Combining single-cell analysis and molecular docking techniques to construct a prognostic model for colon adenocarcinoma and uncovering inhibin subunit βb as a novel therapeutic ta... by Qinqing Wu, Qinqing Wu, Lu Ye, Yuwei Wu, Mengyu Zhao, Mengyu Zhao, Jiaxin Lu, Yanping Yu, Yanping Yu, Yixiao Niu, Yixiao Niu, Luxiao Zhang, Peijun Zuo, Peijun Zuo

“…We also investigated the roles and interactions of these genes in the tumor microenvironment by analyzing single-cell RNA sequencing data. Additionally, we employed molecular docking techniques to evaluate the potential of inhibin subunit beta B (INHBB) as therapeutic targets and to assess the binding affinity of candidate drugs. …”
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Assessment of prognosis and responsiveness to immunotherapy in colorectal cancer patients based on the level of immune cell infiltration by Kaili Liao, Minqi Zhu, Lei Guo, Zijun Gao, Jinting Cheng, Bing Sun, Yihui Qian, Bingying Lin, Jingyan Zhang, Tingyi Qian, Yixin Jiang, Yanmei Xu, Qionghui Zhong, Xiaozhong Wang

“…ObjectiveTo build a new prognostic risk assessment model based on immune cell co-expression networks for predicting overall survival and evaluating the efficacy of immunotherapy for colon cancer patients.MethodsThe Cancer Genome Atlas (TCGA) database was used to obtain mRNA expression profiling data, clinical information, and somatic mutation data from colorectal cancer patients. …”
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3-methyl-4-nitrophenol disturbs the maternal-to-zygotic transition of early embryos by damaging mitochondrial function and histone modification by Fan Chen, An-Feng Luo, Kai-Xin Pan, Hao Gu, Chang-Fan Zhou, Wei Zeng, Song Liu, Adrian Molenaar, Hong-Yan Ren, Li-Jun Huo, Yan-Zhen Bi

“…SMART-seq2 transcriptome sequencing further confirmed that PNMC treatment disrupted global gene expression in 2-cell embryos, with differentially expressed genes enriched in multiple signaling pathways, including those related to autophagy, apoptosis, fertilization, embryonic development, transcription, and mRNA processing. Integration of transcriptome data with open databases revealed that both zygotic genome activation genes and maternal factors experienced significant transcript-level disruptions. …”
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miR-129-5p Regulates the Immunomodulatory Functions of Adipose-Derived Stem Cells via Targeting Stat1 Signaling by He-Yang Zhang, Yu-Han Wang, Yan Wang, Yan-Nv Qu, Xiao-Hui Huang, Hui-Xin Yang, Chang-Ming Zhao, Youdi He, Si-Wei Li, Jin Zhou, Changyong Wang, Xiao-Xia Jiang

“…When fludarabine, an inhibitor of Stat1 activation, was added to ASCs with miR-129-5p knockdown, iNOS mRNA and protein levels were significantly reduced. …”
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Fosab, but not fosaa, plays important role in learning and memory in fish—insights from zebrafish gene knockout study by Qiuling Wang, Qiuling Wang, Qiuling Wang, Lixin Zhang, Lixin Zhang, Lixin Zhang, Chenyuan Zhu, Chenyuan Zhu, Chenyuan Zhu, Ke Lu, Ke Lu, Ke Lu, Jiaqi Wu, Jiaqi Wu, Jiaqi Wu, Xu-Fang Liang, Xu-Fang Liang, Xu-Fang Liang

“…The average time to complete the trial in fosab−/− zebrafish was significantly higher than in WT zebrafish. The relative mRNA expression level of c-jun in fosab−/− zebrafish was significantly higher than that in WT zebrafish, while the fosaa−/− zebrafish has no discernible trend. …”
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Single‐Nucleus and Spatial Transcriptome Profiling Delineates the Multicellular Ecosystem in Hepatocellular Carcinoma After Hepatic Arterial Infusion Chemotherapy by YeXing Huang, ZeFeng Du, ZhiCheng Lai, DongSheng Wen, LiChang Huang, MinKe He, ZiChao Wu, HuiFang Li, HanYue OuYang, WenChao Wu, Anna Kan, Ming Shi

“…Here, we collected tumor samples from treatment‐naïve primary and post‐HAIC HCC, and integrated single‐nucleus RNA sequencing with spatial transcriptomics to characterize the tumor ecosystem in the post‐HAIC HCC. …”
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DNGR-1 limits Flt3L-mediated antitumor immunity by restraining tumor-infiltrating type I conventional dendritic cells by Ignacio Melero, Ruth Conde-Garrosa, David Sancho, Santos Mañes, Alfonso R Sanchez-Paulete, Francisco J Cueto, Carlos del Fresno, Paola Brandi, Alexis J. Combes, Elena Hernández-García, Michel Enamorado, Christian P Bromley, Manuel J Gomez, Santiago Zelenay, Salvador Iborra, Matthew F. Krummel

“…To characterize the immune response, we performed flow cytometry and RNA-Seq of tumor-infiltrating cDC1s.Results Here, we found that cross-presentation of tumor antigens in the steady state was DNGR-1-independent. …”
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Ibuprofen reduces inflammation, necroptosis and protects photoreceptors from light-induced retinal degeneration by Ping-Wu Zhang, Zi-He Wan, Weifeng Li, Abhishek Vats, Kunal Mehta, Laura Fan, Lingli Zhou, Sean Li, Gloria Li, Casey J. Keuthan, Cynthia Berlinicke, Cheng Qian, Noriko Esumi, Elia J Duh, Donald J. Zack

“…Twenty-four hour after LD, retinal mRNA expression for the inflammatory-factors tumor necrosis factor (Tnf), interleukin-1 beta (Il1B), and C-C motif chemokine ligand 2 (Ccl2) increased by 10-, 17-, and 533-fold, respectively; in IBU-treated animals, the expression levels of these inflammatory factors were not significantly different from no-LD controls. …”
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The immune checkpoint molecule B7-H4 regulates β-cell mass and insulin secretion by modulating cholesterol metabolism through Stat5 signalling by Fangzhen Xia, Ziteng Zhang, Zhen Qian, Xiaoyu Fang, Junxue Wang, Yan Wang, Guoting Sun, Yuefeng Yu, Ninjian Wang, Junke Zhen, Yan Liu, Yingli Lu

“…AAV2/8-ins2-B7H4 and a control virus were infused via the pancreatic intraduct into high-fat diet (HFD)-treated mice to elucidate the therapeutic effect of B7-H4. RNA sequencing was conducted on primary islets. …”
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The relationship between dietary branched-chain and aromatic amino acids with the regulation of leptin and FTO genes in adipose tissue of patients undergoing abdominal surgery by Farshad Teymoori, Hossein Farhadnejad, Mostafa Norouzzadeh, Mitra Kazemi Jahromi, Niloufar Saber, Ebrahim Mokhtari, Golaleh Asghari, Emad Yuzbashian, Parvin Mirmiran, Alireza Khalaj, Maryam Zarkesh, Mehdi Hedayati, Mohammadreza Vafa

“…Using the quantitative PCR method, leptin and FTO mRNA expression was measured in both visceral and subcutaneous fat tissues. …”
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Influence of injection technique, drug formulation and tumor microenvironment on intratumoral immunotherapy delivery and efficacy by Patrick Hwu, Ravi Murthy, Aung Naing, Sapna P. Patel, Simon Young, Alda Tam, Nina M. Muñoz, Malea Williams, Katherine Dixon, Crystal Dupuis, Amanda McWatters, Rony Avritscher, Soraya Zorro Manrique, Kevin McHugh, David Leach, Jeffrey D. Hartgerink, Punit Prakash, Rahul A. Sheth

“…The influence of varying needle design and hydrogel-based drug delivery on the immune response to a stimulator of interferon genes (STING) agonist was evaluated using flow cytometry and single cell RNA sequencing. We also evaluated the influence of tumor stiffness on drug injection distribution.Results Variations in needle design, specifically with the use of a multiside hole needle, led to approximately threefold improvements in intratumoral drug deposition relative to conventional end-hole needles. …”
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Stratification system with dual human endogenous retroviruses for predicting immunotherapy efficacy in metastatic clear-cell renal cell carcinoma by Li Xu, Stephane Oudard, Catherine Sautes-Fridman, Xiaoping Su, Gabriel G. Malouf, Virginie Verkarre, Salma Kotti, Fangrong Yan, Yann-Alexandre Vano, Wolf Herve Fridman, Cheng-Ming Sun, Xiaofan Lu, Wenxuan Cheng

“…ERV expression was quantified using the ERVmap algorithm from RNA sequencing data. Our primary objective was to correlate ERV expression with progression-free survival, with overall survival and time-to-second-treatment survival as secondary endpoints. …”
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Neobacillus driksii sp. nov. isolated from a Mars 2020 spacecraft assembly facility and genomic potential for lasso peptide production in Neobacillus by Asif Hameed, Francesca McDonagh, Pratyay Sengupta, Georgios Miliotis, Shobhan Karthick Muthamilselvi Sivabalan, Lukasz Szydlowski, Anna Simpson, Nitin Kumar Singh, Punchappady Devasya Rekha, Karthik Raman, Kasthuri Venkateswaran

“…All four strains exhibited high 16S rRNA gene sequence similarity (>99.2%) and low average nucleotide identity (ANI) with Neobacillus niacini NBRC 15566T, delineating new phylogenetic branches within the genus. …”
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Understanding the Molecular Mechanisms of Incomptine A in Treating Non-Hodgkin Lymphoma Associated with U-937 Cells: Bioinformatics Approaches, Part I by Fernando Calzada, Normand García-Hernández, Elihú Bautista, José Manuel Sánchez-López, Miguel Valdes, Claudia Velázquez, Elizabeth Barbosa

“…Gene ontology, Reactome, and KEGG pathway analysis showed that proteins with altered levels may be implicated in several processes, including gene silencing by RNA, oxidative phosphorylation, glycolysis/gluconeogenesis, cytoskeleton organization, and ATP metabolic and energetic processes. …”
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Deeper response predicts better outcomes in high-risk-smoldering-myeloma: results of the I-PRISM phase II clinical trial by Omar Nadeem, Michelle P. Aranha, Robert Redd, Michael Timonian, Sophie Magidson, Elizabeth D. Lightbody, Jean-Baptiste Alberge, Luca Bertamini, Ankit K. Dutta, Habib El-Khoury, Mark Bustoros, Jacob P. Laubach, Giada Bianchi, Elizabeth O’Donnell, Ting Wu, Junko Tsuji, Kenneth C. Anderson, Gad Getz, Lorenzo Trippa, Paul G. Richardson, Romanos Sklavenitis-Pistofidis, Irene M. Ghobrial

“…Exploratory single-cell RNA sequencing linked tumor MHC class I expression to proteasome inhibitor response, and a lower proportion of GZMB+ T cells within clonally expanded CD8+ T cells associated with suboptimal outcomes.…”
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Potential Probiotic Yeasts of the Pichia Genus Isolated from ‘Dadih’, a Traditional Fermented Food of West Sumatra, Indonesia by Tatenda Calvin Chihombori, Apon Zaenal Mustopa, Rika Indri Astuti, Ilma Mutiara, Redoyan Refli, Rifqiyah Nur Umami, Fatimah, Herman Irawan, Nurlaili Ekawati, Joko P Trinugroho, Rizna Akmaliyah, Sheila Chairunnisa, Febriyanti Nur Amani, Baso Manguntungi, Ai Hertati, Jendri Mamangkey

“…Yeasts were isolated using yeast Extract, peptone, and dextrose (YPD) medium, and molecularly identified through 18S-rRNA sequencing. Probiotic potential was assessed by evaluating resistance to acidic pH, bile salts, proteolytic, lipolytic, and hemolytic activities. …”
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Field-based evidence for the prevalence of soil antibiotic resistomes under long-term antibiotic-free fertilization by Yuhao Fu, Fang Hu, Fang Wang, Min Xu, Zhongjun Jia, Wulf Amelung, Zhi Mei, Xiaozeng Han, Marko Virta, Xin Jiang, James M. Tiedje

“…Long-term fertilization slightly impacts the diversity of antibiotic resistomes, with 85.5 % of total ARGs and mobile genetic elements (MGEs) being common across all treatment types, while significantly increasing their abundances from 0.68 to a maximum of 0.90 copies/16S rRNA. The rise in ARG abundances was less pronounced when using antibiotic-free manure compared to chemical fertilizer, particularly for Rank Ⅱ ARGs. …”
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Bees on the run: Nosema spp. (Microsporidia) in Apis mellifera and related products, Italy by Giovanni Sgroi, Luigi Jacopo D’Auria, Luigi Jacopo D’Auria, Maria Gabriella Lucibelli, Andrea Mancusi, Yolande Thérèsa Rose Proroga, Mauro Esposito, Mauro Esposito, Simona Rea, Daniel Signorelli, Federica Gargano, Nicola D’Alessio, Ranju Ravindran Santhakumari Manoj, Peyman Khademi, Giuseppe Rofrano, Giuseppe Rofrano

“…DNA by specific PCR protocols targeting the 16S rRNA gene. Signs/symptoms of nosemosis were monitored and collected by the cooperation of beekeepers.ResultsOut of 10 apiaries, 6 (i.e., 60%, 95% CI: 31.3–83.2) tested positive for at least one sample to Nosema spp. …”
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Exploring the composition of placental microbiome and its potential origin in preterm birth by Marwa Saadaoui, Mohamed Nadhir Djekidel, Selvasankar Murugesan, Manoj Kumar, Duaa Elhag, Parul Singh, Basirudeen Syed Ahamed Kabeer, Basirudeen Syed Ahamed Kabeer, Alexandra Katharina Marr, Tomoshige Kino, Tobias Brummaier, Rose McGready, Rose McGready, François Nosten, François Nosten, Damien Chaussabel, Annalisa Terranegra, Souhaila Al Khodor

“…Additionally, it’s unclear whether the placental microbiome differs between healthy pregnancies and those with complications like preterm birth (PTB), which remains a leading cause of neonatal morbidity and mortality worldwide.MethodsIn this study, we performed 16S rRNA gene sequencing to investigate the composition of the oral and placental microbiome in samples collected from 18 women who experienced PTB and 36 matched controls who delivered at term (TB), all of whom were part of the Molecular Signature in Pregnancy (MSP) study. …”
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Folic acid alleviates the negative effects of dexamethasone induced stress on production performance in Hyline Brown laying hens by Xi Sun, Chaohui Wang, Sijing Li, Xiaoying Liu, Yun Li, Yumeng Wang, Yuxin Niu, Zhouzheng Ren, Xin Yang, Xiaojun Yang, Yanli Liu

“…Kyoto Encyclopedia of Genes and Genomes enrichment from the transcriptome and metabolomics showed that the reduced production performance may be due to the disturbance of oocyte production, calcium metabolism, and oxidative stress. Analysis of 16S rRNA gene amplicon sequences revealed the differential microbial composition and potential functional changes among the different groups. …”
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