Genetic and molecular characterization of metabolic pathway-based clusters in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive types of squamous cell carcinoma and represents a significant proportion of esophageal cancer. Metabolic reprogramming plays a key role in the occurrence and development of ESCC. Unsupervised clustering analysis was employed to stratify ESCC samples into three clusters: MPC1-lipid type, MPC2-amino acid type, and MPC3-energy type, based on the enrichment scores of metabolic pathways extracted from the Reactome database. The MPC3 cluster exhibited characteristics of energy metabolism, with heightened glycolysis, cofactors, and nucleotide metabolism, showing a trend toward increased aggressiveness and poorer survival rates. On the other hand, MPC1 and MPC2 primarily involved lipid and amino acid metabolism, respectively. In addition, liquid chromatography‒mass spectrometry-based metabolite profiles and potential therapeutic agents were explored and compared among ESCC cell lines with different MPCs. MPC3 amplified energy metabolism markers, especially carnitines. In contrast, MPC1 and MPC2 predominantly had elevated levels of lipids (primarily triacylglycerol) and amino acids, respectively. Furthermore, MPC3 demonstrated a suboptimal clinical response to PD-L1 immunotherapy but showed increased sensitivity to the doramapimod chemotherapy regimen, as evident from drug sensitivity evaluations. These insights pave the way for a more personalized therapeutic approach, potentially enhancing treatment precision for ESCC patients.

Machine learning-based MRI radiomics for assessing the level of tumor infiltrating lymphocytes in oral tongue squamous cell carcinoma: a pilot study

BACKGROUND

To investigate the value of machine learning (ML)-based magnetic resonance imaging (MRI) radiomics in assessing tumor-infiltrating lymphocyte (TIL) levels in patients with oral tongue squamous cell carcinoma (OTSCC).

METHODS

The study included 68 patients with pathologically diagnosed OTSCC (30 with high TILs and 38 with low TILs) who underwent pretreatment MRI. Based on the regions of interest encompassing the entire tumor, a total of 750 radiomics features were extracted from T2-weighted (T2WI) and contrast-enhanced T1-weighted (ceT1WI) imaging. To reduce dimensionality, reproducibility analysis by two radiologists and collinearity analysis were performed. The top six features were selected from each sequence alone, as well as their combination, using the minimum-redundancy maximum-relevance algorithm. Random forest, logistic regression, and support vector machine models were used to predict TIL levels in OTSCC, and 10-fold cross-validation was employed to assess the performance of the classifiers.

RESULTS

Based on the features selected from each sequence alone, the ceT1WI models outperformed the T2WI models, with a maximum area under the curve (AUC) of 0.820 versus 0.754. When combining the two sequences, the optimal features consisted of one T2WI and five ceT1WI features, all of which exhibited significant differences between patients with low and high TILs (all P < 0.05). The logistic regression model constructed using these features demonstrated the best predictive performance, with an AUC of 0.846 and an accuracy of 80.9%.

CONCLUSIONS

ML-based T2WI and ceT1WI radiomics can serve as valuable tools for determining the level of TILs in patients with OTSCC.

Bulk and single-cell alternative splicing analyses reveal roles of TRA2B in myogenic differentiation

Alternative splicing (AS) disruption has been linked to disorders of muscle development, as well as muscular atrophy. However, the precise changes in AS patterns that occur during myogenesis are not well understood. Here, we employed isoform long-reads RNA-seq (Iso-seq) and single-cell RNA-seq (scRNA-seq) to investigate the AS landscape during myogenesis. Our Iso-seq data identified 61,146 full-length isoforms representing 11,682 expressed genes, of which over 52% were novel. We identified 38,022 AS events, with most of these events altering coding sequences and exhibiting stage-specific splicing patterns. We identified AS dynamics in different types of muscle cells through scRNA-seq analysis, revealing genes essential for the contractile muscle system and cytoskeleton that undergo differential splicing across cell types. Gene-splicing analysis demonstrated that AS acts as a regulator, independent of changes in overall gene expression. Two isoforms of splicing factor TRA2B play distinct roles in myogenic differentiation by triggering AS of TGFBR2 to regulate canonical TGF-β signalling cascades differently. Our study provides a valuable transcriptome resource for myogenesis and reveals the complexity of AS and its regulation during myogenesis.

MRI-based radiomics nomogram for distinguishing solitary fibrous tumor from schwannoma in the orbit: a two-center study

OBJECTIVES

To investigate the value of magnetic resonance imaging (MRI) radiomics for distinguishing solitary fibrous tumor (SFT) from schwannoma in the orbit.

MATERIALS AND METHODS

A total of 140 patients from two institutions were retrospectively included. All patients from institution 1 were randomized into a training cohort (n = 69) and a validation cohort (n = 35), and patients from institution 2 were used as an external testing cohort (n = 36). One hundred and six features were extracted from T2-weighted imaging (T2WI) and contrast-enhanced T1-weighted imaging (CET1WI). A radiomics model was built for each sequence using least absolute shrinkage and selection operator logistic regression, and radiomics scores were calculated. A combined model was constructed and displayed as a radiomics nomogram. Two radiologists jointly assessed tumor category based on MRI findings. The performances of the radiomics models and visual assessment were compared via area under the curve (AUC).

RESULTS

The performances of the radiomics nomogram combining T2WI and CET1WI radiomics scores were superior to those of the pooled readers in the training (AUC 0.986 vs. 0.807, p < 0.001), validation (AUC 0.989 vs. 0.788, p = 0.009), and the testing (AUC 0.903 vs. 0.792, p = 0.093), although significant difference was not found in the testing cohort. Decision curve analysis demonstrated that the radiomics nomogram had better clinical utility than visual assessment.

CONCLUSION

MRI radiomics nomogram can be used for distinguishing between orbital SFT and schwannoma, which may help tumor management by clinicians.

CLINICAL RELEVANCE STATEMENT

It is of great importance and challenging for distinguishing solitary fibrous tumor from schwannoma in the orbit. In the present study, an MRI-based radiomics nomogram were developed and independently validated, which could help the discrimination of the two entities.

KEY POINTS

• It is challenging to differentiate solitary fibrous tumor from schwannoma in the orbit due to similar clinical and image features. • A radiomics nomogram based on T2-weighted imaging and contrast-enhanced T1-weighted imaging has advantages over radiologists. • Radiomics can provide a non-invasive diagnostic tool for differentiating between the two entities.

Evaluation of New Folate Receptor-mediated Mitoxantrone Targeting Liposomes In Vitro

Background: Ligand-mediated liposomes targeting folate receptors (FRs) that are overexpressed on the surface of tumor cells may improve drug delivery. However, the properties of liposomes also affect cellular uptake and drug release.

Objective: Mitoxantrone folate targeted liposomes were prepared to increase the enrichment of drugs in tumor cells and improve the therapeutic index of drugs by changing the route of drug administration.

Methods: Liposomes were prepared with optimized formulation, including mitoxantrone folatetargeted small unilamellar liposome (MIT-FSL), mitoxantrone folate-free small unilamellar liposome (MIT-SL), mitoxantrone folate-targeted large unilamellar liposome (MIT-FLL), mitoxantrone folate-free large unilamellar liposomes (MIT-LL). Cells with different levels of folate alpha receptor (FRα) expression were used to study the differences in the enrichment of liposomes, the killing effect on tumor cells, and their ability to overcome multidrug resistance.

The results of the drug release experiment showed that the particle size of liposomes affected their release behavior. Large single-compartment liposomes could hardly be effectively released, while small single-compartment liposomes could be effectively released, MIT-FSL vs MIT-FLL and MIT-SL vs MIT-LL had significant differences in the drug release rate (P<0.0005). Cell uptake experiments results indicated that the ability of liposomes to enter folic acid receptor-expressing tumor cells could be improved after modification of folic acid ligands on the surface of liposomes and it was related to the expression of folate receptors on the cell surface. There were significant differences in cell uptake rates (p<0.0005) for cells with high FRα expression (SPC-A-1 cells), when MIT-FSL vs MIT-SL and MIT-FLL vs MIT-LL. For cells with low FRα expression (MCF-7 cells), their cell uptake rates were still different (p<0.05), but less pronounced than in SPC-A-1 cells. The results of the cell inhibition experiment suggest that MIT-FLL and MIT-LL had no inhibitory effect on cells, MIT-FSL had a significant inhibitory effect on cells and its IC50 value was calculated to be 4502.4 ng/mL, MIT-SL also had an inhibitory effect, and its IC50 value was 25092.1 ng/mL, there was a statistical difference (p<0.05), MIT-FSL had a higher inhibitory rate than MIT-SL at the same drug concentration. Afterward, we did an inhibitory experiment of different MIT-loaded nanoparticles on MCF-7 cells compared to the drug-resistant cells (ADR), Observing the cell growth inhibition curve, both MIT-FSL and MIT-SL can inhibit the growth of MCF-7 and MCF-7/ADR cells. For MCF- 7 cells, at the same concentration, there is little difference between the inhibition rate of MITFSL and MIT-SL, but for MCF-7/ADR, the inhibition rate of MIT-FSL was significantly higher than that of MIT-SL at the same concentration (P<0.05).

Conclusion: By modifying folic acid on the surface of liposomes, tumor cells with high expression of folic acid receptors can be effectively targeted, thereby increasing the enrichment of intracellular drugs and improving efficacy. It can also change the delivery pathway, increase the amount of drug entering resistant tumor cells, and overcome resistance.

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An MRI-based radiomics nomogram for detecting cervical esophagus invasion in hypopharyngeal squamous cell carcinoma

BACKGROUND

Accurate detection of cervical esophagus invasion (CEI) in HPSCC is challenging but crucial. We aimed to investigate the value of magnetic resonance imaging (MRI)-based radiomics for detecting CEI in patients with HPSCC.

METHODS

This retrospective study included 151 HPSCC patients with or without CEI, which were randomly assigned into a training (n = 101) or validation (n = 50) cohort. A total of 750 radiomics features were extracted from T2-weighted imaging (T2WI) and contrast-enhanced T1-weighted imaging (ceT1WI), respectively. A radiomics signature was constructed using the least absolute shrinkage and selection operator method. Multivariable logistic regression analyses were adopted to establish a clinical model and a radiomics nomogram. Two experienced radiologists evaluated the CEI status based on morphological findings. Areas under the curve (AUCs) of the models and readers were compared using the DeLong method. The performance of the nomogram was also assessed by its calibration and clinical usefulness.

RESULTS

The radiomics signature, consisting of five T2WI and six ceT1WI radiomics features, was significantly associated with CEI in both cohorts (all p < 0.001). The radiomics nomogram combining the radiomics signature and clinical T stage achieved significantly higher predictive value than the clinical model and pooled readers in the training (AUC 0.923 vs. 0.723 and 0.621, all p < 0.001) and validation (AUC 0.888 vs. 0.754 and 0.647, all p < 0.05) cohorts. The radiomics nomogram showed favorable calibration in both cohorts and provided better net benefit than the clinical model.

CONCLUSIONS

The MRI-based radiomics nomogram is a promising method for detecting CEI in HPSCC.

Nd-Mn Molecular Cluster with Searched Targets for Oral Cancer Imaging

In this research, we designed a novel NIR II luminescence imaging probe with targeting effect to accurately track oral squamous cell carcinoma (OSCC) cells. Massive gene expression data were processed by weighted gene co-expression network analysis to establish a network of relationships between genes. After clustering, correlation of clinical information, and gene functional enrichment analysis, MMP1 was predicted to be a biomarker/therapeutic target for OSCC cells. To obtain rare-earth probes with better luminescence in the NIR II region, we adjusted the doping ratio of the rare-earth element (Nd, Gd, Er, and Yb) fraction of the Nd-Mn molecular cluster to optimize its luminescence properties. The results of in vitro targeting experiments showed that Nd-Mn-MMP1Ab can target Cal-27 cells, demonstrating at the cellular level that the MMP1 gene is a biomarker for oral cancer, which also proves that the cancer targets predicted by the bioinformatics approach are correct.

Shoulder MRI-based radiomics for diagnosis and severity staging assessment of surgically treated supraspinatus tendon tears

OBJECTIVE

To develop and validate MRI-based radiomics models capable of evaluating supraspinatus tendon tears within the shoulder joints by using arthroscopy as the reference standard.

METHODS

A total of 432 patients (332 in the training set and 100 in the external validation set) with intact supraspinatus tendon (n = 202) and supraspinatus tendon tear (n = 230, 130 full-thickness tears and 100 partial-thickness tears) were enrolled. Radiomics features were extracted from fat-saturated T2-weighted coronal images. Two radiomics signature models for detecting supraspinatus tendon abnormalities (tear or not), and stage lesion severity (full- or partial-thickness tear) and radiomics scores (Rad-score), were constructed and calculated using multivariate logistic regression analysis. The diagnostic performance of the two models was validated using ROC curves on the training and validation datasets.

RESULTS

For the radiomics model of no tears or tears, thirteen features from MR images were used to build the radiomics signature with an AUC value of 0.98 in the training set, 0.97 in the internal validation set, and 0.98 in the external validation set. For the radiomics model of full- or partial-thickness tears, thirteen features from MR images were used to build the radiomics signature with an AUC value of 0.79 in the training set, 0.69 in the internal validation set, and 0.77 in the external validation set.

CONCLUSION

The proposed radiomics models in this study can accurately rule out supraspinatus tendon tears and are capable of assessing the severity staging of tears with moderate accuracy based on shoulder MR images.

KEY POINTS

• The radiomics model of no tears or tears achieved a high overall accuracy of 93.6%, sensitivity of 91.6%, and specificity of 95.2% for supraspinatus tendon tears. • The radiomics model of full- or partial-thickness tears displayed moderate performance with an accuracy of 76.4%, a sensitivity of 79.2%, and a specificity of 74.3% for supraspinatus tendon tears severity staging.

A review of advances in aptamer-based cell detection technology

Since cells are the basic structural and functional units of organisms, the detection or quantitation of cells is one of the most common basic problems in life science research. The established cell detection techniques mainly include fluorescent dye labeling, colorimetric assay, and lateral flow assay, all of which employ antibodies as cell recognition elements. However, the widespread application of the established methods generally dependent on antibodies is limited, because the preparation of antibodies is complicated and time-consuming, and unrecoverable denaturation is prone to occur with antibodies. By contrast, aptamers that are generally selected through the systematic evolution of ligands by exponential enrichment can avoid the disadvantages of antibodies due to their controllable synthesis, thermostability, and long shelf life, etc. Accordingly, aptamers may serve as novel molecular recognition elements like antibodies in combination with various techniques for cell detection. This paper reviews the developed aptamer-based cell detection methods, mainly including aptamer-fluorescent labeling, aptamer-isothermal amplification assay, electrochemical aptamer sensor, aptamer-based lateral flow analysis, and aptamer-colorimetric assay. The principles, advantages, progress of application in cell detection and future development trend of these methods were specially discussed. Overall, different assays are suitable for different detection purposes, and the development of more accurate, economical, efficient, and rapid aptamer-based cell detection methods is always on the road in the future. This review is expected to provide a reference for achieving efficient and accurate detection of cells as well as improving the usefulness of aptamers in the field of analytical applications.

FexO4-enhanced degradation of bisphenol A in visible light/peroxydisulfate system: production of singlet state oxygen

In this study, ferrous composites (Fe_xO₄) were prepared by microreactor to activate peroxydisulfate (PDS) for the degradation of bisphenol A (BPA) with visible (Vis) light irradiation. X-ray diffraction (XRD), energy-dispersive spectrometry (EDS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscope (SEM) were used to characterize the morphology and crystal phase of Fe_XO₄. Photoluminescence (PL) spectroscopy combined with amperometric tests were used to determine the role of PDS on the performance of photocatalytic reaction. The main reactive species and intermediates for BPA removal were determined by electron paramagnetic resonance (EPR) measurement and quenching experiments. The result indicated that singlet state oxygen (¹O₂) contributed more to the BPA degradation than that of other reactive radicals (·OH, SO₄^·- and ·O₂^-); these reactive radicals and ¹O₂ formed by the reaction between photo-generated electrons (e^-) and holes (h⁺) of Fe_xO₄ and PDS. During this process, the consumption of e^- and h⁺ also improved their separation efficiency and thus enhanced the degradation of BPA. In addition, the photocatalytic activity of Fe_xO₄ in Vis/Fe_xO₄/PDS system was 3.2-fold and 6.6-fold higher than that of single Fe_xO₄ and PDS under Vis light, respectively. The Fe²⁺/Fe³⁺ cycle could effectively drive the photocatalytic activation of PDS through indirect electron transfer and the formation of reactive radicals. This work illustrated that the degradation of BPA was rapidly in Vis/Fe_xO₄/PDS system mainly through ¹O₂, which further improve our understanding on the efficient removal of organic contaminants in the environment.

Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1

Feingold syndrome type 1, caused by loss-of-function of MYCN, is characterized by varied phenotypes including esophageal and duodenal atresia. However, no adequate model exists for studying the syndrome's pathological or molecular mechanisms, nor is there a treatment strategy. Here, we developed a zebrafish Feingold syndrome type 1 model with nonfunctional mycn, which had severe intestinal atresia. Single-cell RNA-seq identified a subcluster of intestinal cells that were highly sensitive to Mycn, and impaired cell proliferation decreased the overall number of intestinal cells in the mycn mutant fish. Bulk RNA-seq and metabolomic analysis showed that expression of ribosomal genes was down-regulated and that amino acid metabolism was abnormal. Northern blot and ribosomal profiling analysis showed abnormal rRNA processing and decreases in free 40S, 60S, and 80S ribosome particles, which led to impaired translation in the mutant. Besides, both Ribo-seq and western blot analysis showed that mTOR pathway was impaired in mycn mutant, and blocking mTOR pathway by rapamycin treatment can mimic the intestinal defect, and both L-leucine and Rheb, which can elevate translation via activating TOR pathway, could rescue the intestinal phenotype of mycn mutant. In summary, by this zebrafish Feingold syndrome type 1 model, we found that disturbance of ribosomal biogenesis and blockage of protein synthesis during development are primary causes of the intestinal defect in Feingold syndrome type 1. Importantly, our work suggests that leucine supplementation may be a feasible and easy treatment option for this disease.

Population Pharmacokinetic Modelling for Nifedipine to Evaluate the Effect of Parathyroid Hormone on CYP3A in Patients with Chronic Kidney Disease

Purpose

Parathyroid hormone (PTH) can induce the downregulation of CYP3A in chronic kidney disease (CKD). Nevertheless, the effect of PTH on CYP3A-mediated clearance pathways from a clinical perspective remains unclear.

Methods

This study employed population pharmacokinetic (PopPK) modeling to delineate potential changes in CYP3A activity in patients with CKD. Pharmacokinetic data for nifedipine, a typical CYP3A substrate, as well as covariate information, were prospectively collected from 157 patients with a total of 612 concentrations. PopPK data analysis was performed using a nonlinear mixed-effects model.

Results

The pharmacokinetics of nifedipine were optimally described according to a one-compartment model with zero-order absorption and first-order elimination. The estimated population parameters (and interindividual variability) were apparent clearance (CL/F) 49.61 L/h (58.33%) and apparent volume of distribution (V/F) 2300.26 L (45.62%), and the PTH level negatively correlated with CL/F. In comparison with the reference level, it was observed that the dosage of nifedipine should be reduced with the maximum boundary value of PTH, after a Monte Carlo simulation.

Conclusion

This study provides insight into the effects of PTH on CYP3A-mediated clearance pathways. Moreover, PTH could be used as a guide for the appropriate administration of CYP3A eliminated drugs in patients with CKD.

A multimodal transformer to fuse images and metadata for skin disease classification

Skin disease cases are rising in prevalence, and the diagnosis of skin diseases is always a challenging task in the clinic. Utilizing deep learning to diagnose skin diseases could help to meet these challenges. In this study, a novel neural network is proposed for the classification of skin diseases. Since the datasets for the research consist of skin disease images and clinical metadata, we propose a novel multimodal Transformer, which consists of two encoders for both images and metadata and one decoder to fuse the multimodal information. In the proposed network, a suitable Vision Transformer (ViT) model is utilized as the backbone to extract image deep features. As for metadata, they are regarded as labels and a new Soft Label Encoder (SLE) is designed to embed them. Furthermore, in the decoder part, a novel Mutual Attention (MA) block is proposed to better fuse image features and metadata features. To evaluate the model's effectiveness, extensive experiments have been conducted on the private skin disease dataset and the benchmark dataset ISIC 2018. Compared with state-of-the-art methods, the proposed model shows better performance and represents an advancement in skin disease diagnosis.

Socioeconomic and environmental factors of poverty in China using geographically weighted random forest regression model

Correlations between socioeconomic factors and poverty in regression models do not reflect actual relationships, especially when data exhibit patterns of spatial heterogeneity. Spatial regression models can estimate the relationships between socioeconomic factors and poverty in defined geographical areas, explaining the imbalanced distribution of poverty, but the relationships between these factors and poverty are not always linear however, and conventional simple linear local regression models do not accurately capture these nonlinear relationships. To fill this gap, we used a local regression method, geographically weighted random forest regression (GW-RFR), that integrates a spatial weight matrix (SWM) and random forest (RF). The GW-RFR evaluates the spatial variations in the nonlinear relationships between variables. A county-level poverty data set of China was employed to estimate the performance of the GW-RFR against the random forest (RF). In this poverty application, the value of [Formula: see text] was 0.128 higher than that of the RF, the NRMSE value was 1.6% lower than the RF, and the MAE value was 0.295 lower than the RF. These results showed that the relationship between poverty factors and poverty varies with space at the county level in China, and the GW-RFR was suitable for dealing with nonlinear relationships in local regression analysis.

Polymyxin B-Based Regimens for Patients Infected with Carbapenem-Resistant Gram-Negative Bacteria: Clinical and Microbiological Efficacy, Mortality, and Safety

Background

The increasing prevalence of carbapenem-resistant Gram-negative bacteria (CR-GNB) represents a global healthcare crisis. This study explored the efficacy and safety of Polymyxin B (PMB)-based regimens and factors influencing their effectiveness.

Methods

Patients with CR-GNB infections treated with PMB for more than three days were enrolled in this retrospective study from 1st June 2018 to 30th April 2020. Data were collected on patient characteristics, bacterial culture, and drug-sensitivity test results; anti-infection treatment regimens, particularly details of PMB use; and adverse drug reactions. Clinical and microbiological efficacy, mortality, and safety of PMB-based regimens in CR-GNB infected patients were evaluated. Univariate analysis and multivariate logistic regression analyses were used to assess factors influencing efficacy and mortality.

Results

A total of 373 CR-GNB strains were cultured from 268 patients. About 41.04% of patients used PMB loading dose of 1.01 (0.84–1.69) mg/kg. Maintenance dose was 0.85 (0.82–1.00) mg/kg q12h. The clinical efficacy rate was 36.57% (98/268), the total bacterial clearance rate of PMB was 39.42%, and the all-cause mortality rate was 33.96%. The adverse drug reaction rate was 19.58%, among which the incidence of renal toxicity was highest (8.21%). Multivariate logistic regression analysis showed that clinical efficacy, bacterial clearance rate, and all-cause mortality were associated with patient-related facts, including mechanical ventilation use, underlying diseases (such as respiratory disease), the type and site of CR-GNB infection, and PMB administration timing and loading dose.

Conclusion

PMB is a relatively safe and effective antibiotic drug for treatment of critically ill patients with CR-GNB infection; however, PMB use should be subject to guidelines recommendations for early administration, loading administration, and adequate administration, which could help to improve the clinical efficacy, microbiological efficacy, and mortality.

Abnormalities in lysine degradation are involved in early cardiomyocyte hypertrophy development in pressure-overloaded rats

BACKGROUND

Cardiomyocyte metabolism changes before cardiac remodeling, but its role in early cardiac hypertrophy detection remains unclear. This study investigated early changes in plasma metabolomics in a pressure-overload cardiac hypertrophy model induced by transverse aortic constriction (TAC).

METHODS

The TAC model was constructed by partly ligating the aortic arch. Twelve Sprague-Dawley rats were randomly divided into the TAC group (n = 6) and sham group (n = 6). Three weeks after surgery, cardiac echocardiography was performed to assess cardiac remodeling and function. Hematoxylin/eosin (HE), Masson, and wheat germ agglutinin (WGA) stains were used to observe pathological changes. Plasma metabolites were detected by UPLC-QTOFMS and Q-TOFMS. Specific metabolites were screened by orthogonal partial least squares discriminant analysis (OPLS-DA). Metabolic pathways were characterized by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and the predictive value of the screened metabolites was analyzed by receiver operating characteristic (ROC) curve analysis.

RESULTS

Three weeks after surgery, the TAC and sham groups had similar left heart function and interventricular septum and diastolic left ventricular posterior wall thicknesses. However, on pathological examination, the cross-sectional area of cardiomyocytes and myocardial fibrosis severity were significantly elevated in TAC rats. OPLS-DA showed different metabolic patterns between the TAC and sham groups. Based on the criteria VIP > 1 and P < 0.05, 13 metabolites were screened out. KEGG analysis identified disrupted lysine degradation through the related metabolites 5-aminopentanoic acid, N6-acetyl-L-lysine, and L-lysine, with areas under the ROC curve (AUCs) of 0.917, 0.889, and 0.806, respectively, for predicting compensated cardiomyocyte hypertrophy.

CONCLUSION

Disruption of lysine degradation might be involved in early cardiac hypertrophy development, and related metabolites might be potential predictive and interventional targets for subclinical cardiomyocyte hypertrophy.

Distribution of the environmental and socioeconomic risk factors on COVID-19 death rate across continental USA: a spatial nonlinear analysis

The COVID-19 outbreak has become a global pandemic. The spatial variation in the environmental, health, socioeconomic, and demographic risk factors of COVID-19 death rate is not well understood. Global models and local linear models were used to estimate the impact of risk factors of the COVID-19, but these do not account for the nonlinear relationships between the risk factors and the COVID-19 death rate at various geographical locations. We proposed a local nonlinear nonparametric regression model named geographically weighted random forest (GW-RF) to estimate the nonlinear relationship between COVID-19 death rate and 47 risk factors derived from the US Environmental Protection Agency, National Center for Environmental Information, Centers for Disease Control and the US census. The COVID-19 data were employed to a global regression model random forest (RF) and a local model GW-RF. The adjusted R² of the RF is 0.69. The adjusted R² of the proposed GW-RF is 0.78. The result of GW-RF showed that the risk factors (i.e. going to work by walking, airborne benzene concentration, householder with a mortgage, unemployment, airborne PM_2.5 concentration and per cent of the black or African American) have a high correlation with the spatial distribution of the COVID-19 death rate, and these key factors driven from the GW-RF were mapped, which could provide useful implications for controlling the spread of the COVID-19 pandemic.

Omental Adipose Removal Decreases High Blood Pressure in Hypertensive Patients Independent of Body Mass Index

AIM

Several studies have demonstrated that increased omental adipose is a risk factor for obesity and metabolic syndrome. It remains unclear whether it is responsible for hypertension as an independent risk. This study was designed to assess the impact of omental adipose removal by surgery on blood pressure in cancer patients with or without hypertension.

METHODS AND RESULTS

In this prospective observational study, 133 patients with gastric or gynecological cancer were divided into 3 groups: non-hypertensive and omentum removed (NH&OR), hypertensive and omentum removed (H&OR), and hypertensive and omentum present (H&OP). Patients were followed up with systolic and diastolic blood pressure (SBP and DBP), changes in related body mass index and metabolic indices. The time points of the 2 follow-up visits were 1 month ± 7 days after the operation before the start of chemotherapy and the endpoint of 8 ± 1 month. Omental adipose tissues from both non-hypertensive and hypertensive patients in surgery were collected. We included 133 patients (84.2% female, 20.3% malignant gastric cancer and 79.7% malignant gynecological cancer, 78.2% omentum removal, 48.9% hypertensive), and all completed follow-up. H&OR group showed significant reductions in systolic and diastolic blood pressure compared with the baseline at 1-m (-16.94/-10.50 mmHg, both P < 0.001) and 8-m end point (-16.00/-5.50 mmHg, P < 0.001 and P = 0.004). Little reductions were observed with the body mass index of patients in 3 groups till the endpoint of study (H&OR group: 24.60 kg/m² to 23.57 kg/m², NH&OR group: 23.45 kg/m² to 23.25 kg/m², H&OP group: 25.74 kg/m² to 25.24 kg/m², all P > 0.05). No correlation was found between the baseline body mass index and 8-m change of systolic and diastolic blood pressure in omentum removed groups. In both groups, triglyceride levels were significantly increased at 4 ± 1 week after surgery (NH&OR 0.32 mmol/L, P = 0.006; H&OR 0.40 mmol/L, P = 0.010).

CONCLUSION

Resection of omental adipose tissue represents an effective strategy for reducing systolic and diastolic blood pressure at 8 months in hypertensive patients, even in the non-obese hypertensive population.

A model based on CT radiomic features for predicting RT-PCR becoming negative in coronavirus disease 2019 (COVID-19) patients

BACKGROUND

Coronavirus disease 2019 (COVID-19) has emerged as a global pandemic. According to the diagnosis and treatment guidelines of China, negative reverse transcription-polymerase chain reaction (RT-PCR) is the key criterion for discharging COVID-19 patients. However, repeated RT-PCR tests lead to medical waste and prolonged hospital stays for COVID-19 patients during the recovery period. Our purpose is to assess a model based on chest computed tomography (CT) radiomic features and clinical characteristics to predict RT-PCR negativity during clinical treatment.

METHODS

From February 10 to March 10, 2020, 203 mild COVID-19 patients in Fangcang Shelter Hospital were retrospectively included (training: n = 141; testing: n = 62), and clinical characteristics were collected. Lung abnormalities on chest CT images were segmented with a deep learning algorithm. CT quantitative features and radiomic features were automatically extracted. Clinical characteristics and CT quantitative features were compared between RT-PCR-negative and RT-PCR-positive groups. Univariate logistic regression and Spearman correlation analyses identified the strongest features associated with RT-PCR negativity, and a multivariate logistic regression model was established. The diagnostic performance was evaluated for both cohorts.

RESULTS

The RT-PCR-negative group had a longer time interval from symptom onset to CT exams than the RT-PCR-positive group (median 23 vs. 16 days, p < 0.001). There was no significant difference in the other clinical characteristics or CT quantitative features. In addition to the time interval from symptom onset to CT exams, nine CT radiomic features were selected for the model. ROC curve analysis revealed AUCs of 0.811 and 0.812 for differentiating the RT-PCR-negative group, with sensitivity/specificity of 0.765/0.625 and 0.784/0.600 in the training and testing datasets, respectively.

CONCLUSION

The model combining CT radiomic features and clinical data helped predict RT-PCR negativity during clinical treatment, indicating the proper time for RT-PCR retesting.

Density Structure of the Von Kármán Crater in the Northwestern South Pole-Aitken Basin: Initial Subsurface Interpretation of the Chang'E-4 Landing Site Region

The Von Kármán Crater, within the South Pole-Aitken (SPA) Basin, is the landing site of China's Chang'E-4 mission. To complement the in situ exploration mission and provide initial subsurface interpretation, we applied a 3D density inversion using the Gravity Recovery and Interior Laboratory (GRAIL) gravity data. We constrain our inversion method using known geological and geophysical lunar parameters to reduce the non-uniqueness associated with gravity inversion. The 3D density models reveal vertical and lateral density variations, 2600-3200 kg/m3, assigned to the changing porosity beneath the Von Kármán Crater. We also identify two mass excess anomalies in the crust with a steep density contrast of 150 kg/m3, which were suggested to have been caused by multiple impact cratering. The anomalies from recovered near surface density models, together with the gravity derivative maps extending to the lower crust, are consistent with surface geological manifestation of excavated mantle materials from remote sensing studies. Therefore, we suggest that the density distribution of the Von Kármán Crater indicates multiple episodes of impact cratering that resulted in formation and destruction of ancient craters, with crustal reworking and excavation of mantle materials.

trumpet: transcriptome-guided quality assessment of m6A-seq data

BACKGROUND

Methylated RNA immunoprecipitation sequencing (MeRIP-seq or m6A-seq) has been extensively used for profiling transcriptome-wide distribution of RNA N6-Methyl-Adnosine methylation. However, due to the intrinsic properties of RNA molecules and the intricate procedures of this technique, m6A-seq data often suffer from various flaws. A convenient and comprehensive tool is needed to assess the quality of m6A-seq data to ensure that they are suitable for subsequent analysis.

RESULTS

From a technical perspective, m6A-seq can be considered as a combination of ChIP-seq and RNA-seq; hence, by effectively combing the data quality assessment metrics of the two techniques, we developed the trumpet R package for evaluation of m6A-seq data quality. The trumpet package takes the aligned BAM files from m6A-seq data together with the transcriptome information as the inputs to generate a quality assessment report in the HTML format.

CONCLUSIONS

The trumpet R package makes a valuable tool for assessing the data quality of m6A-seq, and it is also applicable to other fragmented RNA immunoprecipitation sequencing techniques, including m1A-seq, CeU-Seq, Ψ-seq, etc.

Crystal structure of Psb27 from Arabidopsis thaliana determined at a resolution of 1.85 Å

Proper biogenesis and maintenance of photosynthetic thylakoid membrane complexes are essential for the photosynthetic light reactions. A thylakoid lumenal protein, Psb27, plays a vital role in assembly or/and maintenance of photosystem II (PSII). In cyanobacteria, it is a small lipoprotein docked to the lumenal side of PSII, and functions in the assembly of the Mn₄Ca cluster and in the PSII repair cycle. However, Psb27 from Arabidopsis thaliana is not a lipoprotein, and it is involved in PSII repair and acclimation to fluctuating light stress, suggesting a functional divergence between Arabidopsis Psb27 and cyanobacterial Psb27s. To gain a better understanding of Psb27 from higher plants, we determined the crystal structure of Arabidopsis Psb27 by X-ray crystallography at a resolution of 1.85 Å. The structure of Arabidopsis Psb27 is a four-helix bundle, similar to its orthologues from cyanobacteria. However, there are several structural differences between Arabidopsis Psb27 and cyanobacterial Psb27s concerning the overall molecular shape, the N- and C-terminal structures, and the surface charge. These differences suggest that Psb27 from higher plants and cyanobacteria may function differently.

CT and MRI findings in focal eosinophilic infiltration of the liver

OBJECTIVES

To investigate the findings of computed tomography (CT) and magnetic resonance imaging (MRI) of focal eosinophilic infiltration (FEI) of the liver.

METHODS

A retrospective study including 29 patients with confirmed FEI of the liver was performed. We evaluated the lesions' number, distribution, size, shape, margin, attenuation or signal intensity characteristics, the enhancement pattern, and some special features. Spearman correlation analysis was used to analyze the correlation between the number of lesions and the eosinophil counts in peripheral blood.

RESULTS

In all, 108 lesions were detected in 29 cases, including two cases with single lesion and the remaining 27 cases with multiple lesions. The mean size of all lesions was 34 mm (range, from 3 to 61 mm). 95 (88%) lesions were located in subcapsular parenchyma or surrounding the portal vein. Most (66%) subcapsular lesions were wedge shaped and all lesions surrounding portal vein were round shaped. However, the hepatic parenchymal lesions were irregular or round shaped. All lesions showed ill-defined margins. On pre-contrast CT images, the lesions showed slightly low attenuation or iso-attenuating. On T1-weighted and T2-weighted images, the lesions were slightly iso-/hypointense and hyperintense, respectively. A total of 23 (79.3%) cases were gradually enhanced. Branches of portal vein went through the lesions in all cases; 12 had 'stripe sign' and 16 had 'halo ring sign.' Spearman analysis indicated a significant correlation between the number of lesions and the increased eosinophils in peripheral blood (r = 0.627, p = 0.0003).

CONCLUSIONS

Special CT and MRI features and increased eosinophils may strongly suggest the diagnosis of FEI of the liver.

Differential effects of heat shock protein 90 and serine 1179 phosphorylation on endothelial nitric oxide synthase activity and on its cofactors

Endothelial nitric oxide synthase (eNOS) is responsible for maintaining systemic blood pressure, vascular remodeling and angiogenesis. Previous studies showed that bovine eNOS serine 1179 (Serine 1177 for human eNOS) phosphorylation enhanced NO synthesis. Meanwhile, heat shock protein 90 (Hsp90) plays a critical role in maintenance of eNOS structure and function. However, the regulatory difference and importance between Serine 1179 phosphorylation and Hsp90 on eNOS activity have not been evaluated. In current studies, S1179D eNOS was employed to mimic phospho-eNOS and exhibited markedly increased enzyme activity than wild type eNOS (WT eNOS). Hsp90 showed a dose-dependent increase for both WT eNOS and S1179D eNOS activity at the presence of all eNOS cofactors, such as Calcium/Calmodulin (Ca2+ /CaM), BH4, and NADPH etc. The enhancement effects were abolished by dominant-negative mutant Hsp 90 protein. ENOS-cofactors dynamic assay showed that Hsp90 enhanced WT eNOS affinity to NADPH, L-arginine, and CaM but not to Ca2+ and BH4. The impact of eNOS Serine 1179 phosphorylation and Hsp90 on eNOS affinity to cofactors has also been compared. Different from the effect of Hsp90 on eNOS affinity to specific cofactors, Serine 1179 phosphorylation significantly increased eNOS affinity to all cofactors. Moreover, VEGF-induced eNOS phosphorylation in bovine aortic endothelial cells (BAECs) and more NO generation from eNOS compared to control. Inhibition of Hsp90 by geldanamycin decreased eNOS activity and decreased endothelial viability. In conclusion, by changing eNOS structure, Hsp90 profoundly affected eNOS functions, including change of affinity of eNOS to cofactors like Ca2+, L-arginine, BH4 and further affecting NO generation capability. These specific cofactors regulated by Hsp 90 could become potential therapeutic targets of the eNOS-related diseases in future.

Probabilistic Entity-Relationship Diagram: A correlation between functional connectivity and spontaneous brain activity during resting state in major depressive disorder

BACKGROUND

Alterations of functional connectivity (FC) and spontaneous brain activity (SBA) during the resting state has been observed in subjects with major depressive disorder (MDD). Although there are many studies separately describing on the alterations of FC and SBA in major depressive disorder, their correlation are still have not been performed.

METHODS

A literature search based on Pubmed and Embase was conducted until 20 April 2016 to identify studies evaluating the correlation for the alterations between functional connectivity and spontaneous brain activity during resting-state in MDD. Meta-analyses were performed using the Probabilistic Entity-Relationship Diagram (PERD) approach to summarize the relationships among multiple factors in an intuitive manner.

RESULTS

A total of 30 studies (747 individuals with MDD and 757 healthy controls) met the inclusion criteria. In this study, we demonstrated that the functional connectivity and spontaneous brain activity, which was quantitatively measured by the primary analysis methods, was decreased in the parahippocampal gyrus, orbitofrontal cortex (OFC) and postcentral gyrus (PCG), and increased in insula and left dorsal medial prefrontal cortex (DMPFC) in MDD patients. Furthermore, we found that MDD patients presented negative correlation alterations both FC and SBA in the default mode network and the dorsal attention network, but positive correlation alterations both FC and SBA in the insular network, executive control network, the salience network and the other network.

CONCLUSIONS

Our results first suggested that there were correlation alterations between functional connectivity and spontaneous brain activity during resting-state in patients with MDD. Besides, we applied a recent meta-analysis approach (PERD) to summarize and integrate the inconsistence of the existing findings regarding the network dysfunction of MDD.

Association between Triglyceride to HDL-C Ratio (TG/HDL-C) and Insulin Resistance in Chinese Patients with Newly Diagnosed Type 2 Diabetes Mellitus

OBJECTIVES

To explore the association between the triglyceride to HDL-C ratio (TG/HDL-C) and insulin resistance in Chinese patients with newly diagnosed type 2 diabetes mellitus.

METHODS

Patients with newly diagnosed type 2 diabetes mellitus (272 men and 288 women) were enrolled and divided into three groups according to TG/HDL-C tertiles. Insulin resistance was defined by homeostatic model assessment of insulin resistance (HOMA-IR). Demographic information and clinical characteristics were obtained. Spearman's correlation was used to estimate the association between TG/HDL-C and other variables. Multiple logistic regression analyses were adopted to obtain probabilities of insulin resistance. A receiver operating characteristic analysis was conducted to evaluate the ability of TG/HDL-C to discriminate insulin resistance.

RESULTS

TG/HDL-C was associated with insulin resistance in Chinese patients with newly diagnosed T2DM (Spearman's correlation coefficient = 0.21, P < 0.01). Patients in the higher tertiles of TG/HDL-C had significantly higher HOMA-IR values than patients in the lower tertiles [T1: 2.68(1.74-3.70); T2: 2.96(2.29-4.56); T3: 3.09(2.30-4.99)]. Multiple logistic regression analysis showed that TG/HDL-C was significantly associated with HOMA-IR, and patients in the higher TG/HDL-C tertile had a higher OR than those in the lower TG/HDL-C tertile, after adjusting for multiple covariates including indices for central obesity [T1: 1; T2: 4.02(1.86-8.71); T3: 4.30(1.99-9.29)]. Following stratification of waist circumference into quartiles, the effect of TG/HDL-C on insulin resistance remained significant irrespective of waist circumference.

CONCLUSIONS

TG/HDL-C was associated with insulin resistance independent of waist circumference. Whether it could be a surrogate marker for insulin resistance in Chinese patients with newly diagnosed type 2 diabetes mellitus still needs to be confirmed by more researches.