Transcriptomics Analysis of Maize (<i>Zea mays</i> L.) in Response to the Infection by <i>Setosphaeria turcica</i> by Hui Jia, Pan Li, Bu Tao, Yuwei Liu, Zhihang Liu, Mengfang Zhu, He Zhou, Maocun Wang, Jingao Dong, Shouqin Gu, Xiaodong Gong

“…Our study identified 7196 differentially expressed genes (DEGs) involved in the maize leaf response to <i>S. turcica</i> infection compared to the control (CK at 0 hpi). Functional analysis revealed that these DEGs were enriched in multiple metabolic pathways. …”
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Modelling the alpha and beta diversity of copepods across tropical and subtropical Atlantic ecoregions by Lorena Martínez-Leiva, José M. Landeira, Maria Luz Fernández de Puelles, Santiago Hernández-León, Víctor M. Tuset, Effrosyni Fatira

“…To perform the functional analysis, six traits related to the behaviour, growth, and reproduction of copepods were selected. …”
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Exploring MAP3K genes in gastric cancer: biomarkers, tumor microenvironment dynamics, and chemotherapy resistance by Senhui Wei, Ying Li, Jing Zhou, Yongming Xia

“…Methylation profiling further supported the idea that promoter hypomethylation of MAP3K1, MAP3K4, MAP3K7, MAP3K8, MAP3K9, and MAP3K10 genes was associated with their up-regulation. Single-cell functional analysis elucidated the involvement of MAP3K genes in shaping the tumor microenvironment. miRNA-mRNA network analysis revealed intricate regulatory mechanisms, with hsa-mir-200b-3p emerging as a key regulator. …”
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Co-modulation of a circular form of PCDH11Y during neuroendocrine differentiation of prostate cancer by Giovanni Pecoraro, Ilaria Leone, Silvia Nuzzo, Santiago Negueruela, Giovanni Smaldone, Lorena Buono

“…After that, validation and functional analysis by RNA-interference was applied to a selected circRNA to explore its role during NED. …”
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Celastrol promotes DNA damage and apoptosis in uterine corpus endometrial carcinoma via promotion of KAT2B-mediated RBPJ acetylation and repression of MCM4 transcription by Lipeng Pei, Yan Zhu, Wenpeng Li, Bin Xu, Jingli Sun

“…RBPJ could bind to the MCM4 promoter to suppress the luciferase activity. Further functional analysis revealed that the functions of KAT2B in UCEC cell proliferation, DNA damage and apoptosis were mediated by MCM4, and Celastrol enhanced RBPJ acetylation and reduced MCM4 expression. …”
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Does preeclampsia impact the gut microbiota of preterm offspring during early infancy? by Yang Chen, Zhou-Ting Yi, Hai-Long Yu, Xiao-Yan Wu, Jun-Ping Wang, Chuan Nie, Hui Li, Sheng-Hui Li, Qiu-Long Yan, Tian-Wen He, Min-Chai Chen, Xin-Yue Yang, Ji-Ying Wen, Li-Juan Lv

“…The gut virome analysis showed no significant differences among the groups. Functional analysis revealed distinct metabolic pathway activities across the groups, suggesting that early disturbances due to PE impact the establishment of healthy gut microbiota. …”
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Comprehensive bioinformatics analysis identifies hub genes associated with immune cell infiltration in early-onset schizophrenia by Shasha Wu, Tailian Xue, Yilin Li, Weikang Chen, Yan Ren

“…Subsequently, a PPI network was constructed to select the top 10 potential hub genes, and functional analysis was performed by GeneMANIA, resulting in the identification of four immune-related genes. …”
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Identification and Analysis of Potential Immune-Related Biomarkers in Endometriosis by Yanan He, Jixin Li, Yanjun Qu, Liyuan Sun, Xibo Zhao, Han Wu, Guangmei Zhang

“…The top-ranked upregulated DEIRGs were upregulated in the endometra of infertile women. Functional analysis showed that DETFs and DEIRGs may be involved in the biological behaviors and pathways of endometriosis. …”
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Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early‐Stage Nonsmoking Lung Adenocarcinoma Patients by Yaohui Sun, Zhiming Gan, Shijiancong Liu, Sheng Zhang, Wei Zhong, Jian Liu, Xiuting Huang, Wei He, Hongcheng Zhong, Qingdong Cao

“…Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. …”
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Emergence of Self-Identity in Artificial Intelligence: A Mathematical Framework and Empirical Study with Generative Large Language Models by Minhyeok Lee

“…While existing approaches to artificial self-awareness often rely on heuristic implementations or philosophical abstractions, we present a formal framework grounded in metric space theory, measure theory, and functional analysis. Our framework posits that self-identity emerges from two mathematically quantifiable conditions: the existence of a connected continuum of memories <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>C</mi><mo>⊆</mo><mi mathvariant="script">M</mi></mrow></semantics></math></inline-formula> in a metric space <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>(</mo><mi mathvariant="script">M</mi><mo>,</mo><msub><mi>d</mi><mi mathvariant="script">M</mi></msub><mo>)</mo></mrow></semantics></math></inline-formula>, and a continuous mapping <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mi>I</mi><mo>:</mo><mi mathvariant="script">M</mi><mo>→</mo><mi mathvariant="script">S</mi></mrow></semantics></math></inline-formula> that maintains consistent self-recognition across this continuum, where <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mo>(</mo><mi mathvariant="script">S</mi><mo>,</mo><msub><mi>d</mi><mi mathvariant="script">S</mi></msub><mo>)</mo></mrow></semantics></math></inline-formula> represents the metric space of possible self-identities. …”
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A prognostic signature of Glutathione metabolism-associated long non-coding RNAs for lung adenocarcinoma with immune microenvironment insights by Junxi Hu, Junxi Hu, Shuyu Tian, Shuyu Tian, Qingwen Liu, Qingwen Liu, Jiaqi Hou, Jiaqi Hou, Jun wu, Jun wu, Xiaolin Wang, Xiaolin Wang, Yusheng Shu, Yusheng Shu

“…A prognostic model was built with Cox and Least Absolute Shrinkage and Selection Operator (LASSO) methods and validated by Kaplan-Meier analysis, Receiver Operating Characteristic (ROC) curves, and Principal Component Analysis (PCA). Functional analysis revealed immune infiltration and drug sensitivity differences. …”
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Developmental Proteomics Reveals the Dynamic Expression Profile of Global Proteins of <i>Haemaphysalis longicornis</i> (Parthenogenesis) by Min-Xuan Liu, Xiao-Pei Xu, Fan-Ming Meng, Bing Zhang, Wei-Gang Li, Yuan-Yuan Zhang, Qiao-Ying Zen, Wen-Ge Liu

“…In this study, we identified changes in the proteome throughout the <i>H. longicornis</i> development, and functional analysis highlighted the important roles of many key proteins in developmental events (ovarian development, the molting process, the development of midgut, the development and degeneration of salivary glands, etc.). …”
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Transcriptome analysis of jejunal mucosal tissue in breeder hens exposed to acute heat stress by Yongcai Zhu, Satoshi Kubota, Phocharapon Pasri, Sitthipong Rakngam, Supattra Okrathok, Chayanan Pukkung, Shenglin Yang, Sutisa Khempaka

“…Of these, 75 genes including heat shock proteins (HSPs) showed upregulated expression, while 63 genes including a key bile acid transport molecule (SLC10A2) exhibited downregulated expression. Functional analysis through gene ontology classification, pathway mapping via the Kyoto encyclopedia of genes and genomes, and protein interaction networks identified several important regulatory genes in thermal response (HSPA8 and HSPA2), energy homeostasis and fat metabolism (PDK4, PPARA, and CD36), glucose transport (SLC2A5), and cholesterol synthesis pathway (SQLE, CYP51A1, and HSD17B7). …”
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Class III β-Tubulin Overexpression Induces Chemoresistance to Eribulin in a Leiomyosarcoma Cell Line by Kenichiro Yahiro, Yoshihiro Matsumoto, Jun-ichi Fukushi, Ken-ichi Kawaguchi, Makoto Endo, Nokitaka Setsu, Keiichiro IIda, Suguru Fukushima, Makoto Nakagawa, Atsushi Kimura, Yoshinao Oda, Yasuharu Nakashima

“…The resistant cell line showed increased expression of MDR1 transcript, but protein levels and functional analysis results were similar to the parental cell line. …”
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Comprehensive profiling of serum microRNAs in normal and non-alcoholic fatty liver disease (NAFLD) patients by Jian-Wei Zhang, Kamran Ullah, Nauman Khan, Hai-Tao Pan

“…PCR validation confirmed the differential expression of miR-122-5p identified through RNA sequencing. Functional analysis using GO and KEGG pathways revealed a diverse range of biological roles associated with these differentially expressed miRNAs. …”
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Longitudinal DNA methylation profiles in saliva of offspring from mothers with gestational diabetes: associations with early childhood growth patterns by Teresa M. Linares-Pineda, Alfonso Lendínez-Jurado, Alberto Piserra-López, María Suárez-Arana, María Pozo, María Molina-Vega, María José Picón-César, Sonsoles Morcillo

“…Results We identified 6,968 DMPs at the postpartum stage and 5,132 after one year, with 50 sites remaining differentially methylated over time, 16 of which maintained consistent methylation directionality. Functional analysis linked several of these DMPs to genes involved in inflammation and metabolic processes, including CYTH3 and FARP2, both implicated in growth and metabolic pathways. …”
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Reshaping lipid metabolism with long-term alternate day feeding in type 2 diabetes mice by Eleni Beli, Yuanqing Yan, Leni Moldovan, Todd A. Lydic, Preethi Krishman, Sarah A. Tersey, Yaqian Duan, Tatiana E. Salazar, James M. Dominguez, Dung V. Nguyen, Abigail Cox, Sergio Li Calzi, Craig Beam, Raghavendra G. Mirmira, Carmella Evans-Molina, Julia V. Busik, Maria B. Grant

“…Microbiome studies and predicted functional analysis of gut microbiota showed that IF increased beneficial bacteria involved in sphingolipid (SL) metabolism. …”
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Exploration of alcohol dehydrogenase EutG from Bacillus tropicus as an eco-friendly approach for the degradation of polycyclic aromatic compounds by Muhammad Naveed, Fatima Iqbal, Tariq Aziz, Ayesha Saleem, Tayyab Javed, Mahrukh Afzal, Muhammad Waseem, Metab Alharbi, Thamer H. Albekairi

“…Then the computational analysis was conducted where the sequence similarity and functional analysis of alcohol dehydrogenase EutG protein from B.tropicus was analyzed through PSI-BLAT and SMART tool, respectively. …”
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Coupling genome-wide continuous perturbation with biosensor screening reveals the potential targets in yeast isopentanol synthesis network by Qi Xiao, Jingjing Shi, Lixian Wang, Guoping Zhao, Yanfei Zhang

“…Our results confirmed the critical roles of HOM3 and DIP5 in isopentanol production, along with genes associated with the aerobic respiratory chain (SDH3, CYT1, COX7, ROX1, and ATG41) and cofactor balance (BNA2 and NDE1). Additionally, functional analysis of the co-DEGs revealed that MAL33 is associated with the synthesis of branched-chain higher alcohols, expanding the intracellular metabolic network and offering new possibilities for green, cost-effective biofuel production.…”
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FadA antigen of Fusobacterium nucleatum: implications for ceRNA network in colorectal cancer and adenomatous polyps progression by Sama Rezasoltani, Elahe Shams, Moein Piroozkhah, Yaser Aidi, Mehdi Azizmohammad Looha, Parmida Bagheri, Roudabeh Behzadi Andouhjerdi, Amir Sadeghi, Leili Rejali, Ehsan Nazemalhosseini-Mojarad

“…Application of the Spearman test revealed a strong and significant correlation between FadA and LINC00460 (rS = 0.9311, p < 0.0001). Also, the functional analysis of ANXA2 revealed its impact on CRC progression through JAK-STAT and Hippo signaling pathways. …”
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