RETRACTED ARTICLE: A prospective diagnostic model for breast cancer utilizing machine learning to examine the molecular immune infiltrate in HSPB6 by Lizhe Wang, Yu Wang, Yueyang Li, Li Zhou, Sihan Liu, Yongyi Cao, Yuzhi Li, Shenting Liu, Jiahui Du, Jin Wang, Ting Zhu

“…The objective of this research was to perform bioinformatics analyses on breast cancer-related datasets to gain a comprehensive understanding of the molecular mechanisms at play and to identify key genes associated with the disease. …”
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TNF-α Enhances the Therapeutic Effects of MenSC-Derived Small Extracellular Vesicles on Inflammatory Bowel Disease through Macrophage Polarization by miR-24-3p by Huikang Xu, Jiamin Fu, Lijun Chen, Sining Zhou, Yangxin Fang, Qi Zhang, Xin Chen, Li Yuan, Yifei Li, Zhenyu Xu, Charlie Xiang

“…MicroRNAs of small EVs derived from MenSCs before and after TNF-α treatment were sequenced, and the differential microRNAs were analyzed by bioinformatics. The small EVs secreted by TNF-α-stimulating MenSCs were more effective in colonic mice than those secreted directly by MenSCs, as evidenced by the results of histopathology analysis of colonic tissue, immunohistochemistry for tight junction proteins, and enzyme-linked immunosorbent assay (ELISA) for cytokine expression profiles in vivo. …”
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Positional embeddings and zero-shot learning using BERT for molecular-property prediction by Medard Edmund Mswahili, JunHa Hwang, Jagath C. Rajapakse, Kyuri Jo, Young-Seob Jeong

“…The study highlights the robustness of the BERT model in predicting chemical properties and its potential applications in cheminformatics and bioinformatics.…”
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PER3 suppresses tumor metastasis of oral squamous cell carcinoma by promoting HIF-1α degradation by Yaoxu Li, Bing Li, Kai Yang, Lihua Zhu, Hong Tang, Yinpei Huang, Jinhai Deng, Jun Duan

“…Here, we investigated the role and molecular mechanism of PER3 in regulating HIF-1α and metastasis in oral squamous cell carcinoma (OSCC) by using bioinformatics analyses and in vitro and in vivo experiments. …”
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Expanding the Scope of Microvascular Inflammation: Unveiling Its Presence Beyond Antibody-Mediated Rejection Into T-Cell Mediated Contexts by Hilal Varol, Hilal Varol, Anne Wagenmakers, Konrad Hoeft, Konrad Hoeft, Jasper Callemeyn, Jasper Callemeyn, Roos Bodewes, Wichor Bramer, Andrew Stubbs, Andrew Stubbs, Rafael Kramann, Rafael Kramann, Maarten Naesens, Maarten Naesens, Marian C. Clahsen-Van Groningen, Marian C. Clahsen-Van Groningen, Marian C. Clahsen-Van Groningen

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Viral diversity in wild rodents in the regions of Canaã de Carajás and Curionopólis, State of Pará, Brazil by Adriana Freitas Moraes Monteiro, Adriana Freitas Moraes Monteiro, Fábio Silva da Silva, Ana Cecília Ribeiro Cruz, Ana Cecília Ribeiro Cruz, Sandro Patroca da Silva, Alice Louize Nunes Queiroz, Livia Medeiros Neves Casseb, Livia Medeiros Neves Casseb, Livia Carício Martins, Livia Carício Martins, Daniele Barbosa de Almeida Medeiros, Daniele Barbosa de Almeida Medeiros

“…Subsequently, nucleotide sequencing and bioinformatics analyses were conducted on 14 selected samples to characterize the virome. …”
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Physiological arterial pressure improves renal performance during normothermic machine perfusion in a porcine kidney DCD model by Yitian Fang, Gisela Ambagtsheer, Lin Xia, Marian C. Clahsen-van Groningen, Robert C. Minnee, Ron W.F. de Bruin

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Gut Microbiota Composition and Structure of the Ob/Ob and Db/Db Mice by Mingsheng Yang, Yixin Liu, Hengchang Xie, Zhengzheng Wen, Yunxia Zhang, Changjing Wu, Li Huang, Jie Wu, Chensheng Xie, Tao Wang, Weifeng Peng, Shangqi Liu, Long Chen, Xiaomeng Liu

“…The taxa with high abundance in both model mice were identified by bioinformatics analysis. Moreover, the taxa with divergent abundance in one model mice at different ages or in both model mice at the same age were also recognized. …”
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mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms by Barnabé, Christian, Sempéré, Guilhem, Manzanilla, Vincent, Millan, Joel Moo, Amblard-Rambert, Antoine, Waleckx, Etienne

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Adrenomedullin 2 attenuates anxiety-like behaviors by increasing IGF-II in amygdala and re-establishing blood–brain barrier by Denian Wang, Zhi Yang, Pengfei Wu, Qingyan Li, Chunyan Yu, Ying Yang, Yuefan Du, Mengwei Jiang, Junpeng Ma

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Investigating the potential immunomodulatory effects of commercial oral probiotic supplements on equine gastrointestinal tract barrier function by Agnieszka Żak-Bochenek, Paulina Żebrowska-Różańska, Joanna Bajzert, Łukasz Łaczmański, Bogumiła Szponar, Natalia Siwińska, Klaudia Gładysz, Katarzyna Sikorska, Anna Chełmońska-Soyta

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Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability by Amira M. Mahfouz, Walaa A. Eraqi, Hala Nour El Din El Hifnawi, Alaa El Din Shawky, Reham Samir, Mohamed A. Ramadan

“…Conclusions For the detection of single-nucleotide polymorphisms (SNPs) and the identification of all variants (SNPs, insertions, and deletions) in our isolates, the Variation Analysis Service tool available in the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) was used. Compared to the susceptible isolates, the AgNPs-resistant isolates St.L_R.Ag and KP_R.Ag had unique mutations in specific efflux pump systems, stress response, outer membrane proteins, and permeases. …”
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A Pilot Study of Exosome Proteomic Profiling Reveals Dysregulated Metabolic Pathways in Endometrial Cancer by Feras Kharrat, Valeria Capaci, Andrea Conti, Valentina Golino, Pietro Campiglia, Nour Balasan, Michelangelo Aloisio, Danilo Licastro, Lorenzo Monasta, Federica Caponneto, Antonio Paolo Beltrami, Federico Romano, Giovanni di Lorenzo, Giuseppe Ricci, Blendi Ura

“…After quantification and statistical analysis, we identified 373 significantly (<i>p</i> < 0.05) dysregulated proteins involved in neutrophil and platelet degranulation pathways. A more detailed bioinformatics analysis revealed 61 dysregulated enzymes related to metabolic and catabolic pathways linked to tumor invasion. …”
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Unraveling the pathogenesis of Barrett’s esophagus and esophageal adenocarcinoma: the “omics” era by Alberto Barchi, Giuseppe Dell’Anna, Giuseppe Dell’Anna, Luca Massimino, Luca Massimino, Francesco Vito Mandarino, Edoardo Vespa, Edi Viale, Sandro Passaretti, Vito Annese, Vito Annese, Alberto Malesci, Alberto Malesci, Silvio Danese, Silvio Danese, Federica Ungaro

“…Genomics and transcriptomics studies, implemented with the most advanced bioinformatics technologies, have brought to light many new risk loci and genomic alterations connected to BE and its progression to EAC, further exploring the complex pathogenesis of the disease. …”
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Synergetic effects of H2O2 concentration and pH value on corrosion behavior of biomolecular coatings on 3D-printed porous low elastic modulus titanium alloy scaffolds under equilib... by Jia-Yi Wen, Her-Hsiung Huang

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Machine learning prediction of anxiety symptoms in social anxiety disorder: utilizing multimodal data from virtual reality sessions by Jin-Hyun Park, Yu-Bin Shin, Dooyoung Jung, Ji-Won Hur, Seung Pil Pack, Heon-Jeong Lee, Hwamin Lee, Chul-Hyun Cho, Chul-Hyun Cho

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MicroRNA-26b inhibits cardiac remodeling after myocardial infarction by targeting ring finger protein 6 expression by Chun-Mei Tang, Qiang Su, Hai-Xia Zhao, He-Huan Sui, Jing Liang, Li-Sha Zhu, Si-Yun Yang, Tao Liu

“…Consequently, miR-26b was identified to target RNF6 using dual-luciferase reporter assay and bioinformatics prediction. Furthermore, rats injected with a lentiviral vector expressing miR-26b mimic and/or RNF6 were used to evaluate the role of miR-26b and RNF6 in regulating cardiac function, infarct size, and cardiomyocyte apoptosis. …”
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A Case Study Identified a New Mutation in the TTN Gene for Inherited Hypertrophic Cardiomyopathy by Dong J, Liu M, Chen Q, Zha L

“…Candidate variants obtained by WES were verified using Sanger sequencing, pathogenic mutation screening was conducted among family members, and the mutations were systematically analyzed using bioinformatics.Results: WES revealed a novel heterozygous missense mutation, c.20233 C>T (p.R6745C), located in exon 80 of the HCM-related gene TTN, which may be a pathogenic mutation in the family. …”
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Ddx21 mutant peptide is an effective neoantigen in prophylactic lung cancer vaccines and activates long-term anti-tumor immunity by Zhe Zhang, Yimeng Xia, Yimeng Xia, Zhihong Wang, Yaxing Sun, Dan Pu, Yijia He, Ruixian Liu, Yanru Zhang, Yan Liu, Junzhi Yu, Shiyang Ning, Baisui Feng, Yaohe Wang, Na Wang

“…MethodsTo investigate the fundamental reason for the difference between KPL 160302S and KPL 160424S vaccines, we employed bioinformatics methods and immune related experiments to explore the effects and mechanisms of the screened neoantigens. …”
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RBM47 promotes cell proliferation and immune evasion by upregulating PDIA6: a novel mechanism of pancreatic cancer progression by Yihui Ma, Enjie Liu, Huijie Fan, Chenfei Li, Pei Huang, Meiying Cui, Zhengyang Wang, Jing Zhou, Kuisheng Chen

“…Therefore, we supposed that RBM47 might affect PC progression by regulating PDIA6. Methods Bioinformatics analysis was performed to screen the candidate gene affecting PC progression using public databases. …”
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