bluuebunny/crossref_metadata_2025_split huggingface dataset:
Appropriate level of cuproptosis may be involved in alleviating pulmonary fibrosis
Authors: Li Guoxing , Peng Lihua , Wu Mingjun , Zhao Yipin , Cheng Zhe , Li Gang 
Published: December 2022

ObjectiveCuproptosis is a newly discovered form of programmed cell death that has not been studied in pulmonary fibrosis. The purpose of the present study was to explore the relationship between cuproptosis and pulmonary fibrosis.MethodsSingle-cell sequencing (scRNA-seq) data for human and mouse pulmonary fibrosis were obtained online from Gene Expression Omnibus (GEO) database. First, fibroblast lineage was identified and extracted using the Seurat toolkit. The pathway was then evaluated via Gene Set Enrichment Analyses (GSEA), while transcription factor activity was analyzed using DoRothEA. Next, fibroblast differentiation trajectory was inferred via Monocle software and changes in gene expression patterns during fibroblast activation were explored through gene dynamics analysis. The trajectory was then divided into three cell states in pseudotime order and the expression level of genes related to cuproptosis promotion in each cell state was evaluated, in addition to genes related to copper export and buffering and key genes in cellular metabolic pathways.ResultsIn the mouse model of pulmonary fibrosis induced by bleomycin, the genes related to cuproptosis promotion, such as Fdx1, Lias, Dld, Pdha1, Pdhb, Dlat, and Lipt1, were gradually down-regulated in the process of fibroblast differentiation from resting fibroblast to myofibroblast. Consistently, the same results were obtained via analysis of scRNA-seq data for human pulmonary fibrosis. In addition, genes related to copper ion export and buffering gradually increased with the activation of fibroblasts. Metabolism reprogramming was also observed, while fibroblast activation and tricarboxylic acid(TCA) cycle and lipid metabolism were gradually down-regulated and mitochondrial metabolism was gradually up-regulated.ConclusionThe present study is the first to reveal a negative correlation between cuproptosis and fibrosis, suggesting that an appropriate cuproptosis level may be involved in inhibiting fibroblast activation. This may provide a new method for the treatment of pulmonary fibrosis.
A practical scoring model to predict the occurrence of critical illness in hospitalized patients with SARS-CoV-2 omicron infection
Authors: Zhang Yao , Han Jiajia , Sun Feng , Guo Yue , Guo Yifei , Zhu Haoxiang , Long Feng , Xia Zhijie , Mao Shanlin , Zhao Hui , Ge Zi , Yu Jie , Zhang Yongmei , Qin Lunxiu , Ma Ke , Mao Richeng , Zhang Jiming 
Published: December 2022

BackgroundThe variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged repeatedly, especially the Omicron strain which is extremely infectious, so early identification of patients who may develop critical illness will aid in delivering proper treatment and optimizing use of resources. We aimed to develop and validate a practical scoring model at hospital admission for predicting which patients with Omicron infection will develop critical illness.MethodsA total of 2,459 patients with Omicron infection were enrolled in this retrospective study. Univariate and multivariate logistic regression analysis were performed to evaluate predictors associated with critical illness. Moreover, the area under the receiver operating characteristic curve (AUROC), continuous net reclassification improvement, and integrated discrimination index were assessed.ResultsThe derivation cohort included 1721 patients and the validation cohort included 738 patients. A total of 98 patients developed critical illness. Thirteen variables were independent predictive factors and were included in the risk score: age &gt; 65, C-reactive protein &gt; 10 mg/L, lactate dehydrogenase &gt; 250 U/L, lymphocyte &lt; 0.8*10^9/L, white blood cell &gt; 10*10^9/L, Oxygen saturation &lt; 90%, malignancy, chronic kidney disease, chronic cardiac disease, chronic obstructive pulmonary disease, diabetes, cerebrovascular disease, and non-vaccination. AUROC in the derivation cohort and validation cohort were 0.926 (95% CI, 0.903–0.948) and 0.907 (95% CI, 0.860-0.955), respectively. Moreover, the critical illness risk scoring model had the highest AUROC compared with CURB-65, sequential organ failure assessment (SOFA) and 4C mortality scores, and always obtained more net benefit.ConclusionThe risk scoring model based on the characteristics of patients at the time of admission to the hospital may help medical practitioners to identify critically ill patients and take prompt measures.
Elevated VCAM-1, MCP-1 and ADMA serum levels related to pulmonary fibrosis of interstitial lung disease associated with rheumatoid arthritis
Authors: Pulito-Cueto Verónica , Remuzgo-Martínez Sara , Genre Fernanda , Atienza-Mateo Belén , Mora-Cuesta Víctor M. , Iturbe-Fernández David , Lera-Gómez Leticia , Sebastián Mora-Gil María , Prieto-Peña Diana , Portilla Virginia , Blanco Ricardo , Corrales Alfonso , Ocejo-Vinyals J. Gonzalo , Gualillo Oreste , Ferraz-Amaro Iván , Cifrián José M. , López-Mejías Raquel , González-Gay Miguel A. 
Published: December 2022

Introduction: Early diagnosis of interstitial lung disease (ILD) associated with rheumatoid arthritis (RA) constitutes a challenge for the clinicians. Pulmonary vasculopathy is relevant in the development of interstitial lung disease. Accordingly, we aimed to explore the role of vascular cell adhesion molecule-1 (VCAM-1), monocyte chemoattractant protein-1 (MCP-1) and asymmetric dimethylarginine (ADMA), key molecules in the vasculopathy, as potential biomarkers of pulmonary fibrosis in RA-ILD+.Methods: We included 21 RA-ILD+ patients and two comparative groups: 25 RA-ILD- patients and 21 idiopathic pulmonary fibrosis (IPF) patients. Serum levels of the molecules were determined by ELISA, and mRNA expression was quantified by qPCR.Results: VCAM-1, MCP-1 and ADMA serum levels were increased in RA-ILD+ patients in relation to RA-ILD- and IPF patients. Additionally, RA-ILD+ patients exhibited increased CCL2 (gene encoding MCP-1) and decreased PRMT1 (gene related to ADMA synthesis) mRNA expression in relation to RA-ILD- patients. A lower expression of VCAM1, CCL2, and PRMT1 was observed in RA-ILD+ patients when compared with those with IPF. Furthermore, MCP-1 serum levels and PRMT1 mRNA expression were positively correlated with RA duration, and ADMA serum levels were positively associated with C-reactive protein in RA-ILD+ patients.Conclusion: Our study suggests that VCAM-1, MCP-1 and ADMA could be considered as useful biomarkers to identify ILD in RA patients, as well as to discriminate RA-ILD+ from IPF, contributing to the early diagnosis of RA-ILD+.
Different effects of air microembolism through patent foramen ovale in patients with migraine: A quantitative electroencephalogram case series
Authors: Ornello Raffaele , Spezialetti Matteo , Caponnetto Valeria , Frattale Ilaria , Grappasonni Monica , Pistoia Francesca , Placidi Giuseppe , Sacco Simona 
Published: December 2022

BackgroundLiterature suggests an association between patent foramen ovale (PFO) and migraine, mostly migraine with aura (MA). Previous data suggest that air microembolism through PFO can lead to bioelectrical abnormalities detectable at electroencephalogram (EEG) in patients with MA, thus suggesting a pathophysiological mechanism for the MA-PFO association. However, those data lack replication.MethodsPatients with MA or migraine without aura (MO) and large PFO underwent a 19-channel EEG recording before and after injection of air microbubbles. We compared EEG power before and after microbubble injection for each electrode location, for each frequency band (theta: 5–7 Hz; alpha: 8–12 Hz; beta: 13–30 Hz; lower gamma: 31–45 Hz), and for total global power (the average of EEG power at each location and frequency band).ResultsWe included 10 patients, four with MA and six with MO; six patients had medium-to-high migraine frequency (four or more monthly migraine days), while four had low frequency (one monthly migraine day). EEG power changes after air microembolism varied across patients. Considering the overall group, total global EEG power did not change; however, EEG power in the higher frequency ranges (beta and lower gamma) increased in patients with MA.ConclusionsWe did not replicate the effects of air microembolism previously reported in patients with migraine. Aura status, migraine frequency, and medications might influence patients' response to microembolism. More refined EEG measurements are needed to clarify the dynamic role of PFO on migraine occurrence.
A necroptosis-related lncRNA signature was identified to predict the prognosis and immune microenvironment of IDH-wild-type GBM
Authors: Song Chong , Zhu Liwen , Gu Junwei , Wang Tong , Shi Linyong , Li Chiyang , Chen Lei , Xie Sidi , Lu Yuntao 
Published: December 2022

IntroductionNecroptosis-related genes are essential for the advancement of IDH-wild-type GBM. However, the putative effects of necroptosis-related lncRNAs (nrlncRNAs) in IDH-wild-type GBM remain unknown.MethodsBy using the TCGA and GTEx databases, a nrlncRNA prognostic signature was created using LASSO Cox regression. The median risk score was used to categorize the patients into low and high-risk groups. To confirm the validity, univariate, multivariate Cox regression and ROC curves were used. Furthermore, by enrichment analysis, immune correlation analysis, and drug sensitivity analysis, the targeted lncRNAs were selected for further verification. As the highest upregulated expression in tumor than peritumor specimens, RP11-131L12.4 was selected for phenotype and functional experiments in primary GBM cells.ResultsSix lncRNAs were proved to be closely related to necroptosis in IDH-1-wild-type GBM, which were used to create a new signature. For 1-, 2-, and 3-year OS, the AUCs were 0.709, 0.645 and 0.694, respectively. Patients in the low-risk group had a better prognosis, stronger immune function activity, and more immune cell infiltration. In contrast, enrichment analysis revealed that the malignant phenotype was more prevalent in the high-risk group. In vitro experiments indicated that RP11-131L12.4 increased the tumor proliferation, migration and invasion, but decreased the necroptosis. Moreover, this nrlncRNA was also proved to be negatively associated with patient prognosis.ConclusionThe signature of nrlncRNAs may aid in the formulation of tailored and precise treatment for individuals with IDH-wild-type GBM. RP11-131L12.4 may play indispensable role in necroptosis suppression.
Neighborhood segregation and cancer prevention guideline adherence in US Hispanic/Latino adults: Results from the HCHS/SOL
Authors: Pichardo Margaret S. , Pichardo Catherine M. , Talavera Gregory A. , Gallo Linda C. , Castañeda Sheila F. , Sotres-Alvarez Daniela , Molina Yamile , Evenson Kelly R. , Daviglus Martha L. , Hou Lifang , Joyce Brian , Aviles-Santa Larissa , Plascak Jesse 
Published: December 2022

BackgroundAdherence to the American Cancer Society (ACS) guidelines for cancer prevention is associated with a lower risk of cancer and mortality. The role of neighborhood segregation on adherence to the guidelines among Hispanic/Latino adults is relatively unexplored.Materials and methodsThe Hispanic Community Health Study/Study of Latinos is a community-based prospective cohort of 16,462 Hispanic/Latino adults, ages 18-74 years enrolled in 2008-2011 from the Bronx, Chicago, Miami and San Diego. Dimensions of neighborhood segregation were measured using 2010 United States’ census tracts:—evenness (the physical separation of a group), exposure (the propensity for contact between groups), and their joint effect (hypersegregation). ACS guideline adherence levels – low, moderate, high – were created from accelerometry-measured physical activity, dietary intake, alcohol intake, and body mass index. Weighted multinominal logistic regressions estimated relative risk ratios (RRR) and 95% confidence intervals (CI) for guideline adherence levels and its components.ResultsHispanic/Latino adults were classified as low (13.7%), moderate (58.8%) or highly (27.5%) adherent to ACS guidelines. We found no evidence of an association between segregation and overall guideline adherence. Exposure segregation associated with lower likelihood of moderate adherence to alcohol recommendations (RRRmoderate vs. low:0.86, 95%CI:0.75-0.98) but higher likelihood for diet recommendations (RRRmoderate vs. low:1.07, 95%CI:1.01-1.14). Evenness segregation associated with lower likelihood of high adherence to the physical activity recommendations (RRRhigh vs. low:0.73, 95%CI:0.57-0.94). Hypersegregation was associated with individual guideline components.ConclusionWe found evidence of a cross-sectional relationship between neighborhood segregation and ACS cancer prevention guideline components, but not with overall ACS guideline adherence.
A single-center study of two types of upper kidney preservation surgery for complete duplicated kidney in children
Authors: Chu Han , Zhang Xian-sheng , Cao Yong-sheng , Deng Qi-fei 
Published: December 2022

ObjectiveThe objectives of this study were to compare the efficacy, advantages, and disadvantages of insertable ureteral reimplantation (UC group) and ureteral end-to-side anastomosis (UU group) in the treatment of duplicated kidney and summarize the clinical experience in its diagnosis and treatment.MethodsThe current retrospective study enrolled 20 cases with duplicated kidney in Anhui Provincial Children's Hospital from April 2016 to June 2021, including 11 in the UC group and 9 in the UU group. There were 8 boys and 12 girls, with 12 on the left side and 8 on the right side. Meanwhile, there were three cases with urinary tract infection and nine with urinary incontinence. The rest of them were found by B ultrasound during physical examination. The median age of these patients was 33.5 months. Later, preoperative and postoperative renal pelvis separation, ureteral dilation, operation time, and drainage tube indwelling time were compared between the two groups.ResultsThere were statistically significant differences in operation time (282 ± 50.55 vs. 176 ± 61.92, P = 0.03), drainage time (9.36 ± 5.00 vs. 5.33 ± 1.22, P = 0.02), and hospital stay (22.18 ± 5.40 vs. 14.78 ± 5.33, P = 0.007) between the two groups. In addition, the degree of hydronephrosis (UC: 1.86 ± 0.93 vs. 1.08 ± 0.77, P = 0.00; UU: 1.8 ± 0.95 vs. 0.89 ± 0.60, P = 0.02) and ureteral dilatation (UC: 1.57 ± 0.30 vs. 0.72 ± 0.22, P = 0.00; UU: 1.47 ± 0.50 vs. 0.88 ± 0.22, P = 0.001) were statistically different between the two groups before and after surgery.ConclusionCompared with the UC method, the UU method has the advantages of less trauma, faster recovery, and fewer complications. Double J tube or ureter stent placement is beneficial for finding and protecting the lower ureter intraoperatively, without increasing the difficulty in operation, which can also prevent anastomosis or ureteral orifice stenosis.
Characterization of lung adenocarcinoma based on immunophenotyping and constructing an immune scoring model to predict prognosis
Authors: Liu Mengfeng , Xiao Qifan , Yu Xiran , Zhao Yujie , Qu Changfa 
Published: December 2022

Background: Lung cancer poses great threat to human health, and lung adenocarcinoma (LUAD) is the main subtype. Immunotherapy has become first line therapy for LUAD. However, the pathogenic mechanism of LUAD is still unclear.Methods: We scored immune-related pathways in LUAD patients using single sample gene set enrichment analysis (ssGSEA) algorithm, and further identified distinct immune-related subtypes through consistent clustering analysis. Next, immune signatures, Kaplan-Meier survival analysis, copy number variation (CNV) analysis, gene methylation analysis, mutational analysis were used to reveal differences between subtypes. pRRophetic method was used to predict the response to chemotherapeutic drugs (half maximal inhibitory concentration). Then, weighted gene co-expression network analysis (WGCNA) was performed to screen hub genes. Significantly, we built an immune score (IMscore) model to predict prognosis of LUAD.Results: Consensus clustering analysis identified three LUAD subtypes, namely immune-Enrich subtype (Immune-E), stromal-Enrich subtype (Stromal-E) and immune-Deprived subtype (Immune-D). Stromal-E subtype had a better prognosis, as shown by Kaplan-Meier survival analysis. Higher tumor purity and lower immune cell scores were found in the Immune-D subtype. CNV analysis showed that homologous recombination deficiency was lower in Stromal-E and higher in Immune-D. Likewise, mutational analysis found that the Stromal-E subtype had a lower mutation frequency in TP53 mutations. Difference in gene methylation (ZEB2, TWIST1, CDH2, CDH1 and CLDN1) among three subtypes was also observed. Moreover, Immune-E was more sensitive to traditional chemotherapy drugs Cisplatin, Sunitinib, Crizotinib, Dasatinib, Bortezomib, and Midostaurin in both the TCGA and GSE cohorts. Furthermore, a 6-gene signature was constructed to predicting prognosis, which performed better than TIDE score. The performance of IMscore model was successfully validated in three independent datasets and pan-cancer.
Normative values and integrated score of functional fitness among Chinese community-dwelling older adults in Suzhou
Authors: Xu Jing , Chen Ya , Li Jiaojiao , Zhang Hui , Shi Minhao , Meng Hongyan , Wang Li 
Published: December 2022

Objectives: This study was performed to establish the normative values and integrated score of the functional fitness on the basis of the senior fitness test (SFT) among Chinese community-dwelling older adults in Suzhou.Methods: In this cross-sectional descriptive study, 1,122 community-dwelling older adults aged 60 years old and above were recruited at Suzhou, China, by using a multistage stratified sampling method and accepted the SFT measurements. Sex- and age-specific normative values of each index of the SFT were established by using the percentile method. The SFT integrated score was established using factor analysis according to the data of 70% of the participants (construction group) and verified using the error rate from the data of the remaining 30% of the participants (verification group).Results: Normative-referenced percentile values at the 5th, 10th, 25th, 35th, 50th, 65th, 75th, 90th, and 95th percentiles for each index of SFT were established for the men and women among the different age groups. Five indices of the SFT, namely, 2-min step test, 30-s arm curl, 30-s chair stand, chair sit-and-reach, and 8-ft up-and-go (TUGT), gradually declined with age in both sexes (p &lt; .05). The SFT integrated score was calculated as follows: F = 3.8 × 2-min step test + 3.8 × 30-s arm curl + 3.8 × 30-s chair stand + 2.2 × back starch + 2.6 × chair sit-and-reach + 4 × TUGT − .04 × BMI. The formula was verified using the error rate. The error rates of the verification group compared with the construction group in each grade score of SFT were lower than 5%.Conclusion: Based on the data from the community-dwelling older adults in Suzhou, China, the functional fitness normative values for each index of the SFT and the integrated score of SFT were established. The SFT integrated score formula was verified to be reasonable and effective.
Deep learning-based recognition and segmentation of intracranial aneurysms under small sample size
Authors: Zhu Guangyu , Luo Xueqi , Yang Tingting , Cai Li , Yeo Joon Hock , Yan Ge , Yang Jian 
Published: December 2022

The manual identification and segmentation of intracranial aneurysms (IAs) involved in the 3D reconstruction procedure are labor-intensive and prone to human errors. To meet the demands for routine clinical management and large cohort studies of IAs, fast and accurate patient-specific IA reconstruction becomes a research Frontier. In this study, a deep-learning-based framework for IA identification and segmentation was developed, and the impacts of image pre-processing and convolutional neural network (CNN) architectures on the framework’s performance were investigated. Three-dimensional (3D) segmentation-dedicated architectures, including 3D UNet, VNet, and 3D Res-UNet were evaluated. The dataset used in this study included 101 sets of anonymized cranial computed tomography angiography (CTA) images with 140 IA cases. After the labeling and image pre-processing, a training set and test set containing 112 and 28 IA lesions were used to train and evaluate the convolutional neural network mentioned above. The performances of three convolutional neural networks were compared in terms of training performance, segmentation performance, and segmentation efficiency using multiple quantitative metrics. All the convolutional neural networks showed a non-zero voxel-wise recall (V-Recall) at the case level. Among them, 3D UNet exhibited a better overall segmentation performance under the relatively small sample size. The automatic segmentation results based on 3D UNet reached an average V-Recall of 0.797 ± 0.140 (3.5% and 17.3% higher than that of VNet and 3D Res-UNet), as well as an average dice similarity coefficient (DSC) of 0.818 ± 0.100, which was 4.1%, and 11.7% higher than VNet and 3D Res-UNet. Moreover, the average Hausdorff distance (HD) of the 3D UNet was 3.323 ± 3.212 voxels, which was 8.3% and 17.3% lower than that of VNet and 3D Res-UNet. The three-dimensional deviation analysis results also showed that the segmentations of 3D UNet had the smallest deviation with a max distance of +1.4760/−2.3854 mm, an average distance of 0.3480 mm, a standard deviation (STD) of 0.5978 mm, a root mean square (RMS) of 0.7269 mm. In addition, the average segmentation time (AST) of the 3D UNet was 0.053s, equal to that of 3D Res-UNet and 8.62% shorter than VNet. The results from this study suggested that the proposed deep learning framework integrated with 3D UNet can provide fast and accurate IA identification and segmentation.
Global transcriptomic analysis reveals candidate genes associated with different phosphorus acquisition strategies among soybean varieties
Authors: Yang Tongli , Yang Songhua , Chen Zhu , Tan Yuechen , Bol Roland , Duan Honglang , He Jin 
Published: December 2022

IntroductionSoybean adapts to phosphorus-deficient soils through three important phosphorus acquisition strategies, namely altered root conformation, exudation of carboxylic acids, and symbiosis with clumping mycorrhizal fungi. However, the trade-offs and regulatory mechanisms of these three phosphorus acquisition strategies in soybean have not been researched.MethodsIn this study, we investigated the responses of ten different soybean varieties to low soil phosphorus availability by determining biomass, phosphorus accumulation, root morphology, exudation, and mycorrhizal colonization rate. Furthermore, the molecular regulatory mechanisms underlying root phosphorus acquisition strategies were examined among varieties with different low-phosphorus tolerance using transcriptome sequencing and weighted gene co-expression network analysis.Results and discussionThe results showed that two types of phosphorus acquisition strategies—“outsourcing” and “do-it-yourself”—were employed by soybean varieties under low phosphorus availability. The “do-it-yourself” varieties, represented by QD11, Zh30, and Sd, obtained sufficient phosphorus by increasing their root surface area and secreting carboxylic acids. In contrast, the “outsourcing” varieties, represented by Zh301, Zh13, and Hc6, used increased symbiosis with mycorrhizae to obtain phosphorus owing to their large root diameters. Transcriptome analysis showed that the direction of acetyl-CoA metabolism could be the dividing line between the two strategies of soybean selection. ERF1 and WRKY1 may be involved in the regulation of phosphorus acquisition strategies for soybeans grown under low P environments. These findings will enhance our understanding of phosphorus acquisition strategies in soybeans. In addition, they will facilitate the development of breeding strategies that are more flexible to accommodate a variety of production scenarios in agriculture under low phosphorus environments.