bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell RNA sequencing reveals the impaired epidermal differentiation and pathological microenvironment in diabetic foot ulcer
Authors: Liu Yiling , Wang Peng , Li Jingting , Chen Lei , Shu Bin , Wang Hanwen , Liu Hengdeng , Zhao Shixin , Zhou Junli , Chen Xiaodong , Xie Julin 
Published: February 2025

Abstract

Background
Diabetic foot ulcer (DFU) is one of the most common and complex complications of diabetes, but the underlying pathophysiology remains unclear. Single-cell RNA sequencing (scRNA-seq) has been conducted to explore novel cell types or molecular profiles of DFU from various perspectives. This study aimed to comprehensively analyse the potential mechanisms underlying impaired reepithelization of DFU in a single-cell perspective.

Methods
We conducted scRNA-seq on tissues from human normal skin (NS), acute wound (AW) and DFU to investigate the potential mechanisms underlying impaired epidermal differentiation and the pathological microenvironment. Pseudo-time and lineage inference analyses revealed the distinct states and transition trajectories of epidermal cells under different conditions. Transcription factor analysis revealed the potential regulatory mechanism of key subtypes of keratinocytes. Cell–cell interaction analysis revealed the regulatory network between the proinflammatory microenvironment and epidermal cells. Laser-capture microscopy coupled with RNA sequencing (LCM-seq) and multiplex immunohistochemistry (mIHC) were used to validate the expression and location of key subtypes of keratinocytes.

Results
Our research provided a comprehensive map of the phenotypic and dynamic changes that occur during epidermal differentiation, alongside the corresponding regulatory networks in DFU. Importantly, we identified two subtypes of keratinocytes: basal cells (BC-2) and diabetes-associated keratinocytes (DAK) that might play crucial roles in the impairment of epidermal homeostasis. BC-2 and DAK showed a marked increase in DFU, with an inactive state and insufficient motivation for epidermal differentiation. BC-2 was involved in the cellular response and apoptosis processes, with high expression of TXNIP, IFITM1 and IL1R2. Additionally, the pro-differentiation transcription factors (TFs) were downregulated in BC-2 in DFU, indicating that the differentiation process might be inhibited in BC-2 in DFU. DAK was associated with cellular glucose homeostasis. Furthermore, increased CCL2 + CXCL2+ fibroblasts, VWA1+ vascular endothelial cells and GZMA+CD8+ T cells were detected in DFU. These changes in the wound microenvironment could regulate the fate of epidermal cells through the TNFSF12-TNFRSF12A, IFNG-IFNGR1/2 and IL-1B-IL1R2 pathways, which might result in persistent inflammation and impaired epidermal differentiation in DFU.

Conclusions
Our findings offer novel insights into the pathophysiology of DFU and present potential therapeutic targets that could improve wound care and treatment outcomes for diabetic patients.
Flufenamic acid inhibits pyroptosis in ischemic flaps via the AMPK-TRPML1-Calcineurin signaling pathway
Authors: Chen Liang , Yang Ningning , Chen Kongbin , Huang Yingying , Liu Xian , Yu Gaoxiang , Wang Fulin , Gou Yong , Wang Yi , Lu Xiaolang , Wang Yuqi , Zhu Lipeng , Gao Weiyang , Ding Jian 
Published: February 2025

Abstract

Background
Ischemic injury is a primary cause of distal flap necrosis. Previous studies have shown that Flufenamic acid (FFA) can reduce inflammation, decrease oxidative stress (OS), and promote angiogenesis, suggesting its potential role in protecting flaps from ischemic damage. This study investigated the effects and mechanisms of FFA in enhancing the survival of ischemic flaps.

Methods
The viability of ischemic flaps was evaluated using laser doppler blood flow (LDBF) and survival rates. We examined levels of pyroptosis, OS, transcription factor E3 (TFE3)-induced autophagy, and elements of the AMPK-TRPML1-Calcineurin pathway through western blotting (WB), immunofluorescence (IF), molecular docking (MD), cellular thermal shift assay (CETSA) and surface plasmon resonance (SPR).

Results
The findings suggest that FFA significantly enhances the viability of ischemic flaps. The improvement in flap survival associated with FFA can be attributed to increased autophagy, diminished OS, and the suppression of pyroptosis. Notably, the promotion of autophagy flux and an augmented resistance to OS are instrumental in curbing pyroptosis in these flaps. Activation of TFE3 by FFA promoted autophagy and diminished oxidative damage. The therapeutic effects of FFA were negated when TFE3 levels were decreased using adeno-associated virus (AAV)-TFE3shRNA. Additionally, FFA modified TFE3 activity through the AMPK-TRPML1-Calcineurin pathway.

Conclusions
FFA promotes ischemic flap survival via induction of autophagy and suppression of oxidative stress by activation of the AMPK-TRPML1-Calcineurin-TFE3 signaling pathway. These findings could have therapeutic implications.
Deployable machine learning-based decision support system for tracheostomy in acute burn patients
Authors: Li Haisheng , Zhen Ni , Lin Shixu , Li Ning , Zhang Yumei , Luo Wei , Zhang Zhenzhen , Wang Xingang , Han Chunmao , Yuan Zhiqiang , Luo Gaoxing 
Published: February 2025

Abstract

Background
Airway obstruction is a common emergency in acute burns with high mortality. Tracheostomy is the most effective method to keep patency of airway and start mechanical ventilation. However, the indication of tracheostomy is challenging and controversial. We aimed to develop and validate a deployable machine learning (ML)-based decision support system to predict the necessity of tracheostomy for acute burn patients.

Methods
We enrolled 1011 burn patients from Southwest Hospital (2018–2020) for model development and feature selection. The final model was validated on an independent internal cross-temporal cohort (2021, n = 274) and an external cross-institutional cohort (Second Affiliated Hospital of Zhejiang University School of Medicine 2020–2021, n = 376). To improve the model’s deployment and interpretability, an ML-based nomogram, an online calculator, and an abbreviated scale were constructed and validated.

Results
The optimal model was the eXtreme Gradient Boosting classifier (XGB), which achieved an AUROC of 0.973 and AUPRC of 0.879 in training dataset, and AUROCs of greater than 0.95 in both cross-temporal and cross-institutional validation. Moreover, it kept stable discriminatory ability in validation subgroups stratified by sex, age, burn area, and inhalation injury (AUROC ranging 0.903–0.990). The analysis of calibration curve, decision curve, and score distribution proved the feasibility and reliability of the ML-based nomogram, abbreviated scale, and online calculator.

Conclusions
The developed system has strong predictive ability and generalizability in cross-temporal and cross-institutional evaluations. The nomogram, online calculator, and abbreviated scale based on machine learning show comparable prediction performance and can be deployed in broader application scenarios, especially in resource-limited clinical environments.
Brain Pro-TCT: a prospective, quasi-experimental study on early delirium detection with Delirium Observation Screening Scale versus single-channel EEG after cardiac surgery in patients aged over 70 years
Authors: ten Broeke Miarca , Henckens Wim P R , Weierink Anna , Speekenbrink Ron G H , van der Palen Job , Halfwerk Frank R 
Published: February 2025

Abstract

Aim
Delirium is common in patients aged over 70 years after cardiac surgery. Screening to detect delirium in high-risk patients is important, yet hypoactive delirium is often missed in nurse-reported screening. Polymorphic delta waves are associated with delirium, and can be detected with single-channel electroencephalography (SC-EEG). The aim of the study is to assess whether SC-EEG as a screening instrument for delirium will increase the detection rate of postoperative delirium and reduce hospital stay of delirious patients.

Methods and results
A prospective quasi-experimental study compared Delirium Observation Screening Scale (DOSS) screening (442 patients) to SC-EEG screening (462 patients) to detect postoperative delirium in cardiac surgery patients aged over 70 years. Delirium was diagnosed using the Diagnostic and Statistical Manual of Mental Disorders 5th edition.
Detection of delirium was higher in the SC-EEG group (20%) compared to DOSS group (14%), p = 0.016. A difference in length of stay for delirious patients was attributed to baseline differences as pneumonia and EuroSCORE II, but not delirium screening method. Length of stay for all patients was -0.11 (95% CI -0.18 to -0.04) night shorter for SC-EEG cohort patients compared to DOSS cohort patients, p = 0.002.

Conclusion
Screening with SC-EEG increased delirium detection after cardiac surgery. Only length of stay for all patients was significantly reduced in the SC-EEG cohort. This reduction in hospital stay is small, yet relevant for high volume cardiac surgery centres and should be further studied in other centres.

Registration
International Clinical Trials Registry Platform: NL-OMON27069
The differential impact of abdominal obesity on fasting and non-fasting triglycerides and cardiovascular risk
Authors: Christiansen Malene Revsbech , Romero-Lado María J , Carrasquilla German D , Kilpeläinen Tuomas O 
Published: February 2025

Abstract

Aims
We previously showed that abdominal obesity is associated with increased TG levels after a high-fat meal, irrespective of fasting levels. However, whether these findings are applicable to the general population and have implications for cardiovascular disease (CVD) risk remains uncertain. We aimed to examine the effects of abdominal obesity on fasting and non-fasting TG and CVD risk in the UK Biobank.

Methods
Random TG levels were measured in 352,782 individuals and fasting duration was self-reported. We used waist-hip ratio adjusted for BMI (WHRadjBMI) and its polygenic score to assess abdominal obesity and tested for interactions with fasting duration on TG levels. We evaluated the implications for CVD risk by analysing associations with the incidence of myocardial infarction and stroke.

Results
Fasting duration modified the effect of the WHRadjBMI phenotype and its polygenic score on TG levels (PInteraction= 6.5x10-32 and PInteraction=0.034). The polygenic score increased non-fasting TG 0.1 mmol/L more than fasting TG per standard deviation increase in WHRadjBMI. Higher TG levels, regardless of fasting status, were associated with higher CVD risk. The association between WHRadjBMI polygenic score and CVD risk was attenuated by 27% (from HR=1.41 to HR=1.30) after adjusting for non-fasting TG levels, and by 11% (from HR=1.38 to HR=1.34) after adjusting for fasting TG levels.

Conclusions
Polygenic score for abdominal obesity has a stronger effect on non-fasting than fasting TG levels, reflecting impaired postprandial lipid metabolism. Measuring TG levels in fasting state may underestimate CVD risk in individuals with abdominal obesity.
Social Work during Skilled Home Health Care: Prevalence and Determinants
Authors: Burgdorf Julia G , Smiley Adrianne , Barron Yolanda , Goodman Jeri , McDonald Margaret V 
Published: February 2025

Abstract

Background and Objectives
Medicare-funded Home Health (HH) delivers skilled care via visits to patients’ homes. Social work (SW) services are included within the HH benefit and may positively impact outcomes for HH patients with complex needs. However, no prior work has quantitatively assessed SW provision during HH.

Research Design and Methods
We examined 2018 linked HH claims, assessment, and HH agency data for a national sample of 1,372,570 Medicare HH patients. We described the prevalence, number, and timing of SW visits, compared characteristics of those who did vs did not receive SW, and modelled odds of receiving SW using a multilevel logistic model clustering at the HH agency level and adjusting for patient sociodemographic characteristics and clinical status and HH agency characteristics.

Results
Just 11.3% of HH patients received SW. On average, those who received SW had a single SW visit (mean=1.3; SD=0.6) occurring about a week (mean=8.8 days; SD=6.6) after HH admission. The patient-level factors most significantly associated with receiving SW included being Non-Hispanic Black compared to Non-Hispanic White (aOR: 1.70; 95% CI: 1.66-1.74), being Medicaid-enrolled (aOR: 1.26; 95% CI: 1.24-1.28), living alone (aOR: 1.31; 95% CI: 1.28-1.33), having high cognitive impairment (aOR: 2.12; 95% CI: 2.07-2.18), and exhibiting depressive symptoms (aOR: 2.17; 95% CI: 2.10-2.23). Patients also had greater odds of a SW visit if receiving care from a HH agency that was non-profit (aOR: 1.31; 1.19-1.45) and lower odds if the HH agency had a rural service area (aOR: 0.67; 95% CI: 0.61-0.74).

Discussion and Implications
Findings indicate that SW access remains rare during HH and is driven by both demand-side (i.e., patient needs) and supply-side (i.e., agency characteristics) factors. There is a need to identify patient profiles most likely to benefit from SW services during HH and to develop strategies to mitigate agency-level barriers to access.
NSUN2-mediated HCV RNA m5C Methylation Facilitates Viral RNA Stability and Replication
Authors: Li Zhu-Li , Xie Yan , Wang Yafen , Wang Jing , Zhou Xiang , Zhang Xiao-Lian 
Published: February 2025

Abstract
RNA modifications have emerged as new efficient targets against viruses. However, little is known about 5-methylcytosine (m5C) modification in the genomes of Flaviviruses. Herein, we demonstrate that hepatitis C virus (HCV), dengue virus, and Zika virus contain high levels of viral RNA m5C modification. We find that m5C modification in HCV RNA genome is located at C7525 site in the viral NS5A gene. HCV infection increases host m5C machinery NSUN2 expression via transcription factor E2F1. Deficiency of NSUN2 decreases HCV RNA m5C methylation levels, which further reduces viral RNA stability, replication as well as viral assembly and budding. HCV RNA genomic m5C specific abrogating mutation at C7525 site reduces viral replication, assembly, and budding through decreasing viral RNA stability. Deficiency of NSUN2 also reduces host global messenger RNA (mRNA) m5C modification levels during HCV infection, which upregulates antiviral innate immune response genes expression and further suppresses HCV RNA replication. Supported by both cellular and mouse infection models, our findings reveal that NSUN2-mediated HCV RNA and host mRNA m5C methylations facilitate viral RNA replication. HCV infection promotes host NSUN2 expression to facilitate HCV replication, which implies a positive feedback loop. NSUN2 could be a potential new target for Flavivirus therapeutics.
Functional characterization of OXTR-associated enhancers
Authors: Laboy Cintrón Dianne , Sheng Rory R , Ahituv Nadav 
Published: February 2025

Abstract
The oxytocin receptor (OXTR) has a vital role in regulating human behavior, controlling lactation, parturition, pair bonding, maternal behavior, anxiety, and sociability. However, its regulatory elements and how variation in these sequences lead to behavioral changes remain largely unknown. Here, we identified seven OXTR candidate cis-regulatory elements (cCREs) from mouse and human hypothalamus single-cell RNA/ATAC-seq data and characterized them in cells and mice. Luciferase assays in hypothalamus cell lines identified three of the seven to be functional enhancers. Mouse enhancer assays for the most robust enhancer, OXTR candidate enhancer 7 (OCE7), found it to be active in the mouse olfactory bulb at postnatal day 28 and day 56. In summary, using genomic data coupled with cell and mouse enhancer assays, we characterized the OXTR regulatory landscape and identified a novel olfactory bulb OXTR-associated enhancer.
A chromosome-scale genome assembly and Epigenomic profiling reveal temperature-dependent histone methylation in iridoid biosynthesis regulation in Scrophularia ningpoensis
Authors: Xu Qing , Liu Chang , Li Bin , Tian Kewei , You Lei , Xie Li , Wang Huang , Zhang Meide , Zhou Wuxian , Zhang Yonghong , Zhou Chao 
Published: February 2025

Abstract
Understanding how medicinal plants adapt to global warming, particularly through epigenetic mechanisms that modify phenotypes without changing DNA sequences is crucial. Scrophularia ningpoensis Hemsl., a traditional Chinese Medicine (TCM), produces bioactive compounds that are influenced by environmental temperatures, making it an ideal model for studying the biological basis of TCM geoherbalism. However, the adaptive potential of epigenetic marks in S. ningpoensis under varying temperatures remains understudied, partly due to the absence of a reference genome. Here, it was demonstrated that mild warm temperatures contribute to the metabolic accumulation and the cultivated migration of S. ningpoensis using a global dataset. A high-quality chromosome-level genome was assembled, and an atlas of epigenetic, metabolic, and transcriptomic profiles across different tissues. Transcriptome analysis identified 3,401 allele-specific expressed genes (ASEGs) across nine tissues by comparing two haplotypes. ChIP-seq and BS-seq data from leaf and root tissues revealed that ASEGs are associated with distinct epigenetic patterns, particularly the active mark H3K36me3, which functions differently in these tissues. Notably, genes marked with H3K36me3 in iridoid synthesis pathway predominantly expressed in roots. Additionally, the histone methyltransferase SnSDG8 was identified to regulate ectopic H3K36me3 in iridoid biosynthesis in response to warming temperatures. Our results highlight the epigenetic mechanisms of global warming on herb-derived products, significant for medicinal plant breeding under temperature stress.
Genomic insights into the domestication and genetic basis of yield in papaya
Authors: Yang Min , Kong Xiangdong , Zhou Chenping , Kuang Ruibin , Wu Xiaming , Liu Chuanhe , He Han , Xu Ze , Wei Yuerong 
Published: February 2025

Abstract
Papaya (Carica papaya L.) is an important tropical and subtropical fruit crop, and understanding its genome is essential for breeding. In this study, we assembled a high-quality genome of 344.17 Mb for the newly cultivated papaya ‘Zihui,’ which contains 22 250 protein-coding genes. By integrating 201 resequenced papaya genomes, we identified four distinct papaya groups and a 34 Mb genomic region with strong domestication selection signals. Within these regions, two key genes associated with papaya yield were discovered: Cp_zihui06549, encoding a leucine-rich receptor-like protein kinase, and Cp_zihui06768, encoding the accumulation of photosystem one 1 (APO1) protein. Heterologous expression of Cp_zihui06549 in tomato confirmed that the total number of fruits in transgenic lines more than doubled compared to wild-type plants, resulting in a significant yield increase. Furthermore, we constructed a pan-genome of papaya and obtained a 77.41 Mb non-reference sequence containing 1543 genes. Within this pan-genome, 2483 variable genes we detected, including four genes annotated as the ‘terpene synthase activity’ Gene Ontology term, which were lost in cultivars during domestication. Finally, gene retention analyses were performed using gene presence and absence variation (PAV) data and differentially expressed genes across various tissues and organs. This study provides valuable insights into the genes and loci associated with phenotypes and domestication processes, laying a solid foundation for future papaya breeding efforts.
Rapid screening of multiple pesticide residues in Lycii Fructus and raw juice samples by using an automated sample clean-up platform combined with GC-Q-TOF/MS
Authors: Chen Ting , Zhu Renyuan , Zhang Wen , Xu Yanli , Wang Xingzhi 
Published: February 2025

Abstract

Background
Lycii Fructus and its raw juice are widely consumed but may be contaminated with pesticide residues, posing health risks. Traditional methods for pesticide residue detection are often labor-intensive and time-consuming.

Objective
This study aims to develop a rapid, automated method for screening pesticide residues in Lycii Fructus and its raw juice using a combination of micro solid-phase extraction (μ-SPE) and gas chromatography-quadrupole-time-of-flight mass spectrometry (GC-Q-TOF/MS).

Methods
An automated sample clean-up platform (PAL-RTC) was integrated with μ-SPE technology for sample preparation. Matrix-matched external standards were used for quantification, and method validation was conducted to compare μ-SPE with dispersive solid-phase extraction (d-SPE). Performance parameters including linearity, limit of quantitation (LOQ), recovery rates, and relative standard deviations (RSD) were evaluated.

Results
84.5% of the pesticides showed strong linearity (R2 &gt; 0.99) over the concentration range of 2–1000 μg/L. LOQ for 91.4% of pesticides was below 20 μg/kg, with recovery rates between 70% and 120% and RSD ≤ 20%. Screening detection limits (SDLs) were between 1–20 μg/kg, with 96.8% of pesticides having SDLs below 5 μg/kg. The μ-SPE method demonstrated superior reproducibility at the low spiking level (10 μg/kg), detecting 415 pesticides, compared to 369 for d-SPE. Analysis of 100 Lycii Fructus and 50 raw juice samples revealed the presence of 24 pesticides, including 3 restricted types.

Conclusion
The μ-SPE method, integrated with PAL-RTC and GC-Q-TOF/MS, offers a more efficient and accurate approach for detecting pesticide residues in Lycii Fructus and its raw juice compared to traditional methods, reducing labor and improving reproducibility.

Highlights
Compared to the d-SPE method, the μ-SPE method integrated with PAL-RTC demonstrated better reproducibility and stability at low spiking levels, significantly enhancing the efficiency of sample clean-up.
Carcinogenicity assessment: "Modern Toxicology" considerations from an experience in the evaluation of a carbon nanotube
Authors: Kanno Jun 
Published: February 2025

Abstract
The novel properties and functions of nanomaterials have naturally alerted the toxicologists to the fact that such materials may also have novel effects on the human body and living organisms. In particular, materials with high stability or biopersisteny have been shown to have a tendency to accumulate in the body, leading to chronic toxicity including carcinogenicity. However, at the early stages of toxicity research, the information is often limited to the effects of short-term exposure studies, and findings on chronic effects are very much delayed. In this context, it was rather exceptional that studies on multiwall carbon nanotubes (MWCNTs) have started with the verification of their potential to induce mesothelioma. This toxicological endpoint was expected on the basis of existing knowledge of asbestos and asbestos-like fiber particles. This movement has led to the achievement of the original mission of the “Modern Toxicology”, which is “to achieve a win-win situation where both industrial promotion and safety assurance are ensured by communicating and sharing toxicity information to developers and consumers at a stage before mass production and consumption begins, that is, before massive exposure of the general public begins”.
Inaccurate toxicity assessments of asbestos in the 1980s and 1990s allowed its spread to our living environment, which is difficult to decontaminate, and the damage still continues to this day. However, the case described here could be an example of realizing the proposition that ‘nanomaterials, the flagship of high technology, must not repeat the same mistakes.’