Deciphering the therapeutic effects of Xiyanping injection: insights into pulmonary and gut microbiome modulation, SerpinB2/PAI-2 targeting, and alleviation of influenza a virus-in... by Tengwen Liu, Shuping Li, Xuerui Wang, Mingjiang Liu, Yuchen Wang, Jie Ying, Shuwen Zhang, Yan Lin, Ning Wang, Yungjing Bai, Lan Xie, Tengfei Chen, Quansheng Feng, Xiaolong Xu

“…In this study, we established an IAV infection mice model, and utilized 16 S rRNA sequencing, RNA sequencing, protein chips, and molecular docking, to investigate the mechanisms of XYP injection on altering pulmonary and gut microbiota, and identifying its target sites. …”
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A stratified two-stage tumor molecular profiling algorithm to identify clinically actionable molecular alterations in pancreatic cancer☆ by S. Hussung, D. Akhoundova, C. Pistoni, D. Lenggenhager, A. Töpfer, C. Pauli, B. Pestalozzi, C. Britschgi, M. Zoche, M. Rechsteiner, H. Moch, A. Weber, R. Fritsch

“…Stage 1 comprised immunohistochemistry for mismatch repair deficiency and targeted sequencing employing a 33-gene next-generation sequencing panel covering common PC drivers and DNA damage response genes. …”
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Deciphering the generation of heterogeneity in esophageal squamous cell carcinoma metastasis via single-cell multiomics analysis by Kaiwen Sheng, Jun Chen, Ruitang Xu, Haoqiang Sun, Ran Liu, Yongjie Wang, Wenwen Xu, Jiao Guo, Miao Zhang, Shuai Liu, Juan Lei, Yawen Sun, Yang Jia, Dianhao Guo

“…In conjunction, we integrated these data with 55 scRNA-seq datasets, ChIP-seq or CUT&Tag sequencing data, Hi-C sequencing data, bulk RNA-seq data, and bulk ATAC-seq data from ESCC cell lines to dissect the mechanisms underlying the heterogeneity of ESCC and tumor microenvironment (TME). …”
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Treatment Patterns of Follicular Lymphoma in the United States: A Claims Analysis by Scott F. Huntington, Sreevalsa Appukkuttan, Wenyi Wang, Yuxian Du, Sari Hopson, Svetlana Babajanyan

“…**Background:** A consensus is lacking on optimal treatment sequencing for follicular lymphoma (FL), the most common indolent lymphoma. …”
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Genomic, transcriptomic and metabolomic analyses of Amorphophallus albus provides insights into the evolution and resistance to southern blight pathogen by Longfei Duan, Longfei Duan, Jianfeng Qin, Gaoxin Zhou, Chuan Shen, Baofu Qin

“…IntroductionAmorphophallus albus, a perennial herb in the Araceae family, is a valuable cash crop known for its high production of konjac glucomannan and high disease resistance.MethodsIn this study, we present a high-quality, chromosome-scale genome assembly of A. albus using a combination of PacBio HiFi sequencing, DNBSEQ short-read sequencing, and Hi-C technology. …”
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Runaway Train: A Leaky Radiosensitive SCID with Skin Lesions and Multiple Lymphomas by Børre Fevang, Unn Merete Fagerli, Hanne Sorte, Harald Aarset, Håkon Hov, Marit Langmyr, Thomas Morten Keil, Ellen Bjørge, Pål Aukrust, Asbjørg Stray-Pedersen, Tobias Gedde-Dahl

“…The case underscores the importance of next-generation sequencing in the diagnosis of patients with suspected severe immunodeficiency.…”
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HIF-3α-Induced miR-630 Expression Promotes Cancer Hallmarks in Cervical Cancer Cells by Forming a Positive Feedback Loop by Qiaohui Gao, Zhenghua Ren, Shengyuan Jiao, Juan Guo, Xia Miao, Jin Wang, Junye Liu

“…Methods. We conducted RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) experiments to investigate the targets of HIF-3α or miR-630. …”
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Identification of Houge type of X-linked syndromic mental retardation caused by CNKSR2 truncated variants by Si-Hua Chang, Jie-Yuan Jin, Yi-Qiao Hu, Run-Yan Wang, Rong Xiang, Xia Wang

“…Methods Two Chinese MRXSHG families were recruited, and their genetic causes were investigated using whole-exome sequencing (WES), Sanger sequencing, and bioinformatics analysis. …”
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Health benefits of Grifola frondosa polysaccharide on intestinal microbiota in type 2 diabetic mice by Xiaoxiang Gao, Dan Liu, Luying Gao, Yuezhen Ouyang, Yuxi Wen, Chao Ai, Yuqing Chen, Chao Zhao

“…The changes of microbiota in faeces of the diabetic mice upon high fat diet were determined and the V3 region of the 16S rRNA was sequenced by Illumina MiSeq high-throughput sequencing platform. …”
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Soil Alveolata diversity in the undisturbed steppe and wheat agrocenoses under different tillage by N. B. Naumova, P. A. Barsukov, O. A. Baturina, O. A. Rusalimova, M. R. Kabilov

“…Microeukaryotes are vital for maintaining soil quality and ecosystem functioning, however, their communities are less studied than bacterial and fungal ones, especially by high throughput sequencing techniques. Alveolates are important members of soil microbial communities, being consumers and/or prey for other microorganisms. …”
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Genotype B of deformed wing virus and related recombinant viruses become dominant in European honey bee colonies by Fabrice Sircoulomb, Eric Dubois, Frank Schurr, Pierrick Lucas, Marina Meixner, Alicia Bertolotti, Yannick Blanchard, Richard Thiéry

“…Chimeric sequencing reads were used to locate the recombinant junctions along the DWV genome. …”
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Uncovering glycolysis-driven molecular subtypes in diabetic nephropathy: a WGCNA and machine learning approach for diagnostic precision by Chenglong Fan, Guanglin Yang, Cheng Li, Jiwen Cheng, Shaohua Chen, Hua Mi

“…Finally, the expression patterns of these hub genes were validated using single-cell sequencing data and quantitative real-time polymerase chain reaction (qRT-PCR). …”
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Impact of Notch3 Activation on Aortic Aneurysm Development in Marfan Syndrome by Kathryn Jespersen, Chenxin Li, Rishi Batra, Christopher A. Stephenson, Paul Harding, Kylie Sestak, Ryan T. Foley, Harrison Greene, Trevor Meisinger, Jason R. Cook, B. Timothy Baxter, Wanfen Xiong

“…Results. The murine RNA-sequencing data were validated with mouse and human MFS aortic tissue, demonstrating elevated Notch3 activation in MFS. …”
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An Extremely Rare SRD5A2 Gene c.485A>C Mutation in a Compound Heterozygous Newborn with Disorders of Sex Development First Identified in Vietnam by Phan Tuong Quynh Le, Thanh Nha Uyen Le, Thi Thanh Binh Nguyen, Minh Thao Nguyen, Thi Minh Thi Ha

“…This compound heterozygous mutation was first detected by next-generation sequencing. By Sanger sequencing, we confirmed that the c.485A>C mutation was maternal inherited, whereas the c.680G>A mutation was paternal inherited. …”
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Novel MFSD8 Variants in a Chinese Family with Nonsyndromic Macular Dystrophy by Qin Xiang, Yanna Cao, Hongbo Xu, Zhijian Yang, Liang Tang, Ju Xiang, Jianming Li, Hao Deng, Lamei Yuan

“…Ophthalmic examinations were performed, and genomic DNA was extracted from available family members. Whole exome sequencing of two members (the proband and her unaffected mother) and Sanger sequencing in available family members were performed to screen potential pathogenic variants. …”
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scSMD: a deep learning method for accurate clustering of single cells based on auto-encoder by Xiaoxu Cui, Renkai Wu, Yinghao Liu, Peizhan Chen, Qing Chang, Pengchen Liang, Changyu He

“…Abstract Background Single-cell RNA sequencing (scRNA-seq) has transformed biological research by offering new insights into cellular heterogeneity, developmental processes, and disease mechanisms. …”
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Effects of White Quinoa Polysaccharide on Regulation of Glucolipid Metabolism in Type 2 Diabetic Mice by Yanqing ZANG, Yingying CHUANG, Changyuan WANG, Yang CAO

“…The results of 16S rRNA sequencing revealed that the intake of WQP led to an increase in the abundance of the Bacteroidota and a decrease in the Firmicutes in the intestines of diabetic mice. …”
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Efficacy of 0.5% Levofloxacin and 5.0% Povidone-Iodine Eyedrops in Reducing Conjunctival Bacterial Flora: Metagenomic Analysis by Caixia Fan, Baoxia Yang, Yusen Huang

“…In conclusion, the metagenomic analysis using high-throughput sequencing provides a scientific way for evaluating the effectiveness of a disinfection method from the perspective of analyzing the composition and diversity of the conjunctival microbiome. …”
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Discovery of two novel Flavobacterium species with potential for complex polysaccharide degradation by Xu-Dong Lian, Yong Guan, Yue Jiang, Dong-Heui Kwak, Mi-Kyung Lee, Zhun Li

“…Through comprehensive analyses, including 16S rRNA gene sequencing, whole-genome sequencing, and detailed morphological, physiological, and chemotaxonomic characterizations, these strains have been identified as new species within the genus Flavobacterium. …”
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Prevalence and Subtype Analysis of Blastocystis hominis Isolated from Patients in the Northeast of Iran by Mitra Salehi, Jalal Mardaneh, Hamid Reza Niazkar, Mohammadhaasan Minooeianhaghighi, Elahe Arshad, Fateme Soleimani, Alireza Mohammadzadeh

“…Also, PCR was done on the positive samples, and sequencing and phylogenetic analysis were subsequently performed. …”
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