RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications.

Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.

ChIPBase v3.0: the encyclopedia of transcriptional regulations of non-coding RNAs and protein-coding genes.

Non-coding RNAs (ncRNAs) are emerging as key regulators of various biological processes. Although thousands of ncRNAs have been discovered, the transcriptional mechanisms and networks of the majority of ncRNAs have not been fully investigated. In this study, we updated ChIPBase to version 3.0 (https://rnasysu.com/chipbase3/) to provide the most comprehensive transcriptional regulation atlas of ncRNAs and protein-coding genes (PCGs). ChIPBase has identified ∼151 187 000 regulatory relationships between ∼171 600 genes and ∼3000 regulators by analyzing ∼55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified ∼29 000 motif matrices of transcription factors. In addition, we constructed a novel 'Enhancer' module to predict ∼1 837 200 regulation regions functioning as poised, active or super enhancers under ∼1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of ∼65 000 normal and ∼15 000 tumor samples. We built a 'Disease' module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an 'EpiInter' module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed 'Network' module to provide extensive and gene-centred regulatory networks. ChIPBase will serve as a useful resource to facilitate integrative explorations and expand our understanding of transcriptional regulation.

The Evolution of Fluoroquinolone Resistance in Salmonella under Exposure to Sub-Inhibitory Concentration of Enrofloxacin.

The evolution of resistance in Salmonella to fluoroquinolones (FQs) under a broad range of sub-inhibitory concentrations (sub-MICs) has not been systematically studied. This study investigated the mechanism of resistance development in Salmonella enterica serovar Enteritidis (S. Enteritidis) under sub-MICs of 1/128×MIC to 1/2×MIC of enrofloxacin (ENR), a widely used veterinary FQ. It was shown that the resistance rate and resistance level of S. Enteritidis varied with the increase in ENR concentration and duration of selection. qRT-PCR results demonstrated that the expression of outer membrane porin (OMP) genes, ompC, ompD and ompF, were down-regulated first to rapidly adapt and develop the resistance of 4×MIC, and as the resistance level increased (≥8×MIC), the up-regulated expression of efflux pump genes, acrB, emrB amd mdfA, along with mutations in quinolone resistance-determining region (QRDR) gradually played a decisive role. Cytohubba analysis based on transcriptomic profiles demonstrated that purB, purC, purD, purF, purH, purK, purL, purM, purN and purT were the hub genes for the FQs resistance. The 'de novo' IMP biosynthetic process, purine ribonucleoside monophosphate biosynthetic process and purine ribonucleotide biosynthetic process were the top three biological processes screened by MCODE. This study first described the dynamics of FQ resistance evolution in Salmonella under a long-term selection of sub-MICs of ENR in vitro. In addition, this work offers greater insight into the transcriptome changes of S. Enteritidis under the selection of ENR and provides a framework for FQs resistance of Salmonella for further studies.

The Effects of Natural Products and Environmental Conditions on Antimicrobial Resistance.

Due to the extensive application of antibiotics in medical and farming practices, the continued diversification and development of antimicrobial resistance (AMR) has attracted serious public concern. With the emergence of AMR and the failure to treat bacterial infections, it has led to an increased interest in searching for novel antibacterial substances such as natural antimicrobial substances, including microbial volatile compounds (MVCs), plant-derived compounds, and antimicrobial peptides. However, increasing observations have revealed that AMR is associated not only with the use of antibacterial substances but also with tolerance to heavy metals existing in nature and being used in agriculture practice. Additionally, bacteria respond to environmental stresses, e.g., nutrients, oxidative stress, envelope stress, by employing various adaptive strategies that contribute to the development of AMR and the survival of bacteria. Therefore, we need to elucidate thoroughly the factors and conditions affecting AMR to take comprehensive measures to control the development of AMR.

Labor progress determined by ultrasound is different in women requiring cesarean delivery from those who experience a vaginal delivery following induction of labor.

BACKGROUND: The diagnosis of labor dystocia generally is determined by the deviation of labor progress, which is assessed by the use of a partogram. Recently, intrapartum transperineal ultrasound for the assessment of fetal head descent has been introduced to assess labor progress in the first stage of labor in a more objective and noninvasive way. OBJECTIVE: The objective of the study was to determine the differences in labor progress by the use of serial transperineal ultrasound assessment of fetal head descent between women having vaginal and cesarean delivery. STUDY DESIGN: This was a prospective longitudinal study performed in 315 women with singleton pregnancy who were undergoing labor induction at term between December 2016 and December 2017. Paired assessment of cervical dilation and fetal head station by vaginal examination and transperineal ultrasonographic assessment of parasagittal angle of progression and head-perineum distance were made serially after the commencement of labor induction. According to the hospital protocol, assessment was performed every 24 hours and 4 hours, respectively, during latent and active phases of labor. The researchers and the clinical team were blinded to each other's findings. The repeated measures data were analyzed by mixed effect models. To determine the effect of mode of delivery on the association between parasagittal angle of progression and head-perineum distance against fetal head station and cervical dilation, the significance of the interaction term between each mode of delivery and fetal head station or cervical dilation was determined, which accounted for parity and obesity. Area under receiver-operating characteristic curve was used to evaluate the performance of serial intrapartum sonography in predicting women with cesarean delivery because of failure to progress. RESULTS: The total number of paired vaginal examination and ultrasound assessments was 1198, with a median of 3 per woman. The median assessment-to-assessment interval was 4.6 hours (interquartile range, 4.3-5.1 hours). Women who achieved vaginal delivery (n=261) had steeper slopes of parasagittal angle of progression and head-perineum distance against fetal head station and cervical dilation than those who achieved cesarean delivery (n=54). Objectively, an additional decrease of 5.11 and 1.37 degrees in parasagittal angle of progression was observed for an unit increase in fetal head station and cervical dilation, respectively, in women who required cesarean delivery (P<.01; P=.01), compared with women who achieved vaginal delivery, after taking account of repeated measures from individuals and confounding factors. The respective additional increases in head-perineum distance for a unit increase in fetal head station and cervical dilation were 0.27 cm (P<.01) and 0.12 cm (P<.01). A combination of maternal characteristics with the temporal changes of parasagittal angle of progression for an unit increase in fetal head station achieved an area under receiver-operating characteristic curve of 0.85 (95% confidence interval, 0.76-0.94), with sensitivity of 79% and specificity of 80%, for the prediction of women who required cesarean delivery because of failure to progress. CONCLUSION: The differences in labor progress between vaginal and cesarean delivery have been illustrated objectively by serial intrapartum transperineal ultrasonographic assessment of fetal head descent. This tool is potentially predictive of women who will require cesarean delivery because of failure to progress.

SALL4 promotes cancer stem-like cell phenotype and radioresistance in oral squamous cell carcinomas via methyltransferase-like 3-mediated m6A modification.

Radioresistance imposes a great challenge in reducing tumor recurrence and improving the clinical prognosis of individuals having oral squamous cell carcinoma (OSCC). OSCC harbors a subpopulation of CD44(+) cells that exhibit cancer stem-like cell (CSC) characteristics are involved in malignant tumor phenotype and radioresistance. Nevertheless, the underlying molecular mechanisms in CD44( + )-OSCC remain unclear. The current investigation demonstrated that methyltransferase-like 3 (METTL3) is highly expressed in CD44(+) cells and promotes CSCs phenotype. Using RNA-sequencing analysis, we further showed that Spalt-like transcription factor 4 (SALL4) is involved in the maintenance of CSCs properties. Furthermore, the overexpression of SALL4 in CD44( + )-OSCC cells caused radioresistance in vitro and in vivo. In contrast, silencing SALL4 sensitized OSCC cells to radiation therapy (RT). Mechanistically, we illustrated that SALL4 is a direct downstream transcriptional regulation target of METTL3, the transcription activation of SALL4 promotes the nuclear transport of ß-catenin and the expression of downstream target genes after radiation therapy, there by activates the Wnt/ß-catenin pathway, effectively enhancing the CSCs phenotype and causing radioresistance. Herein, this study indicates that the METTL3/SALL4 axis promotes the CSCs phenotype and resistance to radiation in OSCC via the Wnt/ß-catenin signaling pathway, and provides a potential therapeutic target to eliminate radioresistant OSCC.

RGIE: A Gene Selection Method Related to Radiotherapy Resistance in Head and Neck Squamous Cell Carcinoma.

BACKGROUND: Head and Neck Squamous Cell Carcinoma (HNSCC) is a malignant tumor with a high degree of malignancy, invasiveness, and metastasis rate. Radiotherapy, as an important adjuvant therapy for HNSCC, can reduce the postoperative recurrence rate and improve the survival rate. Identifying the genes related to HNSCC radiotherapy resistance (HNSCC-RR) is helpful in the search for potential therapeutic targets. However, identifying radiotherapy resistance-related genes from tens of thousands of genes is a challenging task. While interactions between genes are important for elucidating complex biological processes, the large number of genes makes the computation of gene interactions infeasible. METHODS: We propose a gene selection algorithm, RGIE, which is based on ReliefF, Gene Network Inference with Ensemble of Trees (GENIE3) and Feature Elimination. ReliefF was used to select a feature subset that is discriminative for HNSCC-RR, GENIE3 constructed a gene regulatory network based on this subset to analyze the regulatory relationship among genes, and feature elimination was used to remove redundant and noisy features. RESULTS: Nine genes (SPAG1, FIGN, NUBPL, CHMP5, TCF7L2, COQ10B, BSDC1, ZFPM1, GRPEL1) were identified and used to identify HNSCC-RR, which achieved performances of 0.9730, 0.9679, 0.9767, and 0.9885 in terms of accuracy, precision, recall, and AUC, respectively. Finally, qRT-PCR validated the differential expression of the nine signature genes in cell lines (SCC9, SCC9-RR). CONCLUSION: RGIE is effective in screening genes related to HNSCC-RR. This approach may help guide clinical treatment modalities for patients and develop potential treatments.

NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions.

Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.

[Effect of circulating exosomes in patients with sepsis on T cell function].

OBJECTIVE: To investigate the effect of circulating exosomes (EXO) on T cell function in patients with sepsis. METHODS: Plasma EXO were obtained by ultracentrifugation from 10 patients with sepsis admitted to the emergency intensive care unit of Guangdong Provincial People's Hospital Affiliated to Southern Medical University. Transmission electron microscopy observation, nanoparticle tracking analysis (NTA), and Western blotting were used to detect EXO markers to identify their characteristics. Furthermore, peripheral blood mononuclear cells (PBMC) were isolated from the peripheral blood of 5 healthy volunteers, primary T cells were sorted by magnetic beads and expanded in vitro. After 24 hours of intervention with different doses (0, 1, 2.5, 5, 10 mg/L) of circulating EXO in patients with sepsis, T-cell activity was assessed using a cell counting kit-8 (CCK-8). The expression of T cell activation indicators CD69 and CD25 were observed using flow cytometry. Additional evaluations were performed on immunosuppressive indicators including the expression of programmed cell death 1 (PD-1) in CD4+ T cells and the proportion of regulatory T cell (Treg). RESULTS: The identification results confirmed that the successful isolation of EXO from the plasma of sepsis patients. The expression level of circulating EXO in sepsis patients was higher than that in healthy control group (mg/L: 48.78±5.14 vs. 22.18±2.25, P < 0.01). After 24 hours of intervention with 5 mg/L of plasma EXO from sepsis patients, T cells activity began to show suppression [(85.84±0.56)% vs. (100.00±0.00)%, P < 0.05]. As the dosage increased, after 24 hours of intervention with 10 mg/L of EXO, T cells activity was significantly suppressed [(72.44±2.36)% vs. (100.00±0.00)%, P < 0.01]. Compared with the healthy control group, after T cells intervention with plasma EXO from sepsis patients, the expression of early activation marker CD69 was significantly reduced [(52.87±1.29)% vs. (67.13±3.56)%, P < 0.05]. Meanwhile, there was an upregulation of PD-1 expression in T cells [(57.73±3.06)% vs. (32.07±0.22)%, P < 0.01] and an increase in the proportion of Treg [(54.67±1.19)% vs. (24.60±3.51)%, P < 0.01]. However, the expression of the late activation marker CD25 remained stable [(84.77±3.44)% vs. (85.93±2.32)%, P > 0.05]. CONCLUSIONS: Circulating EXO in sepsis patients induce T cell dysfunction, which may be a novel mechanism lead to immunosuppression in sepsis.

Dynamic mechanical properties of different types of rocks under impact loading.

To study the mechanical properties of different types of rocks under impact loading, static mechanical parameter tests and split-Hopkinson pressure bar (SHPB) dynamic impact experiments were conducted on five typical rock specimens. The mechanical properties and failure modes of different rock specimens under the same static and dynamic loading were investigated. The differences between numerical simulation results and laboratory test results under different constitutive models in LS-DYNA were also compared and analyzed. The results show that with the increase of SHPB impact pressure (0.5-0.8 MPa), the stress peak values of granite, marble, and limestone also increase, while gypsum and reef limestone follow no particular trend. At the same time, both HJC and RHT constitutive models can simulate the laboratory impact test results of granite, marble, and limestone, however, the gypsum and reef limestone are not modelled by the HJC constitutive model, while the RHT constitutive model can describe the deformation-damage-failure process of rock specimens with different strengths. Therefore, the RHT model can better reflect the real deformation and failure of rocks.

Shaping characteristics of excavation contours in sequential controlled fracture blasting of rock-anchored beams in Shuangjiangkou underground powerhouse.

Influences of high in-situ stress generally need to be considered when excavating deep underground caverns. The dynamic fracture behaviors of rocks under blast loads were investigated by using the rock-anchored beam excavation in underground powerhouses of Shuangjiangkou Hydropower Station in Sichuan Province, China as the engineering background. To solve the problems of the poor blasting breakage effect of rocks and the difficulty in protecting surrounding rocks during excavation, mechanical properties of granite under static and dynamic loads were investigated and the sequential controlled fracture blasting (SCFB) method was adopted during in-situ tests. Based on the Riedel-Hiermaier-Thoma constitutive model and the strength criterion, software LS-DYNA was employed to simulate the dynamic propagation of blasting-induced cracks. The contour shaping effect obtained via numerical simulation is generally consistent with the test results. The results show that SCFB can to some extent control the direction of crack initiation and rock fracture behavior of the blasthole wall cracks and the spacing of successive bursting holes is about 10 times the diameter of the blastholes when the cracks between the blastholes are shaped the best effect. Moreover, the magnitude and direction of principal in-situ stress can both affect the propagation path and length of blasting-induced cracks. The results of the research on the excavation and construction of deeply buried underground caverns have a certain reference value.

A fast stop-flow two-dimensional liquid chromatography tandem mass spectrometry and its application in food-derived protein hydrolysates.

Food-derived bioactive peptides have many outstanding features like high safety, easy absorption, etc. However, explorations of the peptides are suffering from the limited knowledge of sample composition and low efficiency of separation techniques. In this work, a fast stop-flow two-dimensional liquid chromatography tandem mass spectrometry (2DLC-MS) was designed and constructed in-house. For chromatographic system optimization, the effects of column pairs and fraction transfer volumes on separation performance were studied. The pair of Protein BEH SEC and HSS T3 columns was found of high orthogonality. The peak capacity detected by the optimized 2DLC reached 1165 (for corn protein hydrolysates), indicating high resolving power. Moreover, the number of peptides identified from corn, soybean and casein protein hydrolysates reached as high as 8330, 8925 and 7215, respectively, demonstrating the high potential of the system. This would help reveal the peptide composition and facilitate the research on exploring bioactive peptides from food-derived protein hydrolysates.

The development of radioresistant oral squamous carcinoma cell lines and identification of radiotherapy-related biomarkers.

BACKGROUND: In the treatment of oral squamous cell carcinoma (OSCC), radiation resistance remains an important obstacle to patient outcomes. Progress in understanding the molecular mechanisms of radioresistance has been limited by research models that do not fully recapitulate the biological features of solid tumors. In this study, we aimed to develop novel in vitro models to investigate the underlying basis of radioresistance in OSCC and to identify novel biomarkers. METHODS: Parental OSCC cells (SCC9 and CAL27) were repeatedly exposed to ionizing radiation to develop isogenic radioresistant cell lines. We characterized the phenotypic differences between the parental and radioresistant cell lines. RNA sequencing was used to identify differentially expressed genes (DEGs), and bioinformatics analysis identified candidate molecules that may be related to OSCC radiotherapy. RESULTS: Two isogenic radioresistant cell lines for OSCC were successfully established. The radioresistant cells displayed a radioresistant phenotype when compared to the parental cells. Two hundred and sixty DEGs were co-expressed in SCC9-RR and CAL27-RR, and thirty-eight DEGs were upregulated or downregulated in both cell lines. The associations between the overall survival (OS) of OSCC patients and the identified genes were analyzed using data from the Cancer Genome Atlas (TCGA) database. A total of six candidate genes (KCNJ2, CLEC18C, P3H3, PIK3R3, SERPINE1, and TMC8) were closely associated with prognosis. CONCLUSION: This study demonstrated the utility of constructing isogenic cell models to investigate the molecular changes associated with radioresistance. Six genes were identified based on the data from the radioresistant cells that may be potential targets in the treatment of OSCC.

Single-base resolution mapping of 2'-O-methylation sites by an exoribonuclease-enriched chemical method.

2'-O-methylation (Nm) is one of the most abundant RNA epigenetic modifications and plays a vital role in the post-transcriptional regulation of gene expression. Current Nm mapping approaches are normally limited to highly abundant RNAs and have significant technical hurdles in mRNAs or relatively rare non-coding RNAs (ncRNAs). Here, we developed a new method for enriching Nm sites by using RNA exoribonuclease and periodate oxidation reactivity to eliminate 2'-hydroxylated (2'-OH) nucleosides, coupled with sequencing (Nm-REP-seq). We revealed several novel classes of Nm-containing ncRNAs as well as mRNAs in humans, mice, and drosophila. We found that some novel Nm sites are present at fixed positions in different tRNAs and are potential substrates of fibrillarin (FBL) methyltransferase mediated by snoRNAs. Importantly, we discovered, for the first time, that Nm located at the 3'-end of various types of ncRNAs and fragments derived from them. Our approach precisely redefines the genome-wide distribution of Nm and provides new technologies for functional studies of Nm-mediated gene regulation.

The expression of CD86 in CD3+CD56+ NKT cells is associated with the occurrence and prognosis of sepsis-associated encephalopathy in sepsis patients: a prospective observational cohort study.

The role of CD3+CD56+ natural killer T (NKT) cells and its co-signaling molecules in patients with sepsis-associated encephalopathy (SAE) is unknown. In this prospective observational cohort study, we initially recruited 260 septic patients and eventually analyzed 90 patients, of whom 57 were in the SAE group and 37 were in the non-SAE group. Compared to the non-SAE group, 28-day mortality was significantly increased in the SAE group (33.3% vs. 12.1%, p = 0.026), while the mean fluorescence intensity (MFI) of CD86 in CD3+CD56+ NKT cells was significantly lower (2065.8 (1625.5 ~ 3198.8) vs. 3117.8 (2278.1 ~ 5349), p = 0.007). Multivariate analysis showed that MFI of CD86 in NKT cells, APACHE II score, and serum albumin were independent risk factors for SAE. Furthermore, the Kaplan-Meier survival analysis indicated that the mortality rate was significantly higher in the high-risk group than in the low-risk group (χ2 = 14.779, p < 0.001). This study showed that the decreased expression of CD86 in CD3+CD56+ NKT cells is an independent risk factor of SAE; thus, a prediction model including MFI of CD86 in NKT cells, APACHE II score, and serum albumin can be constructed for diagnosing SAE and predicting prognosis.

Accelerated Discovery of Macrocyclic CDK2 Inhibitor QR-6401 by Generative Models and Structure-Based Drug Design.

Selective CDK2 inhibitors have the potential to provide effective therapeutics for CDK2-dependent cancers and for combating drug resistance due to high cyclin E1 (CCNE1) expression intrinsically or CCNE1 amplification induced by treatment of CDK4/6 inhibitors. Generative models that take advantage of deep learning are being increasingly integrated into early drug discovery for hit identification and lead optimization. Here we report the discovery of a highly potent and selective macrocyclic CDK2 inhibitor QR-6401 (23) accelerated by the application of generative models and structure-based drug design (SBDD). QR-6401 (23) demonstrated robust antitumor efficacy in an OVCAR3 ovarian cancer xenograft model via oral administration.

ELEVATED PD-1/CD28 RATIO RATHER THAN PD-1 EXPRESSION IN CD8+ T CELLS PREDICTS NOSOCOMIAL INFECTION IN SEPSIS PATIENTS: A PROSPECTIVE, OBSERVATIONAL COHORT STUDY.

ABSTRACTBACKGROUND: The expression of programmed cell death 1 receptor (PD-1) and CD28 on CD8+ T cells is considered to be related to immune function and prognosis markers in patients with sepsis. However, the relationship between the ratio of PD-1/CD28 and nosocomial infection has not been elucidated. Methods: A prospective, observational cohort study was conducted in a general intensive care unit. Patients were enrolled according to the sepsis-3 criteria and peripheral blood samples were collected within 24 hours of enrollment. Programmed cell death 1 receptor and CD28 expression on CD8+ T cells was assayed on day 1. Patients were followed up until 28 days. Multivariate regression analysis was used to assess independent risk factors for nosocomial infection. The accuracy of biomarkers for nosocomial infection and mortality was determined by the area under the receiver operating characteristic curve analysis. The association between biomarkers and 28-day mortality was assessed by Cox regression survival analysis. Results: A total of 181 patients were recruited, and 68 patients were finally included for analysis. Of these, 19 patients (27.9%) died during 28 days and 22 patients (32.4%) acquired nosocomial infection. The PD-1/CD28 ratio of patients with nosocomial infection was significantly higher than those without (0.27 [0.10-0.55] vs. 0.15 [0.08-0.28], P = 0.025). The PD-1/CD28 ratio in CD8+ T cells (odds ratio, 53.33; 95% confidence interval, 2.39-1188.22, P = 0.012) and duration of mechanical ventilation (odds ratio, 1.14; 95% confidence interval, 1.06-1.24; P = 0.001) were independently associated with nosocomial infection. The area under the receiver operating characteristic curve of PD-1/CD28 ratio in CD8+ T cells was 0.67 (0.52-0.82). The PD-1/CD28 ratio in CD8+ T cells of the nonsurvivors was significantly higher than the survivors (0.23 [0.15-0.52] vs. 0.14 [0.07-0.32]); Cox regression analysis showed that the survival time of patients with PD-1/CD28 ratio in CD8+ T cells of 0.13 or greater was shorter compared with patients with lower levels (hazard ratio, 4.42 [1.29-15.20], χ2 = 6.675; P = 0.010). Conclusions: PD-1/CD28 ratio in CD8+ T cells at admission may serve as a novel prognostic biomarker for predicting nosocomial infection and mortality.

Construction of a combined hypoxia and EMT index for head and neck squamous cell carcinoma.

Objectives: In head and neck squamous cell carcinoma (HNSCC), the interaction between epithelial-mesenchymal transformation (EMT) and hypoxia has been confirmed, and corresponding treatment methods have been investigated. Few studies have examined its combined effects and its potential clinical use, however. As a result, we developed a new scoring system based on EMT and hypoxia. Methods: We combined 200 hypoxia-related genes with 1184 EMT-related genes and finally constructed a score risk model containing 14 characteristic factors named the comprehensive index of EMT and hypoxia (CIEH) by the Lasso-Cox regression and univariate Cox regression method, which is used to predict prognosis and to guide treatment planning in HNSCC patients. Furthermore, we examined HNSCC expression of CIEH-related genes using the human protein atlas database. Results: Based on survival analysis results, CIEH value had a high prognostic value in HNSCC patients, a high CIEH value carries a poor prognostic significance in HNSCC. It is noteworthy that the CIEH value was correlated with tumor immune infiltration. Moreover, the CIEH had significant differences in age, stage, N, laterality, and peripheral nerve invasion, and that the CIEH could be an independent prognostic factor. Conclusions: This study constructed a CIEH model containing 14 characteristic factors, including hypoxia-related genes and EMT genes, that may be able to serve as potential biomarkers for HNSCC. According to the 14 characteristic factors in the CIEH model, a diagnostic kit can be packaged in the future to evaluate the survival of patients before tumor surgery and guide the subsequent treatment plan.

Study on timing sequence control fracture blasting excavation of deep rock masses with filled joints.

During the blasting excavation of deep underground caverns, the effects of the structural surface on crack propagation are usually considered in addition to the clamping effects of high in situ stress. Based on the notched borehole and timing sequence control (TSC) fracture blasting method, this paper studies the effects of different borehole shapes on the degree of damage of the surrounding rock and profile flatness of the rock anchor beams and the effects of different filled joint characteristics on the blasting crack propagation rules. The results show that the damage depth of the surrounding rocks by round hole smooth blasting is approximately twice that by notched hole smooth blasting, by which the profile formed is flatter. The notched primary borehole (PBH) remains a strong guidance for crack propagation in a rock mass with filled joints, while the stress concentration effects of the round target borehole (TBH) cannot fully guide the cracks until they fall within a certain distance between the PBH and TBH. It is favourable for cracks to propagate along the lines between boreholes with larger filled joint strengths and larger angles between boreholes.

PPV distribution of sidewalls induced by underground cavern blasting excavation.

The peak particle velocity (PPV) is an important indicator for predicting blasting excavation disturbances. However, the PPV distribution in the deep underground space is significantly different from that on the outdoor ground. Therefore, it is difficult to predict the underground PPV by Sadovsky's vibration formula. The PPV sidewall distribution characteristics were studied during site blasting in an underground cavern in the Taohuazui mine in China, and a similar numerical model was used to verify the site test data. We derived a PPV prediction formula for the underground cavern sidewall surrounding rock using a mechanical analysis model of a simply supported plate and beam in combination with dimensional analysis. The model considered derived boundary constraints, comparison with site measured data, the value predicted by Sadovsky's vibration formula, and numerical simulation results. The results showed that the PPV distribution on the middle 1/3 section of the underground cavern sidewall showed a "platform" or "bulge" different from the curve from Sadovsky's vibration formula. The PPV amplification coefficient in this section was distributed in a drum shape. The PPV prediction formula for the middle section of the sidewall derived in this paper was highly consistent with the data measured on-site and the numerical simulation results. The mechanical analysis model with a simply supported plate and beam included an underground cavern sidewall length-height ratio of 5 and effectively supplemented the PPV prediction formula for the middle section of the traditional underground cavern sidewall.