Comparison of Different 3D Surface Registration-Based Methods to Assess Facial Asymmetry by Annalisa Cappella, Riccardo Solazzo, Luisa Gigante, Alice Gervasoni, Daniele Maria Gibelli, Claudia Dolci, Gianluca Martino Tartaglia, Chiarella Sforza

“…However, we suggest that the methods based on the trigeminal subdivision can be used interchangeably in contexts where the morpho-functional analysis of maxillofacial regions with different embryological origins is considered. …”
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Characterization of private mutations in the spike protein of SARS-CoV-2 correlates with viral prevalence by Shuo Wang, Ziyang Hao, Yuhan Ding, Heng Rong, Shuo Ning, Qiao Qiao, Xiaojuan Zhu, Tao Wu, Kangchen Zhao, Liguo Zhu, Jingxin Li, Yiyue Ge, Lunbiao Cui

“…Conclusions Continuous monitoring and functional analysis of SARS-CoV-2 private mutations can be an effective approach for explaining patterns of viral prevalence. …”
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Macrogenomics-based analysis of rumen microbial composition and their metabolic pathways in yaks under different dietary concentrate-to-forage ratios by Fajie Gou, Fajie Gou, Yincang Han, Yincang Han, Yonggang Sun, Yonggang Sun, Weiqing Ding, Weiqing Ding, Shenwei Jin, Shenwei Jin, Yaqian Liu, Yaqian Liu, Jianyu Chen, Jianyu Chen

“…Bacteroidota, Bacillota, Prevotella, Bacteroides, and Ruminococcus were identified as the dominant bacterial taxa at the phylum and genus levels. Functional analysis of rumen microbial metabolism showed that in the C35 group, pathways related to starch and sucrose metabolism, as well as fructose and mannose metabolism, were significantly different from those in other groups. …”
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Salivary mycobiome alterations in HIV-infected MSM: dominance of Pseudogymnoascus and functional shifts across disease stages by Ying Guo, Ying Guo, Lu Lin, Miao Zhang, Yixi Yu, Yan Wang, Jie Cao, Yuchen Li, Xintong Sun, Meilin Guan, Shuo Wen, Xin Wang, Zhen Fang, Wenshan Duan, Junyi Duan, Tao Huang, Wei Xia, Shan Guo, Feili Wei, Dongxiang Zheng, Xiaojie Huang

“…Statistical analyses (Kruskal-Wallis tests, Spearman’s correlation) assessed associations between fungal profiles, CD4 count, and viral loads.ResultsA total of 51 fungal genera were identified, with Pseudogymnoascus being the most abundant. Functional analysis revealed 113 shared KEGG pathways, of which 69 were unique to Stage 3, primarily related to metabolic and disease-related processes. …”
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Molecular cloning of PRD-like homeobox genes expressed in bovine oocytes and early IVF embryos by Barış Yaşar, Nina Boskovic, Marilin Ivask, Jere Weltner, Eeva-Mari Jouhilahti, Piibe Vill, Tiina Skoog, Ülle Jaakma, Juha Kere, Thomas R. Bürglin, Shintaro Katayama, Tõnis Org, Ants Kurg

“…Subsequently, we observed the prediction of the 9aa transactivation domain (9aaTAD) motif in the putative protein sequence of TPRX3 leading us to conduct functional analysis of this gene. We demonstrated that the TPRX3 overexpression in bovine fibroblast induces not only protein-coding genes but also short noncoding RNAs involved in splicing and RNA editing. …”
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Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches by Wenjie Han, Wenjie Han, Yuhang Zhou, Yuhang Zhou, Yiwen Wang, Yiwen Wang, Xiaolin Liu, Tao Sun, Tao Sun, Junnan Xu, Junnan Xu, Junnan Xu

“…Antibiotic exposure significantly influenced the abundance and functional potential of these key taxa. KEGG-based functional analysis revealed the enrichment of amino acid metabolism pathways in responders. …”
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Comprehensive Analysis Reveals the Potential Diagnostic Value of Biomarkers Associated With Aging and Circadian Rhythm in Knee Osteoarthritis by Hao Li, Yuze Yang, Bo Li, Jiaju Yang, Pengyu Liu, Yuanpeng Gao, Min Zhang, Guangzhi Ning

“…Conclusions Two diagnostic and therapeutic biomarkers associated with aging‐circadian rhythm in KOA were identified. Functional analysis, molecular mechanism exploration, and experimental validation further elucidated their roles in KOA, offering novel perspectives for the prevention and treatment of the disease.…”
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Comparative Study of Structural and Functional Rearrangements in Skeletal Muscle Mitochondria of SOD1-G93A Transgenic Mice at Pre-, Early-, and Late-Symptomatic Stages of ALS Progr... by Natalia V. Belosludtseva, Anna I. Ilzorkina, Mikhail V. Dubinin, Irina B. Mikheeva, Konstantin N. Belosludtsev

“…Transmission electron microscopy followed by quantitative analysis was performed to study ultrastructural alterations in the quadriceps femoris. Functional analysis of skeletal muscle mitochondria was performed using high-resolution Oxygraph-2k (O2K) respirometry and methods for assessing the calcium retention capacity index and the content of lipid peroxidation products in freshly isolated preparations. …”
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Integrated miRNA-seq and functional analyses reveal the regulatory role of sha-miR-92a_L + 2R + 4 via targeting vegfaa in rainbow trout (Oncorhynchus mykiss) responding to acute hy... by Yongjuan Li, Shenji Wu, Jinqiang Huang, Lu Zhao

“…Through miRNA-mRNA interaction and weighted gene co-expression network analysis (WGCNA), five key DE miRNAs (sha-miR-92a_L + 2R + 4, ssa-miR-128-3p, ssa-miR-101b-3p_R + 1, ola-miR-199a-5p_R + 2 and tni-miR-199_1ss18CG) were identified, which can target at least two hypoxia-responsive genes, such as vegfaa, ho, glut1a and junb. Functional analysis found that sha-miR-92a_L + 2R + 4 directly regulated vegfaa expression by targeting its 3′-UTR, overexpression of sha-miR-92a_L + 2R + 4 significantly decreased vegfaa expression in rainbow trout liver cells, while opposite results were obtained after transfection of sha-miR-92a_L + 2R + 4 inhibitor. …”
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Anatomical and functional outcome of surgical correction of optic disc pit maculopathy using autologous scleral patch graft: a long-term retrospective analysis by Naresh Babu Kannan, Avik Dey Sarkar, MuthuKrishnan Vallinayagam, Swikruti Jena, Shraddha Shah, Kim Ramasamy

“…Successful visual rehabilitation was achieved in 45 patients (83.33%) Conclusions Detailed OCT based and functional analysis in this study with long-term follow-up helps to entitle the importance of scleral patch graft based surgical procedure in managing this challenging surgical condition. …”
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Polyamine metabolism related gene index prediction of prognosis and immunotherapy response in breast cancer by Ruoya Wang, Shouliang Cai, Qing Gao, Yidong Chen, Xue Han, Fangjian Shang, Chunyan Liang, Guolian Zhu, Bo Chen

“…The model successfully stratified BC patients into high-risk and low-risk groups, with the high-risk group exhibiting poorer clinical outcomes. Functional analysis revealed significant differences in immune status and drug sensitivity between high-risk and low-risk groups.ConclusionsThis study elucidated the biological characteristics of PMRG expression subtypes in BC, identifying a polyamine-related prognostic signature and four novel biomarkers to accurately predict prognosis and immunotherapy response in BC patients.…”
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Cigarette smoke modulates methylation levels of LEF1-AS1 and impedes its expression: An experimental study by Bader O. Almutairi, Ahmed Rady, Bashayer S. Aljuhani, Mikhlid H. Almutairi

“…The expression analysis of LEF1-AS1 was performed using the GTEx (Genotype-Tissue Expression) database, including an assessment of its expression in various cancers such as lung and brain cancers. The functional analysis of the LEF1-AS1 gene was conducted across multiple tissues using data from the GENT2 databases, along with meta-survival and functional enrichment analysis. …”
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Integrating machine learning and multi-omics analysis to unveil key programmed cell death patterns and immunotherapy targets in kidney renal clear cell carcinoma by Fanyan Ou, Yi Pan, Qiuli Chen, Lixiong Zeng, Kanglai Wei, Delin Liu, Qian Guo, Liquan Zhou, Jie Yang

“…Integrating multi-omics analysis, including immune cell infiltration, phenotyping, functional analysis, immune checkpoint exploration, and gene set enrichment analysis (GSEA), we explored the relationship between key cell death patterns and patients’ responses to immunotherapy. …”
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Effects of saffron-grape intercropping on saffron flower number and rhizosphere microbial community by Yuanyuan Tao, Guifen Zhou, Xingchang Zhang, Mengqing Feng, Liqin Li, Xiaodong Qian

“…Intercropping decreased the dominance of certain microbial taxa, including Fictibacillus, Microbacterium, and Glutamicibacter among bacterial genera, as well as Fusarium and Arthrographis among fungal genera. Additionally, functional analysis revealed that intercropping was significantly higher (P < 0.01) than monoculture in dark hydrogen oxidation, denitrification, nitrate denitrification, nitrous oxide denitrification, nitrite denitrification, and manganese oxidation. …”
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Genome-Wide Identification, Characterization, and Expression Analysis of <i>BES1</i> Family Genes in ‘<i>Tieguanyin</i>’ Tea Under Abiotic Stress by Yanzi Zhang, Yanlin Zhang, Zhicheng Yang, Qingyan Li, Weixiang Chen, Xinyan Wen, Hao Chen, Shijiang Cao

“…Synteny analysis identified 20 syntenic genes, suggesting the conservation of their evolutionary functions. Analysis of the promoter regions revealed two types of light-responsive cis-elements, with <i>CsBES1.4</i> exhibiting the highest number of light-related cis-elements (13), followed by <i>CsBES1.9</i> and <i>CsBES1.10</i>. …”
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Inhibition of the FEN1-PBX1 axis elicits cellular senescence in breast cancer via the increased intracellular reactive oxygen species levels by Min Wu, Benmeng Wu, Xiaoshan Huang, Zirui Wang, Miaolin Zhu, Yaqin Zhu, Lin Yu, Jingjing Liu

“…A xenograft mouse model was employed to validate the effect of FEN1 on breast cancer cell senescence and apoptosis. Results Functional analysis demonstrated that FEN1 suppressed both senescence and apoptosis of breast cancer cells in vitro, while in vivo experiments demonstrated moderate therapeutic effects. …”
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Integration of single-cell sequencing and drug sensitivity profiling reveals an 11-gene prognostic model for liver cancer by Qunfang Zhou, Jingqiang Wu, Jiaxin Bei, Zixuan Zhai, Xiuzhen Chen, Wei Liang, Jing Meng, Mingyu Liu

“…An 11-gene prognostic model was constructed, effectively stratifying patient prognosis (p < 0.05) and achieving an AUC above 0.6 for 5 year survival prediction in multiple cohorts. Functional analysis revealed that upregulated genes in high-risk groups were enriched in cell adhesion pathways, while downregulated genes were enriched in metabolic pathways. …”
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The identification and validation of histone acetylation-related biomarkers in depression disorder based on bioinformatics and machine learning approaches by Lu Zhang, Lu Zhang, YuJing Lv, Mengqing Ma, Jile Lv, Jie Chen, Shang Lei, Yi Man, Guimei Xing, Yu Wang

“…Candidate genes were selected by intersecting DEGs, key module genes, and HAC-RGs, followed by functional analysis. Two machine learning algorithms were used to identify hub genes, which were used for drug prediction, immunological infiltration studies, nomogram construction, and regulatory network building. …”
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Single-cell RNA sequencing of human double-negative T cells reveals a favorable cellular signature for cancer therapy by Li Zhang, Sergio Rutella, Jongbok Lee, Ismat Khatri, Yoosu Na, Enoch Tin, Karen Fang, Michele Nawata, Juan Arteaga, Mark D Minden

“…Here, we performed single-cell RNA sequencing with in vitro and in vivo functional analysis on DNTs. As a significant proportion of DNTs express Vγ9Vδ2 (Vδ2) TCR chain, we compared DNTs with donor-matched conventional Vδ2 T cells expanded with zoledronic acid.Methods Healthy donor-derived allogeneic DNTs and Vδ2 T cells were expanded ex vivo. …”
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Integrative Analysis Provides Insights into Genes Encoding LEA_5 Domain-Containing Proteins in Tigernut (<i>Cyperus esculentus</i> L.) by Zhi Zou, Xiaowen Fu, Xiaoping Yi, Chunqiang Li, Jiaquan Huang, Yongguo Zhao

“…These findings highlight the lineage-specific evolution of the <i>LEA_5</i> family, which facilitates further functional analysis and genetic improvement in tigernut and other species.…”
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