bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning and feature extraction for rapid antimicrobial resistance prediction of Acinetobacter baumannii from whole-genome sequencing data
Authors: Gao Yue , Li Henan , Zhao Chunjiang , Li Shuguang , Yin Guankun , Wang Hui
Published: January 2024

Background

Whole-genome sequencing (WGS) has contributed significantly to advancements in machine learning methods for predicting antimicrobial resistance (AMR). However, the comparisons of different methods for AMR prediction without requiring prior knowledge of resistance remains to be conducted.

Methods

We aimed to predict the minimum inhibitory concentrations (MICs) of 13 antimicrobial agents against Acinetobacter baumannii using three machine learning algorithms (random forest, support vector machine, and XGBoost) combined with k-mer features extracted from WGS data.

Results

A cohort of 339 isolates was used for model construction. The average essential agreement and category agreement of the best models exceeded 90.90% (95%CI, 89.03–92.77%) and 95.29% (95%CI, 94.91–95.67%), respectively; the exceptions being levofloxacin, minocycline and imipenem. The very major error rates ranged from 0.0 to 5.71%. We applied feature selection pipelines to extract the top-ranked 11-mers to optimise training time and computing resources. This approach slightly improved the prediction performance and enabled us to obtain prediction results within 10 min. Notably, when employing these top-ranked 11-mers in an independent test dataset (120 isolates), we achieved an average accuracy of 0.96.

Conclusion

Our study is the first to demonstrate that AMR prediction for A. baumannii using machine learning methods based on k-mer features has competitive performance over traditional workflows; hence, sequence-based AMR prediction and its application could be further promoted. The k-mer-based workflow developed in this study demonstrated high recall/sensitivity and specificity, making it a dependable tool for MIC prediction in clinical settings.
The lncRNA HCG4 regulates the RIG-I-mediated IFN production to suppress H1N1 swine influenza virus replication
Authors: Cheng Jinghua , Tao Jie , Li Benqiang , Shi Ying , Liu Huili
Published: January 2024

Influenza A virus (IAV) non-structural protein 1 (NS1) is a virulence factor that allows the virus to replicate efficiently by suppressing host innate immune responses. Previously, we demonstrated that the serine (S) at position 42 of NS1 in H1N1 swine influenza virus (SIV) is a critical residue in interferon (IFN) resistance, thus facilitating viral infections. Here, by lncRNA-seq, a total of 153 differentially expressed lncRNAs were identified, and the lncRNA HCG4 was selected due to its significantly higher expression after infection with the NS1 S42P mutant virus. Overexpression of HCG4 enhanced IFN-β production and suppressed SIV infection, highlighting the potential antiviral activity of HCG4 against SIV. Further investigation suggested that HCG4 served as a positive feedback mediator for RIG-I signaling. It alleviated the inhibitory effect on RIG-I K63-linked ubiquitination by NS1 protein, thereby resulting in an increase in RIG-I-mediated IFN production. Taken together, our findings demonstrate that HCG4 modulates the innate immune response to SIV infection through K63-linked RIG-I ubiquitination, providing insights into the role of lncRNAs in controlling viral infections.
Multi-omics analysis revealed the differences in lipid metabolism of the gut between adult and juvenile yellowfin tuna (Thunnus albacares)
Authors: Zou Ying , Zhang Yanjie , Wu Di , Lu Zhiyuan , Xiao Juan , Huang Hai , Fu Qiongyao , Guo Zhiqiang
Published: January 2024

Introduction

Tuna has a cost-effective energy supply to support the regional endothermic and high-speed swimming performance. The gut symbiotic microbiotas and their metabolites play essential roles in tuna’s diet digestion, absorption, and energy acquirement, which are often highly related to the ontogenetic development of tuna.

Methods

We compared gut microbial compositions and metabolites, as well as mRNA expression of the intestine between juvenile and adult yellowfin tuna using 16S rRNA sequencing, metabolomic and transcriptomic, respectively.

Results and discussion

The results revealed that adults had a significantly higher microbial diversity and abundance of Acinetobacter than juveniles. Regarding the gut microbiota-derived metabolites, fatty acids, especially glycerophospholipid and sphingolipid, were significantly enriched in adults than in juveniles. Moreover, the short-chain fatty acid (butyrate and isobutyrate) contents were significantly higher in adults than in juveniles. To find the relationship between gut microbiotas and host physiology, intestinal transcriptome analysis demonstrated that the enriched pathways of differential expression genes (DEGs) in adult tuna were the lipid metabolism pathway, including “fat digestion and absorption,” “cholesterol metabolism,” “steroid hormone biosynthesis,” “glycerolipid metabolism,” and “glycerophospholipid metabolism.” However, protein digestion and absorption and pancreatic secretion pathways were significantly enriched in the juveniles. The conjoint analysis indicated that the enriched pathways of both differential metabolites (DMs) and DEGs were remarkably related to the regulation of glycerophospholipids metabolism in adult tunas. This study highlights the role of gut microbiotas in fish nutrition metabolism. These findings provide new insights into the view of ontogenetic shifts of gut microbiotas and their metabolites on host health and gut function in endothermic and high-speed swimming marine fish species.
Plant–microorganism–soil interaction under long-term low-dose ionizing radiation
Authors: Zeng Guoqiang , Wen Yingzi , Luo Chuyang , Zhang Yihong , Li Fei , Xiong Chao
Published: January 2024

As the environmental nuclear radiation pollution caused by nuclear-contaminated water discharge and other factors intensifies, more plant–microorganism–soil systems will be under long-term low-dose ionizing radiation (LLR). However, the regulatory mechanisms of the plant–microorganism–soil system under LLR are still unclear. In this study, we study a system that has been stably exposed to low-dose ionizing radiation for 10 years and investigate the response of the plant–microorganism–soil system to LLR based on the decay of the absorbed dose rate with distance. The results show that LLR affects the carbon and nitrogen migration process between plant–microorganism–soil through the “symbiotic microbial effect.” The increase in the intensity of ionizing radiation led to a significant increase in the relative abundance of symbiotic fungi, such as Ectomycorrhizal fungi and Rhizobiales, which is accompanied by a significant increase in soil lignin peroxidase (LiP) activity, the C/N ratio, and C%. Meanwhile, enhanced radiation intensity causes adaptive changes in the plant functional traits. This study demonstrates that the “symbiotic microbial effect” of plant–microorganism–soil systems is an important process in terrestrial ecosystems in response to LLR.
A computational examination of the therapeutic advantages of fourth-generation ALK inhibitors TPX-0131 and repotrectinib over third-generation lorlatinib for NSCLC with ALK F1174C/L/V mutations
Authors: Balasundaram Ambritha , Doss George Priya C.
Published: January 2024

Background: In non-small-cell lung cancer (NSCLC), a pivotal factor in promoting cancer development is the rearrangement in the anaplastic lymphoma kinase ALK gene, resulting in elevated ALK protein expression. F1174C/L/V is the acquired secondary resistant mutation in ALK. Significant survival improvements have been seen while tyrosine kinase inhibitors specifically target ALK. Nevertheless, the emergence of drug resistance hinders the clinical effectiveness of these drugs.

Objective: This research sought to find the binding affinity/inhibitory effects of the existing drug lorlatinib (LOR) and upcoming TPX-0131 (zotizalkib/TPX) and repotrectinib (TPX-0005/REP) inhibitors against ALK F1174C/L/V mutations using computational approaches to identify potential strategies over resistance.

Methods: We conducted molecular docking, molecular dynamics simulation, and MMPBSA calculations to investigate how compact macrocyclic inhibitors, such as TPX-0131 and repotrectinib, fit within the ATP-binding boundary and differ from LOR.

Results: Our results demonstrated that TPX-0131 and repotrectinib contributed to higher binding energy in F1174C and F1174L mutations than LOR. Repotrectinib showed greater binding energy in the F1174V mutation, whereas LOR and TPX-0131 exhibited similar binding energy. However, all three inhibitors showed significant binding energy toward F1174C/L/V mutations found in NSCLC.

Conclusion: This comparative study of the potential binding effects of fourth-generation inhibitors TPX-0131 and repotrectinib and third-generation inhibitor LOR for ALK F1174C/L/V mutations revealed the atomistic insights of the binding mechanism. These computational findings enable us to carry out further research for the clinical implementation of fourth-generation ALK inhibitors on ALK-positive NSCLC.
Association of social integration with cognitive function trajectories among Chinese older adults: evidence from the China health and retirement longitudinal study (CHARLS)
Authors: Mose Amu , Chen Yanhong , Tan Xiaoshuang , Ren Qingman , Ren Xiaohui
Published: January 2024

Background

The prevalence of cognitive impairment among older adults remains high. It has been proven that social integration is related to cognitive function. However, limited research has examined the association of social integration and its different dimensions with cognitive function trajectories of older adults.

Methods

The data were from the China Health and Retirement Longitudinal Study (CHARLS) spanning 2013 (T1) to 2018 (T3). A total of 3,977 older adults were included in the final analysis. Cognitive function was measured with items from an adapted Chinese version of the Mini-Mini-Mental Mental State Examination (MMSE), while the measurement of social integration included three dimensions: economic integration, relational integration and community integration. A group-based trajectory model (GBTM) was used to identify cognitive trajectory groups among participants and an unordered multinomial logistic regression was employed to explore the association of baseline social integration and its three dimensions with cognitive function trajectories.

Result

Three cognitive function trajectory groups were identified: low-decline group (24.1%), medium-decline group (44.2%) and high-stable group (31.7%). Comparing to the medium-decline trajectory group, older adults with higher social integration scores were more likely to be in the high-stable trajectory group (OR = 1.087, 95%CI: 1.007 ~ 1.174), while less likely to be in the low-decline group (OR = 0.806, 95%CI: 0.736 ~ 0.882). Among the different dimensions of social integration, older adults with higher community integration scores were more likely to be in the high-stable trajectory group (OR = 1.222, 95%CI: 1.026 ~ 1.456); Older adults with higher relational integration scores were less likely to be in the low-decline trajectory group (OR = 0.816, 95%CI: 0.734 ~ 0.906). The economic integration was not found to correlate with the cognitive function trajectories. Stratified analyses revealed that the association between community integration and cognitive trajectories was only significant among older adults aged 60 to 69, and the association between relational integration and cognitive trajectories was only significant among older adults who was agricultural household registration.

Conclusion

The developmental trajectories of cognitive function among Chinese older adults are heterogeneous. Social integration is significantly related to the trajectories of cognitive function in Chinese older adults. Measures should be taken to promote social integration of Chinese older adults to reduce the decline of cognitive function.
Utilizing hiPSC-derived oligodendrocytes to study myelin pathophysiology in neuropsychiatric and neurodegenerative disorders.
Authors: Shim Gina , Romero-Morales Alejandra I. , Sripathy Srinidhi R. , Maher Brady J.
Published: January 2024

Oligodendrocytes play a crucial role in our central nervous system (CNS) by myelinating axons for faster action potential conduction, protecting axons from degeneration, structuring the position of ion channels, and providing nutrients to neurons. Oligodendrocyte dysfunction and/or dysmyelination can contribute to a range of neurodegenerative diseases and neuropsychiatric disorders such as Multiple Sclerosis (MS), Leukodystrophy (LD), Schizophrenia (SCZ), and Autism Spectrum Disorder (ASD). Common characteristics identified across these disorders were either an inability of oligodendrocytes to remyelinate after degeneration or defects in oligodendrocyte development and maturation. Unfortunately, the causal mechanisms of oligodendrocyte dysfunction are still uncertain, and therapeutic targets remain elusive. Many studies rely on the use of animal models to identify the molecular and cellular mechanisms behind these disorders, however, such studies face species-specific challenges and therefore lack translatability. The use of human induced pluripotent stem cells (hiPSCs) to model neurological diseases is becoming a powerful new tool, improving our understanding of pathophysiology and capacity to explore therapeutic targets. Here, we focus on the application of hiPSC-derived oligodendrocyte model systems to model disorders caused by oligodendrocyte dysregulation.
The supplementation of the multi-strain probiotics WHHPRO™ alleviates high-fat diet-induced metabolic symptoms in rats via gut-liver axis
Authors: Chen Cailing , Gao Kan , Chen Zuoguo , Zhang Qiwen , Ke Xueqin , Mao Bingyong , Fan Qiuling , Li Yanjun , Chen Su
Published: January 2024

Metabolic syndrome (MS) has emerged as one of the major global health concerns, accompanied by a series of related complications, such as obesity and type-2 diabetes. The gut-liver axis (GLA) is a bidirectional communication between the gut and the liver. The GLA alterations have been revealed to be closely associated with the development of MS. Probiotics within Lactobacillus and Bifidobacterium confer beneficial effects on improving MS symptoms. WHHPRO™ is a mixture of four probiotic strains, with potential MS-improving abilities. This study aimed to investigate the effects of WHHPRO™ on MS symptoms using a high-fat diet (HFD) rat model. Oral administration of WHHPRO™ for 12 weeks improved glucose tolerance, blood lipid, body weight, and liver index in HFD rats. WHHPRO™ shaped the gut microbiome composition by increasing the abundance of Lactobacillus and Akkermansia and normalized the reduced SCFA levels in HFD rats. Besides, WHHPRO™ modulated the fecal bile acids (BAs) profile, with decreased levels of T-b-MCA and 12-KDCA and increased levels of LCA and ILCA. Meanwhile, WHHPRO™ increased total unconjugated BAs in feces and liver and reduced the accumulation of total hepatic BA pool size in HFD rats. Moreover, WHHPRO™ reversed the expression of genes associated with impaired BA metabolism signaling in the ileum and liver. Our findings suggest that WHHPRO™ exerted beneficial effects on improving MS symptoms, involving the modulation of the gut microbiome composition, SCFAs, and the FXR-FGF15 signaling along the GLA. Supplementation of WHHPRO™ may serve as a novel strategy for improving MS symptoms.
Correlation between sarcopenia and cirrhosis: a meta-analysis
Authors: Cui Yifan , Zhang Mingming , Guo Jing , Jin Jin , Wang Haijiao , Wang Xinran
Published: January 2024

Background

The relationship between sarcopenia and cirrhosis is unclear. In this research, our aim is to evaluate the prevalence of sarcopenia among individuals with liver cirrhosis and its correlation with survival and mortality risks.

Methods

We conducted searches on PubMed, Web of Science, EMBASE, and Cochrane for English articles published up to July 10, 2023, and additionally manually searched the bibliography of relevant articles. We incorporated research on sarcopenia in patients with cirrhosis to examine the connection between sarcopenia and the likelihood of survival and mortality. Statistical analyses were carried out utilizing the Stata version 15.1 software. Depending on the heterogeneity of the results, we employed either fixed-effects models or random-effects models for data synthesis. To assess publication bias, we employed funnel plots and conducted Egger’s test.

Results

We included 40 studies involving 8,945 patients with cirrhosis. The overall prevalence of cirrhosis was 41% (95% CI 34%–48%). Male patients and those with liver cirrhosis and hepatic encephalopathy had a higher prevalence of sarcopenia (44% for male patients and 48% for hepatic encephalopathy patients). Sarcopenia emerged as a risk factor for both survival (HR = 2.57, 95% CI 2.02–3.27, p < 0.001) and mortality (HR = 2.13, 95% CI 1.86–2.44, p < 0.001) in patients with cirrhosis. Subgroup analyses consistently yielded the same results for study sites, whether HCC patients were excluded from the cohort, whether patients were from the liver transplant cohort or had undergone tips surgery, the definition of sarcopenia (L3-SMI or other methods), and the diagnostic criteria used by patients. The presence of sarcopenia was also a significant risk factor for hepatic encephalopathy [HR = 2.27, 95% CI (1.76–2.94), p < 0.001].

Conclusion

This systematic review and meta-analysis reveal that patients with cirrhosis have a prevalence of sarcopenia of 41% and is associated with survival rate and mortality rate. Therefore, we should attach importance to the screening of sarcopenia in patients with cirrhosis, early detection of susceptible populations, and appropriate measures to reduce the occurrence and adverse outcomes.

Systematic review registration:https://www.crd.york.ac.uk/PROSPERO/#recordDetails.
RETRACTED: Dual-phenotype hepatocellular carcinoma: correlation of MRI features with other primary hepatocellular carcinoma and differential diagnosis
Authors: Zhang Liqing , Chen Jing , Lai Xufeng , Zhang Xiaoqian , Xu Jianfeng
Published: January 2024

Objectives

Dual-phenotype hepatocellular carcinoma (DPHCC) is a rare subtype of hepatocellular carcinoma characterized by high invasiveness and a poor prognosis. The study aimed to compare clinical and magnetic resonance imaging (MRI) features of DPHCC with that of non-DPHCC and intrahepatic cholangiocarcinoma (ICC), exploring the most valuable features for diagnosing DPHCC.

Methods

A total of 208 cases of primary liver cancer, comprising 27 DPHCC, 113 non-DPHCC, and 68 ICC, who undergone gadoxetic acid–enhanced MRI, were enrolled in this study. The clinicopathologic and MRI features of all cases were summarized and analyzed. Univariate and multivariate logistic regression analyses were conducted to identify the predictors. Kaplan–Meier survival analysis was used to evaluate the 1-year and 2-year disease-free survival (DFS) and overall survival (OS) rates in the cohorts.

Results

In the multivariate analysis, the absence of tumor capsule (P = 0.046; OR = 9.777), persistent enhancement (P = 0.006; OR = 46.941), arterial rim enhancement (P = 0.011; OR = 38.211), and target sign on DWI image (P = 0.021; OR = 30.566) were identified as independently significant factors for distinguishing DPHCC from non-DPHCC. Serum alpha-fetoprotein (AFP) >20 μg/L (P = 0.036; OR = 67.097) and hepatitis B virus (HBV) positive (P = 0.020; OR = 153.633) were independent significant factors for predicting DPHCC compared to ICC. The 1-year and 2-year DFS rates for patients in the DPHCC group were 65% and 50%, respectively, whereas those for the non-DPHCC group were 80% and 60% and for the ICC group were 50% and 29%, respectively. The 1-year and 2-year OS rates for patients in the DPHCC group were 74% and 60%, respectively, whereas those for the non-DPHCC group were 87% and 70% and for the ICC group were 55% and 37%, respectively. Kaplan–Meier survival analysis revealed significant differences in the 1-year and 2-year OS rates between the DPHCC and non-DPHCC groups (P = 0.030 and 0.027) as well as between the DPHCC and ICC groups (P = 0.029 and 0.016).

Conclusion

In multi-parameter MRI, combining the assessment of the absence of tumor capsule, persistent enhancement, arterial rim enhancement, and target sign on DWI image with clinical data such as AFP >20 μg/L and HBV status may support in the diagnosis of DPHCC and differentiation from non-DPHCC and ICC. Accurate preoperative diagnosis facilitates the selection of personalized treatment options.
Cerebrospinal fluid ctDNA testing shows an advantage over plasma ctDNA testing in advanced non-small cell lung cancer patients with brain metastases
Authors: Liu Xiaocui , Mei Fengjun , Fang Mei , Jia Yaqiong , Zhou Yazhu , Li Chenxi , Tian Panpan , Lu Chufan , Li Guangrui
Published: January 2024

Background

Brain metastases (BM), including brain parenchyma metastases (BPM) and leptomeningeal metastases (LM), are devastating metastatic complications in advanced cancer patients. Next-generation sequencing (NGS) is emerging as a new promising tool for profiling cancer mutation, which could facilitate the diagnosis of cancer. This retrospective study aimed to investigate the molecular genetic characteristics of non-small cell lung cancer (NSCLC) patients with BPM and LM using NGS.

Methods

Cerebrospinal fluid (CSF) samples and paired plasma samples were collected from 37 patients of NSCLC-BM. We profiled genetic mutation characteristics using NGS from NSCLC-BM by comparing CSF circulating tumour DNA (ctDNA) with plasma ctDNA and primary tumour tissues.

Results

Among the 37 patients with NSCLC-BM, 28 patients had LM with or without BPM, while 9 patients only had BPM. Driver and drug-resistant mutations in primary tumours with LM included: EGFR L858R (10, 35.7%), EGFR 19del (6, 21.4%), EGFR L858R+MET (1, 3.6%), EGFR L858R+S768I (1, 3.6%), ALK (2, 7.1%), ROS1 (1, 3.6%), negative (5, 17.9%), and unknown (2, 7.1%). In patients with NSCLC-LM, the detection rate and abundance of ctDNA in the CSF were significantly higher than those in paired plasma. The main driver mutations of NSCLC-LM remained highly consistent with those of the primary tumours, along with other unique mutations. Circulating tumour DNA was negative in the CSF samples of BPM patients. Patients with BMP had a higher ratio of EGFR 19del than L858R mutation (55.6% vs 11.1.%), whereas NSCLC patients with LM had a higher ratio of EGFR L858R than 19del mutation (50.0% vs 25.0%). Most patients with positive plasma ctDNA results were male (p = 0.058) and in an unstable state (p = 0.003).

Conclusion

Our study indicated that the CSF ctDNA detected by NGS may reflect the molecular characteristics and heterogeneity of NSCLC-LM. Timely screening of patients with NSCLC for CSF ctDNA, especially for patients with positive plasma ctDNA, may facilitate the early detection of LM. Furthermore, patients with the EGFR 19del may have a higher risk of developing BPM.
Manipulation of mitochondrial poly(A) polymerase family proteins in Trypanosoma brucei impacts mRNA termini processing
Authors: Smoniewski Clara M. , Mirzavand Borujeni Poorya , Hampton Marshall , Petersen Austin , Faacks Sean P. , Salavati Reza , Zimmer Sara L.
Published: January 2024

RNA-specific nucleotidyltransferases (rNTrs) add nontemplated nucleotides to the 3′ end of RNA. Two noncanonical rNTRs that are thought to be poly(A) polymerases (PAPs) have been identified in the mitochondria of trypanosomes – KPAP1 and KPAP2. KPAP1 is the primary polymerase that adds adenines (As) to trypanosome mitochondrial mRNA 3′ tails, while KPAP2 is a non-essential putative polymerase whose role in the mitochondria is ambiguous. Here, we elucidate the effects of manipulations of KPAP1 and KPAP2 on the 5′ and 3′ termini of transcripts and their 3′ tails. Using glycerol gradients followed by immunoblotting, we present evidence that KPAP2 is found in protein complexes of up to about 1600 kDa. High-throughput sequencing of mRNA termini showed that KPAP2 overexpression subtly changes an edited transcript’s 3′ tails, though not in a way consistent with general PAP activity. Next, to identify possible roles of posttranslational modifications on KPAP1 regulation, we mutated two KPAP1 arginine methylation sites to either mimic methylation or hypomethylation. We assessed their effect on 3′ mRNA tail characteristics and found that the two mutants generally had opposing effects, though some of these were transcript-specific. We present results suggesting that while methylation increases KPAP1 substrate binding and/or initial nucleotide additions, unmethylated KPAP1is more processive. We also present a comprehensive review of UTR termini, and evidence that tail addition activity may change as mRNA editing is initiated. Together, this work furthers our understanding of the role of KPAP1 and KPAP2 on trypanosome mitochondrial mRNA 3′ tail addition, as well as provides more information on mRNA termini processing in general.
Machine learning-based prediction of composite risk of cardiovascular events in patients with stable angina pectoris combined with coronary heart disease: development and validation of a clinical prediction model for Chinese patients
Authors: Wang Zihan , Sun Ziyi , Yu Linghua , Wang Zhitian , Li Lin , Lu Xiaoyan
Published: January 2024

Objective: To develop a risk score model for the occurrence of composite cardiovascular events (CVE) in patients with stable angina pectoris (SA) combined with coronary heart disease (CHD) by comparing the modeling effects of various machine learning (ML) algorithms.

Methods: In this prospective study, 690 patients with SA combined with CHD attending the Department of Integrative Cardiology, China-Japan Friendship Hospital, from October 2020 to October 2021 were included. The data set was randomly divided into a training group and a testing group in a 7:3 ratio in the per-protocol set (PPS). Model variables were screened using the least absolute shrinkage selection operator (LASSO) regression, univariate analysis, and multifactor logistic regression. Then, nine ML algorithms are integrated to build the model and compare the model effects. Individualized risk assessment was performed using the SHapley Additive exPlanation (SHAP) and nomograms, respectively. The model discrimination was evaluated by receiver operating characteristic curve (ROC), the calibration ability of the model was evaluated by calibration plot, and the clinical applicability of the model was evaluated by decision curve analysis (DCA). This study was approved by the Clinical Research Ethics Committee of China-Japan Friendship Hospital (2020-114-K73).

Results: 690 patients were eligible to finish the complete follow-up in the PPS. After LASSO screening and multifactorial logistic regression analysis, physical activity level, taking antiplatelets, Traditional Chinese medicine treatment, Gensini score, Seattle Angina Questionnaire (SAQ)-exercise capacity score, and SAQ-anginal stability score were found to be predictors of the occurrence of CVE. The above predictors are modeled, and a comprehensive comparison of the modeling effectiveness of multiple ML algorithms is performed. The results show that the Light Gradient Boosting Machine (LightGBM) model is the best model, with an area under the curve (AUC) of 0.95 (95% CI = 0.91–1.00) for the test set, Accuracy: 0.90, Sensitivity: 0.87, and Specificity: 0.96. Interpretation of the model using SHAP highlighted the Gensini score as the most important predictor. Based on the multifactorial logistic regression modeling, a nomogram, and online calculators have been developed for clinical applications.

Conclusion: We developed the LightGBM optimization model and the multifactor logistic regression model, respectively. The model is interpreted using SHAP and nomogram. This provides an option for early prediction of CVE in patients with SA combined with CHD.
Bank digital transformation, bank competitiveness and systemic risk
Authors: Jia Kaiwei , Liu Xinbei
Published: January 2024

The aim of this paper is to analyze the impact of the digital transformation of banks on their systemic risks. We find that the digital transformation of commercial banks can significantly inhibit the systemic risk of banks, and this conclusion is still valid after considering the endogeneity of the model. The bank’s digital transformation reduces its systemic risk by increasing its own competitiveness. Further analysis shows that the reduction of banks’ marginal costs due to digital transformation is a key factor in promoting banks’ competitiveness as the mechanism by which digital transformation reduces banks’ systemic risk. The role of bank digital transformation in reducing systemic risk is heterogeneous, which is more obvious in large commercial banks, commercial banks that have not established financial technology subsidiaries, and systemically important banks.
Overexpression of ameloblastin in secretory ameloblasts results in demarcated, hypomineralized opacities in enamel
Authors: Chun Yong-Hee Patricia , Tan Chunyan , Villanueva Omar , Colley Madeline E. , Quintanilla Travis J. , Basiouny Mohamed S. , Hartel Caldonia A. , Critchfield Cameron S. , Bach Stephan B. H. , Fajardo Roberto J. , Pham Cong-Dat
Published: January 2024

Introduction: Developmental defects of the enamel manifest before tooth eruption and include amelogenesis imperfecta, a rare disease of underlying gene mutations, and molar–incisor hypomineralization (MIH), a prevalent disease in children originating from environmental and epigenetic factors. MIH enamel presents as the abnormal enamel marked by loss of translucency, demarcation between the healthy and affected enamel, and reduced mineral content. The pathophysiology of opaque, demarcated enamel lesions is not understood; however, the retention of enamel proteins in the matrix has been suggested. Ameloblastin (Ambn) is an enamel protein of the secreted calcium-binding phosphoproteins (SCPPs) critical for enamel formation. When the Ambn gene is mutated or deleted, teeth are affected by hypoplastic amelogenesis imperfecta.

Methods: In this study, enamel formation in mice was analyzed when transgenic Ambn was overexpressed from the amelogenin promoter encoding full-length Ambn. Ambn was under- and overexpressed at six increasing concentrations in separate mouse lines.

Results: Mice overexpressing Ambn displayed opaque enamel at low concentrations and demarcated lesions at high concentrations. The severity of enamel lesions increased starting from the inner enamel close to the dentino-enamel junction (DEJ) to span the entire width of the enamel layer in demarcated areas. Associated with the opaque enamel were 17-kDa Ambn cleavage products, a prolonged secretory stage, and a thin basement membrane in the maturation stage. Ambn accumulations found in the innermost enamel close to the DEJ and the mineralization front correlated with reduced mineral content. Demarcated enamel lesions were associated with Ambn species of 17 kDa and higher, prolonged secretory and transition stages, a thin basement membrane, and shortened maturation stages. Hypomineralized opacities were delineated against the surrounding mineralized enamel and adjacent to ameloblasts detached from the enamel surface. Inefficient Ambn cleavage, loss of contact between ameloblasts, and the altered basement membrane curtailed the endocytic activity; thus, enamel proteins remained unresorbed in the matrix. Ameloblasts have the ability to distinguish between Ambn concentration and Ambn cleavage products through finely tuned feedback mechanisms. The under- or overexpression of Ambn in murine secretory ameloblasts results in either hypoplastic amelogenesis imperfecta or hypomineralization with opaque or sharply demarcated boundaries of lesions, similar to MIH.
Profiles of Wnt pathway gene expression during tooth morphogenesis
Authors: Raju Resmi , Piña Jeremie Oliver , Roth Daniela M. , Chattaraj Parna , Kidwai Fahad K. , Faucz Fabio R. , Iben James , Fridell Gus , Dale Ryan K. , D’Souza Rena N.
Published: January 2024

Mouse and human genetic studies indicate key roles of the Wnt10a ligand in odontogenesis. Previous studies have identified effectors and regulators of the Wnt signaling pathway actively expressed during key stages of tooth morphogenesis. However, limitations in multiplexing and spatial resolution hindered a more comprehensive analysis of these signaling molecules. Here, profiling of transcriptomes using fluorescent multiplex in situ hybridization and single-cell RNA-sequencing (scRNA-seq) provide robust insight into the synchronized expression patterns of Wnt10a, Dkk1, and Sost simultaneously during tooth development. First, we identified Wnt10a transcripts restricted to the epithelium at the stage of tooth bud morphogenesis, contrasting that of Sost and Dkk1 localization to the dental mesenchyme. By embryonic day 15.5 (E15.5), a marked shift of Wnt10a expression from dental epithelium to mesenchyme was noted, while Sost and Dkk1 expression remained enriched in the mesenchyme. By postnatal day 0 (P0), co-localization patterns of Wnt10a, Dkk1, and Sost were observed in both terminally differentiating and secreting odontoblasts of molars and incisors. Interestingly, Wnt10a exhibited robust expression in fully differentiated ameloblasts at the developing cusp tip of both molars and incisors, an observation not previously noted in prior studies. At P7 and 14, after the mineralization of dentin and enamel, Wnt10a expression was limited to odontoblasts. Meanwhile, Wnt modulators showed reduced or absent signals in molars. In contrast, strong signals persisted in ameloblasts (for Wnt10a) and odontoblasts (for Wnt10a, Sost, and Dkk1) towards the proximal end of incisors, near the cervical loop. Our scRNA-seq analysis used CellChat to further contextualize Wnt pathway-mediated communication between cells by examining ligand-receptor interactions among different clusters. The co-localization pattern of Wnt10a, Dkk1, and Sost in both terminally differentiating and secreting odontoblasts of molars and incisors potentially signifies the crucial ligand-modulator interaction along the gradient of cytodifferentiation starting from each cusp tip towards the apical region. These data provide cell type-specific insight into the role of Wnt ligands and mediators during epithelial-mesenchymal interactions in odontogenesis.
Weed detection in soybean fields using improved YOLOv7 and evaluating herbicide reduction efficacy
Authors: Li Jinyang , Zhang Wei , Zhou Hong , Yu Chuntao , Li Qingda
Published: January 2024

With the increasing environmental awareness and the demand for sustainable agriculture, herbicide reduction has become an important goal. Accurate and efficient weed detection in soybean fields is the key to test the effectiveness of herbicide application, but current technologies and methods still have some problems in terms of accuracy and efficiency, such as relying on manual detection and poor adaptability to some complex environments. Therefore, in this study, weeding experiments in soybean fields with reduced herbicide application, including four levels, were carried out, and an unmanned aerial vehicle (UAV) was utilized to obtain field images. We proposed a weed detection model—YOLOv7-FWeed—based on improved YOLOv7, adopted F-ReLU as the activation function of the convolution module, and added the MaxPool multihead self-attention (M-MHSA) module to enhance the recognition accuracy of weeds. We continuously monitored changes in soybean leaf area and dry matter weight after herbicide reduction as a reflection of soybean growth at optimal herbicide application levels. The results showed that the herbicide application level of electrostatic spraying + 10% reduction could be used for weeding in soybean fields, and YOLOv7-FWeed was higher than YOLOv7 and YOLOv7-enhanced in all the evaluation indexes. The precision of the model was 0.9496, the recall was 0.9125, the F1 was 0.9307, and the mAP was 0.9662. The results of continuous monitoring of soybean leaf area and dry matter weight showed that herbicide reduction could effectively control weed growth and would not hinder soybean growth. This study can provide a more accurate, efficient, and intelligent solution for weed detection in soybean fields, thus promoting herbicide reduction and providing guidance for exploring efficient herbicide application techniques.
Non-destructive real-time analysis of plant metabolite accumulation in radish microgreens under different LED light recipes
Authors: Garegnani Marco , Sandri Carla , Pacelli Claudia , Ferranti Francesca , Bennici Elisabetta , Desiderio Angiola , Nardi Luca , Villani Maria Elena
Published: January 2024

Introduction

The future of human space missions relies on the ability to provide adequate food resources for astronauts and also to reduce stress due to the environment (microgravity and cosmic radiation). In this context, microgreens have been proposed for the astronaut diet because of their fast-growing time and their high levels of bioactive compounds and nutrients (vitamins, antioxidants, minerals, etc.), which are even higher than mature plants, and are usually consumed as ready-to-eat vegetables.

Methods

Our study aimed to identify the best light recipe for the soilless cultivation of two cultivars of radish microgreens (Raphanus sativus, green daikon, and rioja improved) harvested eight days after sowing that could be used for space farming. The effects on plant metabolism of three different light emitting diodes (LED) light recipes (L1—20% red, 20% green, 60% blue; L2—40% red, 20% green, 40% blue; L3—60% red, 20% green, 20% blue) were tested on radish microgreens hydroponically grown. A fluorimetric-based technique was used for a real-time non-destructive screening to characterize plant methabolism. The adopted sensors allowed us to quantitatively estimate the fluorescence of flavonols, anthocyanins, and chlorophyll via specific indices verified by standardized spectrophotometric methods. To assess plant growth, morphometric parameters (fresh and dry weight, cotyledon area and weight, hypocotyl length) were analyzed.

Results

We observed a statistically significant positive effect on biomass accumulation and productivity for both cultivars grown under the same light recipe (40% blue, 20% green, 40% red). We further investigated how the addition of UV and/or far-red LED lights could have a positive effect on plant metabolite accumulation (anthocyanins and flavonols).

Discussion

These results can help design plant-based bioregenerative life-support systems for long-duration human space exploration, by integrating fluorescence-based non-destructive techniques to monitor the accumulation of metabolites with nutraceutical properties in soilless cultivated microgreens.
Differences in primary metabolism related to quality of raspberry (Rubus idaeus L.) fruit under open field and protected soilless culture growing conditions
Authors: Fuentealba Claudia , Álvarez Fernanda , Ponce Excequel , Veas Sebastian , Salazar Martina , Romero Diego , Ayala-Raso Anibal , Alvaro Juan E. , Valdenegro Monika , Figueroa Carlos R. , Fuentes Lida
Published: January 2024

Introduction

The raspberry (Rubus idaeus) fruit is characterized by good taste and high acceptability by consumers. Thus, the impact on the quality attributes and metabolites related to raspberry taste should be evaluated in crop alternatives such as the protected soilless culture. This study aimed to evaluate the metabolic changes during fruit development and postharvest of raspberry grown in open field and protected soilless culture and their relationship with quality parameters and sensory perception.

Methods

In this study, the quality parameters and polar metabolites -sugar and amino acids- content were evaluated during raspberry ripening. In addition, ripe fruit was stored at 1 °C for five days, followed by one day of shelf life at 20 °C.

Results

The physiological and quality parameters showed typical changes during ripening in both growing conditions: a constant production of CO2, a drastic loss of firmness, an increase in weight and soluble solids content, loss of acidity, and a turning to red color from the green to fully ripe fruit stages in both growing conditions. Fruit from the protected soilless culture had significantly higher weight but a lower soluble solids content. The metabolic analysis showed differences in primary metabolites content during ripening and storage at 1 °C between both growing conditions. The raspberries grown in the open field showed higher contents of sugars such as D-glucose and D-fructose. On the contrary, the fruit from the protected soilless culture showed higher contents of some amino acids such as L-alanine, L-serine and L-valine, among others. The sensorial panel showed significant differences in the perception of the sweetness, acidity, color and firmness of ripe fruit from both growing conditions.

Discussion

The present study provides interesting and useful results with direct commercial application for this alternative growing system, mainly in areas where soil and water scarcity are a reality.
Principles, developments, and applications of spatially resolved spectroscopy in agriculture: a review
Authors: Xia Yu , Liu Wenxi , Meng Jingwu , Hu Jinghao , Liu Wenbo , Kang Jie , Luo Bin , Zhang Han , Tang Wei
Published: January 2024

Agriculture is the primary source of human survival, which provides the most basic living and survival conditions for human beings. As living standards continue to improve, people are also paying more attention to the quality and safety of agricultural products. Therefore, the detection of agricultural product quality is very necessary. In the past decades, the spectroscopy technique has been widely used because of its excellent results in agricultural quality detection. However, traditional spectral inspection methods cannot accurately describe the internal information of agricultural products. With the continuous research and development of optical properties, it has been found that the internal quality of an object can be better reflected by separating the properties of light, such as its absorption and scattering properties. In recent years, spatially resolved spectroscopy has been increasingly used in the field of agricultural product inspection due to its simple compositional structure, low-value cost, ease of operation, efficient detection speed, and outstanding ability to obtain information about agricultural products at different depths. It can also separate optical properties based on the transmission equation of optics, which allows for more accurate detection of the internal quality of agricultural products. This review focuses on the principles of spatially resolved spectroscopy, detection equipment, analytical methods, and specific applications in agricultural quality detection. Additionally, the optical properties methods and direct analysis methods of spatially resolved spectroscopy analysis methods are also reported in this paper.
The tenure track employment system in colleges and universities in China: a scoping review of the Chinese literature
Authors: Wang Xin , Wang Wen Li
Published: January 2024

Chinese higher education institutions have adopted a US-style tenure track system since the 1990s. This is an important reform aimed at modernizing China’s higher education system. In response, authors have begun to carry out close examination of the career system and analyse its implications in a national context (Republic of China). This study aims to present the key research themes, identify research gaps and offer recommendations from the increasing pool of Chinese-language literature on the tenure track system. A scoping review of Chinese language papers was conducted using the China National Knowledge Infrastructure (including the China Academic Journals Full-text Database, China Core Newspapers Full-text Database, China Doctoral Dissertations Full-text Database, China Masters’ Thesis Full-text Database, and China Yearbooks Full-text Database) (CNKI) database. Four major research themes were identified in Chinese discourse: (1) examining the tenure track system, (2) providing suggestions for better adaptation of the tenure track system in the Chinese context, (3) analysing the negative effects of the tenure track system, and (4) analysing the positive effects of the tenure track system. Generally, authors were concerned with the adaptation and cultivation of the US-originated tenure track system in the Chinese context and emphasized the importance of acknowledging its perceived negative influences on early-career scholars who have not received adequate attention. Overall, the authors demonstrate increasing interest in the tenure track system in China, and the literature is of variable quality. Further empirical studies are needed to analyse, evaluate and guide future improvement of the career system in the Chinese context in practice.
A structural equation model of online learning: investigating self-efficacy, informal digital learning, self-regulated learning, and course satisfaction
Authors: Zheng Yi , Xiao Ao
Published: January 2024

Introduction

English as a Foreign Language (EFL) education increasingly relies on online learning, necessitating a nuanced understanding of crucial factors impacting learning experiences. This research investigates the intricate relationships among online learning self-efficacy, online self-regulated learning, informal digital learning of English (IDLE), and online course satisfaction within the unique context of EFL learners.

Methods

The study involved 563 intermediate college students from various national universities in China. Structural Equation Modeling (SEM) was employed to analyze the data, providing comprehensive insights into the relationships among the identified variables.

Results

The results revealed significant insights. Both online learning self-efficacy and IDLE exhibited direct and positive influences on online course satisfaction. Furthermore, the study uncovered that online self-regulated learning acted as a partial mediator in the connection between online learning self-efficacy and IDLE with online course satisfaction. This mediation implies that learners’ self-regulatory behaviors significantly affect how self-efficacy and informal digital language learning experiences impact overall satisfaction with online courses.

Discussion

The findings highlight the pivotal role of nurturing learners’ self-efficacy beliefs, fostering IDLE, and promoting effective self-regulated learning strategies in the realm of online language learning. These initiatives are instrumental in enhancing learners’ satisfaction and success in online courses.

Conclusion

The implications of these findings for EFL instruction are substantial. By emphasizing the importance of self-efficacy, IDLE, and self-regulated learning strategies, educators can significantly contribute to creating more satisfying and successful online learning experiences for EFL students.