The expression landscape and clinical significance of methyltransferase-like 17 in human cancer and hepatocellular carcinoma: a pan-cancer analysis using multiple databases by Yezhou Ding, Mingyang Feng, Wanqing Chi, Xiaoyin Wang, Baoyan An, Kehui Liu, Shike Lou, Xiaolin Wang, Hui Wang

“…First, we comprehensively analyzed RNA-seq data from the HPA database of 25 human tissues. An array of bioinformatics methods was employed to explore the potential oncogenic roles of METTL17, including analyzing its related prognosis, mutation, landscapes, tumor stemness index, immune cell infiltration, and other factors among different tumors. …”
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CDK9 Expression Shows Role as a Potential Prognostic Biomarker in Breast Cancer Patients Who Fail to Achieve Pathologic Complete Response after Neoadjuvant Chemotherapy by Ashley J. Schlafstein, Allison E. Withers, Soumon Rudra, Diana Danelia, Jeffrey M. Switchenko, Donna Mister, Saul Harari, Hui Zhang, Waaqo Daddacha, Shahrzad Ehdaivand, Xiaoxian Li, Mylin A. Torres, David S. Yu

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Comprehensive analysis of full genome sequence and Bd-milRNA/target mRNAs to discover the mechanism of hypovirulence in Botryosphaeria dothidea strains on pear infection with BdCV1... by Wangcheng Hu, Hui Luo, Yuekun Yang, Qiong Wang, Ni Hong, Guoping Wang, Aiming Wang, Liping Wang

“…B. dothidea was predicted to express 3833 secreted proteins. In bioinformatics analysis, 351 CAZy members, 552 transporters, 128 kinases, and 1096 proteins associated with plant-host interaction (PHI) were identified. …”
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Effect of miR-144-3p-Targeted Regulation of PTEN on Proliferation, Apoptosis, and Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells under Stretch by Shiyong Ling, Xi Luo, Bo Lv, Hua Wang, Mengzhi Xie, Kai Huang, Jingchuan Sun

“…Real-time quantitative reverse transcription PCR (qRT-PCR) was used to detect the expression of miR-144-3p and PTEN in the two groups of cells after osteogenic differentiation. Bioinformatics website and dual luciferase reporter were used to detect the relationship between miR-144-3p and PTEN. …”
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Genomic Characterization of Carbapenemase-Producing Enterobacteriaceae from Clinical and Epidemiological Human Samples by Alexander Tristancho-Baró, Laura Eva Franco-Fobe, Monica Pilar Ariza, Ana Milagro, Ana Isabel López-Calleja, Blanca Fortuño, Concepción López, Miriam Latorre-Millán, Laura Clusa, Rosa Martínez, Carmen Torres, Antonio Rezusta

“…De novo assembly was used to generate draft genomes in order to determine their complete taxonomic classification, resistome, plasmidome, sequence type (ST), core–genome multilocus sequence typing (cgMLST), and phylogenetic relationships using a suite of bioinformatics tools and in-house scripts. <b>Results</b>: Between 2021 and 2023, 0.4% out of 38,145 Enterobacteriaceae isolates were CPE. …”
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Candidate SNP markers of changes in the expression levels of the human <i>SCN9A</i> gene as a hub gene for pain generation, perception, response and anesthesia by P. A. Dotsenko, K. A. Zolotareva, R. A. Ivanov, I. V. Chadaeva, N. L. Podkolodnyy, V. A. Ivanisenko, P. S. Demenkov, S. A. Lashin, M. P. Ponomarenko

“…In this work, we for the first time performed a comprehensive bioinformatics analysis of 568 human genes that, according to the NCBI Gene database as on September 15, 2024, were associated with pain generation, perception and anesthesia. …”
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The Effect of Diabetes-Associated Autoantigens on Cell Processes in Human PBMCs and Their Relevance to Autoimmune Diabetes Development by Jana Vcelakova, Radek Blatny, Zbynek Halbhuber, Michal Kolar, Ales Neuwirth, Lenka Petruzelkova, Tereza Ulmannova, Stanislava Kolouskova, Zdenek Sumnik, Pavlina Pithova, Maria Krivjanska, Dominik Filipp, Katerina Stechova

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The PHD transcription factor Cti6 is involved in the fungal colonization and aflatoxin B1 biological synthesis of Aspergillus flavus by Zhang Mengjuan, Lin Guanglan, Pan Xiaohua, Song Weitao, Tan Can, Chen Xuan, Yang Yanling, Zhuang Zhenhong

“…Crops models analysis showed that A. flavus Cti6 plays vital role in colonization and the production of AFB1 on the host grains mainly via PHD domain. Bioinformatics analysis showed Cti6 is conservative in Aspergillus spp., and mCherry mediated subcellular localization showed that most Cti6 accumulated in the nuclei, which reflected that Cti6 performed its important biological function in the nuclei in Aspergillus spp.. …”
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High trophic similarity between non-native common carp and gibel carp in Turkish freshwaters: Implications for management by Sadi Aksu, Özgür Emiroğlu, Paride Balzani, J. Robert Britton, Esengül Köse, Irmak Kurtul, Sercan Başkurt, Oğuzcan Mol, Emre Çınar, Phillip J. Haubrock, Pinar Oztopcu-Vatan, Ali Serhan Tarkan

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UBE2T/CDC42/CD276 signaling axis mediates brain metastasis of triple-negative breast cancer via lysosomal autophagy by Lin Li, Rong Fu, Yan Chen, Jin Yao, Xiaobing Jiang, Tao Liang, Jun jun Li, Qian zhi Chen, Liang Liang Shi, Ming Xing Xie, Xin Wei Qiao, Qi Hong Cheng, Min Jie Wang

“…Here, we used public databases and bioinformatics analysis as well as clinical samples from different cohorts to investigate the interrelationship between UBE2T/CDC42/CD276. …”
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Protocol for a randomised ‘screen-and-treat’ Helicobacter pylori eradication trial in 14–18-years-old adolescents residing in three regions of Chile: effectiveness and microbiologi... by Ximena Aguilera, Camila Cabrera, Sergio George, Yalda Lucero, Beatriz Zabala Torres, Lilian Fernández, Nora Mamani, Anne Lagomarcino, Miguel O'Ryan

“…The gut microbiome will be characterised by amplifying and sequencing the 16S rRNA gene from stool samples, followed by bioinformatics analysis.Ethics and dissemination Approved by the Human Research Ethics Committee at the Faculty of Medicine, University of Chile (073–2022). …”
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Mathematical modeling in autoimmune diseases: from theory to clinical application by Yaroslav Ugolkov, Yaroslav Ugolkov, Yaroslav Ugolkov, Antonina Nikitich, Antonina Nikitich, Cristina Leon, Gabriel Helmlinger, Kirill Peskov, Kirill Peskov, Kirill Peskov, Kirill Peskov, Victor Sokolov, Victor Sokolov, Alina Volkova, Alina Volkova

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Overcoming beta-lactam resistance in Pseudomonas aeruginosa by targeting metallo-beta-lactamase VIM-1: a one-microsecond molecular dynamics simulation study by Mohammed Salleh M. Ardawi, Samar A. Badreddine, Muhammad Yasir, Muhammad Yasir, Aiah M. Khateb, Aiah M. Khateb, Safaa A. Turkistani, Ahmed Afandi, Samah O. Noor, Adhari Alselmi, Adhari Alselmi, Vivek Dhar Dwivedi, Vivek Dhar Dwivedi, Esam I. Azhar, Esam I. Azhar

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Circular RNA circBNC2 inhibits tumorigenesis by modulating ferroptosis and acts as a nanotherapeutic target in prostate cancer by Xiang Pan, Kailai Chen, Wei Gao, Meiqi Xu, Fanlong Meng, Mengyuan Wu, Zi Qi Wang, Yun Qi Li, Wanhai Xu, Manjie Zhang, Yakun Luo

“…Results We identified a novel tumor-suppressive circRNA, circBNC2, in human PCa, CRPC and NEPC samples via bioinformatic analysis. CircBNC2 expression was significantly downregulated in PCa tissues and PCa cell lines. …”
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Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from companion animals and human infections in Europe by Adrien Biguenet, Benoit Valot, Farid El Garch, Xavier Bertrand, Didier Hocquet

“…The aim of this study was to compare the genomes of third-generation cephalosporin-resistant (3GC-R) Escherichia coli responsible for human and pet infections in Europe.Whole-genome sequencing data from 3GC-R E. coli isolated from clinical samples of humans, dogs and cats, and published in eight European studies were re-analyzed using bioinformatics tools. The acquired genes responsible for 3GC-R were identified. …”
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Sugarcane: an unexpected habitat for black yeasts in Chaetothyriales by Flávia de F. Costa, Rafael S. C. de Souza, Morgana F. Voidaleski, Renata R. Gomes, Guilherme F. Reis, Bruna J. F. de S. Lima, Giovanna Z. Candido, Marlon R. Geraldo, Jade M. B. Soares, Gabriela X. Schneider, Edvaldo da S. Trindade, Israel H. Bini, Leandro F. Moreno, Amanda Bombassaro, Flávio Queiroz-Telles, Roberto T. Raittz, Yu Quan, Paulo Arruda, Derlene Attili-Angelis, Sybren de Hoog, Vania A. Vicente

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Erroneous Classification and Coding as a Limitation for Big Data Analyses: Causes and Impacts Illustrated by the Diagnosis of Clavicle Injuries by Robert Raché, Lara-Sophie Claudé, Marcus Vollmer, Lyubomir Haralambiev, Denis Gümbel, Axel Ekkernkamp, Martin Jordan, Stefan Schulz-Drost, Mustafa Sinan Bakir

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Activated CD27+PD-1+ CD8 T Cells and CD4 T Regulatory Cells Dominate the Tumor Microenvironment in Refractory Celiac Disease Type II by Tessa Dieckman, Mette Schreurs, Ciska Lindelauf, Ahmed Mahfouz, Caroline R. Meijer, Louise Pigeaud, Vincent van Unen, Gerd Bouma, Frits Koning

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Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorecta... by Romy Walker, Jihoon E. Joo, Khalid Mahmood, Mark Clendenning, Julia Como, Susan G. Preston, Sharelle Joseland, Bernard J. Pope, Ana B.D. Medeiros, Brenely V. Murillo, Nicholas Pachter, Kevin Sweet, Allan D. Spigelman, Alexandra Groves, Margaret Gleeson, Krzysztof Bernatowicz, Nicola Poplawski, Lesley Andrews, Emma Healey, Steven Gallinger, Robert C. Grant, Aung K. Win, John L. Hopper, Mark A. Jenkins, Giovana T. Torrezan, Christophe Rosty, Finlay A. Macrae, Ingrid M. Winship, Daniel D. Buchanan, Peter Georgeson

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Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs by Michel, Elisa, Masson, Estelle, Bubbendorf, Sandrine, Lapicque, Léocadie, Nidelet, Thibault, Segond, Diego, Guézenec, Stéphane, Marlin, Thérèse, Devillers, Hugo, Rué, Olivier, Onno, Bernard, Legrand, Judith, Sicard, Delphine

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