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"Liu, Jinhui"
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Group B Streptococcus: Virulence Factors and Pathogenic Mechanism
2022
Group B Streptococcus (GBS) or Streptococcus agalactiae is a major cause of neonatal mortality. When colonizing the lower genital tract of pregnant women, GBS may cause premature birth and stillbirth. If transmitted to the newborn, it may result in life-threatening illnesses, including sepsis, meningitis, and pneumonia. Moreover, through continuous evolution, GBS can use its original structure and unique factors to greatly improve its survival rate in the human body. This review discusses the key virulence factors that facilitate GBS invasion and colonization and their action mechanisms. A comprehensive understanding of the role of virulence factors in GBS infection is crucial to develop better treatment options and screen potential candidate molecules for the development of the vaccine.
Journal Article
Phytohormones Regulate the Development of Arbuscular Mycorrhizal Symbiosis
by
Liu, Jinhui
,
Xu, Guohua
,
Liao, Dehua
in
Gibberellins - pharmacology
,
Indoleacetic Acids - pharmacology
,
Mycorrhizae - drug effects
2018
Most terrestrial plants are able to form a root symbiosis with arbuscular mycorrhizal (AM) fungi for enhancing the assimilation of mineral nutrients. AM fungi are obligate symbionts that depend on host plants as their sole carbon source. Development of an AM association requires a continuous signal exchange between the two symbionts, which triggers coordinated differentiation of both partners, to enable their interaction within the root cells. The control of the AM symbiosis involves a finely-tuned process, and an increasing number of studies have pointed to a pivotal role of several phytohormones, such as strigolactones (SLs), gibberellic acids (GAs), and auxin, in the modulation of AM symbiosis, through the early recognition of events up to the final arbuscular formation. SLs are involved in the presymbiotic growth of the fungus, while auxin is required for both the early steps of fungal growth and the differentiation of arbuscules. GAs modulate arbuscule formation in a dose-dependent manner, via DELLA proteins, a group of GRAS transcription factors that negatively control the GA signaling. Here, we summarize the recent findings on the roles of these plant hormones in AM symbiosis, and also explore the current understanding of how the DELLA proteins act as central regulators to coordinate plant hormone signaling, to regulate the AM symbiosis.
Journal Article
Improving prediction accuracy in agricultural markets through the CIMA-AttGRU model
2024
In the Chinese futures market, agricultural product futures play a crucial role. While previous studies have primarily relied on historical price data and fundamental financial indicators of agricultural product futures, there is a growing recognition of the value that lies within the vast amounts of textual data generated in the financial domain. Our study specifically focuses on the limitations of existing methods in capturing the complex relationships and rich semantic information embedded in these textual sources. This article designs a CIMA AttGRU (CIMA-AttGRU) model for soybean futures, which is a forecasting method for the agricultural product market. This model uniquely integrates Collective Intrinsic Mode Analysis (CIMA) with an Attention-Gated Recurrent Unit (AttGRU), leveraging the strengths of both techniques to enhance predictive accuracy and adaptability. The rationale behind employing the CIMA-AttGRU model lies in its ability to effectively tackle the inherent challenges of financial market analysis. By incorporating CIMA, the model adeptly filters out market noise, directly addressing the challenge of high volatility. Additionally, with its attention mechanism, the CIMA-AttGRU targets the issue of non-linear patterns by allowing dynamic adjustment to temporal dependencies, offering differential learning capabilities crucial for capturing the nuanced fluctuations in futures prices. Complementing the CIMA and AttGRU, the integration of Class-wise Adversarial Domain Adaptation (CADA) further refines the model’s robustness, addressing the critical challenge of domain adaptivity. This aspect is particularly vital for edamame futures, where price determinants can vary significantly over time and across regions. Our empirical results demonstrate a significant improvement in forecasting precision, with the CIMA-AttGRU model achieving a Mean Absolute Error (MAE) reduction of 15% and a Mean Squared Error (MSE) reduction of 20% compared to conventional models. This superior performance, especially in terms of prediction accuracy and handling market fluctuations, highlights the improve of the model compared to existing methods and has made significant explorations in agricultural market forecasting.
Journal Article
Mast cell marker gene signature: prognosis and immunotherapy response prediction in lung adenocarcinoma through integrated scRNA-seq and bulk RNA-seq
by
Li, Jun
,
Liu, Jinhui
,
Pei, Shengbin
in
Adenocarcinoma
,
Adenocarcinoma of Lung - genetics
,
Adenocarcinoma of Lung - therapy
2023
Mast cells, comprising a crucial component of the tumor immune milieu, modulate neoplastic progression by secreting an array of pro- and antitumorigenic factors. Numerous extant studies have produced conflicting conclusions regarding the impact of mast cells on the prognosis of patients afflicted with lung adenocarcinoma (LUAD).
Employing single-cell RNA sequencing (scRNA-seq) analysis, mast cell-specific marker genes in LUAD were ascertained. Subsequently, a mast cell-related genes (MRGs) signature was devised to stratify LUAD patients into high- and low-risk cohorts based on the median risk value. Further investigations were conducted to assess the influence of distinct risk categories on the tumor microenvironment. The prognostic import and capacity to prognosticate immunotherapy benefits of the MRGs signature were corroborated using four external cohorts. Ultimately, the functional roles of SYAP1 were validated through
experimentation.
After scRNA-seq and bulk RNA-seq data analysis, we established a prognostic signature consisting of nine MRGs. This profile effectively distinguished favorable survival outcomes in both the training and validation cohorts. In addition, we identified the low-risk group as a population more effective for immunotherapy. In cellular experiments, we found that silencing SYAP1 significantly reduced the proliferation, invasion and migratory capacity of LUAD cells while increasing apoptosis.
Our MRGs signature offers valuable insights into the involvement of mast cells in determining the prognosis of LUAD and may prove instrumental as a navigational aid for immunotherapy selection, as well as a predictor of immunotherapy response in LUAD patients.
Journal Article
Circadian rhythm-related genes index: A predictor for HNSCC prognosis, immunotherapy efficacy, and chemosensitivity
2023
Head and neck squamous cell carcinoma (HNSCC) is the most common head and neck cancer and is highly aggressive and heterogeneous, leading to variable prognosis and immunotherapy outcomes. Circadian rhythm alterations in tumourigenesis are of equal importance to genetic factors and several biologic clock genes are considered to be prognostic biomarkers for various cancers. The aim of this study was to establish reliable markers based on biologic clock genes, thus providing a new perspective for assessing immunotherapy response and prognosis in patients with HNSCC.
We used 502 HNSCC samples and 44 normal samples from the TCGA-HNSCC dataset as the training set. 97 samples from GSE41613 were used as an external validation set. Prognostic characteristics of circadian rhythm-related genes (CRRGs) were established by Lasso, random forest and stepwise multifactorial Cox. Multivariate analysis revealed that CRRGs characteristics were independent predictors of HNSCC, with patients in the high-risk group having a worse prognosis than those in the low-risk group. The relevance of CRRGs to the immune microenvironment and immunotherapy was assessed by an integrated algorithm.
6-CRRGs were considered to be strongly associated with HNSCC prognosis and a good predictor of HNSCC. The riskscore established by the 6-CRRG was found to be an independent prognostic factor for HNSCC in multifactorial analysis, with patients in the low-risk group having a higher overall survival (OS) than the high-risk group. Nomogram prediction maps constructed from clinical characteristics and riskscore had good prognostic power. Patients in the low-risk group had higher levels of immune infiltration and immune checkpoint expression and were more likely to benefit from immunotherapy.
6-CRRGs play a key predictive role for the prognosis of HNSCC patients and can guide physicians in selecting potential responders to prioritise immunotherapy, which could facilitate further research in precision immuno-oncology.
Journal Article
Effect of Wettability Heterogeneity on Water-Gas Two-Phase Displacement Behavior in a Complex Pore Structure by Phase-Field Model
2022
Understanding the immiscible displacement mechanism in porous media is vital to enhancing the hydrocarbon resources in the oil and gas reservoir. Improving resource recovery requires quantitatively characterizing the effect of wettability heterogeneity on the immiscible displacement behaviors at the pore scale, which can be used to predict the displacement distribution of multiphase fluids and evaluate the optimal wettability strategy in porous media. The heterogeneity of fluid wettability in a natural rock makes it extremely hard to directly observe the fluid displacement behaviors in the reservoir rocks and quantify the sensitivity of preferential displacement path and displacement efficiency to wettability distribution. In this study, the phase-field model coupling wettability heterogeneity was established. The gas-water two-phase displacement process was simulated under various wettability distributions and injecting flux rates in a complex pore structure. The effect of wettability heterogeneity on immiscible displacement behavior was analyzed. The results indicated that wettability heterogeneity significantly affects the fluid displacement path and invasion patterns, while the injecting flux rate negatively influences the capillary–viscous crossover flow regime. The continuous wetting patches enhanced the preferential flow and hindered displacement, whereas the dalmatian wetting patches promoted a higher displacement efficiency. The results of the fractal dimensions and specific surface area also quantitatively show the effects of wettability distribution and heterogeneity on the complexity of the two-phase fluid distribution. The research provides the theoretical foundation and analysis approach for designing an optimal wettability strategy for injecting fluid into unconventional oil and gas reservoirs.
Journal Article
Study on the water-richness law and zoning assessment of mine water-bearing aquifers based on sedimentary characteristics
2022
To study and prevent the water hazards of deep coal mines roof in the Inner Mongolia–Shaanxi (IM–S) mining area, it is essential to correctly evaluate the water-richness distributions of water-bearing aquifers in roof. This paper puts forward a sediment control method for water-richness law and zoning in the roof aquifers of deep Jurassic coals. To determine the vertical distance of direct water-bearing aquifers, the height of fractured water-conducting zone was detected by an underground network parallel electrical method. The plane and lateral spatial distribution patterns of the water-bearing aquifers and the control of the water-richness distribution was analyzed with the sediment control method. An evaluation system that consisted of four indicators, i.e., sedimentary environmental impact index, interlayer ratio of sandstone and mudstone, sandstone thickness, geophysical water-richness anomaly index was constructed. Furthermore, an Analytic Hierarchy Process (AHP) was introduced to establish the comprehensive zoning map. Finally, through the example analysis of Muduchaideng coal mine, the zoning evaluation results of water-richness were verified by the mine inflow. The findings of this study provide scientific guidance for prevention and control of mine water hazards in the IM–S mining area.
Journal Article
ALKBH5-HOXA10 loop-mediated JAK2 m6A demethylation and cisplatin resistance in epithelial ovarian cancer
2021
Background
Chemotherapy resistance remains a barrier to improving the prognosis of epithelial ovarian cancer (EOC). ALKBH5 has recently been shown to be one of the RNA N6-methyladenosine (m6A) demethyltransferases associated with various cancers, but its role in cancer therapeutic resistance remains unclear. This study aimed to investigate the role of AlkB homolog 5 (ALKBH5) in cisplatin-resistant EOC.
Methods
Functional assays were performed both in vitro and in vivo. RNA sequencing (RNA-seq), m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq), chromatin immunoprecipitation, RNA immunoprecipitation, and luciferase reporter and actinomycin-D assays were performed to investigate RNA/RNA interaction and m6A modification of the ALKBH5-HOXA10 loop.
Results
ALKBH5 was upregulated in cisplatin-resistant EOC and promoted cancer cell cisplatin resistance both in vivo and in vitro. Notably, HOXA10 formed a loop with ALKBH5 and was found to be the upstream transcription factor of ALKBH5. HOXA10 overexpression also facilitated EOC cell chemoresistance both in vivo and in vitro. Collective results of MeRIP-seq and RNA-seq showed that JAK2 is the m6A-modified gene targeted by ALKBH5. The JAK2/STAT3 signaling pathway was activated by overexpression of the ALKBH5-HOXA10 loop, resulting in EOC chemoresistance. Cell sensitivity to cisplatin was rescued by ALKBH5 and HOXA10 knockdown or inhibition of the JAK2/STAT3 signaling pathway in EOC cells overexpressing ALKBH5-HOXA10.
Conclusions
The ALKBH5-HOXA10 loop jointly activates the JAK2/STAT3 signaling pathway by mediating JAK2 m6A demethylation, promoting EOC resistance to cisplatin. Thus, inhibition of the expression of the ALKBH5-HOXA10 loop may be a potential strategy to overcome cisplatin resistance in EOC.
Journal Article
Model test and numerical simulation on the dynamic stability of the bedding rock slope under frequent microseisms
2020
Shake table testing was performed to investigate the dynamic stability of a mid-dip bedding rock slope under frequent earthquakes. Then, numerical modelling was established to further study the slope dynamic stability under purely microseisms and the influence of five factors, including seismic amplitude, slope height, slope angle, strata inclination and strata thickness, were considered. The experimental results show that the natural frequency of the slope decreases and damping ratio increases as the earthquake loading times increase. The dynamic strength reduction method is adopted for the stability evaluation of the bedding rock slope in numerical simulation, and the slope stability decreases with the increase of seismic amplitude, increase of slope height, reduction of strata thickness and increase of slope angle. The failure mode of a mid-dip bedding rock slope in the shaking table test is integral slipping along the bedding surface with dipping tensile cracks at the slope rear edge going through the bedding surfaces. In the numerical simulation, the long-term stability of a mid-dip bedding slope is worst under frequent microseisms and the slope is at risk of integral sliding instability, whereas the slope rock mass is more broken than shown in the shaking table test. The research results are of practical significance to better understand the formation mechanism of reservoir landslides and prevent future landslide disasters.
Journal Article
Comprehensive of N1-Methyladenosine Modifications Patterns and Immunological Characteristics in Ovarian Cancer
by
Liu, Jinhui
,
Xing, Yan
,
Chen, Can
in
Adenosine - metabolism
,
Algorithms
,
Carcinoma, Ovarian Epithelial - immunology
2021
recently, many researches have concentrated on the relevance between N1-methyladenosine (m1A) methylation modifications and tumor progression and prognosis. However, it remains unknown whether m1A modification has an effect in the prognosis of ovarian cancer (OC) and its immune infiltration.
Based on 10 m1A modulators, we comprehensively assessed m1A modification patterns in 474 OC patients and linked them to TME immune infiltration characteristics. m1Ascore computed with principal component analysis algorithm was applied to quantify m1A modification pattern in OC patients. m1A regulators protein and mRNA expression were respectively obtained by HPA website and RT-PCR in clinical OC and normal samples.
We finally identified three different m1A modification patterns. The immune infiltration features of these m1A modification patterns correspond to three tumor immune phenotypes, including immune-desert, immune-inflamed and immune-excluded phenotypes. The results demonstrate individual tumor m1A modification patterns can predict patient survival, stage and grade. The m1Ascore was calculated to quantify individual OC patient's m1A modification pattern. A high m1Ascore is usually accompanied by a better survival advantage and a lower mutational load. Research on m1Ascore in the treatment of OC patients showed that patients with high m1Ascore showed marked therapeutic benefits and clinical outcomes in terms of chemotherapy and immunotherapy. Lastly, we obtained four small molecule drugs that may potentially ameliorate prognosis.
This research demonstrates that m1A methylation modification makes an essential function in the prognosis of OC and in shaping the immune microenvironment. Comprehensive evaluation of m1A modifications improves our knowledge of immune infiltration profile and provides a more efficient individualized immunotherapy strategy for OC patients.
Journal Article