bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between vessel density and thickness in the retina and choroid of severe non-proliferative diabetic retinopathy patients
Authors: He Kai , Wei-Zhang Selena , Li Ziqi , Kaysar Parhat , Yang Tianjing , Sun Zhiyong , Zhou Wei , Yan Hua 
Published: May 2024

ObjectivesTo explore the correlation between the vessel density (VD) of the retina and choroid vascular plexuses and the thicknesses of their respective retinal layers and choroid membranes in participants with severe non-proliferative diabetic retinopathy (NPDR).MethodsWe retrospectively analyzed the data of 42 eyes of 42 participants with diabetes mellitus (DM) and severe NPDR. In addition, 41 eyes of 41 healthy controls were evaluated. Measurements were taken for both groups using optical coherence tomography angiography (OCTA), including the area and perimeter of the foveal vascular zone (FAZ) and the vascular density (VD) in the superficial capillary plexus (SCP), deep capillary plexus (DCP), and choroid capillary (CC). These measurements were compared with the retinal thickness (RT) of the inner/intermediate retinal layers and choroidal thickness (CT). The study evaluated the correlation between RT or CT and VD in the respective vascular networks, namely superficial capillary plexus (SCP), deep capillary plexus (DCP), or CC.ResultsThe inner RT and VD in all plexuses were significantly lower in the severe NPDR group than in the healthy controls. Furthermore, the FAZ area and perimeter were larger in the severe NPDR group. Inner RT was correlated with VD in the SCP group (r=0.67 and r=0.71 in the healthy control and severe NPDR groups, respectively; p&lt;0.05). CT negatively correlated with VD in the CC (r=-0.697 and r=-0.759 in the healthy control and severe NPDR groups, respectively; p&lt;0.05). Intermediate RT significantly correlated with VD in the DCP of the severe NPDR group (r=-0.55, p&lt;0.05), but not in the healthy control group.ConclusionsRetinal or choroidal thickness strongly correlated with VD. Therefore, patients with severe NPDR must consider the distinct anatomical and functional entities of the various retinal layers and the choroid.
Influence of maximum diameter on fine-needle aspiration biopsy outcomes in ACR TI-RADS 5 thyroid nodules
Authors: Cao Shi-Liang , Shi Wan-Ying , Niu Yi-Ru , Zhao Zhen-Long , Wei Ying , Wu Jie , Peng Li-Li , Li Yan , Yu Ming-An 
Published: May 2024

IntroductionFine needle aspiration (FNA) biopsy is a widely accepted method for diagnosing thyroid nodules. However, the influence of maximum diameter (MD) of ACR TIRADS 5 (TR5) thyroid nodules on the FNA outcomes remains debated. This study examined the influence of MD on the FNA outcomes and investigated the optimal MD threshold for FNA in TR5 nodules.MethodsWe conducted a retrospective analysis of 280 TR5 thyroid nodules from 226 patients who underwent FNA from January to June 2022 in our department. Probably malignant (PM) group was defined as Bethesda V in cytopathology with confirmed BRAF V600E mutation or Bethesda VI, the other cytopathology outcomes were defined as probably benign (PB) group. We examined factors influencing malignant cytopathology outcomes and determined the optimal MD threshold for FNA in TR5 nodules using logistic regression and restricted cubic spline (RCS) analysis.ResultsAmong these nodules, 58.2% (163/280) had PM outcomes. The PM group had a significantly larger MD than the PB group [6.5mm (range 5.0-8.4) vs. 5.3mm (range 4.0-7.0), p &lt; 0.001]. In multivariate logistic regression fully adjusted for confounders, MD was significantly associated with PM outcomes [odds ratio 1.16, 95%CI 1.05-1.31; p = 0.042]. The highest quartile of MD had a greater likelihood of PM outcomes compared to the lowest quartile [odds ratio 4.71, 95% CI 1.97-11.69, p = 0.001]. The RCS analysis identified 6.2 mm as the optimal MD threshold for FNA in TR5 nodules.ConclusionMD significantly affects the probability of malignant outcomes in FNA of TR5 thyroid nodules. A MD threshold of ≥6.2mm is suggested for FNA in these nodules.
Incorporating leys in arable systems as a mitigation strategy to reduce soil organic carbon losses during land-use change
Authors: Nyameasem John Kormla , De Los Rios Josue , Kluß Christof , Reinsch Thorsten , Poyda Arne , Taube Friedhelm , Loges Ralf 
Published: May 2024

The intensification of dairy and biogas production in Northwestern Europe has led to the conversion of permanent grasslands to arable land, mainly for silage maize production, resulting in significant soil organic carbon (SOC) losses, highlighting the need for implementing alternative management practices during land use change (LUC) for effective climate change mitigation. This study evaluated the impact of incorporating annual grass-clover leys in 3-year arable rotations and slurry application to mitigate SOC losses during LUC. We compared this approach to a continuous silage maize and a permanent grassland on sandy loam soil in Northern Germany. The experiments were simultaneously established at two adjacent 17-year-old sites of permanent grassland and arable cropping, with different levels of initial SOC when the experiment was established. The SOC dynamics in the upper soil layer (0–30 cm) were evaluated by annual 12-year sampling (2011–2022). The cropping systems were unfertilized (N0) or fertilized (N1) using cattle slurry at a rate of 240 kg N ha-1 year-1. The study reveals substantial SOC losses following the conversion of the permanent grassland to grass-clover (ley) based rotation or continuous silage maize, with reductions of 22% and 31%, respectively, compared to baseline levels of the permanent grassland. However, over the 12-year period, the grass-clover ley-based crop rotation demonstrated a 30% reduction in SOC losses compared to continuous silage maize, without compromising dry matter yield. Conversely, the conversion of arable land to grasslands led to SOC increases ranging from 10% to 30%. This recovery was only half the SOC losses observed in the grassland conversion for the same period, indicating a slow-in, fast-out effect during LUC. However, the transition from ley-containing forage rotation to continuous silage maize incurred significant SOC losses of 11%. Overall, these findings underscore the imperative of integrating ley phases to mitigate SOC losses, particularly in high-biomass-yield cropping systems. As a 1-year ley phase was insufficient to sustain carbon sequestration in arable crop rotations, extended ley residence times should be considered.
Comprehensive analysis of differential long non-coding RNA and messenger RNA expression in cholelithiasis using high-throughput sequencing and bioinformatics
Authors: Sun Yanbo , Xu Conghui , Luo Jing , Li Shumin , Chen Shi , Cen Yunyun , Xu Pengyuan 
Published: May 2024

BackgroundThe etiology of gallstone disease (GSD) has not been fully elucidated. Consequently, the primary objective of this study was to scrutinize and provisionally authenticate the distinctive expression profiles of long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in GSD.MethodsRiboNucleic Acid (RNA) sequencing was used on four paired human gallbladder samples for the purpose of this study. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were identified and subjected to analysis of their biological functions. The Pearson’s correlation coefficients between DElncRNAs and DEmRNAs were computed to construct a co-expression network delineating their associations. Furthermore, both cis- and trans-regulatory networks of selected lncRNAs were established and visualized. Additionally, a competing endogenous RNA (ceRNA) regulatory network was constructed. To validate the RNA-sequencing data, we performed a Quantitative Real-time Polymerase Chain Reaction (RT-qPCR) on 10 paired human gallbladder samples, assessing the expressions of the top 4 DEmRNAs and DElncRNAs in gallstone and control samples.ResultsA total of 934 DEmRNAs and 304DElncRNAs were successfully identified. Functional enrichment analysis indicated a predominant involvement in metabolic-related biological functions. Correlation analysis revealed a strong association between the expressions of 597 DEmRNAs and 194 DElncRNAs. Subsequently, both a cis-lncRNA-mRNA and a trans-lncRNA-Transcription Factor (TF)-mRNA regulatory network were meticulously constructed. Additionally, a ceRNA network, comprising of 24 DElncRNAs, 201 DEmRNAs, and 120 predicted miRNAs, was established. Furthermore, using RT-qPCR, we observed significant upregulation of AC004692.4, HECW1-IT1, SFRP4, and COMP, while LINC01564, SLC26A3, RP1-27K12.2, and GSTA2 exhibited marked downregulation in gallstone samples. Importantly, these findings were consistent with the sequencing.ConclusionWe conducted a screening process to identify DElncRNAs and DEmRNAs in GSD. This approach contributes to a deeper understanding of the genetic factors involved in the etiology of gallstones.
Integrated analysis of muscle transcriptome, miRNA, and proteome of Chinese indigenous breed Ningxiang pig in three developmental stages
Authors: Chen Wenwu , Xiao Yu , Yang Fang , Liufu Sui , Gong Yan , Li Zhi , Zhang Shuo , Tang Shengguo , Li Biao , Ma Haiming 
Published: May 2024

The Ningxiang pig, a distinguished local breed in China, is recognized for its good meat quality traits. This study examines the proteomics of Ningxiang pigs at three developmental stages and delves into the upstream transcriptomics of these proteomics. Such an analysis facilitates a deeper understanding of the molecular interplay between proteins and transcriptomes in the Ningxiang pig muscle, influencing muscle growth and development. In this research, we analyzed the muscles of Ningxiang pigs at three developmental stages: 30 days in weaned piglets, 90 days in nursery pigs, and 210 days in late fattening pigs. There a total of 16 differentially co-expressed miRNAs (ssc-miRNA-1, ssc-miRNA-378, ssc-miRNA-143, ssc-miRNA-30e, etc.), 74 differentially co-expressed mRNA (PLIN3, CPT2, IGF2 and HSP90AB1, etc.) have been identified in the three stages. 572 differentially abundant proteins (DAPs) (APOC3, NDUFA2, HSPD1, ATP5E, PDHA1, etc.) were readily identified by comparing different time periods. According to the KEGG enrich pathway results that DAPs most enriched in growth and development pathways, immune mechanism pathways and maintaining functions of physical. Through short time-series expression miner (STEM) association analysis, a total of 571 negative miRNA-mRNA interaction pairs and 2 negative miRNA-mRNA-protein (Chr05_11955-Pig.17268.1-ATP5F1B, ssc-miR-194a-3p-Pig.15802.1-ACY1) interaction pairs were found. Our study provides a theoretical basis on molecular mechanism for the study of IMF deposition, muscle growth and immunity in Ningxiang pig breed.
A whole-exome sequencing study of patent foramen ovale: investigating genetic variants and their association with cardiovascular disorders
Authors: Li Xinyi , Xie Lingling , Dai Jin , Zhou Xinbin , Chen Tingting , Mao Wei 
Published: May 2024

BackgroundPatent foramen ovale (PFO) has a genetic predisposition and is closely associated with cryptogenic stroke (CS), migraine, decompression sickness, and hypoxemia. Identifying PFO-related mutant genes through whole-exome sequencing (WES) can help in the early recognition of cardiovascular genetic risk factors, guide timely clinical intervention, and reduce the occurrence of cardiovascular events.MethodsWe analyzed mutant genes from ClinVar and OMIM databases. WES was performed on 25 PFO patients from Zhejiang Provincial Hospital of Chinese Medicine. Pathogenicity of variants was evaluated using American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology. (AMP) guidelines.ResultsIn ClinVar (4 Feb 2023), 113 coding gene mutations were found, including 83 associated with PFO. From OMIM (18 Apr 2023), 184 gene mutations were analyzed, with 110 mutant coding genes. WES identified pathogenic mutations in two of 25 PFO patients (8%). LDLR, SDHC, and NKX2-5 genes were linked to PFO and primarily involved in myocardial tissue function. NKX2-5 may play a crucial role in PFO development, interacting with NOTCH1, GATA4, MYH6, SCN5A signaling pathways regulating cardiomyocyte characteristics.ConclusionWe identified pathogenic mutations in LDLR, SDHC, and NKX2-5 genes, implying their role in PFO development. Functional enrichment analysis revealed NKX2-5’s interaction with signaling pathways regulating cardiomyocyte function. These findings enhance our understanding of PFO’s genetic basis, suggesting potential therapeutic targets for future research.
Development and verification of a manganese metabolism- and immune-related genes signature for prediction of prognosis and immune landscape in gastric cancer
Authors: Han Xiaoxi , Leng Chuanyu , Zhao Shufen , Wang Shasha , Chen Shuming , Wang Shibo , Zhang Mengqi , Li Xiangxue , Lu Yangyang , Wang Bing , Qi Weiwei 
Published: May 2024

BackgroundGastric cancer (GC) poses a global health challenge due to its widespread prevalence and unfavorable prognosis. Although immunotherapy has shown promise in clinical settings, its efficacy remains limited to a minority of GC patients. Manganese, recognized for its role in the body’s anti-tumor immune response, has the potential to enhance the effectiveness of tumor treatment when combined with immune checkpoint inhibitors.MethodsGene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases was utilized to obtain transcriptome information and clinical data for GC. Unsupervised clustering was employed to stratify samples into distinct subtypes. Manganese metabolism- and immune-related genes (MIRGs) were identified in GC by univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analysis. We conducted gene set variation analysis, and assessed the immune landscape, drug sensitivity, immunotherapy efficacy, and somatic mutations. The underlying role of NPR3 in GC was further analyzed in the single-cell RNA sequencing data and cellular experiments.ResultsGC patients were classified into four subtypes characterized by significantly different prognoses and tumor microenvironments. Thirteen genes were identified and established as MIRGs, demonstrating exceptional predictive effectiveness in GC patients. Distinct enrichment patterns of molecular functions and pathways were observed among various risk subgroups. Immune infiltration analysis revealed a significantly greater abundance of macrophages and monocytes in the high-risk group. Drug sensitivity analysis identified effective drugs for patients, while patients in the low-risk group could potentially benefit from immunotherapy. NPR3 expression was significantly downregulated in GC tissues. Single-cell RNA sequencing analysis indicated that the expression of NPR3 was distributed in endothelial cells. Cellular experiments demonstrated that NPR3 facilitated the proliferation of GC cells.ConclusionThis is the first study to utilize manganese metabolism- and immune-related genes to identify the prognostic MIRGs for GC. The MIRGs not only reliably predicted the clinical outcome of GC patients but also hold the potential to guide future immunotherapy interventions for these patients.
Serum NfL and EGFR/NfL ratio mRNAs as biomarkers for phenotype and disease severity of myelin oligodendrocyte glycoprotein IgG-associated disease
Authors: Wang Xin , Qu Yi , Fan Jiayu , Ren Huiqiang 
Published: May 2024

Background and purposeMyelin oligodendrocyte glycoprotein (MOG) IgG is frequently elevated in pediatric patients with acquired demyelinating syndrome (ADS). However, no specific biomarkers exist for phenotype classification, symptom severity, prognosis, and treatment guidance of MOG-IgG-associated disease (MOGAD). This study evaluated neurofilament light chain (NfL) and endothelial growth factor receptor (EGFR) mRNA expression levels in serum and cerebrospinal fluid (CSF) as potential biomarkers for MOGAD in Chinese children.MethodsThis was a cross-sectional and single-center study. We enrolled 22 consecutive pediatric patients hospitalized with MOGAD and 20 control pediatric patients hospitalized for noninflammatory neurological diseases in Hebei Children’s Hospital. Serum and CSF were collected from MOGAD patients within 3 days before immunotherapy. The mRNA levels of NfL and EGFR in serum and CSF were measured by real-time polymerase chain reaction (qPCR), and the EGFR/NfL ratio mRNA was calculated. These measurement values were then compared between disease groups and among MOGAD phenotypes. In addition, the correlations between the mRNAs of three markers (NfL, EGFR, EGFR/NfL ratio), extended disability status scale (EDSS) scores, and clinical phenotypes were analyzed.ResultsSerum and CSF NfL mRNA levels were significantly higher of acute-stage MOGAD patients than those of control patients (p&lt; 0.05 and p&lt; 0.01, respectively), while the mRNA levels of serum EGFR and EGFR/NfL ratio were significantly lower of MOGAD patients than those of controls (p &lt; 0.05, p &lt; 0.0001). Serum NfL mRNA was significantly correlated with mRNA of serum EGFR (r =0.480, p &lt; 0.05). Serum and CSF NfL mRNA levels in MOGAD patients with the ADEM-like phenotype were also significantly higher than those in control patients (p &lt; 0.01, p &lt; 0.01) and optic neuritis (ON) phenotype (p &lt; 0.05, p &lt; 0.05). Both mRNAs of NfL in CSF and EGFR/NfL ratio in serum were correlated with EDSS scores (p &lt; 0.05, r = 0.424; p &lt; 0.05, r= -0.521).ConclusionThe mRNA levels of elevated NfL in serum and CSF as well as lower EGFR and EGFR/NfL ratio in serum could help distinguish acute-phase MOGAD. Higher mRNA levels of NfL in serum and CSF of MOGAD patients help distinguish ADEM-like phenotype. In addition, serum EGFR/NfL mRNA ratio is indicative of disease severity in pediatric patients with MOGAD. Further investigations are warranted to elucidate the pathological mechanisms underlying these associations.
Transient heat stress protects from severe endothelial damage and dysfunction during prolonged experimental ex-vivo lung perfusion
Authors: Parapanov Roumen , Debonneville Anne , Allouche Manon , Lugrin Jérôme , Rodriguez-Caro Helena , Liaudet Lucas , Krueger Thorsten 
Published: May 2024

IntroductionThe pulmonary endothelium is the primary target of lung ischemia-reperfusion injury leading to primary graft dysfunction after lung transplantation. We hypothesized that treating damaged rat lungs by a transient heat stress during ex-vivo lung perfusion (EVLP) to elicit a pulmonary heat shock response could protect the endothelium from severe reperfusion injury.MethodsRat lungs damaged by 1h warm ischemia were reperfused on an EVLP platform for up to 6h at a constant temperature (T°) of 37°C (EVLP37°C group), or following a transient heat stress (HS) at 41.5°C from 1 to 1.5h of EVLP (EVLPHS group). A group of lungs exposed to 1h EVLP only (pre-heating conditions) was added as control (Baseline group). In a first protocol, we measured lung heat sock protein expression (HSP70, HSP27 and Hsc70) at selected time-points (n=5/group at each time). In a second protocol, we determined (n=5/group) lung weight gain (edema), pulmonary compliance, oxygenation capacity, pulmonary artery pressure (PAP) and vascular resistance (PVR), the expression of PECAM-1 (CD31) and phosphorylation status of Src-kinase and VE-cadherin in lung tissue, as well as the release in perfusate of cytokines (TNFα, IL-1β) and endothelial biomarkers (sPECAM, von Willebrand Factor -vWF-, sE-selectin and sICAM-1). Histological and immunofluorescent studies assessed perivascular edema and formation of 3-nitrotyrosine (a marker of peroxinitrite) in CD31 lung endothelium.ResultsHS induced an early (3h) and persisting expression of HSP70 and HSP27, without influencing Hsc70. Lungs from the EVLP37°C group developed massive edema, low compliance and oxygenation, elevated PAP and PVR, substantial release of TNFα, IL-1β, s-PECAM, vWF, E-selectin and s-ICAM, as well as significant Src-kinase activation, VE-cadherin phosphorylation, endothelial 3-NT formation and reduced CD31 expression. In marked contrast, all these alterations were either abrogated or significantly attenuated by HS treatment.ConclusionThe therapeutic application of a transient heat stress during EVLP of damaged rat lungs reduces endothelial permeability, attenuates pulmonary vasoconstriction, prevents src-kinase activation and VE-cadherin phosphorylation, while reducing endothelial peroxinitrite generation and the release of cytokines and endothelial biomarkers. Collectively, these data demonstrate that therapeutic heat stress may represent a promising strategy to protect the lung endothelium from severe reperfusion injury.
Multifidelity topology design of a maritime survey operation with UUVs
Authors: Morey Danielle F. , Plate Randall S. , Wakayama Cherry Y. , Zabinsky Zelda B. 
Published: May 2024

Advances in autonomous systems, maritime communications, and sensing technologies lead to increasing applications of unmanned underwater vehicles (UUVs). In this paper, we study a maritime survey operation topology design problem with UUVs that traverse an ocean environment and collect data from prespecified sensors or locations. This maritime scenario is analyzed via several models and simulation for the purpose of topology design for mission planning. We use a multifidelity approach to examine the trade-offs between different potential topology configurations of assigning UUVs to data collection sensors or locations. We develop three low-fidelity models that make simplifying assumptions. These models provide insight into the design characteristics and allow for sensitivity analysis with low computational cost. They are used to down-select potential configuration designs for further evaluation using a high-fidelity simulation model. A high-fidelity simulation model removes many simplifying assumptions and predicts how a topology design would perform under more realistic conditions. It gathers detailed performance metrics at the expense of higher computational cost. Our study uses this multifidelity approach to demonstrate key trade-offs for topology design. The optimal design of UUVs depends on mission-specific goals.