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Abstract Background Numerous studies have characterized the gut microbiome (GM) in lung cancer (LC). Yet, the causality between GM and LC and its subtypes remain uncharacterized. Methods Two‐sample Mendelian randomization (MR) was designed to investigate the causal relationship between the GM and LC and its subtypes, using publicly available summary data of genome‐wide association studies. The researchers ran two groups of MR analyses, including the genome‐wide statistical significance threshold (5 × 10−8) and the locus‐wide significance level (1 × 10−5). Results Using MR analysis, we ascertained 42 groups of GM that are intimately linked to LC and its subtypes at the locus‐wide significance level. Of the 42 groups, 12 were in LC, nine in non‐small cell lung cancer (NSCLC), six in small cell lung cancer (SCLC), two in lung adenocarcinomas, and 13 in lung squamous carcinomas. After false discovery rate correction, we still found a remarkable causal interaction between the Eubacterium ruminantium group and SCLC. Moreover, five groups of GM closely linked to LC and its subtypes were recognised at the genome‐wide statistical significance threshold. This finding included one group each in LC, NSCLC and SCLC, two groups in lung adenocarcinoma and none in lung squamous carcinoma. None of the foregoing findings were heterogeneous or horizontal pleiotropy. Reverse MR revealed that genetic susceptibility to LC and its subtypes caused significant changes in three groups of GM. Conclusion Our findings substantiate the causality between GM and LC and its subtypes. This study offers fresh insights into the function of GM in mediating the progression of LC.

Background: The long-term prognosis for patients with osteosarcoma (OS) metastasis remains unfavourable, highlighting the urgent need for research that explores potential biomarkers using innovative methodologies. Methods: This study explored potential biomarkers for OS metastasis by analysing data from the Cancer Genome Atlas Program (TCGA) and Gene Expression Omnibus (GEO) databases. The synthetic minority oversampling technique (SMOTE) was employed to tackle class imbalances, while genes were selected using four feature selection algorithms (Monte Carlo feature selection [MCFS], Borota, minimum-redundancy maximum-relevance [mRMR], and light gradient-boosting machine [LightGBM]) based on the gene expression matrix. Four machine learning (ML) algorithms (support vector machine [SVM], extreme gradient boosting [XGBoost], random forest [RF], and k-nearest neighbours [kNN]) were utilized to determine the optimal number of genes for building the model. Interpretable machine learning (IML) was applied to construct prediction networks, revealing potential relationships among the selected genes. Additionally, enrichment analysis, survival analysis, and immune infiltration were performed on the featured genes. Results: In DS1, DS2, and DS3, the IML algorithm identified 53, 45, and 46 features, respectively. Using the merged gene set, we obtained a total of 79 interpretable prediction rules for OS metastasis. We subsequently conducted an in-depth investigation on 39 crucial molecules associated with predicting OS metastasis, elucidating their roles within the tumour microenvironment. Importantly, we found that certain genes act as both predictors and differentially expressed genes. Finally, our study unveiled statistically significant differences in survival between the high and low expression groups of TRIP4, S100A9, SELL and SLC11A1, and there was a certain correlation between these genes and 22 various immune cells. Conclusions: The biomarkers discovered in this study hold significant implications for personalized therapies, potentially enhancing the clinical prognosis of patients with OS.

Summary: The typical genomic feature of acute myeloid leukemia (AML) M3 subtype is the fusion event of PML/RARα, and ATRA/ATO-based combination therapy is current standard treatment regimen for M3 subtype. Here, a machine-learning model based on expressions of PML/RARα targets was developed to identify M3 patients by analyzing 1228 AML patients. Our model exhibited high accuracy. To enable more non-M3 AML patients to potentially benefit from ATRA/ATO therapy, M3-like patients were further identified. We found that M3-like patients had strong GMP features, including the expression patterns of M3 subtype marker genes, the proportion of myeloid progenitor cells, and deconvolution of AML constituent cell populations. M3-like patients exhibited distinct genomic features, low immune activity and better clinical survival. The initiative identification of patients similar to M3 subtype may help to identify more patients that would benefit from ATO/ATRA treatment and deepen our understanding of the molecular mechanism of AML pathogenesis.

Abstract Communications between tumor cells and surrounding immune cells help shape the tumor immunity continuum. Recent breakthroughs in high-throughput technologies as well as computational algorithms had reported many important tumor-immune cell (TIC) communications, which were scattered in thousands of published studies and impeded systematical characterization of the TIC communications across cancer. Here, a comprehensive database, TICCom, was developed to model TIC communications, containing 739 experimentally-validated or manually-curated interactions collected from more than 3,000 literatures as well as 4,537,709 predicted interactions inferred via six computational algorithms by reanalyzing 32 scRNA-seq datasets and bulk RNA-seq data across 25 cancer types. The communications between tumor cells and 14 types of immune cells were characterized, and the involved ligand-receptor interactions were further integrated. 14190 human and 3650 mouse integrated ligand-receptor interactions with supplemented corresponding function information were also stored in the TICCom database. Our database would serve as a valuable resource for investigating TIC communications.

In this study, a cationic amphiphilic self-assembling peptide (SAP) Z23 was designed, and a simple bisphenol a (BPA) sensor, based on SAP Z23/multiwalled carbon nanotubes (Z23/MWCNTs) composite, was successfully fabricated on the surface of a glassy carbon electrode (GCE). The composite material was formed by π-π stacking interaction between the aromatic group on the hydrophobic side of Z23 and the side-wall of MWCNTs, with the charged hydrophilic group of Z23 exposed. During the electrocatalytic process of BPA, a synergistic effect was observed between Z23 and MWCNTs. The current response of the sensor based on composite material was 3.24 times that of the MWCNTs-modified electrode, which was much higher than that of the peptide-based electrode. Differential pulse voltammetry (DPV) was used to optimize the experimental conditions affecting the analytical performance of the modified electrode. Under optimal conditions, the linear range of the sensor was from 10 nM to 100 μM by amperometric measurement with sensitivity and limit of detection (LOD) at 6.569 μAμM−1cm−2 and 1.28 nM (S/N = 3), respectively. Consequently, the sensor has excellent electrochemical performance and is easy to fabricate, making it a good prospect in the field of electrochemical detection in the future.

Hawthorn leaves also known as crataegi foilum, are a combination of botanical drugs used commonly in Traditional Chinese Medicine. Hawthorn, the plant from which hawthorn leaves are prepared, is distributed in Northeast China, North China, and other regions in China. Hawthorn leaves are known to activate blood circulation and eliminate stasis, invigorating Qi, eliminating turbidity, and reducing the levels of lipids. So far, over a hundred compounds have been isolated from hawthorn leaves, including flavonoids, terpenoids, lignans, organic acids, and nitrogenous compounds. Hawthorn leaves are used for the treatment of hypertension, protecting against ischemic injury, angina, hyperglycemia, hyperlipidemia, and certain other conditions. Several of the currently available clinical preparations also use hawthorn leaves as raw materials, such as Yixintong capsules, Xinan capsules, etc. The present report systematically reviews the chemical composition, biological activities, and quality standards of hawthorn leaves, to provide a scientific basis and reference for detailed research on hawthorn leaves.

Abstract Finding effective strategies to design efficient photocatalysts and decompose refractory organic compounds in wastewater is a challenging problem. Herein, by coupling element doping and constructing heterostructures, S‐scheme CdS QDs/La‐Bi2WO6 (CS/LBWO) photocatalysts are designed and synthesized by a simple hydrothermal method. As a result, the RhB degradation efficiency of the optimized 5% CS/LBWO reached 99% within 70 min of illumination with excellent stability and recyclability. CS/LBWO shows improvement in the adsorption range of visible light and promotes electron–hole pair generation/migration/separation, attributing the superior degradation performance. The degradation RhB mechanism is proposed by a free radical capture experiment, electron paramagnetic resonance, and high‐performance liquid chromatography‐mass spectrometry results, indicating that h+ and •O2– play a significant role during four degradation processes: de‐ethylation, chromophore cleavage, ring opening, and mineralization. Based on in situ irradiated X‐ray photoelectron spectroscopy, Mulliken electronegativity theory, and the work function results, the S‐scheme heterojunction of CS/LBWO promotes the transfer of photogenerated electron–hole pairs and promotes the generation of reactive radicals. This work not only reports that 5% CS/LBWO is a promising photocatalyst for degradation experiments but also provides an approach to design advanced photocatalysts by coupling element doping and constructing heterostructures.

LncRNA-lncRNA immune cooperative regulations are identified by integrating multi-omics data across 20 cancer types and the roles of immune cooperative lncRNAs in tumor-immune functions are explored.

The synuclein family, consisting of α-, β-, and γ-synuclein, is primarily expressed in neurons. Mutations of α- and β-synuclein have been linked to Parkinson’s disease and dementia with Lewy bodies, respectively. Recent studies have shown that synucleins are upregulated in various tumors, including breast, ovarian, meningioma, and melanoma, and high synuclein expression is associated with poor prognosis and drug resistance. We report a novel rearrangement of β-synuclein in a pediatric T-cell acute lymphoblastic leukemia (T-ALL) case, where β-synuclein (SNCB) is fused in-frame with ETS variant transcription factor 6 (ETV6), a gene frequently rearranged in acute leukemia including acute myeloid leukemia (AML), B-cell acute lymphoblastic leukemia (B-ALL), and T-ALL. An additional case of β-synuclein rearrangement was identified in a squamous cell carcinoma of the lung through analysis of the public TCGA database. Both rearrangements involve the C-terminal of β-synuclein. Since β-synuclein shares extensive amino acid similarities with α-synuclein and α-synuclein binds to 14-3-3, an important regulator of apoptosis, the rearranged β-synuclein may contribute to tumorigenesis by deregulating apoptosis. In addition, overexpression of synucleins has been shown to increase cell proliferation, suggesting that the rearranged β-synuclein may also deregulate the cell cycle.

The electronic, optical, and magnetic properties of Nd-doped ZnO systems were calculated using the DFT/GGA + U method. According to the results, the Nd dopant causes lattice parameter expansion, negative formation energy, and bandgap narrowing, resulting in the formation of an N-type degenerate semiconductor. Overlapping of the generated impurity and Fermi levels results in a significant trap effect that prevents electron-hole recombination. The absorption spectrum demonstrates a redshift in the visible region, and the intensity increased, leading to enhanced photocatalytic performance. The Nd-doped ZnO system displays ferromagnetic, with FM coupling due to strong spd-f hybridization through magnetic exchange interaction between the Nd-4f state and O-2p, Zn-4s, and Zn-3p states. These findings imply that Nd-doped ZnO may be a promising material for DMS spintronic devices.

BackgroundThis study aimed to establish an effective model for preoperative prediction of tumor deposits (TDs) in patients with rectal cancer (RC). MethodsIn 500 patients, radiomic features were extracted from magnetic resonance imaging (MRI) using modalities such as high-resolution T2-weighted (HRT2) imaging and diffusion-weighted imaging (DWI). Machine learning (ML)-based and deep learning (DL)-based radiomic models were developed and integrated with clinical characteristics for TD prediction. The performance of the models was assessed using the area under the curve (AUC) over five-fold cross-validation.ResultsA total of 564 radiomic features that quantified the intensity, shape, orientation, and texture of the tumor were extracted for each patient. The HRT2-ML, DWI-ML, Merged-ML, HRT2-DL, DWI-DL, and Merged-DL models demonstrated AUCs of 0.62 ± 0.02, 0.64 ± 0.08, 0.69 ± 0.04, 0.57 ± 0.06, 0.68 ± 0.03, and 0.59 ± 0.04, respectively. The clinical-ML, clinical-HRT2-ML, clinical-DWI-ML, clinical-Merged-ML, clinical-DL, clinical-HRT2-DL, clinical-DWI-DL, and clinical-Merged-DL models demonstrated AUCs of 0.81 ± 0.06, 0.79 ± 0.02, 0.81 ± 0.02, 0.83 ± 0.01, 0.81 ± 0.04, 0.83 ± 0.04, 0.90 ± 0.04, and 0.83 ± 0.05, respectively. The clinical-DWI-DL model achieved the best predictive performance (accuracy 0.84 ± 0.05, sensitivity 0.94 ± 0. 13, specificity 0.79 ± 0.04).ConclusionsA comprehensive model combining MRI radiomic features and clinical characteristics achieved promising performance in TD prediction for RC patients. This approach has the potential to assist clinicians in preoperative stage evaluation and personalized treatment of RC patients.

Based on density functional theory (DFT), theoretical models of three kinds of lanthanide rare earth metal ion-doped γ-Bi2MoO6 were constructed (Ln-BMO (Ln=Gd, Ho, Yb)). The geometric structure, electronic structure, and optical properties of the model were calculated, and the influence of doped Ln3+ ions on the structures and properties of the system was analyzed. The results revealed that the substitution of smaller ionic radius Ln3+ ions for Bi3+ ions caused a contraction of the lattice parameters. At the same time, the contribution of the [Ln]4d near valence band and conduction band reduced the bandwidth of γ-Bi2MoO6, forming the Ln-O ionic bond with different strengths to obtain higher charge conductivity and charge-separation ability. Secondly, Ln3+ ions have a strongly ionic charge, which leads to the appearance of optical absorption bands in the infrared region and part of the visible region. This reduces the reflection in the visible region, improves the utilization rate, delays the loss of electron energy, and promotes phase matching in the visible region. And the Gd3+-doped system has better photocatalytic activity than the other Ln3+-doped system. This research provides theoretical insights into doped lanthanide rare earth ions and also provides strategies for the modification of γ-Bi2MoO6 nanomaterials.

Based on the density functional theory, the effect of rare-earth La doping at different concentrations on the electronic structure, optical properties, and magnetic properties of ZnO was calculated by using the GGA+U method under the condition of spin polarization. The calculation results show that the cell of a La-doped ZnO system is distorted, resulting in a formation energy less than zero, in which case it is easy to dope. After La doping, the band gap narrows, the Fermi level enters the conduction band, and the excess carriers induced by La atoms degenerate to form n-type degenerate semiconductor materials. In the visible light region, a blue shift in the optical absorption edge of the La-doped ZnO system causes an increased average static dielectric constant, stronger polarization ability, stronger binding ability on charges, and the photoconductivity of the doped ZnO system is improved. The magnetic moment of the La-doped ZnO system is zero, so it is not magnetic.

ObjectiveTo investigate the association between pretreatment prognostic nutritional index (PNI) and clinical survival outcomes for advanced-stage cancer patients treated with immune checkpoint inhibitors (ICIs).MethodsWe conducted a comprehensive literature search to identify eligible studies concerning the relationship between pretreatment PNI and survival outcomes in advanced cancer patients treated with ICIs. Published data were extracted and pooled odds ratio (pOR) for objective response rate (ORR), disease control rate (DCR), and pooled hazard ratio (pHR) for overall survival (OS), progressive-free survival (PFS), along with 95% confidence intervals (95% CIs) were calculated.ResultsTwelve studies with 1,359 participants were included in our study. A higher level of PNI indicated a greater ORR (pOR = 2.17, 95% CI = 1.52–3.10) and favorable DCR (pOR = 2.48, 95% CI = 1.87–3.29). Low PNI was associated with a shorter OS (pHR = 2.24, 95% CI = 1.57–3.20) and unfavorable PFS (pHR = 1.61, 95% CI = 1.37–1.88).ConclusionLow PNI might be an effective biomarker of poor tumor response and adverse prognosis of advanced cancer patients with ICIs. Further studies are needed to verify the prognostic value of PNI in clinical practice.

AimsTo compare the antifungal efficacy of corneal cross-linking (CXL) and voriconazole in experimental Aspergillus keratitis models.MethodsThirty-nine New Zealand rabbits were divided into three groups: a control group, a voriconazole group (M group), and a voriconazole combined with CXL group (CXL-M group). The ulcer area was measured via slit lamp imaging, the corneal and corneal epithelial thickness, and ulcer depth was measured via anterior segment optical coherence tomography (AS-OCT). The existence time of the hyphae was observed via in vivo confocal microscopy (IVCM), and the cornea was taken for pathological examination after modeling and at the end of the study to determine the hyphae and corneal repair. The observation times were as follows: at successful modeling and at 1, 4, 7, 14, 21, and 28 days after intervention.ResultsIn the CXL-M group, ulcer area and depth decreased continuously from Day 4 to Day 28 after CXL (all P < 0.05). In the CXL-M group, ulcer area and depth were smaller than those in the other two groups from Day 4 to Day 21 after CXL (all P < 0.05, except ulcer area in the CXL-M vs. M group on Day 21). The duration of hyphae in the CXL-M group was significantly shorter than in the other two groups (P = 0.025). On Day 28, in CXL-M group, corneal thickness was thicker than baseline (P < 0.05). Meanwhile, in CXL-M group, corneal and corneal epithelial thickness were significantly thinner than in the other two groups (P < 0.001). The CXL-M group had no complications, such as corneal perforation, at the end of the study.ConclusionsVoriconazole combined with CXL is effective in treating Aspergillus-infected keratitis. Combined therapy could effectively inhibit Aspergillus, accelerate corneal repair, and shorten the course of the disease.

The incidence of hepatocellular carcinoma (HCC) is increasing worldwide. Extracellular vesicles (EVs) contain sufficient bioactive substances and are carriers of intercellular information exchange, as well as delivery vehicles for nucleic acids, proteins and drugs. Although EVs show great potential for the treatment of HCC and their role in HCC progression has been extensively studied, there are still many challenges such as time-consuming extraction, difficult storage, easy contamination, and low drug loading rate. We focus on the biogenesis, morphological characteristics, isolation and extraction of EVs and their significance in the progression of HCC, tumor invasion, immune escape and cancer therapy for a review. EVs may be effective biomarkers for molecular diagnosis of HCC and new targets for tumor-targeted therapy.

Objective To explore independent risk factors for incomplete radiofrequency ablation (iRFA) of colorectal cancer liver metastases (CRLM) and evaluate adverse outcomes following iRFA. Materials and Methods Magnetic resonance imaging data of CRLM patients who received percutaneous RFA were randomized into training (70%) and validation set 1 (30%) data sets. An independent validation set 2 was derived from computed tomography scans. Uni- and multivariate analyses identified independent risk factors for iRFA. Area under the curve (AUC) values were used to evaluate the predictive model performance. Risk points were assigned to independent predictors, and iRFA was predicted according to the total risk score. Kaplan–Meier curves were used to assess new intrahepatic metastases (NIHM), unablated tumor progression, and overall survival (OS). Results Multivariate regression determined as independent iRFA risk factors perivascular tumor location, subcapsular tumor location, tumor size ≥20 mm, and minimal ablative margin ≤5 mm. The AUC values of the model in the training set, validation set 1, and validation set 2 were 0.867, 0.772, and 0.820, respectively. The respective AUC values of the total risk score were 0.864, 0.768, and 0.817. During the 6-year follow-up, the cumulative OS was significantly shorter in the iRFA than in the complete RFA group, and NIHM (hazard ratio [HR] = 2.79; 95% confidence interval [CI]: 1.725, 4.513) and unablated tumor progression (HR = 3.473; 95% CI: 1.506, 8.007) were more severe. Conclusions Perivascular tumor location, subcapsular tumor location, tumor size ≥20 mm, and minimal ablative margin ≤5 mm were independent risk factors for iRFA. iRFA may be a potential predictor of NIHM, unablated tumor progression, and OS.

PurposeTo evaluate peripapillary vascular reactivity in primary open-angle glaucoma (POAG) with and without high myopia (HM) by using optical coherence tomography angiography (OCTA).MethodsThis prospective study enrolled 48 eyes with POAG, including 16 and 32 eyes with and without HM, respectively. The retinal peripapillary vessel density (VD) was repeatedly assessed using OCTA at baseline and after a hyperoxia test (breathing 80% oxygen). The VD changes between different oxygenation conditions were calculated to reflect the vasoreactivity. Linear regression was performed to determine the relationship between myopia and retinal vascular reactivity in patients with POAG. Systemic hemodynamic characteristics were also evaluated under both conditions.ResultsThe VD was significantly reduced after hyperoxia in the whole image (baseline and hyperoxia: 41.4 ± 4.5 and 38.8 ± 4.4, respectively, P < 0.001) and in the peripapillary regions (44.3 ± 5.7 and 41.1 ± 5.4, respectively, P < 0.001) in POAG eyes without HM. However, in eyes with HM, the whole-image VD in hyperoxia was not significantly different from the baseline (baseline and hyperoxia: 40.5 ± 6.2 and 40.2 ± 6.2, respectively, P = 0.481). The VD changes in eyes with HM were significantly smaller than those in eyes without HM in both the whole image (0.3 ± 1.8 and 2.6 ± 2.0, respectively, P < 0.001) and peripapillary regions (1.1 ± 2.0 and 3.2 ± 2.3, respectively, P = 0.003). Linear regression results showed a significant correlation between retinal vascular reactivity and spherical equivalent (SE) (β = 0.28, P < 0.001, R2 = 0.31) and axial length (AL) (β = −0.72, P < 0.001, R2 = 0.33).ConclusionRetinal vasoreactivity of peripapillary capillaries in POAG eyes with HM was significantly impaired in comparison with that in POAG eyes without HM. A lower peripapillary vascular response was significantly associated with worse SE and elongated AL.

Abstract Background Long noncoding RNAs (lncRNAs) are emerging as critical regulatory elements and play fundamental roles in the biology of various cancers. However, we are still lack of knowledge about their expression patterns and functions in human colorectal cancer (CRC). Methods Differentially expressed lncRNAs in CRC were identified by bioinformatics screen and the level of MIR22HG in CRC and control tissues were determined by qRT-PCR. Cell viability and migration capacities were examined by MTT and transwell assay. Mouse model was used to examine the function and rational immunotherapy of MIR22HG in vivo. Results We systematically investigated the expression pattern of lncRNAs and revealed MIR22HG acts as a tumor suppressor in CRC. The expression of MIR22HG was significantly decreased in CRC, which was mainly driven by copy number deletion. Reduced expression of MIR22HG was significantly associated with poor overall survival. Silencing of MIR22HG promoted cell survival, proliferation and tumor metastasis in vitro and in vivo. Mechanistically, MIR22HG exerts its tumor suppressive activity by competitively interacting with SMAD2 and modulating the activity of TGFβ pathway. Decreased MIR22HG promoted the epithelial-mesenchymal transition in CRC. Importantly, we found that MIR22HG expression is significantly correlated with CD8A and overexpression of MIR22HG triggers T cell infiltration, enhancing the clinical benefits of immunotherapy. Conclusion MIR22HG acts as a tumor suppressor in CRC. Our data provide mechanistic insights into the regulation of MIR22HG in TGFβ pathway and facilitates immunotherapy in cancer.

Introduction. To compare accelerated and standard corneal collagen cross-linking (CXL) treatments in experimental Aspergillus keratitis models. Methods. Twenty-six New Zealand rabbits were divided into two groups: a 1% voriconazole combined with standard CXL group, and a 1% voriconazole combined with accelerated CXL group. The ulcer area, corneal opacity, and corneal neovascularization score were measured via slit-lamp imaging, and the corneal and corneal epithelial thickness and ulcer depth were measured via anterior segment optical coherence tomography (AS-OCT). The duration of the hyphae was observed via in vivo confocal microscopy (IVCM), and the cornea was taken for pathological examination after modeling and at the end of the study to determine the hyphae and corneal repair. The observation times were as follows: at successful modeling (day 0) and at 1, 4, 7, 14, 21, and 28 days after the intervention. Results. The area and depth of the ulcer decreased in both groups after CXL (all P

Overlapping disease aetiologies associated with multiple altered biological processes have been identified that change the endometrial function leading to recurrent implantation failure (RIF) and recurrent early pregnancy loss (REPL). We aimed to provide a detailed insight into the nature of the biological malfunction and related pathways of differentially expressed genes in RIF and REPL. Endometrial biopsies were obtained from 9 women experiencing RIF, REPL and control groups. Affymetrix microarray analysis was performed to measure the gene expression level of the endometrial biopsies. Unsupervised clustering of endometrial samples shows scattered distribution of gene expression between the RIF, REPL and control groups. 2556 and 1174 genes (p value < 0.05, Fold change > 1.2) were significantly altered in the endometria of RIF and REPL patients’ group, respectively compared to the control group. Downregulation in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the differentially expressed genes (DEGs) in RIF and REPL including ribosome and oxidative phosphorylation pathways. Gene Ontology (GO) analysis revealed ribosomes and mitochondria inner membrane as the most significantly downregulated cellular component (CC) affected in RIF and REPL. Determination of the dysregulated genes and related biological pathways in RIF and REPL will be key in understanding their molecular pathology and of major importance in addressing diagnosis, prognosis, and treatment issues

Human papillomavirus (HPV) is a double-stranded DNA (dsDNA) virus, and its high-risk subtypes increase cancer risks. However, the mechanism of HPV infection and pathogenesis still remain unclear. Therefore, understanding the molecular mechanisms and the pathogenesis of HPV are crucial in the prevention of HPV-related cancers. In this study, we analyzed cervix squamous cell carcinoma (CESC) and head and neck carcinoma (HNSC) combined data to investigate various HPV-induced cancer common features. We showed that epidermal growth factor receptor (EGFR) was downregulated in HPV-positive (HPV+) cancer, and that HPV+ cancer patients exhibited better prognosis than HPV-negative (HPV−) cancer patients. Our study also showed that TP53 mutation rate is lower in HPV+ cancer than in HPV− cancer and that TP53 can be modulated by HPV E7 protein. However, there was no significant difference in the expression of wildtype TP53 in both groups. Subsequently, we constructed HPV-human interaction network and found that EGFR is a critical factor. From the network, we also noticed that EGFR is regulated by HPV E7 protein and hsa-miR-944. Moreover, while phosphorylated EGFR is associated with a worse prognosis, EGFR total express level is not significantly correlated with prognosis. This indicates that EGFR activation will induce a worse outcome in HPV+ cancer patients. Further enrichment analysis showed that EGFR downstream pathway and cancer relative pathway are diversely activated in HPV+ cancer and HPV− cancer. In summary, HPV E7 protein downregulates EGFR that downregulates phosphorylated EGFR and inhibit EGFR-related pathways which in turn and consequently induce better prognosis.

Using cetyltrimethylammonium bromide (CTAB) as the surfactant from the precursors of SnCl2·2H2O, the flower-shaped nano composite of tin oxide (SnO2) is prepared by the simple eco-friendly hydrothermal method. We can see that the as-prepared SnO2 sample has a rutile phase crystal structure with regular-shaped nanosheets, and the nanosheets were cross-assembled to form nanoflowers. The band gap of the as-prepared SnO2 sample is 2.26 eV, which is close to the calculated energy gap of 2.58 eV based on density functional theory. The sample is used to degrade the organic dye, and this preliminary application study indicates that the as-prepared SnO2 sample has good stability and reusability in the visible light assisted degradation of methyl orange. Through capture experiments, it is determined that electrons and holes play a major role in the degradation process. The reaction mechanism is also analyzed to indicate the internal relationship between the as-prepared SnO2 samples and its photocatalytic properties.

Background: Effective treatments for coronavirus disease 2019 (COVID-19) are urgently needed. The real role of corticosteroid use in COVID-19 has long been of interest and is disputable.Methods: We aimed to quantitatively reevaluate the efficacy of corticosteroids on COVID-19. Databases were searched for eligible meta-analyses/systematic reviews with available outcome data. For each association, we estimated the summary effect size with fixed- and random-effects models, 95% confidence intervals, and 95% prediction intervals. Heterogeneity, Egger’s test, evidence of small-study effects and excess significance bias, and subgroup analyses were rigorously evaluated.Results: Intended outcomes of 12 eligible studies were mortality, clinical improvement, hospitalization, mechanical ventilation (MV), adverse events (AEs), intensive care unit (ICU) stay, hospital stay, virus clearance time (VCT), and negative conversion. Corticosteroid administration was associated with a 27% risk reduction in MV [hazard ratio (HR): 0.73 (0.64–0.83)] and a 20% reduction in mortality of critically ill/severe COVID-19 patients [HR: 0.80 (0.65–0.98)]. Interestingly, shorter ICU stays and, conversely, potentially longer hospital stays, a longer VCT, and a longer time to negative conversion were associated with corticosteroid use. There was no significant impact of different corticosteroid doses on mortality. Only one study showed slightly excess significant bias. Caution should be applied given the weak nature of the evidence, and it has been confirmed by sensitivity analyses too.Conclusion: This umbrella study found benefits from corticosteroids on MV and especially the mortality of critically ill/severe patients with shorter ICU stays but prolonged hospital stays and VCT. The benefits and harms should be reevaluated and balanced before corticosteroids are cautiously prescribed in clinical practice.

Although accumulating evidence has demonstrated the key roles of enhancers in gene expression regulation, the contribution of genome-wide enhancer-enhancer interactions to developmental decisions remains unclear. Here we explored the cooperative regulation patterns among enhancers to understand their regulatory mechanism. We first filtered robust enhancers in embryonic stem cells (ESCs) through integrating bidirectional transcription, genomic location, and epigenetic modification. Genome-wide enhancer-enhancer interactions were then identified based on enhancer-promoter relationships that were derived from Hi-C data. We further explored the interacting principles of the identified enhancer-enhancer interactions. The results revealed that the observed cooperativity occurred mainly between enhancers distributed within a 1-kb to 10-Mb distance across the genome. In addition, enhancer-enhancer pairs had higher expression correlations than non-interacting pairs. Finally, we identified robust enhancers during human cardiac commitment, and we found that enhancers exhibited strong stage-specific expression patterns. We further inferred the enhancer-enhancer interactions based on RNA sequencing (RNA-seq) data in heart development, according to the regulatory principles characterized from Hi-C data. The identified enhancer-enhancer interaction networks (EEINs) presented highly dynamic linkages. Moreover, enhancers cooperatively targeted many marker genes in each developmental stage to regulate stage-specific functions, which contribute to the organization of cell identity in heart development. Our work will increase the understanding of enhancer regulation in human heart development. Keywords: enhancer, eRNA, histone modification, cooperative regulation, heart development, Hi-C, RNA-seq

Abstract Background Acute myeloid leukemia (AML) pertains to a hematologic malignancy with heterogeneous therapeutic responses. Improvements in risk stratification in AML patients are warranted. MicroRNAs have been associated with the pathogenesis of AML. Methods To examine the prognostic value of miR-25, 162 cases with de novo AML were classified into two groups according to different treatment regimens. Results In the chemotherapy group, cases with upregulated miR-25 expression showed relatively longer overall survival (OS; P = 0.0086) and event-free survival (EFS; P = 0.019). Multivariable analyses revealed that miR-25 upregulation is an independent predictor for extended OS (HR = 0.556, P = 0.015) and EFS (HR = 0.598, P = 0.03). In addition, allogeneic hematopoietic stem cell transplantation (allo-HSCT) circumvented the poor prognosis that was related to miR-25 downregulation with chemotherapy. The expression level pattern of miR-25 coincided with AML differentiation and proliferation, which included HOXA and HOXB cluster members, as well as the HOX cofactor MEIS1. The MYH9 gene was identified as a direct target of miR-25. Conclusions The miR-25 levels are correlated with prognosis in AML independently of other powerful molecular markers. The expression of miR-25 may contribute to the selection of the optimal treatment regimen between chemotherapy and allo-HCST for AML patients.

Abstract In the age of big data, service recommendation has provided an effective manner to filter valuable information from massive data. Generally, by observing the past service invocation records (Boolean values) distributed across different cloud platforms, a recommender system can infer personalized preferences of a user and recommend him/her new services to gain more profits. However, the historical service invocation records are a kind of private information for users. Therefore, how to protect sensitive user data distributed across multiple cloud platforms is becoming a necessity for successful service recommendations. Additionally, the historical service invocation records often update with time, which call for an efficient and scalable service recommendation method. In view of these challenges, we introduce the multi-probe Simhash technique in information retrieval domain into the recommendation process and further put forward a privacy-preserving recommendation method based on historical service invocation records. At last, we design several experiments on the real-world service quality data in set WS-DREAM. Experimental results show the feasibility of the proposal in terms of producing accurate recommended results while protecting users’ private information contained in historical service invocation records.

Abstract Background Acute myeloid leukemia (AML) is a highly heterogeneous malignancy with various outcomes, and therefore needs better risk stratification tools to help select optimal therapeutic options. Methods In this study, we identify miRNAs that could predict clinical outcome in a heterogeneous AML population using TCGA dataset. Results We found that MiR-363 is a novel prognostic factor in AML patients undergoing chemotherapy. In multivariable analyses, high miR-363 remained predictive for shorter OS (HR = 2.349, P = 0.012) and EFS (HR = 2.082, P = 0.001) independent of other well-known prognostic factors. More importantly, allogeneic hematopoietic stem cell transplantation (allo-HSCT) overcame the adverse outcomes related to high miR-363 expression. In gene expression profiling, high miR-363 expression was positively correlated with the amounts of leukemogenic transcription factors, including Myb, RUNX3, GATA3, IKZF3, ETS1 and MLLT3. Notably, we found that the in silico predicted target genes (EZH2, KLF6 and PTEN) of miR-363 were downregulated in association with high miR-363 expression. Conclusions In summary, miR-363 expression may help identify patients in need of strategies to select the optimal therapy between chemotherapeutic and allo-HCST regimens. AML patients with high miR-363 expression may be highly recommended for early allo-HSCT regimen.

Abstract Background To evaluate the ocular surface characteristics and the infestation of Demodex in Chinese paediatric and adult blepharokeratoconjunctivitis (BKC). Methods Fifty consecutive patients with BKC and 50 age- and sex-matched healthy subjects were enrolled. Lid margin characteristics and corneal disorders were evaluated under slit-lamp illumination. Four eyelashes were collected from each eye to examine Demodex infestation by light microscopy. Results Corneal neovascularization (P = 0.001) and scarring (P = 0.040) were significantly worse in children than in adults with BKC, whereas meibum quality was worse in adults (P = 0.008). Diagnosis delay was longer in children with BKC than in adults (2.2 vs 1.2 years, P = 0.022). Demodex infestation was more frequent in subjects with BKC than in healthy subjects (56% vs 26%, P = 0.002). The lid margin inflammation and meibomian gland dysfunction were worse in Demodex-positive subjects than in Demodex-negative subjects with BKC. Conclusions Children with BKC had severer corneal disorders compared with adult BKC patients, which may be caused by a long-delayed diagnosis. Ocular demodicosis was more common in subjects with BKC. Ocular Demodex infestation was associated with worse lid margin inflammation and meibomian gland dysfunction.

Long noncoding RNAs (lncRNAs) have been implicated in cancer biogenesis and prognosis. However, we still lack knowledge on their function during glioma progression. In this study, we analyzed the lncRNA expression profile across 907 glioma patients in grades II, III, and IV. Widespread dynamic expression of lncRNAs during glioma progression was revealed, and we identified 33 onco-lncRNAs and 61 tumor suppressor lncRNAs. We found that the expression of these oncogenic lncRNAs is regulated by grade-specific expressed transcription factors. Based on the “guilt by association” rule, we predicted the potential functions of oncogenic lncRNAs, and the majority of these lncRNAs are involved in cancer hallmarks. Especially we found that CARD8-AS1 regulates the metastatic potential of glioma cell lines in vitro. Integrating clinical information, we identified the 12 protective and 8 risk lncRNAs (such as PWAR6 and CARD8-AS1) in glioma. Finally, an lncRNA-gene functional module was identified to be associated with the survival of patients. The predictive ability of this module signature was further validated in an independent dataset. Our results revealed the dynamic transcriptome transition during glioma progression, indicating that the lncRNA signature could be a useful biomarker that may improve upon our understanding of the molecular mechanisms underlying glioma progression. Keywords: glioma progression, long noncoding RNA, transcription regulation, cancer hallmark, survival

Genome mining is more and more widely used in identifying new enzymes from database. In the present study, we reported a putative xylanase, Pg-Xyn (WP_053166147.1), which originated from a psychrotolerant strain Planomicrobium glaciei CHR 43, and was identified from Genbank by genome mining. Sequence analysis and homology modeling showed that Pg-Xyn belongs to glycosyl hydrolase family 10. On the basis of heterologous expression in E. coli and biochemical characterization, we found Pg-Xyn was most active at pH 9.0 and 80°C and exhibited good stability from pH 5.0 to 12.0 and below 90°C. Pg-Xyn was slightly activated in the presence of Ca2+ and Mg2+, while it was strongly inhibited by Mn2+. The analysis of hydrolysis products showed that Pg-Xyn was an endo-β-1,4-xylanase. In addition, Pg-Xyn performed good deinking ability in a paper deinking test. In consideration of its unique properties, Pg-Xyn might be a promising candidate for application in the paper and pulp industries.

With the increasing growth of web services shared in various mobile edge platforms, it becomes necessary to evaluate all the candidates based on their quality of services to reduce the users’ service selection cost. However, the service quality data released by service providers cannot be simply deemed as trusted due to various subjective or objective reasons, which further produce a series of serious trust-aware service evaluation problems, including service quality data sparsity and lack of feedback incentive. In view of this, we summarize the challenging issues existing in the current research field of trusted mobile edge service evaluation. Afterward, we review the current research status of the trusted service evaluation in the mobile edge environment and discuss one of the typical application scenarios based on trusted service evaluation, that is, recommender systems, as well as their diverse categories. We believe this research could be helpful in assisting a mobile edge platform to build a trusted reputation system for various smart applications hosted in the mobile edge platform.

Long non-coding RNAs (lncRNAs), as important ncRNA regulators, play crucial roles in the regulation of various biological processes, and their aberrant expression is related to the occurrence and development of diseases, which is gradually validated by more and more studies. Alzheimer’s disease (AD) is a chronic neurodegenerative disease that often develops slowly and gradually deteriorates over time. However, which functions the lncRNAs perform in AD are almost unknown. In this study, we performed transcriptome analysis in AD, containing 12,892 known lncRNAs and 19,053 protein-coding genes (PCGs). Further, 14 down-regulated and 39 up-regulated lncRNAs were identified, compared with normal brain samples, which indicated that these lncRNAs might play critical roles in the pathogenesis of AD. In addition, 19 down-regulated and 28 up-regulated PCGs were also detected. Using the differentially expressed lncRNAs and PCGs through the WGCNA method, an lncRNA–mRNA co-expressed network was constructed. The results showed that lncRNAs RP3-522J7, MIR3180-2, and MIR3180-3 were frequently co-expressed with known AD risk PCGs. Interestingly, PCGs in the network are significantly enriched in brain- or AD-related biological functions, including the brain renin–angiotensin system, cell adhesion, neuroprotective role of THOP1 in AD, and so on. Furthermore, it was shown that 18 lncRNAs and 7 PCGs were highly expressed in normal brain tissue relative to other normal tissue types, suggesting their potential as diagnostic markers of AD, especially RP3-522J7, MIR3180-2, MIR3180-3, and CTA-929C8. In total, our study identified a compendium of AD-related dysregulated lncRNAs and characterized the corresponding biological functions of these lncRNAs in AD, which will be helpful to understand the molecular basis and pathogenesis of AD.

Abstract Background Acute myeloid leukemia (AML) is a highly heterogeneous disease. MicroRNAs function as important biomarkers in the clinical prognosis of AML. Methods This study identified miR-425 as a prognostic factor in AML by screening the TCGA dataset. A total of 162 patients with AML were enrolled for the study and divided into chemotherapy and allogeneic hematopoietic stem cell transplantation (allo-HSCT) groups. Results In the chemotherapy group, patients with high miR-425 expression had significantly longer overall survival (OS) and event-free survival (EFS) compared with patients with low miR-425 expression. In multivariate analyses, high miR-425 expression remained independently predictive of a better OS (HR = 0.502, P = 0.005) and EFS (HR = 0.432, P = 0.001) compared with patients with low miR-425 expression. Then, all patients were divided into two groups based on the median expression levels of miR-425. Notably, the patients undergoing allo-HSCT had significantly better OS (HR = 0.302, P

LincRNAs enriched with high H3K4me1 and low H3K4me3 signals often have the enhancer-like features which are named as enhancer-associated lincRNAs (elincRNAs). ElincRNAs are considered to be indispensable for target gene transcription, which play important roles in development, signaling events, and even diseases. In this study, we developed a regularized regression model to identify elincRNAs by integrating the genomic, epigenomic, and regulatory data. Application of the proposed method to mouse ESCs reveals that besides the basic well-known epigenetic features H3K4me1 and H3K4me3, more specific epigenetic features, such as high DNA methylation, high H3K122ac, and H3K36me3 were contributed to mark elincRNAs with the best accuracy and precision. Finally, 3729 elincRNAs were identified in mouse ESCs. Furthermore, the elincRNAs and canonical lincRNAs exhibit distinct genomic features, and elincRNAs have the higher CGI enrichment and lower sequence conservation. Through the analysis of transcription regulation, we found that elincRNAs were significantly regulated by NANOG, POU5F1, SOX2 and ESRRB, and were involved in the core transcriptional regulatory circuitry controlling ES cell state Function enrichment analysis further discovered that elincRNAs tended to regulate specific embryonic development biological processes. These results indicated that these two types of lincRNAs had both specific epigenetic and transcriptional regulation mechanism and display distinct functional characters. In conclusion, we presented a credible computational model to prioritize novel elincRNAs, and depicted the atlas of elincRNAs in mouse ESCs, which would help dissect the function roles of lncRNAs during the mammalian development and diseases.

Acute myeloid leukemia (AML) requires refined risk stratification tools to drive decisions concerning effective therapeutic strategies. Here, genome-wide screening was carried out for identifying miRNA molecules capable of predicting treatment outcome in AML patients based on the TCGA dataset. We identified miR-340 as a prognostic factor for selecting treatment between chemotherapy and allogeneic transplantation (allo-HSCT). In multivariable analyses, low miR-340 expression independently predicted reduced OS (HR = 2.07, P = 0.004) and EFS (HR = 1.909, P = 0.01) independent of other well-known prognostic factors. Meanwhile, allo-HSCT overcome deleterious outcomes related to low miR-340. Cases administered allo-HSCT showed markedly improved OS (HR = 0.316, P < 0.0001) and EFS (HR = 0.391, P = 0.002) in comparison with those receiving chemotherapy in the low miR-340 group. Gene expression assessment revealed that elevated miR-340 amounts were negatively correlated with HOXA/HOXB cluster levels, as well as the amounts of the HOX cofactor MEIS1. Strikingly, in silico analysis pointing to HOXA10, HOXB2, and MEIS1 as miR-340 targets. The miR-340 expression may help identify cases requiring strategies for selecting the optimal therapeutic option between chemotherapy and allo-HCST. AML cases showing low miR-340 levels should be strongly considered for early allo-HSCT treatment.

Background and objective Mediastinal involvement in lung cancer is a highly significant prognostic factor for survival, and accurate staging of the mediastinum will correctly identify patients who will benefit the most from surgery. Positron emission tomography/computed tomography (PET/CT) has become the standard imaging modality for the staging of patients with lung cancer. The aim of this study is to investigate 18-fluoro-2-deoxy-glucose (18F-FDG) PET/CT imaging in the detection of mediastinal disease in lung cancer. Methods A total of 72 patients newly diagnosed with non-small cell lung cancer (NSCLC) who underwent preoperative whole-body 18F-FDG PET/CT were retrospectively included. All patients underwent radical surgery and mediastinal lymph node dissection. Mediastinal disease was histologically confirmed in 45 of 413 lymph nodes. PET/CT doctors analyzed patients’ visual images and evaluated lymph node’s short axis, lymph node’s maximum standardized uptake value (SUVmax), node/aorta density ratio, node/aorta SUV ratio, and other parameters using the histopathological results as the reference standard. The optimal cutoff value for each ratio was determined by receiver operator characteristic curve analysis. Results Using a threshold of 0.9 for density ratio and 1.2 for SUV ratio yielded high accuracy for the detection of mediastinal disease. The lymph node’s short axis, lymph node’s SUVmax, density ratio, and SUV ratio of integrated PET/CT for the accuracy of diagnosing mediastinal lymph node was 95.2%. The diagnostic accuracy of mediastinal lymph node with conventional PET/CT was 89.8%, whereas that of PET/CT comprehensive analysis was 90.8%. Conclusion Node/aorta density ratio and SUV ratio may be complimentary to conventional visual interpretation and SUVmax measurement. The use of lymph node’s short axis, lymph node’s SUVmax, and both ratios in combination is better than either conventional PET/CT analysis or PET/CT comprehensive analysis in the assessment of mediastinal disease in NSCLC patients.

The electronic structure, band structure, density of state, and magnetic properties of Ni-doped zinc-blende (ZB) ZnO are studied by using the first-principles method based on the spin-polarized density-functional theory. The calculated results show that Ni atoms can induce a stable ferromagnetic (FM) ground state in Ni-doped ZB ZnO. The magnetic moments mainly originate from the unpaired Ni 3d orbitals, and the O 2p orbitals contribute a little to the magnetic moments. The magnetic moment of a supercell including a single Ni atom is 0.79 μB. The electronic structure shows that Ni-doped ZB ZnO is a half-metallic FM material. The strong spin-orbit coupling appears near the Fermi level and shows obvious asymmetry for spin-up and spin-down density of state, which indicates a significant hybrid effects from the Ni 3d and O 2p states. However, the coupling of the anti-ferromagnetic (AFM) state show metallic characteristic, the spin-up and spin-down energy levels pass through the Fermi surface. The magnetic moment of a single Ni atom is 0.74 μB. Moreover, the results show that the Ni 3d and O 2p states have a strong p-d hybridization effect near the Fermi level and obtain a high stability. The above theoretical results demonstrate that Ni-doped zinc blende ZnO can be considered as a potential half-metal FM material and dilute magnetic semiconductors.

Background: Infectious keratitis after pterygium surgery is a rare but potentially devastating complication. The present study presents 5 cases of herpes simplex keratitis (HSK) after pterygium surgery. Case Report: This study was conducted in our clinic in a 5-year period from February 2017 to September 2021. The 5 patients were men, aged between 42 and 73 years, with no prior history of herpes simplex virus (HSV) infections. Symptoms appeared near 1 month (median 30 days, range 10 to 70 days) after primary pterygium surgery. Diagnosis was based on clinical symptoms and laboratory test results, such as tear HSV-sIgA, corneal tissue polymerase chain reaction, and next-generation sequencing of metagenomics. The epithelial (1/5) and stromal (4/5) subtypes of HSK were identified. The patients received topical ganciclovir gel, immunosuppressive eyedrops, and oral acyclovir tablets, along with additional surgical interventions if necessary. Three were healed with conservative therapy, 1 eye required amniotic membrane transplantation due to corneal melt, and 1 was perforated and followed by corneal grafting. Finally, a literature review of previous publications on HSK after ocular surgeries was conducted. Conclusions: HSK is a rare but serious complication that can arise after uneventful pterygium surgery. It is worthy of attention that both epithelial and stromal forms can occur. Timely diagnosis and treatment are crucial to prevent unfavorable outcomes. Consequently, routine corneal fluorescein staining, tear sIgA examination, and corneal scraping for polymerase chain reaction or next-generation sequencing of metagenomics should be performed in any suspected cases. [ABSTRACT FROM AUTHOR]

By adopting the first principle method based on density functional theory framework, the geometric structure, electronic structure and optical properties of BiOBr were studied by generalized gradient approximate. Theoretical calculation results have shown that BiOBr is an indirect wide-band gap semiconductor material with a band gap width of 2.19 ev. The analyses of state density and atomic charge arrangement number have shown that the valence band top of BiOBr is mainly contributed by 4p orbitals of O 2p and Br 4p, while the lowest conduction band is mainly formed by Bi 6p orbital. In addition, the charge density has revealed that BiOBr is a hybrid bond semiconductor with strong covalent and weak ionic properties, and has a strong p orbital distribution. The calculation results of optical properties have shown that two obvious dielectric peaks appear in the energy range of 0-15 eV, and the absorption band edge is 448 nm, which is consistent with the experimental results. The above outcomes have the theoretical guiding significance for exploring the potential applications of BiOBr materials, and provide theoretical basis for us to accurately monitor and control the growth of BiOBr materials. [ABSTRACT FROM AUTHOR]

The co-pyrolysis of Salix psammophila and coal was conducted in a pyrolysis reactor. The interaction between coal and S. psammophila at different ratios was investigated. It was found that the promotion and inhibition effects of the co-pyrolysis experiment were more obvious at 20 wt.% and 40 wt.% Salix psammophila, respectively, indicating a certain synergistic effect. The results of the N2 adsorption-desorption experiment showed that the addition of S. psammophila increased the surface area and decreased the pore size of the co-pyrolysis char. The Fourier transform infrared (FT-IR) spectra indicated that the pyrolysis tar contained mainly aromatic rings and fatty compounds. The addition of S. psammophila was beneficial to the decomposition of phenolic hydroxyls, ether bonds, and oxygen-containing heterocyclic rings in the coal tar. However, the addition of 50 wt.% S. psammophila blocked the pores of the coal and thus obstructed its pyrolysis, while the porosity of the copyrolysis char became more abundant. Richer porosity of the char implies great potential to be widely used in the sewage treatment industry. [ABSTRACT FROM AUTHOR]