bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of low-intensity pulsed ultrasound on tissue resident stem cells: Potential for ophthalmic diseases
Authors: Lin Zichun , Gao Liyu , Hou Ning , Zhi Xushuang , Zhang Yupeng , Che Zelin , Deng Aijun 
Published: March 2023

IntroductionTissue-resident stem cells (TRSCs) have the ability to self-renew and differentiate throughout an individual’s lifespan, and they utilize both mechanisms to maintain homeostasis and regenerate damaged tissues. Several studies suggest that these stem cells can serve as a potential source for cell-replacement-based therapy by promoting differentiation or expansion. In recent years, low-intensity pulsed ultrasound (LIPUS) has been demonstrated to effectively stimulate stem cell proliferation and differentiation, promote tissue regeneration, and inhibit inflammatory responses.AimsTo present a comprehensive overview of current application and mechanism of LIPUS on tissue resident stem cells.MethodsWe searched PubMed, Web of Science for articles on the effects of LIPUS on tissue resident stem cells and its application.ResultsThe LIPUS could modulate cellular activities such as cell viability, proliferation and differentiation of tissue resident stem cells and related cells through various cellular signaling pathways. Currently, LIPUS, as the main therapeutic ultrasound, is being widely used in the treatment of preclinical and clinical diseases.ConclusionThe stem cell research is the hot topic in the biological science, while in recent years, increasing evidence has shown that TRSCs are good targets for LIPUS-regulated regenerative medicine. LIPUS may be a novel and valuable therapeutic approach for the treatment of ophthalmic diseases. How to further improve its efficiency and accuracy, as well as the biological mechanism therein, will be the focus of future research.
Construction of an ecological security pattern for the Guanzhong Plain urban agglomeration: Scale perspective and hierarchy demand
Authors: Ye Hao , Song Yongyong , Xue Dongqian , Xia Siyou , Tang Yu , Zhang Liwei 
Published: March 2023

As areas of dense populations and high economic activity, urban agglomerations have driven an overall increase in economic efficiency; however, the associated ecological risks are becoming increasingly apparent. The construction of ecological security patterns (ESPs) is an important approach for ensuring the ecological security of urban agglomerations, thereby achieving coordinated development of society, economy and ecology. Previous studies on ESPs have rarely considered the demand for ecosystem services at multiple scales and have accordingly failed to accurately identify important ecological sources. Here, we propose a novel method based on multi-scale ecosystem service demand to identify ecological sources, which can more accurately identify the ecological source meeting the regional sustainable development. Selecting the Guanzhong Plain urban agglomeration (GPUA) as study area, we constructed a resistance surface by comprehensively considering natural and anthropogenic disturbances. We found high resistance areas are mainly concentrated in highly urbanized areas with Xi’an as the core. In addition, we performed minimum cumulative resistance and gravity model to obtain and classify ecological corridors. The results revealed that the ecological sources identified in this study can enhance the connectivity of the inner regions of the GPUA and the linkage between north and south ecological corridors. The ecological sources were found to be concentrated in the southern Qinling Mountains, with an area of 28,780.02 km2, accounting for 26.85% of entire region. Furthermore, we identified 121 potential ecological corridors, 47 ecological nodes, and 49 ecological breakpoints, and established that the extent of land with a high level of ecological security accounts for 21.98% of the entire regional area. This study offers a new perspective for ESPs construction, which can provide a scientific basis and policy guidance for the optimization of spatial structure and the maintenance of ecological security in ecologically fragile urban agglomerations.
Identification of the cuproptosis-related hub genes and therapeutic agents for sarcopenia
Authors: Zhu Yingqian , Chen Xin , Geng Shasha , Li Qingqing , Li Yang , Yuan Huixiao , Jiang Hua 
Published: March 2023

Background: Along with acceleration of population aging, the increasing prevalence of sarcopenia has posed a heavy burden on families as well as society. In this context, it is of great significance to diagnose and intervene sarcopenia as early as possible. Recent evidence has indicated the role of cuproptosis in the development of sarcopenia. In this study, we aimed to seek the key cuproptosis-related genes that can be used for identification and intervention of sarcopenia.Methods: The GSE111016 dataset was retrieved from GEO. The 31 cuproptosis-related genes (CRGs) were obtained from previous published studies. The differentially expressed genes (DEGs) and Weighed gene co-expression network analysis (WGCNA) were subsequently analyzed. The core hub genes were acquired by the intersection of DEGs, WGCNA and CRGs. Through logistic regression analysis, we established a diagnostic model of sarcopenia based on the selected biomarkers and was validated in muscle samples from GSE111006 and GSE167186. In addition, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analysis were performed on these genes. Furthermore, the gene set enrichment analysis (GSEA), and immune cell infiltration were also conducted on the identified core genes. Finally, we screened the potential drugs targeting the potential biomarkers of sarcopenia.Results: A total of 902 DEGs and WGCNA containing 1,281 significant genes were preliminarily selected. Intersection of DEGs, WGCNA and CRGs yielded four core genes (PDHA1, DLAT, PDHB, and NDUFC1) as potential biomarkers for the prediction of sarcopenia. The predictive model was established and validated with high AUC values. KEGG pathway and Gene Ontology biological analysis indicated these core genes may play a crucial role in energy metabolism in mitochondria, oxidation process, and aging-related degenerative diseases. In addition, the immune cells may be involved in the development of sarcopenia through mitochondrial metabolism. Finally, metformin was identified as a promising strategy of sarcopenia treatment via targeting NDUFC1.Conclusion: The four cuproptosis-related genes PDHA1, DLAT, PDHB and NDUFC1 may be the diagnostic biomarkers for sarcopenia, and metformin holds great potential to be developed as a therapy for sarcopenia. These outcomes provide new insights for better understanding of sarcopenia and innovative therapeutic approaches.
Genetic architecture for skeletal muscle glycolytic potential in Chinese Erhualian pigs revealed by a genome-wide association study using 1.4M SNP array
Authors: Xie Xinke , Huang Cong , Huang Yizhong , Zou Xiaoxiao , Zhou Runxin , Ai Huashui , Huang Lusheng , Ma Junwu 
Published: March 2023

Introduction: Muscle glycolytic potential (GP) is a key factor affecting multiple meat quality traits. It is calculated based on the contents of residual glycogen and glucose (RG), glucose-6-phosphate (G6P), and lactate (LAT) contents in muscle. However, the genetic mechanism of glycolytic metabolism in skeletal muscle of pigs remains poorly understood. With a history of more than 400 years and some unique characteristics, the Erhualian pig is called the “giant panda” (very precious) in the world’s pig species by Chinese animal husbandry.Methods: Here, we performed a genome-wide association study (GWAS) using 1.4M single nucleotide polymorphisms (SNPs) chips for longissimus RG, G6P, LAT, and GP levels in 301 purebred Erhualian pigs.Results: We found that the average GP value of Erhualian was unusually low (68.09 μmol/g), but the variation was large (10.4–112.7 μmol/g). The SNP-based heritability estimates for the four traits ranged from 0.16–0.32. In total, our GWAS revealed 31 quantitative trait loci (QTLs), including eight for RG, nine for G6P, nine for LAT, five for GP. Of these loci, eight were genome-wide significant (p &lt; 3.8 × 10−7), and six loci were common to two or three traits. Multiple promising candidate genes such as FTO, MINPP1, RIPOR2, SCL8A3, LIFR and SRGAP1 were identified. The genotype combinations of the five GP-associated SNPs also showed significant effect on other meat quality traits.Discussion: These results not only provide insights into the genetic architecture of GP related traits in Erhualian, but also are useful for pig breeding programs involving this breed.
Type I interferon score is associated with the severity and poor prognosis in anti-MDA5 antibody-positive dermatomyositis patients
Authors: Qian Jinjing , Li Rui , Chen Zhiwei , Cao Zehui , Lu Liangjing , Fu Qiong 
Published: March 2023

ObjectivesTo investigate the clinical significance of the interferon (IFN) score, especially the IFN-I score, in patients with anti-melanoma differentiation-associated gene 5 (MDA5) antibody-positive dermatomyositis (anti-MDA5+ DM).MethodsWe enrolled 262 patients with different autoimmune diseases, including idiopathic inflammatory myopathy, systemic lupus erythematosus, rheumatoid arthritis, adult-onset Still’s disease, and Sjögren’s syndrome, as well as 58 healthy controls. Multiplex quantitative real-time polymerase chain reaction (RT-qPCR) using four TaqMan probes was used to evaluate type I IFN-stimulated genes (IFI44 and MX1), one type II IFN-stimulated gene (IRF1), and one internal control gene (HRPT1), which were used to determine the IFN-I score. The clinical features and disease activity index were compared between the high and low IFN-I score groups in 61 patients with anti-MDA5+ DM. The associations between laboratory findings and the predictive value of the baseline IFN-I score for mortality were analyzed.ResultsThe IFN score was significantly higher in patients with anti-MDA5+ DM than in healthy controls. The IFN-I score was positively correlated with the serum IFN-α concentration, ferritin concentration, and Myositis Disease Activity Assessment Visual Analogue Scale (MYOACT) score. Compared with patients with a low IFN-I score, patients with a high IFN-I score showed a higher MYOACT score, C-reactive protein concentration, aspartate transaminase concentration, ferritin concentration, plasma cell percentage, and CD3+ T-cell percentage, as well as lower lymphocyte, natural killer cell, and monocyte counts. The 3-month survival rate was significantly lower in patients with an IFN-I score of &gt;4.9 than in those with an IFN-I score of ≤4.9 (72.9% vs. 100%, respectively; P = 0.044).ConclusionThe IFN score, especially the IFN-I score, measured by multiplex RT-qPCR is a valuable tool to monitor disease activity and predict mortality in patients with anti-MDA5+ DM.
Prognostic signatures of sphingolipids: Understanding the immune landscape and predictive role in immunotherapy response and outcomes of hepatocellular carcinoma
Authors: Zhang Xin , Zhuge Jinke , Liu Jinhui , Xia Zhijia , Wang Huixiong , Gao Qiang , Jiang Hao , Qu Yanyu , Fan Linlin , Ma Jiali , Tan Chunhua , Luo Wei , Luo Yong 
Published: March 2023

BackgroundHepatocellular carcinoma (HCC) is a complex disease with a poor outlook for patients in advanced stages. Immune cells play an important role in the progression of HCC. The metabolism of sphingolipids functions in both tumor growth and immune infiltration. However, little research has focused on using sphingolipid factors to predict HCC prognosis. This study aimed to identify the key sphingolipids genes (SPGs) in HCC and develop a reliable prognostic model based on these genes.MethodsThe TCGA, GEO, and ICGC datasets were grouped using SPGs obtained from the InnateDB portal. A prognostic gene signature was created by applying LASSO-Cox analysis and evaluating it with Cox regression. The validity of the signature was verified using ICGC and GEO datasets. The tumor microenvironment (TME) was examined using ESTIMATE and CIBERSORT, and potential therapeutic targets were identified through machine learning. Single-cell sequencing was used to examine the distribution of signature genes in cells within the TME. Cell viability and migration were tested to confirm the role of the key SPGs.ResultsWe identified 28 SPGs that have an impact on survival. Using clinicopathological features and 6 genes, we developed a nomogram for HCC. The high- and low-risk groups were found to have distinct immune characteristics and response to drugs. Unlike CD8 T cells, M0 and M2 macrophages were found to be highly infiltrated in the TME of the high-risk subgroup. High levels of SPGs were found to be a good indicator of response to immunotherapy. In cell function experiments, SMPD2 and CSTA were found to enhance survival and migration of Huh7 cells, while silencing these genes increased the sensitivity of Huh7 cells to lapatinib.ConclusionThe study presents a six-gene signature and a nomogram that can aid clinicians in choosing personalized treatments for HCC patients. Furthermore, it uncovers the connection between sphingolipid-related genes and the immune microenvironment, offering a novel approach for immunotherapy. By focusing on crucial sphingolipid genes like SMPD2 and CSTA, the efficacy of anti-tumor therapy can be increased in HCC cells.
Prognostic value of COL10A1 and its correlation with tumor-infiltrating immune cells in urothelial bladder cancer: A comprehensive study based on bioinformatics and clinical analysis validation
Authors: Wang Xiaoming , Bai Yunjin , Zhang Facai , Li Dengxiong , Chen Kai , Wu Ruicheng , Tang Yin , Wei Xin , Han Ping 
Published: March 2023

IntroductionBladder cancer (BLCA) is one of the most lethal diseases. COL10A1 is secreted small-chain collagen in the extracellular matrix associated with various tumors, including gastric, colon, breast, and lung cancer. However, the role of COL10A1 in BLCA remains unclear. This is the first research focusing on the prognostic value of COL10A1 in BLCA. In this research, we aimed to uncover the association between COL10A1 and the prognosis, as well as other clinicopathological parameters in BLCA.MethodsWe obtained gene expression profiles of BLCA and normal tissues from the TCGA, GEO, and ArrayExpress databases. Immunohistochemistry staining was performed to investigate the protein expression and prognostic value of COL10A1 in BLCA patients. GO and KEGG enrichment along with GSEA analyses were performed to reveal the biological functions and potential regulatory mechanisms of COL10A1 based on the gene co-expression network. We used the “maftools” R package to display the mutation profiles between the high and low COL10A1 groups. GIPIA2, TIMER, and CIBERSORT algorithms were utilized to explore the effect of COL10A1 on the tumor immune microenvironment.ResultsWe found that COL10A1 was upregulated in the BLCA samples, and increased COL10A1 expression was related to poor overall survival. Functional annotation of 200 co-expressed genes positively correlated with COL10A1 expression, including GO, KEGG, and GSEA enrichment analyses, indicated that COL10A1 was basically involved in the extracellular matrix, protein modification, molecular binding, ECM-receptor interaction, protein digestion and absorption, focal adhesion, and PI3K-Akt signaling pathway. The most commonly mutated genes of BLCA were different between high and low COL10A1 groups. Tumor immune infiltrating analyses showed that COL10A1 might have an essential role in recruiting infiltrating immune cells and regulating immunity in BLCA, thus affecting prognosis. Finally, external datasets and biospecimens were used, and the results further validated the aberrant expression of COL10A1 in BLCA samples.ConclusionsIn conclusion, our study demonstrates that COL10A1 is an underlying prognostic and predictive biomarker in BLCA.
Biomineralization of struvite induced by indigenous marine bacteria of the genus Alteromonas
Authors: He Wei , Xue Hua-Peng , Liu Chuang , Zhang Ai Hua , Huang Jian-Ke , Zhang Dao-Feng 
Published: March 2023

Biomineralization is a universal phenomenon in the ocean that plays an important role in marine geochemical circulation. The genus Alteromonas is an indigenous taxon with a wide distribution and various ecological roles in the ocean, but biomineralization by this genus has not been reported. In this study, five Alteromonas spp. were found to induce mineral crystal formation of different shapes and sizes in agar media. Further studies on deep-sea strains A. alteriprofundi HHU 13199T and A. alterisediminis N102T showed that they could produce mineral crystals with similar morphology when grown in agar or broth media with different concentrations of sea salts (i.e., 2%, 4%, 6%, and 8%), and that their growth was dependent on Ca2+ and/or Mg2+ ion concentrations. Genomic analysis showed that the genus Alteromonas universally possessed the ammonification metabolism pathway and that, during the culture of these bacteria, the production of mineral crystals was accompanied by an increase in ammonia concentration and pH value and a decrease in nitrate nitrogen concentration. The addition of ammonia to broth media (≈ 572.7 mg/L) simulated the ammonia content in media on days 5 and 6 of bacterial growth and also induced mineral crystals to form. Through the analysis using scanning electron microscope–energy-dispersive spectrometry (SEM-EDS), X-ray diffraction (XRD), Fourier-transform infrared microscopy (FTIR), thermogravimetric (TG) analysis, and differential thermal gravity and differential scanning calorimetry (DTG–DSC), mineral crystals induced by bacterial strains and the non-strain (ammonia-added sample) were all identified as struvite mineral. In addition, the characteristics of the struvite mineral induced by bacterial strains were different from the characteristics of the struvite synthesized by non-strain and of a struvite mineral standard. Thus, this study deduces that Alteromonas spp. possess the ability to induce struvite formation. The mechanism mainly lies in the presence of an ammonification metabolism pathway to produce ammonia, which should be recognized as biologically induced mineralization (BIM). This study provides insight into a new ecological role of indigenous marine taxa of the genus Alteromonas.
Carbonic anhydrase IX-related tumoral hypoxia predicts worse prognosis in breast cancer: A systematic review and meta-analysis
Authors: Numprasit Warapan , Yangngam Supaporn , Prasopsiri Jaturawitt , Quinn Jean A. , Edwards Joanne , Thuwajit Chanitra 
Published: March 2023

BackgroundTumoral hypoxia is associated with aggressiveness in many cancers including breast cancer. However, measuring hypoxia is complicated. Carbonic anhydrase IX (CAIX) is a reliable endogenous marker of hypoxia under the control of the master regulator hypoxia-inducible factor-1α (HIF-1α). The expression of CAIX is associated with poor prognosis in many solid malignancies; however, its role in breast cancer remains controversial.MethodsThe present study performed a meta-analysis to evaluate the correlation between CAIX expression and disease-free survival (DFS) and overall survival (OS) in breast cancer.ResultsA total of 2,120 publications from EMBASE, PubMed, Cochrane, and Scopus were screened. Of these 2,120 publications, 272 full texts were reviewed, and 27 articles were included in the meta-analysis. High CAIX was significantly associated with poor DFS (HR = 1.70, 95% CI = 1.39–2.07, p &lt; 0.00001) and OS (HR = 2.02, 95% CI 1.40–2.91, p = 0.0002) in patients with breast cancer. When stratified by subtype, the high CAIX group was clearly associated with shorter DFS (HR = 2.09, 95% CI =1.11–3.92, p = 0.02) and OS (HR = 2.50, 95% CI =1.53–4.07, p = 0.0002) in TNBC and shorter DFS in ER+ breast cancer (HR = 1.81 95% CI =1.38–2.36, p &lt; 0.0001).ConclusionHigh CAIX expression is a negative prognostic marker of breast cancer regardless of the subtypes.
Evaluation of the contribution of gut microbiome dysbiosis to cardiac surgery-associated acute kidney injury by comparative metagenome analysis
Authors: Li Ying , Jiang Xinyi , Chen Jingchun , Hu Yali , Bai Yunpeng , Xu Wang , He Linling , Wang Yirong , Chen Chunbo , Chen Jimei 
Published: March 2023

IntroductionCardiac surgery-associated acute kidney injury (CSA-AKI) is a common hospital-acquired AKI that carries a grave disease burden. Recently, gut-kidney crosstalk has greatly changed our understanding of the pathogenesis of kidney diseases. However, the relationship between gut microbial dysbiosis and CSA-AKI remains unclear. The purpose of this study was to investigate the possible contributions of gut microbiota alterations in CSA-AKI patients.MethodsPatients undergoing cardiac surgery were enrolled and divided into acute kidney injury (AKI) and Non_AKI groups. Faecal samples were collected before the operation. Shotgun metagenomic sequencing was performed to identify the taxonomic composition of the intestinal microbiome. All groups were statistically compared with alpha- and beta-diversity analysis, and linear discriminant analysis effect size (LEfSe) analysis was performed.ResultsA total of 70 individuals comprising 35 AKI and 35 Non_AKI were enrolled in the study. There was no significant difference between the AKI and Non_AKI groups with respect to the alpha-and beta-diversity of the Shannon index, Simpson or Chao1 index values except with respect to functional pathways (p &lt; 0.05). However, the relative abundance of top 10 gut microbiota in CSA-AKI was different from the Non_AKI group. Interestingly, both LEfSe and multivariate analysis confirmed that the species Escherichia coli, Rothia mucilaginosa, and Clostridium innocuum were associated with CSA-AKI. Moreover, correlation heat map indicated that altered pathways and disrupted function could be attributed to disturbances of gut microbiota involving Escherichia coli.ConclusionDysbiosis of the intestinal microbiota in preoperative stool affects susceptibility to CSA-AKI, indicating the crucial role of key microbial players in the development of CSA-AKI. This work provides valuable knowledge for further study of the contribution of gut microbiota in CSA-AKI.