of dealumination and sterilization for ready-to-eat jellyfish.展开更多
Aim:This study aimed to translate a known drug-resistance mechanism of long-term CSFIR inhibition into multicellu-lar biomarkers that can serve as potential therapeutic targets as well as predictive markers for the su...Aim:This study aimed to translate a known drug-resistance mechanism of long-term CSFIR inhibition into multicellu-lar biomarkers that can serve as potential therapeutic targets as well as predictive markers for the survival of glioma patients.Methods:Using existing data from a published mouse study of drug resistance in immunotherapy for glioma,we identified mulicellular differentially expressed genes(DEGs)between drug-sensitive and drug-resistant mice and translated the DEGs in mouse genome to human homolog.We constructed correlation gene networks for drug re-sistance in mice and glioma patients and selected candidate genes via concordance analysis of human with mouse gene networks.Markers of drug resistance and an associated predictive signature for patient survival were developed using regularized Cox models with data of glioma patients from The Cancer Genome Atlas(TCGA)database.Predic-tive performance of the identified predictive signature was evaluated using an independent human dataset from the Chinese Glioma Genome Atlas(CGGA)database.Results:Fourteen genes(CCL22,ADCY2,PDK1,ZFP36,CP,CD2,PLAUR,ACAPI,COL5A1,FAM83D,PBK,FANCA,ANXA7,and TACC3)were identified as genetic biomarkers that were all associated with pathways in glioma progression and drug resistance.Five of the 14 genes(CCL22,ADCY2,PDK1,CD2,and COL5A1)were used to construct a signature that is predictive of patient survival in the proneural subtype GBM patients with an AUC under the time-dependent receiver operating characteristic(ROC)of 2-year survival equal to 0.89.This signature also shows promising predic-tive accuracy for the survival of LGG patients but not for non-proneural type GBMs.Conclusion:Our translational approach can utilize gene correlation networks from multiple types of cells in the tu-mor microenvironment of an imals.The identified biomarkers of drug resistance have good power to predict patient survival in some major subtypes of gliomas(the proneural subtype of GBM and LGG).The expression levels of the biomarkers of drug resistance may be modified for the development of personalized immunotherapies to prolong survival for a large portion of glioma patients.展开更多
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 11875042 and 11505114)the Shanghai Project for Construction of Top Disciplines (Grant No. USST-SYS-01)。
文摘Detecting coupling pattern between elements in a complex system is a basic task in data-driven analysis. The trajectory for each specific element is a cooperative result of its intrinsic dynamic, its couplings with other elements, and the environment. It is subsequently composed of many components, only some of which take part in the couplings. In this paper we present a framework to detect the component correlation pattern. Firstly, the interested trajectories are decomposed into components by using decomposing methods such as the Fourier expansion and the Wavelet transformation. Secondly, the cross-correlations between the components are calculated, resulting into a component cross-correlation matrix(network).Finally, the dominant structure in the network is identified to characterize the coupling pattern in the system. Several deterministic dynamical models turn out to be characterized with rich structures such as the clustering of the components. The pattern of correlation between respiratory(RESP) and ECG signals is composed of five sub-clusters that are mainly formed by the components in ECG signal. Interestingly, only 7 components from RESP(scattered in four sub-clusters) take part in the realization of coupling between the two signals.
基金supported by the National Natural Science Foundation of China (31271959)National Basic Research Program (2011CB100604) of China
文摘Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid （AsA）, which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato （Solanum lycopersicum L.） fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty- four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.
文摘This article discusses the covariance correlation tensor (CCT) in quantum network theory for four Bell bases in detail. Furthermore, it gives the expression of the density operator in terms of CCT for a quantum network of three nodes, thus gives the criterion of entanglement for this case, i.e. the conditions of complete separability and partial separability for a given quantum state of three bodies. Finally it discusses the general case for the quantum network of nodes.
基金suppor ted by the US Depar tment of Defense Congressionally Directed Medical Research Program (CDMRP)awards (http://cdmrp.army.mil/) W81XWH-16-1-0632 (Craddock PI),W81XWH-16-1-0552 (Craddock PI),W81XWH-18-1-0549 (Sullivan PI),W81XWH-13-2-0072 (Sullivan PI),and W81XWH-09-2-0071 (Klimas PI)a Veterans Affairs Merit Award (4987.69) to Dr.Nancy Klimas。
文摘Background:One-third of veterans returning from the 1990–1991 Gulf War reported a myriad of symptoms including cognitive dysfunction,skin rashes,musculoskeletal discomfort,and fatigue.This symptom cluster is now referred to as Gulf War Illness(GWI).As the underlying mechanisms of GWI have yet to be fully elucidated,diagnosis and treatment are based on symptomatic presentation.One confounding factor tied to the illness is the high presence of post-traumatic stress disorder(PTSD).Previous research efforts have demonstrated that both GWI and PTSD are associated with immunological dysfunction.As such,this research endeavor aimed to provide insight into the complex relationship between GWI symptoms,cytokine presence,and immune cell populations to pinpoint the impact of PTSD on these measures in GWI.Methods:Symptom measures were gathered through the Multidimensional fatigue inventory(MFI)and 36-item short form health survey(SF-36)scales and biological measures were obtained through cytokine&cytometry analysis.Subgrouping was conducted using Davidson Trauma Scale scores and the Structured Clinical Interview for Diagnostic and statistical manual of mental disorders(DSM)-5,into GWI with high probability of PTSD symptoms(GWIH)and GWI with low probability of PTSD symptoms(GWIL).Data was analyzed using analysis of variance(ANOVA)statistical analysis along with correlation graph analysis.We mapped correlations between immune cells and cytokine signaling measures,hormones and GWI symptom measures to identify patterns in regulation between the GWIH,GWIL,and healthy control groups.Results:GWI with comorbid PTSD symptoms resulted in poorer health outcomes compared with both healthy control(HC)and the GWIL subgroup.Significant differences were found in basophil levels of GWI compared with HC at peak exercise regardless of PTSD symptom comorbidity(ANOVA F=4.7,P=0.01)indicating its potential usage as a biomarker for general GWI from control.While the unique identification of GWI with PTSD symptoms was less clear,the GWIL subgroup was found to be delineated from both GWIH and HC on measures of IL-15 across an exercise challenge(ANOVA F>3.75,P<0.03).Additional differences in natural killer(NK)cell numbers and function highlight IL-15 as a potential biomarker of GWI in the absence of PTSD symptoms.Conclusions:We conclude that disentangling GWI and PTSD by defining trauma-based subgroups may aid in the identification of unique GWI biosignatures that can help to improve diagnosis and target treatment of GWI more effectively.
基金funded by the National Key R&D Program of China(2023YFD1401401)the China Agriculture Research System(CARS27)。
文摘Defensin,an essential component of plant development,is indispensable in pathogen resistance.However,the molecular function of defensins under pathological conditions of Cytospora canker has not been characterized in apple plants.The present study exhibits a detailed overview of the phylogeny and structure of 29 defensins(MdDEF)in apple.Expression analysis revealed that MdDEF genes were spatiotemporally diverse across apple tissues.Five MdDEF genes were found to be significantly up-regulated following a challenge with Cytospora mali.The transgenic overexpression of five defensin genes in apple calli enhanced resistance to C.mali.Among them,MdDEF30 was strongly induced and conferred the highest resistance level in vivo.Meanwhile,antifungal activity assays in vitro demonstrated that a recombinant protein produced from MdDEF30could inhibit the growth of C.mali.Notably,MdDEF30 promoted the accumulation of reactive oxygen species(ROS)and activated defense-related genes such as PR4,PR10,CML13,and MPK3.Co-expression regulatory network analysis showed that MdWRKY75 may regulate the expression of MdDEF30.Further yeast onehybrid(Y1H),luciferase,and chromatin Immunoprecipitation quantitative polymerase chain reaction(ChIPqPCR)assays verified that MdWRKY75 could directly bind to the promoter of MdDEF30.Importantly,pathogen inoculation assays confirmed that MdWRKY75 positively regulates resistance by transcriptionally activating MdDEF30.Overall,these results demonstrated that MdDEF30 promotes resistance to C.mali in apple plants and that MdWRKY75 regulates MdDEF30 expression during the induction of resistance,thereby clarifying biochemical mechanisms of resistance to C.mali in apple trees.
基金Supported by Science and Technology Project of Quzhou of China,No.2021Y011Beijing Science and Technology Innovation Medical Development Foundation,No.KC2021-JX-0186-81.
文摘BACKGROUND Voltage-gated sodium channels(VGSCs,or Navs)are highly expressed in various tumors and play a critical role in tumor metastasis and invasion.AIM To identify Nav1.6-associated cancer genes through bioinformatics analysis and experimental validation,with the goal of determining the role of Nav1.6 in colorectal cancer(CRC)metastasis.METHODS The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)data were analyzed using weighted correlation network analysis(WGCNA)and Venn analysis to identify Nav1.6-associated genes in CRC.siRNA,real-time PCR,and western blotting were employed to validate the Nav1.6-associated cancer genes and signaling pathways identified in CRC.Cell counting kit-8 and Transwell migration assays were used to assess the proliferation and migration of CRC cells.RESULTS The analysis of TCGA and GEO datasets,along with WGCNA,identified 575 differentially expressed genes associated with SCN8A(Nav1.6)in CRC,which were particularly enriched in MAPK signaling pathways.Tissue microarray analysis of surgical samples revealed elevated Nav1.6 levels in CRC tissues,which were predominantly in the cytoplasm and nucleus rather than in the membrane.Cytoplasmic Nav1.6 expression increased with T stage increases,consistent with the TCGA findings.SCN8A knockdown in colon tumor cells significantly reduced cell proliferation and invasion and downregulated key proteins in the RAF-MAPK pathway.CONCLUSION These findings suggest that Nav1.6 promotes CRC cell proliferation and invasion which is related to the MAPK signaling pathway.
文摘This article discusses the separability of the pure states and mixed states of the quantum network of two nodes by means of the criterion of no entanglement in terms of the covariance correlation tensor in quantum network theory, i.e. for a composite system consisting of two nodes. The covariance correlation tensor is equal to zero for all possible and .
基金Supported by Chulabhorn Royal Academy(Fundamental Fund:Fiscal year 2022 by National Science Research and Innovation Fund),No.FRB650039/0240 Project Code 165422.
文摘BACKGROUND Colorectal polyps that develop via the conventional adenoma-carcinoma sequence[e.g.,tubular adenoma(TA)]often progress to malignancy and are closely associated with changes in the composition of the gut microbiome.There is limited research concerning the microbial functions and gut microbiomes associated with colorectal polyps that arise through the serrated polyp pathway,such as hyperplastic polyps(HP).Exploration of microbiome alterations asso-ciated with HP and TA would improve the understanding of mechanisms by which specific microbes and their metabolic pathways contribute to colorectal carcinogenesis.AIM To investigate gut microbiome signatures,microbial associations,and microbial functions in HP and TA patients.METHODS Full-length 16S rRNA sequencing was used to characterize the gut microbiome in stool samples from control participants without polyps[control group(CT),n=40],patients with HP(n=52),and patients with TA(n=60).Significant differences in gut microbiome composition and functional mechanisms were identified between the CT group and patients with HP or TA.Analytical techniques in this study included differential abundance analysis,co-occurrence network analysis,and differential pathway analysis.RESULTS Colorectal cancer(CRC)-associated bacteria,including Streptococcus gallolyticus(S.gallolyticus),Bacteroides fragilis,and Clostridium symbiosum,were identified as characteristic microbial species in TA patients.Mediterraneibacter gnavus,associated with dysbiosis and gastrointestinal diseases,was significantly differentially abundant in the HP and TA groups.Functional pathway analysis revealed that HP patients exhibited enrichment in the sulfur oxidation pathway exclusively,whereas TA patients showed dominance in pathways related to secondary metabolite biosynthesis(e.g.,mevalonate);S.gallolyticus was a major contributor.Co-occurrence network and dynamic network analyses revealed co-occurrence of dysbiosis-associated bacteria in HP patients,whereas TA patients exhibited co-occurrence of CRC-associated bacteria.Furthermore,the co-occurrence of SCFA-producing bacteria was lower in TA patients than HP patients.CONCLUSION This study revealed distinct gut microbiome signatures associated with pathways of colorectal polyp development,providing insights concerning the roles of microbial species,functional pathways,and microbial interactions in colorectal carcinogenesis.
基金conducted with the funds from the Oat Whole Industry Chain Technology Innovation Teamthe National Key Research and Development Program of China(No.2018YFE0107900)+2 种基金the National Modern Agricultural Industry Technology System(No.CARS-07)the Inner Mongolia Autonomous Region Oat Engineering Laboratory Capacity Building Project(No.BR221023)the Inner Mongolia University Oat Engineering Research Center,the Oat Engineering Laboratory of Inner Mongolia Autonomous Region,and the Inner Mongolia Agricultural University Coarse-grain Industry Collaborative Innovation Center,China.
文摘Drought,as major abiotic stress,primarily restricts the production of oat(Avena sativa)around the world.With the aim of elucidating oat leaves’early response to drought stress,this study focused on examining the contents of malondialdehyde(MDA),soluble sugar(SS),and proline(Pro)and the transcriptome of oat leaves under 0,12,24,36,and 48 h of drought treatment,revealing that the content of MDA increased with drought duration,whereas the contents of SS and Pro reached their maximum at 24 h of treatment,with a total between 0 h of treatment and the other groups.Differentially expressed genes(DEGs)presented significant enrichment in the phenylpropanoid biosynthetic pathway,flavonoid biosynthetic pathway,galactose metabolism,and glutathione metabolism.The biological changes caused by drought stress resulted in the obvious activation of antioxidase genes.The sugar and flavonoid biosynthetic genes were studied based on the detailed temporal patterns of expression of four major metabolic pathways.Additionally,14 candidate hub genes,such as the genes that encoded galactinol synthase,serine/threonineprotein kinase,and 1-aminocyclopropane-1-carboxylate oxidase,were identified by virtue of weighted gene co-expression network analysis.Differential transcription factor(TF)analysis showed that NAM,ATAF1/2,CUC2(NAC),Heat Shock(HS),Trihelix,TEOSINTE BRANCHED1/CYCLOIDEA/PCF(TCP),and other 11 TF families were closely related to drought stress.These findings help us understand the early responses of oat to drought stress from new perspectives and can guide further research.
基金supported by the National Natural Science Foundation of China (81101234 to Lei Tong 81571999, 81871652 to Zhaohua Zhong+9 种基金 31470260 to Xingyi Ge 81672007 to Wenran Zhao 81772188 to Yan Wang)the Foundation of Heilongjiang Provincial Postdoctor of China (LBH-Z11076 to Lei Tong)the China Postdoctoral Science Foundation (2015M580269 to Lexun Lin)the Research Foundation of Education Bureau of Heilongjiang Province (12511176 to Lei Tong)the Hu-Xiang Youth Talents Scholar Program of Hunan Province (2017RS3017 to Xingyi Ge)Health and Family Planning Commission of Heilongjiang Province (2016-165 to Lexun Lin)the Provincial Natural Science Foundation of Hunan Province (Grant Number 2019JJ50035 to Ye Qiu)the Fundamental Research Funds for the Central Universities of China (Grant Number 531107051162 to Ye Qiu)
文摘The roles of lnc RNAs in the infection of enteroviruses have been barely demonstrated. In this study, we used coxsackievirus B3(CVB3), a typical enterovirus, as a model to investigate the expression profiles and functional roles of lnc RNAs in enterovirus infection. We profiled lnc RNAs and m RNA expression in CVB3-infected He La cells by lnc RNA-m RNA integrated microarrays. As a result, 700 differentially expressed lnc RNAs(431 up-regulated and 269 down-regulated) and665 differentially expressed m RNAs(299 up-regulated and 366 down-regulated) were identified in CVB3 infection. Then we performed lnc RNA-m RNA integrated pathway analysis to identify potential functional impacts of the differentially expressed m RNAs, in which lnc RNA-m RNA correlation network was built. According to lnc RNA-m RNA correlation, we found that XLOC-001188, an lnc RNA down-regulated in CVB3 infection, was negatively correlated with NFAT5 m RNA,an anti-CVB3 gene reported previously. This interaction was supported by q PCR detection following si RNA-mediated knockdown of XLOC-001188, which showed an increase of NFAT5 m RNA and a reduction of CVB3 genomic RNA. In addition, we observed that four most significantly altered lnc RNAs, SNHG11, RP11-145 F16.2, RP11-1023 L17.1 and RP11-1021 N1.2 share several common correlated genes critical for CVB3 infection, such as BRE and IRF2 BP1. In all, our studies reveal the alteration of lnc RNA expression in CVB3 infection and its potential influence on CVB3 replication,providing useful information for future studies of enterovirus infection.
基金Supported by National Key Research and Development Program of China(Grant No.2021YFB1600402)National Natural Science Foundation of China(Grant No.52072212)+1 种基金Dongfeng USharing Technology Co.,Ltd.,China Intelli‑gent and Connected Vehicles(Beijing)Research Institute Co.,Ltd.“Shuimu Tsinghua Scholarship”of Tsinghua University of China.
文摘Environment perception is one of the most critical technology of intelligent transportation systems(ITS).Motion interaction between multiple vehicles in ITS makes it important to perform multi-object tracking(MOT).However,most existing MOT algorithms follow the tracking-by-detection framework,which separates detection and tracking into two independent segments and limit the global efciency.Recently,a few algorithms have combined feature extraction into one network;however,the tracking portion continues to rely on data association,and requires com‑plex post-processing for life cycle management.Those methods do not combine detection and tracking efciently.This paper presents a novel network to realize joint multi-object detection and tracking in an end-to-end manner for ITS,named as global correlation network(GCNet).Unlike most object detection methods,GCNet introduces a global correlation layer for regression of absolute size and coordinates of bounding boxes,instead of ofsetting predictions.The pipeline of detection and tracking in GCNet is conceptually simple,and does not require compli‑cated tracking strategies such as non-maximum suppression and data association.GCNet was evaluated on a multivehicle tracking dataset,UA-DETRAC,demonstrating promising performance compared to state-of-the-art detectors and trackers.
基金supported by the State Key Laboratory of Medical Genomics,the Double First-Class Project(No.WF510162602)from the Ministry of Educationthe Shanghai Collaborative Innovation Program on Regenerative Medicine and Stem Cell Research(No.2019CXJQ01)+5 种基金the Overseas Expertise Introduction Project for Discipline Innovation(111 Project,No.B17029)the National Natural Science Foundation of China(Nos.82230006 and 32170663)the Shanghai Clinical Research Center for Hematological disease(No.19MC1910700)the Shanghai Shenkang Hospital Development Center(No.SHDC2020CR5002)the Shanghai Major Project for Clinical Medicine(No.2017ZZ01002)the Innovative Research Team of High-level Local Universities in Shanghai and the Yangfan Program of the Science and Technology Commission of Shanghai Municipality(No.22YF1425500)。
文摘The treatment of PML/RARA+acute promyelocytic leukemia(APL)with all-trans-retinoic acid and arsenic trioxide(ATRA/ATO)has been recognized as a model for translational medicine research.Though an altered microenvironment is a general cancer hallmark,how APL blasts shape their plasma composition is poorly understood.Here,we reported a cross-sectional correlation network to interpret multilayered datasets on clinical parameters,proteomes,and metabolomes of paired plasma samples from patients with APL before or after ATRA/ATO induction therapy.Our study revealed the two prominent features of the APL plasma,suggesting a possible involvement of APL blasts in modulating plasma composition.One was characterized by altered secretory protein and metabolite profiles correlating with heightened proliferation and energy consumption in APL blasts,and the other featured APL plasma-enriched proteins or enzymes catalyzing plasma-altered metabolites that were potential trans-regulatory targets of PML/RARA.Furthermore,results indicated heightened interferon-gamma signaling characterizing a tumor-suppressing function of the immune system at the first hematological complete remission stage,which likely resulted from therapy-induced cell death or senescence and ensuing supraphysiological levels of intracellular proteins.Overall,our work sheds new light on the pathophysiology and treatment of APL and provides an information-rich reference data cohort for the exploratory and translational study of leukemia microenvironment.
基金financially supported by the National Key R&D Program of China(2019YFD0901903)the China Agriculture Research System of MOF and MARA(CARS-46,CARS-47)+3 种基金the Guangdong Basic and Applied Basic Research Foundation(2021A1515010872)the Young S&T Talent Training Program of Guangdong Provincial Association for S&T,China(SKXRC202210)the Pearl River S&T Nova Program of Guangzhou(201906010081)the Central Public-interest Scientific Institution Basal Research Fund,CAFS(2020TD69).
文摘Fermented foods are a potential source to produce novel dipeptidyl peptidase-IV inhibitory peptides(D4IPs).In this study,the fermented mandarin fish(Chouguiyu)was used to screen D4IPs and their formation mechanism was studied by metagenomics and peptidomics.A total of 400 D4IPs with DPP-IV inhibition structure and high hydrophobicity were identified.The correlation network map showed that Lactococcus,Bacillus,Lysobacter,Pelagivirga,Kocuria,Escherichia,Streptococcus,and Peptostreptococcus were significantly correlated with the most D4IPs.Four stable D4IPs,including KAGARALTDAETAT,GEKVDFDDIQK,VVDADEMYLKGK,and GQKDSYVGDEAQ were respectively from the precursor proteins parvalbumin,troponin,myosin,and actin,and were mainly formed by the hydrolysis of subtilisin(EC 3.4.21.62),aspartic proteinase(EC 3.4.23.1),thermolysin(EC 3.4.24.27),oligopeptidase B(EC 3.4.21.83),and proteinase P1(EC 3.4.21.96)from Bacillus,Kocuria,Lysobacter,Lactococcus,and Peptostreptococcus.The inhibition mainly resulted from the hydrogen bond and salt bridge between D4IPs and DPP-IV enzyme.This study provides important information on the proteases and related microbial strains to directionally prepare D4IPs in Chouguiyu.
基金Supported by the basic research programs of Shenzhen Science and Technology Innovation Committee to XU Xin Yun[JCYJ20170413101713324]Shenzhen Key Medical Discipline Construction Fund[SZXK067].
文摘Objective To screen the differentially expressed proteins(DEPs)in human bronchial epithelial cells(HBE)treated with atmospheric fine particulate matter(PM2.5).Methods HBE cells were treated with PM2.5 samples from Shenzhen and Taiyuan for 24 h.To detect overall protein expression,the Q Exactive mass spectrometer was used.Gene ontology(GO),Kyoto encyclopedia of genes and genomes(KEGG),and Perseus software were used to screen DEPs.Results Overall,67 DEPs were screened in the Shenzhen sample-treated group,of which 46 were upregulated and 21 were downregulated.In total,252 DEPs were screened in the Taiyuan sampletreated group,of which 134 were upregulated and 118 were downregulated.KEGG analysis demonstrated that DEPs were mainly enriched in ubiquitin-mediated proteolysis and HIF-1 signal pathways in Shenzhen PM2.5 samples-treated group.The GO analysis demonstrated that Shenzhen sample-induced DEPs were mainly involved in the biological process for absorption of various metal ions and cell components.The Taiyuan PM2.5-induced DEPs were mainly involved in biological processes of protein aggregation regulation and molecular function of oxidase activity.Additionally,three important DEPs,including ANXA2,DIABLO,and AIMP1,were screened.Conclusion Our findings provide a valuable basis for further evaluation of PM2.5-associated carcinogenesis.
文摘Stomach adenocarcinoma (STAD) is the fifth most prevalent cancer and the third leading cause of cancer-related death in the world and is more common in Asia than in most Western countries. There is an urgent need to identify potential novel oncogenes and tumor suppressor genes, and biomarkers for STAD. 6652 differentially expressed genes were identified between STAD and normal samples based on the transcriptome data analysis of the TCGA and GEO databases. 13 key modules were identified in STAD by WGCNA analysis. 293 potential STAD associated genes were identified from intersection by Venn Diagram. The 293 intersected genes were enriched in cell cortex and infection by GO and KEGG analysis. 10 hub genes were identified from PPI and Cytoscape analyses of the intersected genes. KLF4/CGN low and SHH/LIF high expression were associated with short overall survival of Asian STAD patients. Bioinformatics analysis revealed potential novel tumor suppressors (KLF4/CGN), oncogenes (SHH/LIF) and biomarkers for diagnosis, therapy and prognosis of STAD, specifically for Asian patients.
基金supported by Natural Science Foundation of China(41274061 and 40374019)
文摘The Kunlunshan Mountain Ms8.1 earthquake, occurred in Nov.14, 2001, is the first event with magnitude more than 8 in the China earthquake monitoring history, specifically at the beginning of digital techniques in precursor monitoring networks. Any investigation of recorded data on this earthquake is very important for testing the operation of the digital monitoring networks and understanding the preparation, occurrence, and adjustment of stress/strain of strong continental earthquakes. In this paper we investigated the coseismic response changes of well water level of groundwater and volume strain meter of bore hole in digital earthquake monitoring network of Capital area and its vicinity, due to the Nov.14, 2001 Ms8.1 Kunlun Mountain earthquake. The responding time, shapes or manners, amplitudes, and lasting time of well water level and strain-meters to seismic wave are studied in comparison. Then we discussed the possibility that the response changes of groundwater to strong distant earthquakes can be understood as one kind of observing evidence of stress/strain changes induced by distant earthquake.
文摘From the comparison of correlation tensor in the theory of quantum network, the Alexander relation matrix in the theory of knot crystals and the identical inversion relations under the action of Pauli matrices, we show that there is a one to one correspondence between four Bell bases and four oriented links of the linkage in knot theory.
基金supported by the General Program of Natural Science Foundation of Chongqing(cstc2019jcyj msxmx0468)Chongqing Talents Program—Basic Research and Frontier Exploration(cstc2021ycjh bgzxm0152)+1 种基金Chongqing Agricultural Development Fund Project—Resource Plant New Variety Breeding and Application(NKY-2020AB015)the Fundamental Research Funds for the Central Universities(2022CDJXY-004),China.
文摘Maize is an essential source of nutrition for humans and animals and is rich in various metabolites that determine its quality.Different maize varieties show significant differences in metabolite content.Two kinds of waxy maize parental materials,S181 and 49B,created by the Chongqing Academy of Agricultural Sciences,are widely grown in China.S181 shows higher starch and sugar contents than 49B.This study generated metabolic profiles to assess the differences between the two varieties.A total of 674 metabolites that were significantly differentially expressed between the two varieties were identified by gas chromatography and untargeted metabolomics technology.These metabolites were associated with 21 categories,including antioxidant metabolites.Moreover,6415 differentially expressed genes(DEGs)were identified by RNA-seq.Interestingly,these DEGs comprised starch and sugar synthesis pathway genes and 72 different transcription factor families.Among these,six families that were reported to play an essential role in plant antioxidant action accounted for 39.2%of the transcription factor families.Using the Kyoto Encyclopedia of Genes and Genomes(KEGG)classification,the DEGs were mainly involved in amino acid biosynthesis,glycolysis/glucose metabolism,and the synthetic and metabolic pathways of antioxidant active substances.Furthermore,the correlation analysis of transcriptome and metabolomics identified five key transcription factors(ZmbHLH172,ZmNAC44,ZmNAC-like18,ZmS1FA2,ZmERF172),one ubiquitin ligase gene(ZmE25A)and one sucrose synthase gene(ZmSS1).They likely contribute to the quality traits of waxy corn through involvement in the metabolic regulatory network of antioxidant substances.Thus,our results provide new insights into maize quality-related antioxidant metabolite networks and have potential applications for waxy corn breeding.
基金financially supported by the Guangdong Provincial Special Fund For Modern Agriculture Industry Technology Innovation Teams(2023KJ151)the Youth Talent Support Programme of Guangdong Provincial Association for Science and Technology(SKXRC202210)+1 种基金the Central Public-interest Scientific Institution Basal Research Fund,CAFS(2020TD69)the Key Laboratory of Aquatic Product Processing,Ministry of Agriculture and Rural Affairs,China(NYJG201309).
文摘Ready-to-eat jellyfish production is restricted by the high aluminum residue and unable use of thermal sterilization.In this study,the combined dealumination and sterilization by slightly acidic electrolyzed water(SAEW)were used to produce ready-to-eat jellyfish.The optimal aluminum removal amount reaching 120.17 mg/kg was obtained after response surface analysis.Structure observation through optical microscope after Masson staining and scanning electron microscope showed that the microstructure of jellyfish was not destroyed after SAEW treatment.The increase of total plate count(TPC)and pH value during storage was significantly inhibited by SAEW,while the other properties did not changed significantly.Staphylococcus,especially Staphylococcus epidermidis was dominant in the ready-to-eat jellyfish and many spoilage bacteria were inhibited by SAEW.The correlation network maps showed that Pseudomonas and Shewanella contributed most to the increase of TPC and pH value in the control group,while the correlated microbial genera mainly changed to Acinetobacter,Cutibacterium,and Pseudomonas after SAEW treatment,resulting in the decrease of hardness and chewiness of ready-to-eat jellyfish during storage.The inhibited Pseudomonas contributed most to the decrease of TPC and pH value after SAEW treatment.This study provides a novel technology of dealumination and sterilization for ready-to-eat jellyfish.
基金supported by research grants P30CA016087,P50CA225450,P30AG066512 from the National Institute of Health(NIH).
文摘Aim:This study aimed to translate a known drug-resistance mechanism of long-term CSFIR inhibition into multicellu-lar biomarkers that can serve as potential therapeutic targets as well as predictive markers for the survival of glioma patients.Methods:Using existing data from a published mouse study of drug resistance in immunotherapy for glioma,we identified mulicellular differentially expressed genes(DEGs)between drug-sensitive and drug-resistant mice and translated the DEGs in mouse genome to human homolog.We constructed correlation gene networks for drug re-sistance in mice and glioma patients and selected candidate genes via concordance analysis of human with mouse gene networks.Markers of drug resistance and an associated predictive signature for patient survival were developed using regularized Cox models with data of glioma patients from The Cancer Genome Atlas(TCGA)database.Predic-tive performance of the identified predictive signature was evaluated using an independent human dataset from the Chinese Glioma Genome Atlas(CGGA)database.Results:Fourteen genes(CCL22,ADCY2,PDK1,ZFP36,CP,CD2,PLAUR,ACAPI,COL5A1,FAM83D,PBK,FANCA,ANXA7,and TACC3)were identified as genetic biomarkers that were all associated with pathways in glioma progression and drug resistance.Five of the 14 genes(CCL22,ADCY2,PDK1,CD2,and COL5A1)were used to construct a signature that is predictive of patient survival in the proneural subtype GBM patients with an AUC under the time-dependent receiver operating characteristic(ROC)of 2-year survival equal to 0.89.This signature also shows promising predic-tive accuracy for the survival of LGG patients but not for non-proneural type GBMs.Conclusion:Our translational approach can utilize gene correlation networks from multiple types of cells in the tu-mor microenvironment of an imals.The identified biomarkers of drug resistance have good power to predict patient survival in some major subtypes of gliomas(the proneural subtype of GBM and LGG).The expression levels of the biomarkers of drug resistance may be modified for the development of personalized immunotherapies to prolong survival for a large portion of glioma patients.
