Machine learning identifies lipid-associated genes and constructs diagnostic and prognostic models for idiopathic pulmonary fibrosis by Xingren Liu, Junmei Song, Shujin Guo, Yi Liao, Jun Zou, Liqing Yang, Caiyu Jiang

“…Weighted gene co-expression network analysis (WGCNA) was performed on the identified clusters to determine core modules and hub genes associated with IPF. Machine learning algorithms were applied to these hub genes to construct diagnostic and prognostic models, which were validated across multiple datasets. …”
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SIGLEC1 has the potential to be an immune-related prognostic indicator in colon adenocarcinoma: a study based on transcriptomic data and Mendelian randomization analysis by Jue Gu, Yaxuan Wang, Hui Zhang, Haijuan Gu, Haixia Zhu

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Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission. by David W Eyre, Madeleine L Cule, David Griffiths, Derrick W Crook, Tim E A Peto, A Sarah Walker, Daniel J Wilson

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The role of mitochondria-related genes and immune infiltration in carotid atherosclerosis: identification of hub targets through bioinformatics and machine learning approaches by Dan Liu, Kun Guo, Min Li, Xiaochen Yu, Xue Guan, Xiuru Guan

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Integration of bulk RNA-seq and scRNA-seq reveals transcriptomic signatures associated with deep vein thrombosis by Bao-ze Pan, Ming-jun Jiang, Li-ming Deng, Jie Chen, Xian-peng Dai, Zi-xuan Wu, Zhi-he Deng, Dong-yang Luo, Yang-yi-jing Wang, Dan Ning, Guo-zuo Xiong, Guo-shan Bi

“…Furthermore, scRNA-seq demonstrated that B cells, T cells and monocytes play an active role in DVT. In the external validation set, CXCR4 was validated as a potential target by the ML algorithm and IF. …”
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Using Propensity Score Matching Technique to Estimate Utilization and Costs of General Practitioners’ Services associated with Alzheimer’s Disease by Rajan Sharma, Elizaveta Sopina, Jan Sørensen

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Novel insights into the molecular mechanisms of sepsis-associated acute kidney injury: an integrative study of GBP2, PSMB8, PSMB9 genes and immune microenvironment characteristics by Haiting Ye, Xiang Zhang, Pengyan Li, Mei Wang, Ruolan Liu, Dingping Yang

“…Immune cell infiltration was analyzed using the CIBERSORT algorithm, and potential associations between the hub genes and clinicopathological features were explored based on the Nephroseq database. …”
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MAP17 is a Novel NASH Progression Biomarker Associated with Macrophage Infiltration, Immunotherapy Response, and Oxidative Stress by Huang Z, Chen J, Liu S, Xiang X, Long Y, Tan P, Fu W

“…Zhiwei Huang,1,* Jiatong Chen,1,* Shenglu Liu,1 Xin Xiang,2 Yang Long,3 Peng Tan,1,4 Wenguang Fu1,4 1Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, People’s Republic of China; 2Department of General Surgery, The First People’s Hospital of Neijiang, Neijiang, 641000, People’s Republic of China; 3Department of Endocrinology and Metabolism, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, People’s Republic of China; 4Metabolic Hepatobiliary and Pancreatic Diseases Key Laboratory of Luzhou City, Academician (Expert) Workstation of Sichuan Province, Department of General Surgery (Hepatopancreatobiliary surgery), The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, People’s Republic of China*These authors contributed equally to this workCorrespondence: Peng Tan; Wenguang Fu, Department of General Surgery (Hepatopancreatobiliary Surgery), The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, People’s Republic of China, Email tanpeng@swmu.edu.cn; fuwg@swmu.edu.cnBackground: Nonalcoholic steatohepatitis (NASH) has recently garnered increased attention due to immune infiltration. However, the role of membrane-associated protein 17 (MAP17) in NASH remains unclear, which prompted this study to explore its relationship with immune infiltration and its regulatory mechanisms.Methods: We employed weighted correlation network analysis (WGCNA) to construct a gene co-expression network aimed at identifying key genes associated with NASH progression. …”
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Deciphering the role of cuproptosis in the development of intimal hyperplasia in rat carotid arteries using single cell analysis and machine learning techniques by Miao He, Hui Chen, Zhengli Liu, Boxiang Zhao, Xu He, Qiujin Mao, Jianping Gu, Jie Kong

“…Methods: We downloaded single-cell sequencing and bulk transcriptome data from the GEO database to screen for copper-growth-associated genes (CAGs) using machine-learning algorithms, including Random Forest and Support Vector Machine. …”
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Predicting protein–protein interactions in microbes associated with cardiovascular diseases using deep denoising autoencoders and evolutionary information by Senyu Zhou, Jian Luo, Mei Tang, Chaojun Li, Yang Li, Wenhua He

“…IntroductionProtein–protein interactions (PPIs) are critical for understanding the molecular mechanisms underlying various biological processes, particularly in microbes associated with cardiovascular disease. Traditional experimental methods for detecting PPIs are often time-consuming and costly, leading to an urgent need for reliable computational approaches.MethodsIn this study, we present a novel model, the deep denoising autoencoder for protein–protein interaction (DAEPPI), which leverages the denoising autoencoder and the CatBoost algorithm to predict PPIs from the evolutionary information of protein sequences.ResultsOur extensive experiments demonstrate the effectiveness of the DAEPPI model, achieving average prediction accuracies of 97.85% and 98.49% on yeast and human datasets, respectively. …”
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Identification and predictive machine learning models construction of gut microbiota associated with lymph node metastasis in colorectal cancer by Yongzhi Wu, Chengen Deng, Zigui Huang, Yongqi Huang, Chuanbin Chen, Mingjian Qin, Zhen Wang, Fuhai He, Shenghai Liu, Rumao Zhong, Jun Liu, Chenyan Long, Jungang Liu, Weizhong Tang, Xiaoliang Huang

“…ABSTRACT This study focuses on the significant role between gut microbiota and lymph node metastasis (LNM) in colorectal cancer (CRC). …”
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Machine learning-based identification of histone deacetylase-associated prognostic factors and prognostic modeling for low-grade glioma by Keshan Wen, Weijie Zhu, Ziyi Luo, Wei Wang

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Machine learning based screening of biomarkers associated with cell death and immunosuppression of multiple life stages sepsis populations by Jie Yang, Fanyan Ou, Binbin Li, Lixiong Zeng, Qiuli Chen, Houyu Gan, Jianing Yu, Qian Guo, Jihua Feng, Jianfeng Zhang

“…Six key DEGs associated with Ferroptosis were identified (AKR1C3, GCLM, PEBP1, CARS, MAP1LC3B, SCL11A2), among which MAP1LC3B, playing a role in mitochondrial reactive oxygen species energy metabolism, showed the strongest predictive ability (AUC = 0.883, P < 0.05). …”
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Associations of absolute risk of osteoporotic fractures (FRAX®) and total cardiovascular risk (SCORE) in urban population of the Russian Federation by M. A. Myagkova, I. A. Skripnikova, O. V. Kosmatova, S. A. Shalnova, V. A. Vygodin

“…The risk of fracture, determined using the FRAX® algorithm, is positively associated with cumulative CVR (SCORE) in both men and women. …”
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Simultaneous determination of 7 thiols associated proteins in lymphoma patients’serum and cerebrospinal fluid by UHPLC-HRMS technique by Qingkun Ma, Mei Zhang, Yongshuai Fan, Han Zhao, Kun Wang, Xiaojing Wang, Yanling Mu

“…This study aims to measure thiols associated proteins and develop novel diagnostic models in serum and cerebrospinal fluid from PCNSL to verify potential association and early warning effectiveness. …”
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Identification and validation of a KRAS-macrophage-associated gene signature as prognostic biomarkers and potential therapeutic targets in melanoma by Beichen Cai, Beichen Cai, Beichen Cai, Qian Lin, Qian Lin, Qian Lin, Ruonan Ke, Ruonan Ke, Ruonan Ke, Jiaqi Yu, Jiaqi Yu, Jiaqi Yu, Lu Chen, Lu Chen, Xuejun Ni, Xuejun Ni, Hekun Liu, Xiuying Shan, Xiuying Shan, Biao Wang, Biao Wang, Biao Wang

“…Gene set enrichment analysis (GSEA) was utilized to characterize the molecular pathways associated with KRAS signaling. Single-cell RNA sequencing (scRNA-seq) was leveraged to investigate the cellular heterogeneity within the SKCM tumor microenvironment, and macrophage populations were categorized using the Monocle2 algorithm. …”
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Causal role of the pyrimidine deoxyribonucleoside degradation superpathway mediation in Guillain-Barré Syndrome via the HVEM on CD4 + and CD8 + T cells by Xianghua Liu, Lingling Liu, Jiuchang Zhang

“…Abstract Immune system regulation is a key indicator of the gut microbiota (GM) influencing disease development. The causal role of the GM in Guillain-Barré syndrome (GBS) and whether it can be mediated by immune cells is unknown. …”
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Chromatin accessibility reveals potential prognostic value of the peak set associated with smoking history in patients with lung adenocarcinoma by Han Liang, Jianlian Deng, Tian Luo, Huijuan Luo, Fuqiang Li, Kui Wu, Cong Lin

“…Further examination of the gene set related to those peaks revealed that the comprising genes, such as KRT19, B3GNT3, CLDN7 and CLDN3 are strongly associated with LUAD development. They are consistent with the important roles of the associated pathways in LUAD oncogenesis induced by smoking, including estrogen response, apical junction and glycolysis pathways. …”
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The Diagnosis and Management of Patients With Findings Consistent With a Breast Implant Associated–Somatic Symptom Disorder (BIA-SSD) by Stephen D. Bresnick, MD, Kate Faasse, PhD, Patricia McGuire, MD

“…Findings from the current literature combined with both surgical and psychological therapeutic principles were used to develop methods for diagnosing and managing patients with BIA-SSD. Results:. Algorithms for the diagnosis of SSD associated with breast implants, as well as treatment options, are presented so that plastic surgeons can identify, counsel, diagnose, and offer treatment to patients with BII and findings consistent with BIA-SSD. …”
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ERBB3-related gene PBX1 is associated with prognosis in patients with HER2-positive breast cancer by Shufen Mo, Haiming Zhong, Weiping Dai, Yuanyuan Li, Bin Qi, Taidong Li, Yongguang Cai

“…Conclusion PBX1, IGHM and CXCL13 are associated with the expression level of the ERBB3 and are prognostic markers for HER2-positive in BC, which may play an important role in the development and progression of BC.…”
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