Construction of a high-density genetic map for yardlong bean and identification of ANT1 as a regulator of anthocyanin biosynthesis

Because its long, tender pods supply essential proteins, vitamins, and fibers to humans, yardlong bean (Vigna unguiculata ssp. sesquipedalis) is a commonly consumed vegetable, especially in Southeast Asia. To provide insights into the genetic bases of key agricultural traits in yardlong bean, we here created a high-density bin-map with 2084 bin markers using 514 227 SNPs from a recombinant-inbred line (RIL) population. Quantitative trait loci (QTL) mapping was carried out to identify loci associated with anthocyanin content (ANT), vitamin E content (VE), total soluble protein content (TSP), pod length (PL), hundred-seed weight (HSW), seed length and width (SL and SW, respectively), and seed coat color (SCC). In total, 20 related QTLs were isolated, explaining 7.58-56.03% of the phenotypic variation. Of these, five major QTLs (qANT5, qTSP11, qVE7, qPL3, and qSCC9) were detected in 2020, 2021, and the combined environment, explaining 11.96-56.03% of the phenotypic variation. VuANT1 was identified as a causal gene for the QTL qANT5, which regulated anthocyanin content; VuANT1 was highly expressed in immature purple pods but barely detectable in white pods. VuANT1 overexpression in tobacco leaves and yardlong bean hairy roots resulted in purple coloration as a result of anthocyanin accumulation. These findings suggested that VuANT1 was a key regulator of anthocyanin accumulation in yardlong bean. Our results lay a firm foundation for target agricultural trait improvement and clarification of the genetic mechanisms underlying agricultural traits in yardlong bean.

Preoperative MRI features predicting very early recurrence of intrahepatic mass-forming cholangiocarcinoma after R0 resection: a comparison with the AJCC 8th edition staging system

PURPOSE

This study aimed to establish a nomogram based on preoperative magnetic resonance imaging (MRI) features to predict the very early recurrence (VER, less than 6 months) of intrahepatic mass-forming cholangiocarcinoma (IMCC) after R0 resection.

METHODS

This study enrolled a group of 193 IMCC patients from our institution between March 2010 and January 2022. Patients were allocated into the development cohort (n = 137) and the validation cohort (n = 56), randomly, and the preoperative clinical and MRI features were collected. Univariate and multivariate stepwise logistic regression assessments were adopted to assess predictors of VER. Nomogram was constructed and certificated in the validation cohort. The performance of the prediction nomogram was evaluated by its discrimination, calibration, and clinical utility. The performance of the nomogram was compared with the T stage of the American Joint Committee on Cancer (AJCC) 8th edition staging system.

RESULTS

Fifty-three patients (27.5%) experienced VER of the tumor and 140 patients (72.5%) with non-VER, during the follow-up period. After multivariate stepwise logistic regression, number of lesions, diffuse hypoenhancement on arterial phase, necorsis and suspicious lymph nodes were independently associated with VER. The nomogram demonstrated significantly higher area under the curve (AUC) of 0.813 than T stage (AUC = 0.666, P = 0.006) in the development cohort, whereas in the validation cohort, the nomogram showed better discrimination performance, with an AUC of 0.808 than T stage (0.705) with no significantly difference (P = 0.230). Decision curve analysis reflected the clinical net benefit of the nomogram.

CONCLUSION

The nomogram based on preoperative MRI features is a reliable tool to predict VER for patients with IMCC after R0 resection. This nomogram will be helpful to improve survival prediction and individualized treatment.

The causal relationship between psoriasis and artificial joint re-operation after arthroplasty: A two-sample Mendelian randomization study

BACKGROUND

Psoriasis is observationally associated with a higher risk of complications of arthroplasty; however, the causal effects of psoriasis on complications of arthroplasty are yet to be established. This study was to explore the causal effect of psoriasis on artificial joint re-operation after arthroplasty through two-sample Mendelian randomization (MR).

METHODS

In the MR analysis, psoriasis was selected as the exposure in this study while single-nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) were selected as the instrumental variables (IVs). Summary statistics data on artificial joint re-operation was extracted from publicly available GWAS data, including 218 792 European descent individuals. MR analysis was performed using the standard inverse variance weighted method (IVW). Furthermore, MR Egger, weighted median, simple mode, weighted mode, and the MR-PRESSO (Mendelian Randomization Pleiotropy Residual Sum and Outlier) test were also done to verify the results. Finally, the sensitivity analysis was executed.

RESULTS

The IVW showed that psoriasis increases the risk of artificial joint re-operation (OR = 1.12; 95% CI = (1.01, 1.25); p = 0.036). This outcome was also verified by other methods including weighted median (OR = 1.16; 95% CI = (1.03, 1.31); p = 0.015), MR Egger (OR = 1.22; 95% CI = (1.03, 1.44); p = 0.038), and weighted mode (OR = 1.16; 95% CI = (1.03, 1.30); p = 0.025). No heterogeneity and directional pleiotropy were observed upon sensitivity analysis.

CONCLUSION

The present study showed that psoriasis has a potential causal effect on artificial joint re-operation after arthroplasty. Further studies are warranted to elucidate the underlying mechanisms of causal associations between psoriasis on re-operation.

Baseline C-reactive protein predicts efficacy of the first-line immune checkpoint inhibitors plus chemotherapy in advanced lung squamous cell carcinoma: a retrospective, multicenter study

AIMS

To investigate the predictive value of baseline C-reactive protein (CRP) levels on the efficacy of chemotherapy plus immune checkpoint inhibitors (ICI) in patients with advanced lung squamous cell carcinoma (LSCC).

MATERIALS AND METHODS

In this retrospective multicenter study spanning from January 2016 to December 2020, advanced LSCC patients initially treated with chemotherapy or a combination of chemotherapy and ICI were categorized into normal and elevated CRP subgroups. The relationship between CRP levels and treatment outcomes was analyzed using multivariate Cox proportional hazards models and multivariate logistic regression, focusing primarily on the progression-free survival (PFS) endpoint, and secondarily on overall survival (OS) and objective response rate (ORR) endpoints. Survival curves were generated using the Kaplan-Meier method, with the log-rank test used for comparison between groups.

RESULTS

Of the 245 patients evaluated, the 105 who received a combination of chemotherapy and ICI with elevated baseline CRP levels exhibited a significant reduction in PFS (median 6.5 months vs. 11.8 months, HR, 1.78; 95% CI: 1.12-2.81; p = 0.013) compared to those with normal CRP levels. Elevated CRP was identified as an independent risk factor for poor PFS through multivariate-adjusted analysis. However, among the 140 patients receiving chemotherapy alone, baseline CRP levels did not significantly influence PFS. Furthermore, within the combination therapy group, there was a notable decrease in the ORR (51% vs. 71%, p = 0.035), coupled with a significantly shorter OS (median 20.9 months vs. 31.5 months, HR, 2.24; 95% CI: 1.13-4.44; p = 0.033).

CONCLUSION

In patients with advanced LSCC, elevated baseline CRP levels were identified as an independent predictive factor for the efficacy of combination therapy with chemotherapy and ICI, but not in chemotherapy alone. This suggests that CRP may be a valuable biomarker for guiding treatment strategies.

Cytotoxic CD4+ tissue-resident memory T cells are associated with asthma severity

BACKGROUND

Patients with severe uncontrolled asthma represent a distinct endotype with persistent airway inflammation and remodeling that is refractory to corticosteroid treatment. CD4+ TH2 cells play a central role in orchestrating asthma pathogenesis, and biologic therapies targeting their cytokine pathways have had promising outcomes. However, not all patients respond well to such treatment, and their effects are not always durable nor reverse airway remodeling. This observation raises the possibility that other CD4+ T cell subsets and their effector molecules may drive airway inflammation and remodeling.

METHODS

We performed single-cell transcriptome analysis of >50,000 airway CD4+ T cells isolated from bronchoalveolar lavage samples from 30 patients with mild and severe asthma.

FINDINGS

We observed striking heterogeneity in the nature of CD4+ T cells present in asthmatics' airways, with tissue-resident memory T (TRM) cells making a dominant contribution. Notably, in severe asthmatics, a subset of CD4+ TRM cells (CD103-expressing) was significantly increased, comprising nearly 65% of all CD4+ T cells in the airways of male patients with severe asthma when compared to mild asthma (13%). This subset was enriched for transcripts linked to T cell receptor activation (HLA-DRB1, HLA-DPA1) and cytotoxicity (GZMB, GZMA) and, following stimulation, expressed high levels of transcripts encoding for pro-inflammatory non-TH2 cytokines (CCL3, CCL4, CCL5, TNF, LIGHT) that could fuel persistent airway inflammation and remodeling.

CONCLUSIONS

Our findings indicate the need to look beyond the traditional T2 model of severe asthma to better understand the heterogeneity of this disease.

FUNDING

This research was funded by the NIH.

LINC01936 inhibits the proliferation and metastasis of lung squamous cell carcinoma probably by EMT signaling and immune infiltration

Purpose

To discover the biological function and potential mechanism of LINC01936 in the development of lung squamous cell carcinoma (LUSC).

Methods

Transcriptome data of LUSC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to analyze the differentially expressed lncRNAs in LUSC and normal tissues by R "DEseq2", "edgeR" and "limma" packages. The subcellular localization of LINC01936 was predicted by lncLocator. Cell proliferation and apoptosis were measured by CCK-8, MTT assay and Hoechst fluorescence staining. The migration and invasion were detected by Transwell assay. The function and pathway enrichment analysis were performed by Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene set variation analysis (GSVA). The downstream targets of LINC01936 were predicted using RNA-Protein Interaction Prediction (RPISeq) program. The effect of LINC01936 on tumor immune infiltration was analyzed using Pearson Correlation Analysis using R "ggpubr" package.

Results

Based on the gene expression data of LUSC from TCGA database, 1,603, 1,702 and 529 upregulated and 536, 436 and 630 downregulated lncRNAs were obtained by DEseq2, edgeR and limma programs, respectively. For GSE88862 dataset, we acquired 341 differentially expressed lncRNAs (206 upregulated and 135 downregulated). Venn plot for the intersection of above differential expressed lncRNAs showed that there were 29 upregulated and 23 downregulated genes. LINC01936 was one of downregulated lncRNAs in LUSC tissues. The biological analysis showed that the overexpression of LINC01936 significantly reduced proliferation, migration and invasion of LUSC cells, and promoted cell apoptosis. The knockdown of LINC01936 promoted cell proliferation and metastasis. Pathway and GSVA analysis indicated that LINC01936 might participated in DNA repair, complement, cell adhesion and EMT, etc. LINC01936 was predicted to interact with TCF21, AOC3, RASL12, MEOX2 or HSPB7, which are involved in EMT and PI3K-AKT-MTOR pathway, etc. The expression of LINC01936 was also positively correlated with the infiltrating immune cells in LUSC.

Conclusions

LINC01936 is downregulated in LUSC. LINC01936 affected proliferation, migration and invasion of LUSC cells probably by EMT and immune infiltration, which might serve as a new target for the treatment of LUSC.

Changes in serum tumor markers in type 2 diabetes mellitus with microalbuminuria

Objectives

The objective of this study was to investigate changes in serum tumor markers in type 2 diabetes mellitus (T2DM) with microalbuminuria and analyze the relationship between tumor markers and microalbuminuria.

Methods

A total of 956 T2DM patients aged 40-70 years hospitalized in the Department of Endocrinology, Xinhua Hospital, China, affiliated with Shanghai Jiaotong University School of Medicine, were enrolled from January 2018 to December 2020. The sample comprised 313 T2DM patients with microalbuminuria and 643 T2DM patients with normal urinary microalbumin levels. After assessing the changes in serum tumor markers in T2DM with microalbuminuria, we analyzed the risk of microalbuminuria by the serum tumor marker category using multiple logistic regression analysis.

Results

Serum CEA, CA199, CA125, CA153, CA211, SCC, CA242, and CA50 levels were significantly higher in T2DM patients with microalbuminuria than in those without microalbuminuria, while serum AFP levels were lower in the microalbuminuria group (P < 0.05). Following adjustment of confounders, serum CEA, CA211, and SCC were independently associated with microalbuminuria in T2DM. An ROC curve was used to estimate the cutoff point of tumor markers for microalbuminuria. Taking the values under the cutoff points as a reference, values for CEA, CA211, and SCC above the cutoff points indicated a significantly high risk of microalbuminuria. The OR of increased CEA for microalbuminuria was 2.006 (95%CI 1.456-2.765), the OR of increased CA211 for microalbuminuria was 1.505 (95%CI 1.092-2.074), and the OR of increased SCC for microalbuminuria was 1.958 (95%CI 1.407-2.724).

Conclusion

Several serum tumor markers were related to microalbuminuria in T2DM. Serum tumor markers such as CEA, SCC, and CA211 may indicate early diabetic nephropathy, particularly when elevated in combination.

Comparison of the main pathogenic microorganisms of various common oral diseases in children and adults

The microorganisms in the human body gradually change and maintain a dynamic balance with the development of physiology and pathology. Oral microbiota is one of the most important microbiota in human body. It is not only closely related to the occurrence and development of oral diseases, but also plays an important role in the overall health. In childhood, the population of oral microorganisms is relatively small, but with the growth of age and tooth development, the species and quantity of oral microorganisms are gradually increasing. Different oral diseases also have their corresponding main microorganisms, and these dominant microorganisms change at different stages of the disease. In this review, we summarized and compared the main pathogenic microorganisms of several common oral diseases in children and adults. In addition, the possible association and difference between adults and children of the main pathogenic microorganisms in different stages of the same or different diseases are also discussed in order to provide research data for the development and diagnosis of common oral diseases in children and adults.

Risk stratification for overall survival and recurrence-free survival after R0 resection for solitary intrahepatic mass-forming cholangiocarcinoma based on preoperative MRI and clinical features

PURPOSE

This study aimed to establish two nomograms for predicting overall survival (OS) and recurrence-free survival (RFS) in patients with solitary intrahepatic mass-forming cholangiocarcinoma (IMCC) based on preoperative magnetic resonance imaging (MRI) features.

METHODS

This retrospective study included 120 consecutive patients who were diagnosed with solitary IMCC. Preoperative MRI and clinical features were collected. Based on the univariate and multivariate Cox regression analyses, two nomograms were constructed to predict OS and RFS, respectively. The effective performance of the nomograms was evaluated using concordance index (C-index). The prognostic stratification systems for OS and RFS were developed and used to classify patients into high- and low-risk groups.

RESULTS

Suspicious lymph nodes, arterial phase (AP) enhancement patterns, and bile duct dilatation were independent predictors of OS, while suspicious lymph nodes, AP enhancement patterns, and necrosis were independent predictors of RFS. The nomograms achieved the C-index values of 0.705/0.710 for OS and 0.721/0.759 for RFS in the development/validation cohorts, which were significantly higher than those of the T and TNM stages (P < 0.05). Patients were stratified into high- and low-risk groups, the 1-year OS and RFS rates of high-risk patients were poorer than those of patients with low-risk in the development cohort (OS: 93.5% vs 76.3%, P < 0.001; RFS: 74.5% vs 22.4%, P < 0.001). Similar results were observed in the validation cohort.

CONCLUSIONS

Two nomograms were constructed based on preoperative MRI features in patients with solitary IMCC for predicting the OS and RFS and facilitate further prognostic stratification.

A multifunctional chitosan composite aerogel based on high density amidation for chronic wound healing

The management of chronic wounds remains a challenging clinical problem worldwide, mainly because of secondary infections, excessive oxidative stress, and blocked angiogenesis. Aerogel is a novel material with high porosity and specific surface area that allows gas exchange and rapid absorption of a large amount of exudate as well as loading bioactive molecules. Therefore, functional aerogel can be an ideal material for chronic wound treatment. The multifunctional aerogel (CG-DA-VEGF) was prepared by a simple and eco-friendly freeze-drying process combined with harmless EDC/NHS as crosslinking agents using chitosan and dopamine-grafted gelatin as raw materials. The physicochemical characterization revealed that the CG-DA-VEGF aerogel had excellent water absorption, water retention, and mechanical properties, and could release VEGF continuously and stably. In vitro experiments demonstrated that the CG-DA-VEGF aerogel exhibited effective antioxidant and antibacterial properties, as well as superb cytocompatibility. In vivo experiments further confirmed that the CG-DA-VEGF aerogel could significantly improve angiogenesis and re-epithelialization, and promote collagen deposition, thus accelerating wound healing with excellent biosafety. These results suggest that the as-prepared CG-DA-VEGF aerogel may be adopted as a promising multifunctional graft for the treatment of chronic wounds.

Development and validation of a nomogram model for predicting low muscle mass in patients undergoing hemodialysis

BACKGROUND

Muscle mass is important in determining patients' nutritional status. However, measurement of muscle mass requires special equipment that is inconvenient for clinical use. We aimed to develop and validate a nomogram model for predicting low muscle mass in patients undergoing hemodialysis (HD).

METHODS

A total of 346 patients undergoing HD were enrolled and randomly divided into a 70% training set and a 30% validation set. The training set was used to develop the nomogram model, and the validation set was used to validate the developed model. The performance of the nomogram was assessed using the receiver operating characteristic (ROC) curve, a calibration curve, and the Hosmer-Lemeshow test. A decision curve analysis (DCA) was used to evaluate the clinical practicality of the nomogram model.

RESULTS

Age, sex, body mass index (BMI), handgrip strength (HGS), and gait speed (GS) were included in the nomogram for predicting low skeletal muscle mass index (LSMI). The diagnostic nomogram model exhibited good discrimination with an area under the ROC curve (AUC) of 0.906 (95% CI, 0.862-0.940) in the training set and 0.917 (95% CI, 0.846-0.962) in the validation set. The calibration analysis also showed excellent results. The nomogram demonstrated a high net benefit in the clinical decision curve for both sets.

CONCLUSIONS

The prediction model included age, sex, BMI, HGS, and GS, and it can successfully predict the presence of LSMI in patients undergoing HD. This nomogram provides an accurate visual tool for medical staff for prediction, early intervention, and graded management.

A Dual-Antioxidative Coating on Transmucosal Component of Implant to Repair Connective Tissue Barrier for Treatment of Peri-Implantitis

Since the microgap between implant and surrounding connective tissue creates the pass for pathogen invasion, sustained pathological stimuli can accelerate macrophage-mediated inflammation, therefore affecting peri-implant tissue regeneration and aggravate peri-implantitis. As the transmucosal component of implant, the abutment therefore needs to be biofunctionalized to repair the gingival barrier. Here, a mussel-bioinspired implant abutment coating containing tannic acid (TA), cerium and minocycline (TA-Ce-Mino) is reported. TA provides pyrogallol and catechol groups to promote cell adherence. Besides, Ce3+ /Ce4+  conversion exhibits enzyme-mimetic activity to remove reactive oxygen species while generating O2 , therefore promoting anti-inflammatory M2 macrophage polarization to help create a regenerative environment. Minocycline is involved on the TA surface to create local drug storage for responsive antibiosis. Moreover, the underlying therapeutic mechanism is revealed whereby the coating exhibits exogenous antioxidation from the inherent properties of Ce and TA and endogenous antioxidation through mitochondrial homeostasis maintenance and antioxidases promotion. In addition, it stimulates integrin to activate PI3K/Akt and RhoA/ROCK pathways to enhance VEGF-mediated angiogenesis and tissue regeneration. Combining the antibiosis and multidimensional orchestration, TA-Ce-Mino repairs soft tissue barriers and effector cell differentiation, thereby isolating the immune microenvironment from pathogen invasion. Consequently, this study provides critical insight into the design and biological mechanism of abutment surface modification to prevent peri-implantitis.

Single- and combined-phthalate exposures are associated with biological ageing among adults

BACKGROUND

Previous research has emphasized the effects of lifestyle and genetics on ageing. However, the association between exposure to phthalates, which are extensively used in cosmetics and personal care products, and ageing is still unclear.

METHOD

Data for 4711 subjects from the National Health and Nutrition Examination Survey (NHANES) from 2005 to 2010 were incorporated in the present study. The acceleration of the Klemera-Doubal method-biological age (KDM-BA) and phenotypic Age (PhenoAge) were measured by the composite of 13 biomarkers. Multiple-linear and weighted-quantile sum (WQS) regression models were constructed to explore the relationships of single- and combined-phthalate exposures, as indicated by urinary phthalate metabolites, with KDM-BA and PhenoAge. A generalized additive model (GAM) was fitted to explore the potential nonlinear relationships among the above variables.

RESULTS

Except for mono-(carboxynonyl), all urinary phthalate metabolites were associated with biological ageing, with correlation coefficients ranging from 0.241 to 0.526; however, mono-ethyl presented a negative correlation. The WQS models revealed mixed effects of combined urinary phthalate metabolites on ageing, with a 0.22-year ((95 % CI) 0.09, 0.32) increase in KDM-BA acceleration and a 0.27-year ((95 % CI) 0.13, 0.37) increase in PhenoAge acceleration for each decile increase in urinary phthalate metabolites. Moreover, MCPP, MEOHP, and MBzP seemed to be the top three phthalates in terms of biological ageing, with weights of 33.3 % and 32.2 %, 29.2 % and 17.2 %, and 21.5 % and 30.1 % in KDM-BA and PhenoAge acceleration, respectively.

CONCLUSION

Single-phthalate exposure was mostly associated with the ageing process, and combined-phthalate exposure presented mixed effects on biological ageing, emphasizing phthalate exposure as a significant risk factor for ageing.

Predicting the microvascular invasion and tumor grading of intrahepatic mass-forming cholangiocarcinoma based on magnetic resonance imaging radiomics and morphological features

Background

Preoperative diagnosis of microvascular invasion (MVI) and tumor grading of intrahepatic mass-forming cholangiocarcinoma (IMCC) using imaging findings can facilitate patient treatment decision-making. This study was conducted to establish and validate nomograms based on magnetic resonance imaging (MRI) radiomics and morphological features for predicting the MVI and tumor grading of IMCC before radical hepatectomy.

Methods

A total of 235 patients with resected IMCC at the Chinese Academy of Medical Sciences and Peking Union Medical College were divided into a training set (n=167) and a validation set (n=68), retrospectively. Clinical data and MRI morphological features were recorded. Univariate and multivariate analyses were conducted to identify the significant features for the prediction of MVI and tumor grading. Radiomics features were extracted from T2-weighted imaging fat-suppressed and diffusion-weighted imaging (DWI). Radiomics signatures (rad_scores) were built based on the least absolute shrinkage and selection operator (LASSO) method. Then, the nomograms were constructed by combining the rad_scores and the significant clinical or MRI morphologic features. The predictive performances for MVI and tumor grading were evaluated by the area under the receiver operating characteristic curve (AUC), calibration, and clinical utility.

Results

Totals of 16 and 9 radiomics features were selected to build the rad_scores for the prediction of MVI and tumor grading for the training and validation set, respectively. The nomogram for the prediction of MVI comprised the morphologic features including number of tumors, tumor margin, and rad_score. For the prediction of tumor grading, the nomogram comprised the number of tumors, tumor necrosis, and rad_score. The best discriminations were observed in the training and validation sets for the MVI nomogram [AUCs of 0.874, 95% confidence interval (CI): (0.822-0.926) and 0.869 (0.783-0955)] and tumor grading nomogram [AUCs of 0.827 (0.763-0.891) and 0.848 (0.759-0.937)]. Decision curve analysis (DCA) further confirmed the clinical utilities of the nomograms.

Conclusions

Nomograms based on MRI radiomics and morphological features can effectively predict the individualized risks of MVI and tumor grading for IMCC.

FAR in systemic lupus erythematosus: a potential biomarker of disease activity and lupus nephritis

The fibrinogen-to-albumin ratio (FAR), a novel inflammatory marker, has been studied in various diseases. However, the significance of FAR in systemic lupus erythematosus (SLE) has not been fully elucidated. This study was to investigate the connection between FAR and SLE. A retrospective analysis of 154 SLE patients and 77 healthy individuals was performed. The clinical and laboratory data were reviewed. Receiver operating characteristic (ROC) curves were conducted for FAR at baseline to predict disease activity and lupus nephritis (LN) in SLE patients. Pearson correlation was also applied. FAR in the SLE group was found to be significantly higher than that of the healthy control group (83.71 mg/g vs. 53.14 mg/g, P < 0.001). It was also significantly higher in patients with LN than that in patients without (107.64 mg/g vs. 67.75 mg/g, P < 0.001). The ROC curve for predicting LN showed that the area under the curve (AUC) of FAR (0.859, 95% CI 0.803-0.914) was the largest when compared to albumin (0.852, 95% CI 0.789-0.916) or fibrinogen (0.736, 95% CI 0.659-0.814) alone. In addition, FAR was a good predictor of severe disease activity in SLE (AUC = 0.721, 95% CI 0.612-0.830) and LN patients (AUC = 0.789, 95% CI 0.680-0.898). Pearson correlation analysis indicated that FAR demonstrated a strong correlation with SLE disease activity index 2000 (r = 0.4288, P < 0.001). FAR was significantly increased in SLE patients. It is a possible biomarker for disease activity and renal involvement in SLE.

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

BACKGROUND

Domestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.

RESULTS

To comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the "hair follicle maturation" Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with "regulation of heart contraction" in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.

CONCLUSION

This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

Identifying phenotype-associated subpopulations through LP_SGL

Single-cell RNA sequencing (scRNA-seq) enables the resolution of cellular heterogeneity in diseases and facilitates the identification of novel cell types and subtypes. However, the grouping effects caused by cell-cell interactions are often overlooked in the development of tools for identifying subpopulations. We proposed LP_SGL which incorporates cell group structure to identify phenotype-associated subpopulations by integrating scRNA-seq, bulk expression and bulk phenotype data. Cell groups from scRNA-seq data were obtained by the Leiden algorithm, which facilitates the identification of subpopulations and improves model robustness. LP_SGL identified a higher percentage of cancer cells, T cells and tumor-associated cells than Scissor and scAB on lung adenocarcinoma diagnosis, melanoma drug response and liver cancer survival datasets, respectively. Biological analysis on three original datasets and four independent external validation sets demonstrated that the signaling genes of this cell subset can predict cancer, immunotherapy and survival.

Nimotuzumab Plus Gemcitabine for K-Ras Wild-Type Locally Advanced or Metastatic Pancreatic Cancer

PURPOSE

In a phase IIb trial of nimotuzumab plus gemcitabine, substantial clinical benefits were observed in patients with locally advanced or metastatic pancreatic cancer (PC). Therefore, we conducted a phase III clinical study to verify the efficacy and safety of this combination regimen in patients with K-Ras wild-type tumors (ClinicalTrials.gov identifier: NCT02395016).

PATIENTS AND METHODS

Eligible patients were randomly assigned to receive nimotuzumab (400 mg once per week) or placebo followed by gemcitabine (1,000 mg/m2 on days 1, 8, and 15, once every 4 weeks) until disease progression or unacceptable toxicity. The primary end point was overall survival (OS) and the secondary end points were progression-free survival (PFS), response rates, and safety.

RESULTS

A total of 480 patients were screened; 92 patients were enrolled and 82 patients with K-Ras wild-type tumors were eligible. In the full analysis set, the median OS was 10.9 versus 8.5 months, while the restricted mean survival time (RMST) was 18.05 versus 11.14 months for the investigational versus control arm (ratio of control v investigation = 0.62 [0.40-0.97]; P = .036). Median PFS was 4.2 versus 3.6 months in the investigational versus control arm (log-rank P = .04; hazard ratio, 0.60 [0.37-0.99]) and the restricted mean PFS time was 8.08 versus 4.76 months (RMST ratio, 0.58 [0.38-0.90]; P = .036). Both OS and PFS were longer in the nimotuzumab group than in the placebo group. The objective response rates and disease control rates were 7% versus 10% and 68% versus 63% for the investigational and control groups, respectively. The incidence of adverse events were comparable between the two groups.

CONCLUSION

In patients with locally advanced or metastatic K-Ras wild-type PC, nimotuzumab plus gemcitabine significantly improved OS and PFS with a good safety profile.

Construction of EMT related prognostic signature for kidney renal clear cell carcinoma, through integrating bulk and single-cell gene expression profiles

Introduction: Kidney renal clear cell carcinoma (KIRC), as a main type of malignant kidney cancers, has a poor prognosis. Epithelial-mesenchymal transformation (EMT) exerts indispensable role in tumor progression and metastasis, including in KIRC. This study aimed to mine more EMT related details and build prognostic signature for KIRC. Methods: The KIRC scRNA-seq data and bulk data were downloaded from GEO and TCGA databases, respectively. The cell composition in KIRC was calculated using CIBERSORT. Univariate Cox regression analysis and LASSO Cox regression analysis were combined to determine the prognostic genes. Gene set variation analysis and cell-cell communication analysis were conducted to obtain more functional information. Additionally, functional analyses were conducted to determine the biological roles of si-LGALS1 in vitro. Results: We totally identified 2,249 significant differentially expressed genes (DEGs) in KIRC samples, meanwhile a significant distinct expression pattern was found in KIRC, involving Epithelial Mesenchymal Transition pathway. Among all cell types, significantly higher proportion of epithelial cells were observed in KIRC, and 289 DEGs were identified in epithelial cells. After cross analysis of all DEGs and 970 EMT related genes, SPARC, TMSB10, LGALS1, and VEGFA were optimal to build prognostic model. Our EMT related showed good predictive performance in KIRC. Remarkably, si-LGALS1 could inhibit migration and invasion ability of KIRC cells, which might be involved in suppressing EMT process. Conclusion: A novel powerful EMT related prognostic signature was built for KIRC patients, based on SPARC, TMSB10, LGALS1, and VEGFA. Of which, si-LGALS1 could inhibit migration and invasion ability of KIRC cells, which might be involved in suppressing EMT process.

Screening and early diagnosis of chronic obstructive pulmonary disease: a population study

BACKGROUND AND OBJECTIVE

Although chronic obstructive pulmonary disease (COPD) is a common disease leading to further morbidity and significant mortality, there is still limited data on screening for COPD. The purpose of this study was to establish an early chronic obstructive pulmonary disease (COPD) screening system for the community and hospitals in Nanshan District in Shenzhen City, to improve the rate of early diagnosis and treatment of patients with COPD.

METHODS

We identified individuals at high risk of COPD using a questionnaire survey and analyzed the relevant influencing factors in the early stages of COPD in high-risk groups.

RESULTS

We collected a total of 5,000 COPD screening questionnaires, and a total of 449 patients were diagnosed with COPD by pulmonary function examination. The prevalence of COPD in people aged 20 and above in Nanshan District of Shenzhen City was estimated to be 8.98%, with a base of 5000. The severity classification as per the Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria was as follows: GOLD I accounted for 34.74%; GOLD II accounted for 37.64%; GOLD III accounted for 16.04%; and GOLD IV accounted for 11.58%. Common features of early COPD that we identified were: (1) patients were mainly males, accounting for 68.0%; (2) COPD was common among people aged 50-59 years, comprising 31%; (3) 96.0% of patients often had severe respiratory symptoms and had frequent coughs when they did not have a cold; (4) 57.2% of patients experienced shortness of breath when walking quickly on level ground or climbing gentle slopes; (5) 72.6% of patients had a family history of bronchial asthma and COPD. Multivariate ordinal multi-classification logistic regression showed that gender, age, shortness of breath, and the use of firewood, grass, and coal stoves were all influencing factors in pulmonary function grading.

CONCLUSION

A screening questionnaire combined with a pulmonary function test should be adopted as a COPD screening strategy to be implemented at the primary level as a public health priority in China to reduce the incidence, disability, and mortality from COPD.

Artificial Light for Improving Tomato Recovery Following Grafting: Transcriptome and Physiological Analyses

Grafting is widely used to enhance the phenotypic traits of tomatoes, alleviate biotic and abiotic stresses, and control soil-borne diseases of the scion in greenhouse production. There are many factors that affect the healing and acclimatization stages of seedlings after grafting. However, the role of light has rarely been studied. In this study, we compared the effects of artificial light and traditional shading (under shaded plastic-covered tunnels) on the recovery of grafted tomato seedlings. The results show that the grafted tomato seedlings recovered using artificial light had a higher healthy index, leaf chlorophyll content, shoot dry weight, and net photosynthetic rate (Pn) and water use efficiency (WUE) compared with grafted seedling recovered using the traditional shading method. Transcriptome analysis showed that the differentially expressed genes (DEGs) of grafted seedlings restored using artificial light were mainly enriched in the pathways corresponding to plant hormone signal transduction. In addition, we measured the endogenous hormone content of grafted tomato seedlings. The results show that the contents of salicylic acid (SA) and kinetin (Kin) were significantly increased, and the contents of indoleacetic acid (IAA) and jasmonic acid (JA) were decreased in artificial-light-restored grafted tomato seedlings compared with those under shading treatments. Therefore, we suggest that artificial light affects the morphogenesis and photosynthetic efficiency of grafted tomato seedlings, and it can improve the performance of tomato seedlings during grafting recovery by regulating endogenous hormone levels.

CompNet: Complementary network for single-channel speech enhancement

Recent multi-domain processing methods have demonstrated promising performance for monaural speech enhancement tasks. However, few of them explain why they behave better over single-domain approaches. As an attempt to fill this gap, this paper presents a complementary single-channel speech enhancement network (CompNet) that demonstrates promising denoising capabilities and provides a unique perspective to understand the improvements introduced by multi-domain processing. Specifically, the noisy speech is initially enhanced through a time-domain network. However, despite the waveform can be feasibly recovered, the distribution of the time-frequency bins may still be partly different from the target spectrum when we reconsider the problem in the frequency domain. To solve this problem, we design a dedicated dual-path network as a post-processing module to independently filter the magnitude and refine the phase. This further drives the estimated spectrum to closely approximate the target spectrum in the time-frequency domain. We conduct extensive experiments with the WSJ0-SI84 and VoiceBank + Demand datasets. Objective test results show that the performance of the proposed system is highly competitive with existing systems.

Micro Electromechanical System Navigation Assists Femoral Extramedullary Alignment Osteotomy in Total Knee Arthroplasty: A Single-Blind Randomizing Study

OBJECTIVE

A micro-electromechanical system (MEMS) was developed based on spatial alignment and navigation technology to assist femoral extramedullary alignment osteotomy (FEAO) in total knee arthroplasty (TKA). The system can locate and adjust the femoral distal condylar osteotomy (FDCO) to obtain a better femoral prosthesis placement. It is a portable navigation device and provides an innovative approach for FDCO.

METHODS

Sixty patients who suffered from severe knee osteoarthritis who underwent unilateral TKA from May 14, 2021 to May 30, 2022 were randomly divided into a MEMS-FEAO group and a conventional femoral intramedullary alignment osteotomy (FIAO) group, with 30 cases in each group for a controlled retrospective study. The hip-knee-ankle angle (HKAA) of the lower limb was measured before and after surgery, the femoral valgus angle (FVA) was measured preoperatively, and the femoral prosthesis valgus angle (FPVA) and the femoral prosthesis flexion angle (FPFA) were measured postoperatively following computed tomography imaging protocols. Measurement data is statistically described as mean ± standard deviation c. The count data is described by frequency (constituent ratio) using the rank sum test.

RESULT

A total of 6.7% (2/30) of FEAO compared to 20.0% (6/30) of FIAO cases were postoperative deviations where the HKAA exceeded ±3° of neutral alignment (p < 0.05). The postoperative HKAA was 178.74° ± 1.56° versus 176.64° ± 3.39° (p < 0.05), the HKAA deviation was 1.25° ± 1.56° versus 3.36° ± 3.40° (p < 0.05), and the FPFA was 4.85° ± 2.46° versus 6.60° ± 1.86°(p < 0.05). Therefore, the differences were all statistically significant between the two groups. However, the FPVA was -0.59° ± 2.73° versus -0.80° ± 2.85° (p > 0.05), and there was no statistical significance between the two groups.

CONCLUSION

The MEMS-FEAO system can improve the accurate alignment and can be utilized as a locator to obtain the best femoral prosthesis placement in TKA and significantly reduce the rate of poor force line of the lower limb.

The genetic background determines material-induced bone formation through the macrophage-osteoclast axis

Osteoinductive materials are characterized by their ability to induce bone formation in ectopic sites. Thus, osteoinductive materials hold promising potential for repairing bone defects. However, the mechanism of material-induced bone formation remains unknown, which limits the design of highly potent osteoinductive materials. Here, we demonstrated a genetic background link among macrophage polarization, osteoclastogenesis and material-induced bone formation. The intramuscular implantation of an osteoinductive material in FVB/NCrl (FVB) mice resulted in more M2 macrophages at week 1, more osteoclasts at week 2 and increased bone formation after week 4 compared with the results obtained in C57BL/6JOlaHsd (C57) mice. Similarly, in vitro, with a greater potential to form M2 macrophages, monocytes derived from FVB mice formed more osteoclasts than those derived from C57 mice. A transcriptomic analysis identified Csf1, Cxcr4 and Tgfbr2 as the main genes controlling macrophage-osteoclast coupling, which were further confirmed by related inhibitors. With such coupling, macrophage polarization and osteoclast formation of monocytes in vitro successfully predicted in vivo bone formation in four other mouse strains. Considering material-induced bone formation as an example of acquired heterotopic bone formation, the current findings shed a light on precision medicine for both bone regeneration and the treatment of pathological heterotopic bone formation.

Prediction of adult asthma risk in early childhood using novel adult asthma predictive risk scores

BACKGROUND

Numerous risk scores have been developed to predict childhood asthma. However, they may not predict asthma beyond childhood. We aim to create childhood risk scores that predict development and persistence of asthma up to young adult life.

METHODS

The Isle of Wight Birth Cohort (n = 1456) was prospectively assessed up to 26 years of age. Asthma predictive scores were developed based on factors during the first 4 years, using logistic regression and tested for sensitivity, specificity and area under the curve (AUC) for prediction of asthma at (i) 18 and (ii) 26 years, and persistent asthma (PA) (iii) at 10 and 18 years, and (iv) at 10, 18 and 26 years. Models were internally and externally validated.

RESULTS

Four models were generated for prediction of each asthma outcome. ASthma PredIctive Risk scorE (ASPIRE)-1: a 2-factor model (recurrent wheeze [RW] and positive skin prick test [+SPT] at 4 years) for asthma at 18 years (sensitivity: 0.49, specificity: 0.80, AUC: 0.65). ASPIRE-2: a 3-factor model (RW, +SPT and maternal rhinitis) for asthma at 26 years (sensitivity: 0.60, specificity: 0.79, AUC: 0.73). ASPIRE-3: a 3-factor model (RW, +SPT and eczema at 4 years) for PA-18 (sensitivity: 0.63, specificity: 0.87, AUC: 0.77). ASPIRE-4: a 3-factor model (RW, +SPT at 4 years and recurrent chest infection at 2 years) for PA-26 (sensitivity: 0.68, specificity: 0.87, AUC: 0.80). ASPIRE-1 and ASPIRE-3 scores were replicated externally. Further assessments indicated that ASPIRE-1 can be used in place of ASPIRE-2-4 with same predictive accuracy.

CONCLUSION

ASPIRE predicts persistent asthma up to young adult life.