Fasting increases microbiome-based colonization resistance and reduces host inflammatory responses during an enteric bacterial infection.

Reducing food intake is a common host response to infection, yet it remains unclear whether fasting is detrimental or beneficial to an infected host. Despite the gastrointestinal tract being the primary site of nutrient uptake and a common route for infection, studies have yet to examine how fasting alters the host's response to an enteric infection. To test this, mice were fasted before and during oral infection with the invasive bacterium Salmonella enterica serovar Typhimurium. Fasting dramatically interrupted infection and subsequent gastroenteritis by suppressing Salmonella's SPI-1 virulence program, preventing invasion of the gut epithelium. Virulence suppression depended on the gut microbiota, as Salmonella's invasion of the epithelium proceeded in fasting gnotobiotic mice. Despite Salmonella's restored virulence within the intestines of gnotobiotic mice, fasting downregulated pro-inflammatory signaling, greatly reducing intestinal pathology. Our study highlights how food intake controls the complex relationship between host, pathogen and gut microbiota during an enteric infection.

Performance enhancement and population structure of denitrifying phosphorus removal system over redox mediator at low temperature.

The development of denitrifying polyphosphate accumulating organisms (DPAOs) presents a strategy to carbon competition between denitrifying bacteria and phosphorus removing bacteria. However, low temperature inhibits the rate of enzyme-catalyzed and substrate diffusion during denitrifying phosphorus removal (DPR). Therefore, the present study assessed the addition of NQS (100 µmol/L) for enhancing the removal of TP and TN in DPR reactors operated at alternating anaerobic and anoxic phases and different influent phosphate concentrations. The results showed that the removal efficiency of TP and TN in NQS-DPR system at 10 °C were 99.9% and 42.0%, respectively, which were 2.1 and 2.0 times higher than that of DPR system. Adding NQS significantly alleviated the increase of pH under anoxic condition and decreased the ORP value of the reactor, which in turn enhanced the PHAs accumulation process. The determination of functional genes (nirK, narG and phoD) showed that Dechloromonas, Lentimicrobium, and Terrimonas were the dominant functional bacteria in NQS-DPR system at 10 °C with the relative abundance of 3.09%, 2.99% and 2.28%, respectively. This study can provide valuable information for the effects of the addition of the redox mediator on denitrifying phosphorus removal technology.

EspF is crucial for Citrobacter rodentium-induced tight junction disruption and lethality in immunocompromised animals.

Attaching/Effacing (A/E) bacteria include human pathogens enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and their murine equivalent Citrobacter rodentium (CR), of which EPEC and EHEC are important causative agents of foodborne diseases worldwide. While A/E pathogen infections cause mild symptoms in the immunocompetent hosts, an increasing number of studies show that they produce more severe morbidity and mortality in immunocompromised and/or immunodeficient hosts. However, the pathogenic mechanisms and crucial host-pathogen interactions during A/E pathogen infections under immunocompromised conditions remain elusive. We performed a functional screening by infecting interleukin-22 (IL-22) knockout (Il22-/-) mice with a library of randomly mutated CR strains. Our screen reveals that interruption of the espF gene, which encodes the Type III Secretion System effector EspF (E. coli secreted protein F) conserved among A/E pathogens, completely abolishes the high mortality rates in CR-infected Il22-/- mice. Chromosomal deletion of espF in CR recapitulates the avirulent phenotype without impacting colonization and proliferation of CR, and EspF complement in ΔespF strain fully restores the virulence in mice. Moreover, the expression levels of the espF gene are elevated during CR infection and CR induces disruption of the tight junction (TJ) strands in colonic epithelium in an EspF-dependent manner. Distinct from EspF, chromosomal deletion of other known TJ-damaging effector genes espG and map failed to impede CR virulence in Il22-/- mice. Hence our findings unveil a critical pathophysiological function for EspF during CR infection in the immunocompromised host and provide new insights into the complex pathogenic mechanisms of A/E pathogens.

Observation of Transient and Asymptotic Driven Structural States of Tungsten Exposed to Radiation.

Combining spatially resolved x-ray Laue diffraction with atomic-scale simulations, we observe how ion-irradiated tungsten undergoes a series of nonlinear structural transformations with increasing radiation exposure. Nanoscale defect-induced deformations accumulating above 0.02 displacements per atom (dpa) lead to highly fluctuating strains at ∼0.1 dpa, collapsing into a driven quasisteady structural state above ∼1 dpa. The driven asymptotic state is characterized by finely dispersed vacancy defects coexisting with an extended dislocation network and exhibits positive volumetric swelling, due to the creation of new crystallographic planes through self-interstitial coalescence, but negative lattice strain.

Bacterial quorum-sensing signal IQS induces host cell apoptosis by targeting POT1-p53 signalling pathway.

Pseudomonas aeruginosa, an opportunistic life-threatening human bacterial pathogen, employs quorum-sensing (QS) signal molecules to modulate virulence gene expression. 2-(2-hydroxyphenyl)-thiazole-4-carbaldehyde (IQS) is a recently identified QS signal that integrates the canonical lasR-type QS of P. aeruginosa and host phosphate stress response to fine-tune its virulence production for a successful infection. To address the role of IQS in pathogen-host interaction, we here present that IQS inhibits host cell growth and stimulates apoptosis in a dosage-dependent manner. By downregulating the telomere-protecting protein POT1 in host cells, IQS activates CHK1, CHK2, and p53 in an Ataxia telangiectasia mutated (ATM)/ATM and RAD3-related (ATR)-dependent manner and induces DNA damage response. Overexpression of POT1 in host cells presents a resistance to IQS treatment. These results suggest a pivotal role of IQS in host apoptosis, highlighting the complexity of pathogenesis mechanisms developed by P. aeruginosa during infection.

Experiential learning for children's dental anxiety: a cluster randomized trial.

BACKGROUND: Dental anxiety (DA) has an impact on the quality of dental treatment and may have long-lasting implications for children. A recent study introducing experiential learning (EL) into children's oral health promotion resulted in better oral hygiene. The purpose of the study is to evaluate whether EL can reduce children's DA. METHODS: In September 2018, we recruited 988 children aged 7-8 years from 24 classes to participate in a cluster-randomized trial. Classes were randomly assigned to EL (in which children received a lively presentation on oral health and participated in a role play in a simulated dental clinic in the classroom) or the Tell-Show-Do (TSD) group (in which children received a conventional TSD behavior management). The primary outcome was the prevalence of high DA after the procedure of pit and fissure sealant (PFS), assessed by a modified Children's Fear Survey Schedule-Dental Subscale. Secondary outcomes were changes in blood pressures (BP) and pulse rates (PR) before and after the PFS procedure. The intervention effects were estimated by means of mixed effect models, which included covariates of gender and school (and baseline value for BP and PR only), and a random cluster effect. RESULTS: In 396 children of the EL group who received the PFS treatment, the prevalence of high DA (score ≥ 38) was 18.5%, compared with 24.3% in 391 children of the TSD group (OR = 0.65; 95% confidence interval, 0.46-0.93; P = 0.019). The increases in BP and PR after the PFS were also significantly less in the EL group. CONCLUSION: School-based experiential learning intervention before a dental visit is feasible and effective in reducing children's dental anxiety during PFS. TRIAL REGISTRATION: The trial was registered in Chinese Clinical Trial Registry on 5 January 2020 (No.: ChiCTR2000028878 , retrospectively registered).

Analysis of 2 Reverse Syphilis Testing Algorithms in Diagnosis of Syphilis: A Large-Cohort Prospective Study.

Background: Two serologic syphilis screening algorithms recommended by the US Centers for Disease Control and Prevention (US CDC) and the European Centre for Disease Prevention and Control (ECDC), respectively, are commonly used for syphilis screening; however, which one is optimal remains to be determined. Methods: We conducted a prospective study of 119891 subjects to analyze the consistency of the US CDC- and ECDC-recommended algorithms. The US CDC-recommended algorithm begins with a treponemal immunoassay, followed by a rapid plasma reagin (RPR) test. RPR-nonreactive samples are confirmed by the Treponema pallidum particle agglutination assay (TPPA). The ECDC-recommended algorithm begins with a treponemal immunoassay, followed by a confirmatory treponemal test. If the confirmatory test is reactive, a quantitative nontreponemal assay is used to assess the disease activity and treatment response. In the present study, a total of 119891 serum samples from a large hospital (sixth largest in China) were included, and each sample was screened with a chemiluminescent immunoassay (CIA). CIA-reactive samples were then simultaneously tested with RPR and TPPA. The consistency of these 2 algorithms was determined by calculating the percentage of agreement and κ coefficient. Results: The overall percentage of agreement and κ value between these 2 algorithms were 99.996% and 0.999, respectively. The positivity rate for syphilis as determined by the US CDC- and ECDC-recommended algorithms was 1.43% and 1.42%, respectively. Conclusions: Our results suggest that the US CDC-recommended algorithm and the ECDC-recommended algorithm have comparable performances for syphilis screening in low-prevalence populations.

SLC26A3 (DRA) prevents TNF-alpha-induced barrier dysfunction and dextran sulfate sodium-induced acute colitis.

SLC26A3 encodes a Cl-/HCO3- ion transporter that is also known as downregulated in adenoma (DRA) and is involved in HCO3-/mucus formation. The role of DRA in the epithelial barrier has not been previously established. In this study, we investigated the in vivo and in vitro mechanisms of DRA in the colon epithelial barrier. Immunofluorescence (IF) and co-immunoprecipitation (co-IP) studies reveal that DRA binds directly to tight junction (TJ) proteins and affects the expression of TJ proteins in polarized Caco-2BBe cells. Similarly, DRA colocalizes with ZO-1 in the intestinal epithelium. Knockdown or overexpression of DRA leads to alterations in TJ proteins and epithelial permeability. In addition, TNF-α treatment downregulates DRA by activating NF-кB and subsequently affecting intestinal epithelial barrier integrity. Furthermore, overexpression of DRA partly reverses the TNF-α-induced damage by stabilizing TJ proteins. Neutralization of TNF-α in dextran sulfate sodium (DSS)-induced colitis mice demonstrates improved the outcomes, and the therapeutic effect of the TNF-α neutralizing mAb is mediated in part by the preservation of DRA expression. These data suggest that DRA may be one of the therapeutic targets of TNF-α. Moreover, DRA delivered by adenovirus vector significantly prevents the exacerbation of colitis and improves epithelial barrier function by promoting the recovery of TJ proteins in DSS-treated mice. In conclusion, DRA plays a role in protecting the epithelial barrier and may be a therapeutic target in gut homeostasis.

Frontline defenders: goblet cell mediators dictate host-microbe interactions in the intestinal tract during health and disease.

Goblet cells (GCs) are the predominant secretory epithelial cells lining the luminal surface of the mammalian gastrointestinal (GI) tract. Best known for their apical release of mucin 2 (Muc2), which is critical for the formation of the intestinal mucus barrier, GCs have often been overlooked for their active contributions to intestinal protection and host defense. In part, this oversight reflects the limited tools available to study their function but also because GCs have long been viewed as relatively passive players in promoting intestinal homeostasis and host defense. In light of recent studies, this perspective has shifted, as current evidence suggests that Muc2 as well as other GC mediators are actively released into the lumen to defend the host when the GI tract is challenged by noxious stimuli. The ability of GCs to sense and respond to danger signals, such as bacterial pathogens, has recently been linked to inflammasome signaling, potentially intrinsic to the GCs themselves. Moreover, further work suggests that GCs release Muc2, as well as other mediators, to modulate the composition of the gut microbiome, leading to both the expansion as well as the depletion of specific gut microbes. This review will focus on the mechanisms by which GCs actively defend the host from noxious stimuli, as well as describe advanced technologies and new approaches by which their responses can be addressed. Taken together, we will highlight current insights into this understudied, yet critical, aspect of intestinal mucosal protection and its role in promoting gut defense and homeostasis.

Metalloprotease NleC suppresses host NF-κB/inflammatory responses by cleaving p65 and interfering with the p65/RPS3 interaction.

Attaching/Effacing (A/E) pathogens including enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC) and the rodent equivalent Citrobacter rodentium are important causative agents of foodborne diseases. Upon infection, a myriad of virulence proteins (effectors) encoded by A/E pathogens are injected through their conserved type III secretion systems (T3SS) into host cells where they interfere with cell signaling cascades, in particular the nuclear factor kappaB (NF-κB) signaling pathway that orchestrates both innate and adaptive immune responses for host defense. Among the T3SS-secreted non-LEE-encoded (Nle) effectors, NleC, a metalloprotease, has been recently elucidated to modulate host NF-κB signaling by cleaving NF-κB Rel subunits. However, it remains elusive how NleC recognizes NF-κB Rel subunits and how the NleC-mediated cleavage impacts on host immune responses in infected cells and animals. In this study, we show that NleC specifically targets p65/RelA through an interaction with a unique N-terminal sequence in p65. NleC cleaves p65 in intestinal epithelial cells, albeit a small percentage of the molecule, to generate the p65¹â»³8 fragment during C. rodentium infection in cultured cells. Moreover, the NleC-mediated p65 cleavage substantially affects the expression of a subset of NF-κB target genes encoding proinflammatory cytokines/chemokines, immune cell infiltration in the colon, and tissue injury in C. rodentium-infected mice. Mechanistically, the NleC cleavage-generated p65¹â»³8 fragment interferes with the interaction between p65 and ribosomal protein S3 (RPS3), a 'specifier' subunit of NF-κB that confers a subset of proinflammatory gene transcription, which amplifies the effect of cleaving only a small percentage of p65 to modulate NF-κB-mediated gene expression. Thus, our results reveal a novel mechanism for A/E pathogens to specifically block NF-κB signaling and inflammatory responses by cleaving a small percentage of p65 and targeting the p65/RPS3 interaction in host cells, thus providing novel insights into the pathogenic mechanisms of foodborne diseases.

NFATc2 mediates epigenetic modification of dendritic cell cytokine and chemokine responses to dectin-1 stimulation.

The transcription factor NFATc2 regulates dendritic cell (DC) responses to microbial stimulation through the C-type lectin receptor dectin-1. But the genetic targets of NFATc2 and their effects on DC function remain largely unknown. Therefore we used ChIP-seq to conduct genome-wide mapping of NFATc2 target sites in dectin-1-activated DCs. By combining binding-site data with a comprehensive gene expression profile, we found that NFATc2 occupancy regulates the expression of a subset of dectin-1-activated genes. Surprisingly, NFATc2 targeted an extensive range of DC-derived cytokines and chemokines, including regulatory cytokines such as IL2, IL23a and IL12b. Furthermore, we demonstrated that NFATc2 binding is required to induce the histone 3 lysine 4 trimethylation (H3K4me3) epigenetic mark, which is associated with enhanced gene expression. Together, these data show that the transcription factor NFATc2 mediates epigenetic modification of DC cytokine and chemokine genes leading to activation of their expression.

The Serine Protease Autotransporter Pic Modulates Citrobacter rodentium Pathogenesis and Its Innate Recognition by the Host.

Bacterial pathogens produce a number of autotransporters that possess diverse functions. These include the family of serine protease autotransporters of Enterobacteriaceae (SPATEs) produced by enteric pathogens such as Shigella flexneri and enteroaggregative Escherichia coli. Of these SPATEs, one termed "protein involved in colonization," or Pic, has been shown to possess mucinase activity in vitro, but to date, its role in in vivo enteric pathogenesis is unknown. Testing a pic null (ΔpicC) mutant in Citrobacter rodentium, a natural mouse pathogen, found that the C. rodentium ΔpicC strain was impaired in its ability to degrade mucin in vitro compared to the wild type. Upon infection of mice, the ΔpicC mutant exhibited a hypervirulent phenotype with dramatically heavier pathogen burdens found in intestinal crypts. ΔpicC mutant-infected mice suffered greater barrier disruption and more severe colitis and weight loss, necessitating their euthanization between 10 and 14 days postinfection. Notably, the virulence of the ΔpicC mutant was normalized when the picC gene was restored; however, a PicC point mutant causing loss of mucinase activity did not replicate the ΔpicC phenotype. Exploring other aspects of PicC function, the ΔpicC mutant was found to aggregate to higher levels in vivo than wild-type C. rodentium. Moreover, unlike the wild type, the C. rodentium ΔpicC mutant had a red, dry, and rough (RDAR) morphology in vitro and showed increased activation of the innate receptor Toll-like receptor 2 (TLR2). Interestingly, the C. rodentium ΔpicC mutant caused a degree of pathology similar to that of wild-type C. rodentium when infecting TLR2-deficient mice, showing that despite its mucinase activity, PicC's major role in vivo may be to limit C. rodentium's stimulation of the host's innate immune system.

Global impact of Salmonella pathogenicity island 2-secreted effectors on the host phosphoproteome.

During the late stages of infection, Salmonella secretes numerous effectors through a type III secretion system that is encoded within Salmonella pathogenicity island 2 (SPI2). Despite the importance of SPI2 as a major virulence factor leading to the systemic spread of the bacteria and diseases, a global view of its effects on host responses is still lacking. Here, we measured global impacts of SPI2 effectors on the host phosphorylation and protein expression levels in RAW264.7 and in HeLa cells, as macrophage and nonphagocytic models of infection. We observe that SPI2 effectors differentially modulate the host phosphoproteome and cellular processes (e.g. protein trafficking, cytoskeletal regulation, and immune signaling) in a host cell-dependent manner. Our unbiased approach reveals the involvement of many previously unrecognized proteins, including E3 ligases (HERC4, RanBP2, and RAD18), kinases (CDK, SIK3, and WNK1), and histones (H2B1F, H4, and H15), in late stages of Salmonella infection. Furthermore, from this phosphoproteome analysis and other quantitative screens, we identified HSP27 as a direct in vitro and in vivo molecular target of the only type III secreted kinase, SteC. Using biochemical and cell biological assays, we demonstrate that SteC phosphorylates multiple sites in HSP27 and induces actin rearrangement through this protein. Together, these results provide a broader landscape of host players contributing to specific processes/pathways mediated by SPI2 effectors than was previously appreciated.

Coassembly of REST and its cofactors at sites of gene repression in embryonic stem cells.

The differentiation of pluripotent embryonic stem cells is regulated by networks of activating and repressing transcription factors that orchestrate determinate patterns of gene expression. With the recent mapping of target sites for many transcription factors, it has been a conundrum that so few of the genes directly targeted by these factors are transcriptionally responsive to the binding of that factor. To address this, we generated genome-wide maps of the transcriptional repressor REST and five of its corepressors in mouse embryonic stem cells. Combining these binding-site maps with comprehensive gene-expression profiling, we show that REST is functionally heterogeneous. Approximately half of its binding sites apparently are nonfunctional, having weaker binding of REST and low recruitment of corepressors. In contrast, the other sites strongly recruit REST and corepressor complexes with varying numbers of components. Strikingly, the latter sites account for almost all observed gene regulation. These data support a model where productive gene repression by REST requires assembly of a multimeric "repressosome" complex, whereas weak recruitment of REST and its cofactors is insufficient to repress gene expression.

NFAT control of innate immunity.

The calcineurin/nuclear factor of activated T cells (NFAT) signaling pathway mediates multiple adaptive T-cell functions, but recent studies have shown that calcineurin/NFAT signaling also contributes to innate immunity and regulates the homeostasis of innate cells. Myeloid cells, including granulocytes and dendritic cells, can promote inflammation, regulate adaptive immunity, and are essential mediators of early responses to pathogens. Microbial ligation of pattern-recognition receptors, such as TLR4, CD14, and dectin 1, is now known to induce the activation of calcineurin/NFAT signaling in myeloid cells, a finding that has provided new insights into the molecular pathways that regulate host protection. Inhibitors of calcineurin/NFAT binding, such as cyclosporine A and FK506, are broadly used in organ transplantation and can act as potent immunosuppressive drugs in a variety of different disorders. There is increasing evidence that these agents influence innate responses as well as inhibiting adaptive T-cell functions. This review focuses on the role of calcineurin/NFAT signaling in myeloid cells, which may contribute to the various unexplained effects of immunosuppressive drugs already being used in the clinic.

Integrating TCGA and Single-Cell Sequencing Data for Hepatocellular Carcinoma: A Novel Glycosylation (GLY)/Tumor Microenvironment (TME) Classifier to Predict Prognosis and Immunotherapy Response.

The major liver cancer subtype is hepatocellular carcinoma (HCC). Studies have indicated that a better prognosis is related to the presence of tumor-infiltrating lymphocytes (TILs) in HCC. However, the molecular pathways that drive immune cell variation in the tumor microenvironment (TME) remain poorly understood. Glycosylation (GLY)-related genes have a vital function in the pathogenesis of numerous tumors, including HCC. This study aimed to develop a GLY/TME classifier based on glycosylation-related gene scores and tumor microenvironment scores to provide a novel prognostic model to improve the prediction of clinical outcomes. The reliability of the signatures was assessed using receiver operating characteristic (ROC) and survival analyses and was verified with external datasets. Furthermore, the correlation between glycosylation-related genes and other cells in the immune environment, the immune signature of the GLY/TME classifier, and the efficacy of immunotherapy were also investigated. The GLY score low/TME score high subgroup showed a favorable prognosis and therapeutic response based on significant differences in immune-related molecules and cancer cell signaling mechanisms. We evaluated the prognostic role of the GLY/TME classifier that demonstrated overall prognostic significance for prognosis and therapeutic response before treatment, which may provide new options for creating the best possible therapeutic approaches for patients.

Removal of PCP-Na from aqueous systems using monodispersed pompon-like magnetic nanoparticles as adsorbents.

Novel monodispersed pompon-like magnetite/chitosan (Fe3O4/CS) composite nanoparticles were synthesized by a solvothermal method and used as adsorbents for the removal of toxic sodium pentachlorophenate (PCP-Na) from aqueous media. The adsorption behavior of PCP-Na on Fe3O4/CS obeyed the Langmuir isotherm and fitted the pseudo-second-order kinetics model. Thermodynamic parameters showed that the adsorption process was exothermic and spontaneous. Moreover, the adsorption was strongly pH-dependent. The results of XPS, thermodynamics, pH-dependent and desorption studies suggested that electrostatic attraction, hydrogen bonding and π-π interactions were all believed to play a role in PCP-Na adsorption on Fe3O4/CS. Having a saturation magnetization of 22.2 emu · g(-1), the Fe3O4/CS can be easily separated from water with magnets within 2 min. The adsorption equilibrium was achieved quite rapidly (within 30 min) and the maximum removal of PCP-Na (91.5%) was obtained at 25 °C and pH 6.5. The Fe3O4/CS investigated can be used to remove PCP-Na and other contaminants from wastewater.

New insights of anaerobic performance, antibiotic resistance gene removal, microbial community structure: applying graphite-based materials in wet anaerobic digestion.

The addition of carbonaceous materials into anaerobic digestion (AD) has gained widespread attention due to their significant effects on anaerobic performance and antibiotic resistance gene (ARG) removal. This study selected graphite, graphene, and graphene oxide (GO) as additives to investigate variations in AD performance, ARG removal, microbial community diversity and structure in wet AD systems. The results indicated that the addition of graphite-based materials in wet AD systems could increase degradation of solid organic matters by 0.91%-3.41% and utilization of soluble organic fractions by 10.43%-13.67%, but could not stimulate methane production. After the addition of graphite and graphene, ARG removal rates were effectively increased to 90.85% and 94.22%, respectively. However, the total ARG removal rate was reduced to 77.46% with the addition of GO. In addition, the microbial diversity in the wet AD process was enhanced with the addition of GO only, graphite and graphene led to a reduction in it. As for bacterial community, graphite and graphene increased the abundance of Thermotogae from 43.43% to 57.42% and 58.74%, while GO increased the abundance of Firmicute from 49.90% to 56.27%. For the archaeal community, the proportion of hydrogenotrophic methanogens was improved when adding each graphite-based material; however, only GO increased Methanosaeta that was acetoclastic methanogens. Finally, methanogens were found as the ARG host, and ARGs that belong to the same subtype might exist in the same host bacteria.

Single-cell transcriptome analysis reveals the metabolic changes and the prognostic value of malignant hepatocyte subpopulations and predict new therapeutic agents for hepatocellular carcinoma.

Background: The development of HCC is often associated with extensive metabolic disturbances. Single cell RNA sequencing (scRNA-seq) provides a better understanding of cellular behavior in the context of complex tumor microenvironments by analyzing individual cell populations. Methods: The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) data was employed to investigate the metabolic pathways in HCC. Principal component analysis (PCA) and uniform manifold approximation and projection (UMAP) analysis were applied to identify six cell subpopulations, namely, T/NK cells, hepatocytes, macrophages, endothelial cells, fibroblasts, and B cells. The gene set enrichment analysis (GSEA) was performed to explore the existence of pathway heterogeneity across different cell subpopulations. Univariate Cox analysis was used to screen genes differentially related to The Overall Survival in TCGA-LIHC patients based on scRNA-seq and bulk RNA-seq datasets, and LASSO analysis was used to select significant predictors for incorporation into multivariate Cox regression. Connectivity Map (CMap) was applied to analysis drug sensitivity of risk models and targeting of potential compounds in high risk groups. Results: Analysis of TCGA-LIHC survival data revealed the molecular markers associated with HCC prognosis, including MARCKSL1, SPP1, BSG, CCT3, LAGE3, KPNA2, SF3B4, GTPBP4, PON1, CFHR3, and CYP2C9. The RNA expression of 11 prognosis-related differentially expressed genes (DEGs) in normal human hepatocyte cell line MIHA and HCC cell lines HCC-LM3 and HepG2 were compared by qPCR. Higher KPNA2, LAGE3, SF3B4, CCT3 and GTPBP4 protein expression and lower CYP2C9 and PON1 protein expression in HCC tissues from Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases. The results of target compound screening of risk model showed that mercaptopurine is a potential anti-HCC drug. Conclusion: The prognostic genes associated with glucose and lipid metabolic changes in a hepatocyte subpopulation and comparison of liver malignancy cells to normal liver cells may provide insight into the metabolic characteristics of HCC and the potential prognostic biomarkers of tumor-related genes and contribute to developing new treatment strategies for individuals.

Self-paced Multi-view Learning for CT-based severity assessment of COVID-19.

Prior studies for the task of severity assessment of COVID-19 (SA-COVID) usually suffer from domain-specific cognitive deficits. They mainly focus on visual cues based on single cognitive functions but fail to reconcile the valuable information from other alternative views. Inspired by the cognitive process of radiologists, this paper shifts naturally from single-symptom measurements to a multi-view analysis, and proposes a novel Self-paced Multi-view Learning (SPML) framework for automated SA-COVID. Specifically, the proposed SPML framework first comprehensively aggregates multi-view contexts in lung infection with different measure paradigms, i.e., Global Feature Branch, Texture Feature Branch, and Volume Feature Branch. In this way, multiple-perspective clues are taken into account to reflect the most essential pathological manifestation on CT images. To alleviate small-sample learning problems, we also introduce an optimization with self-paced learning strategy to cognitively increase the characterization capabilities of training samples by learning from simple to complex. In contrast to traditional batch-wise learning, a pure self-paced way can further guarantee the efficiency and accuracy of SPML when dealing with small and biased samples. Furthermore, we construct a well-established SA-COVID dataset that contains 300 CT images with fine annotations. Extensive experiments on this dataset demonstrate that SPML consistently outperforms the state-of-the-art baselines. The SA-COVID dataset is publicly released at https://github.com/YishuLiu/SA-COVID.