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

“…BackgroundSubstantial interstudy heterogeneity in cancer immunotherapy-associated biomarkers has hindered their clinical applicability. …”
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The Significant Effects of Threshold Selection for Advancing Nitrogen Use Efficiency in Whole Genome of Bread Wheat by Mohammad Bahman Sadeqi, Agim Ballvora, Said Dadshani, Md. Nurealam Siddiqui, Mohammad Kamruzzaman, Ahossi Patrice Koua, Jens Léon

“…In the GWAS model, thresholding is common strategy to indicate deviation of expected range of p‐value(s), and it can be used to find the distribution of true positive associations under or over of test statistics. Therefore, the threshold plays a critical role to identify reliable and significant associations in wide genome, while the proportion of false positive results is relatively low. …”
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Regulatory T cells and matrix-producing cancer associated fibroblasts contribute on the immune resistance and progression of prognosis related tumor subtypes in ccRCC by Chao Zhang, Yisu Song, Xiaobo Cui, Yina Wang, Jiang Liu, Zhouji Shen

“…By analyzing public single cell RNA-sequencing and bulk RNA-sequencing data with the Scissor algorithm, we have identified three distinct prognosis related cancer cell subtypes which play an indispensable role on tumor metastasis, immune response and proliferation respectively. …”
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Digital Pathology Tailored for Assessment of Liver Biopsies by Alina-Iuliana Onoiu, David Parada Domínguez, Jorge Joven

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Revealing key regulatory factors in lung adenocarcinoma: the role of epigenetic regulation of autophagy-related genes from transcriptomics, scRNA-seq, and machine learning by Xianchang Zeng, Lingyun Wei, Lu Lv, Di Wu, Yingying Shen, Xinliang Lu, Xianghui Kong, Zhijian Cai, Jianli Wang, Jianli Wang

“…Autophagy, a key cellular process, is tightly linked to cancer development; genes like ATG5 and ATG10 influence lung cancer progression, and epigenetic regulators modulate autophagy-related carcinogenesis. However, the role of epigenetic-autophagy genes in LUAD’s tumor microenvironment is under-researched.MethodsWe used the “limma”” package to identify differential epigenetic-related genes associated with altered autophagy regulation (A-ERGs) in LUAD. …”
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Current Evidence Supporting the Role of miRNA as a Biomarker for Lung Cancer Diagnosis Through Exhaled Breath Condensate Collection: A Narrative Review by Paolo Albino Ferrari, Cosimo Bruno Salis, Antonio Macciò

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Multi-Omics Profiling Reveals Glycerolipid Metabolism-Associated Molecular Subtypes and Identifies ALDH2 as a Prognostic Biomarker in Pancreatic Cancer by Jifeng Liu, Shurong Ma, Dawei Deng, Yao Yang, Junchen Li, Yunshu Zhang, Peiyuan Yin, Dong Shang

“…<b>Background</b>: The reprogramming of lipid metabolism, especially glycerolipid metabolism (GLM), plays a key role in cancer progression and response to therapy. …”
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Identification of PRKCQ-AS1 as a Keratinocyte-Derived Exosomal lncRNA That Promotes Th17 Differentiation and IL-17&amp;nbsp;secretion in Psoriasis Through Bioinformatics, Machine L... by Gao P, Gao X, Lin L, Zhang M, Luo D, Chen C, Li Y, He Y, Liu X, Shi C, Yang R

“…Subsequently, exosome-related ncRNAs in psoriasis lesions were identified primarily through weighted gene co-expression network analysis and five machine learning algorithms. Additionally, large-scale integrated single-cell RNA sequencing data and genome-wide association study (GWAS) data were included to investigate the mechanisms of key ncRNA, primarily through immune infiltration analysis, gene set enrichment analysis (GSEA), co-expression analysis, and Mendelian randomization. …”
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Single-cell transcriptomics and machine learning unveil ferroptosis features in tumor-associated macrophages: Prognostic model and therapeutic strategies for lung adenocarcinoma by Ting Ji, Ting Ji, Juanli Jiang, Juanli Jiang, Xin Wang, Xin Wang, Kai Yang, Kai Yang, Shaojin Wang, Shaojin Wang, Bin Pan, Bin Pan

“…BackgroundLung adenocarcinoma (LUAD) is a major cause of cancer-related mortality worldwide. Tumor-associated macrophages (TAMs) play a crucial role in the tumor microenvironment (TME), influencing tumor progression and immune response. …”
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Integrative analyses of 16S rDNA sequencing and serum metabolomics demonstrate significant roles for the oral microbiota and serum metabolites in post-kidney transplant diabetes me... by Chao Liu, Sheng Chao, Lei Jia, Qizhen Yang, Qian Chen, Yulin Niu

“…ABSTRACT Oral microbiota and serum metabolites play crucial roles in diabetes, but their relationship with post-transplant diabetes mellitus (PTDM), a common complication post-kidney transplantation, is not well characterized. …”
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Role of low-frequency integrase strand transfer inhibitor resistance mutations on virological outcomes in antiretroviral therapy-naïve individuals initiating second-generation inte... by Daniele Armenia, Greta Marchegiani, Daniele Spalletta, Luca Carioti, Alessandro Tavelli, Maria Concetta Bellocchi, Vincenzo Spagnuolo, Valentina Mazzotta, Eugenia Quiros-Roldan, Valeria Bono, Stefania Carrara, Sergio Lo Caputo, Antonella D’Arminio Monforte, Francesca Ceccherini-Silberstein, Stefano Rusconi, Maria Mercedes Santoro

“…Conditional logistic regression was used to evaluate the association between INSTI resistance and risk of VR. …”
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Embedded feature fusion for multi-label criteria selection via local search strategy and particle swarm optimization by Suhua Chen, Xu Fang, Feng Zhai, Li Wang, Lin Lv

“…By incorporating this operator, the proposed method achieves superior convergence speed compared to previous algorithms in the field. The performance of the proposed method was evaluated across several datasets against some of the most widely used feature fusion selection algorithms. …”
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A novel tertiary lymphoid structure-associated signature accurately predicts patient prognosis and facilitates the selection of personalized treatment strategies for HNSCC by Jinhao Zhang, Lu Zeng, Lu Zeng, Guobin Song, Gaoge Peng, Gaoge Peng, Zhezheng Chen, Zhezheng Chen, Yamin Yuan, Taowu Chen, Tao Zhong, Shixi Chen, Zhengzhou Luo, Zhengzhou Luo, Jingang Xiao, Jingang Xiao, Jingang Xiao, Lin Liu, Lin Liu, Lin Liu

“…Distinct TLS-related subgroups were identified through unsupervised clustering analysis, and the associated genes were explored. Prognostic genes were identified via univariate Cox and Boruta algorithms, and a novel TLS-related scoring system was developed via the GSVA algorithm.ResultsOur study revealed that patients with higher TLS-related scores had improved overall survival and were more likely to benefit from immunotherapy. …”
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Proteomic associations with cognitive variability as measured by the Wisconsin Card Sorting Test in a healthy Thai population: A machine learning approach. by Chen Chen, Bupachad Khanthiyong, Benjamard Thaweetee-Sukjai, Sawanya Charoenlappanit, Sittiruk Roytrakul, Phrutthinun Surit, Ittipon Phoungpetchara, Samur Thanoi, Gavin P Reynolds, Sutisa Nudmamud-Thanoi

“…This study investigated the association between serum protein expression profiles and cognitive variability in a healthy Thai population using machine learning algorithms. …”
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Identification of M2 macrophage-related genes associated with diffuse large B-cell lymphoma via bioinformatics and machine learning approaches by Jiayi Zhang, Zhixiang Jia, Jiahui Zhang, Xiaohui Mu, Limei Ai

“…Abstract M2 macrophages play a crucial role in the initiation and progression of various tumors, including diffuse large B-cell lymphoma (DLBCL). …”
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Associations Between Intracranial Pressure Extremes and Continuous Metrics of Cerebrovascular Pressure Reactivity in Acute Traumatic Neural Injury: A Scoping Review by Kevin Y. Stein, Fiorella Amenta, Logan Froese, Alwyn Gomez, Amanjyot Singh Sainbhi, Nuray Vakitbilir, Younis Ibrahim, Abrar Islam, Tobias Bergmann, Izabella Marquez, Frederick A. Zeiler

“…Cerebrovascular pressure reactivity plays a key role in maintaining constant cerebral blood flow. …”
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Association of microtubule-based processes gene expression with immune microenvironment and its predictive value for drug response in oestrogen receptor-positive breast cancer by Zhenfeng Huang, Minghui Zhang, Nana Zhang, Mengyao Zeng, Yao Qian, Meng Zhu, Xiangyan Meng, Ming Shan, Guoqiang Zhang, Feng Liu

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The role of endothelial cell-related gene COL1A1 in prostate cancer diagnosis and immunotherapy: insights from machine learning and single-cell analysis by Gujun Cong, Jingjing Shao, Feng Xiao, Haixia Zhu, Peipei Kang

“…A diagnostic model was then constructed and validated using a combination of 108 machine learning algorithms. The XGBoost and Random Forest algorithms highlighted the significant role of COL1A1, and we further analyzed the expression and correlation of COL1A1, AR, and EGFR through multiplex immunofluorescence staining. …”
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Does the hepatologist still need to rely on aminotransferases in clinical practice? A reappraisal of the role of a classic biomarker in the diagnosis and clinical management of chr... by Patrizia Burra, Calogero Cammà, Pietro Invernizzi, Fabio Marra, Maurizio Pompili

“…This study aims to explore the evolving role of ALT as a biomarker. A comprehensive review of evidence was conducted, focusing on studies evaluating ALT thresholds, diagnostic accuracy, and integration with non-invasive liver assessment tools. …”
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Machine learning identification of a novel vasculogenic mimicry-related signature and FOXM1’s role in promoting vasculogenic mimicry in clear cell renal cell carcinoma by Chao Xu, Sujing Zhang, Jingwei Lv, Yilong Cao, Yao Chen, Hao Sun, Shengtao Dai, Bowei Zhang, Meng Zhu, Yuepeng Liu, Junfei Gu

“…Methods: Consensus clustering identified VRG-associated subtypes. We developed a machine learning framework integrating 12 algorithms to establish a consistent VM-related signature (VRG_score). …”
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