Deciphering Ascorbic Acid Regulatory Pathways in Ripening Tomato Fruit Using a Weighted Gene Correlation Network Analysis Approach

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.

Criterion of Quantum Entanglement and the Covariance Correlation Tensor in the Theory of Quantum Network

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.

Separability of Pure States and Mixed States of the Quantum Network of Two Nodes

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 .

Distinct gut microbiomes in Thai patients with colorectal polyps

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.

Cross-sectional network analysis of plasma proteins/metabolites correlated with pathogenesis and therapeutic response in acute promyelocytic leukemia

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.

Novel insight into the formation and inhibition mechanism of dipeptidyl peptidase-Ⅳ inhibitory peptides from fermented mandarin fish(Chouguiyu)

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.

Characteristics of Atmospheric Fine Particulate Matter(PM2.5)Induced Differentially Expressed Proteins Determined by Proteomics and Bioinformatics Analyses

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.

End-to-End Joint Multi-Object Detection and Tracking for Intelligent Transportation Systems

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.

Bioinformatics Analysis Revealed Potential Tumor Suppressors (KLF4/CGN), Oncogenes (SHH/LIF) and Biomarkers of Asian Stomach Adenocarcinoma

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.

Co-seismic changes of well water level and volume strain meter in capital area and its vicinity,due to the Nov.14,2001 Ms8.1 Kunlun Mountain earthquake,China

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.

Correspondence Between Bell Bases and Oriented Links in Knot Theory

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.

Combinatorial analysis of transcription and metabolism reveals the regulatory network associated with antioxidant substances in waxy corn

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.

Expression Profile and Function Analysis of Long Non-coding RNAs in the Infection of Coxsackievirus B3

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.

Multicellular biomarkers of drug resistance as promis-ing targets for glioma precision medicine and predic-tors of patient survival

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.

Textual-geographical-social aware point-of-interest recommendation

The rapid development of location-based social networks（LBSNs） has provided an unprecedented opportunity for better location-based services through point-of-interest（POI） recommendation. POI recommendation is personalized, location-aware, and context depended. However, extreme sparsity of user-POI matrix creates a severe challenge. In this paper we propose a textual-geographical-social aware probabilistic matrix factorization method for POI recommendation. Our model is textual-geographical-social aware probabilistic matrix factorization called TGS-PMF, it exploits textual information, geographical information, social information, and incorporates these factors effectively. First, we exploit an aggregated latent Dirichlet allocation（LDA） model to learn the interest topics of users and infer the interest POIs by mining textual information associated with POIs and generate interest relevance score. Second, we propose a kernel estimation method with an adaptive bandwidth to model the geographical correlations and generate geographical relevance score. Third, we build social relevance through the power-law distribution of user social relations to generate social relevance score. Then, our exploit probabilistic matrix factorization model（PMF） to integrate the interest, geographical, social relevance scores for POI recommendation. Finally, we implement experiments on a real LBSN check-in dataset. Experimental results show that TGS-PMF achieves significantly superior recommendation quality compared to other state-of-the-art POI recommendation techniques.

Efficient aluminum removal and microorganism inhibition in ready-to-eat jellyfish by slightly acidic electrolyzed water

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.