The Gut Microbiota and Its Relevance to Peripheral Lymphocyte Subpopulations and Cytokines in Patients with Rheumatoid Arthritis by Yuan Li, Sheng-Xiao Zhang, Xu-Fang Yin, Ming-Xing Zhang, Jun Qiao, Xiao-Hong Xin, Min-Jing Chang, Chong Gao, Ya-Feng Li, Xiao-Feng Li

“…Alpha and beta diversity of gut microbiome were explored by bioinformatics analysis. Spearman rank correlation test was used to explore the relationships between gut microbiome and lymphocyte subsets as well as serum cytokines. …”
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Curdione combined with borneol treats bacterial mixed HPV infection by regulating the crosstalk among immune cells by Jingwei Liu, Jingwei Liu, Tong Shu, Yiheng Mu, Wanlin Zheng, Xiaohuan Lu, Xiaohuan Lu, Hong Tao, Hong Tao

“…This study aims to explore the molecular mechanisms of curdione and borneol in treating HPV infection.MethodsWe conducted a retrospective cohort analysis of medical records from a single-center study involving 205 HPV patients, focusing on the correlation between HPV clearance and co-infection with other pathogens, confirming the efficacy of Baofukang suppository. Bioinformatics and network pharmacology approaches were employed to identify therapeutic targets of Baofukang suppository for BV/HPV co-infections. qRT-PCR, Western blot, immunofluorescence staining, and flow cytometry were utilized to validate the therapeutic targets of curdione and borneol, along with the associated immune molecular changes. …”
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Unveiling the role of melatonin‐related gene CSNK1D in osteoclastogenesis and its implications for osteoporosis treatment by Jiewen Zhang, Shaobo Wu, Fangze Xing, Ning Kong, Yiwei Zhao, Xudong Duan, Yiyang Li, Kunzheng Wang, Run Tian, Pei Yang

“…This study aimed to identify the relationship between melatonin‐related genes and OP through bioinformatics methods and to verify it experimentally.We analysed microarray data from the GSE35959 dataset, identifying differentially expressed genes in OP patients. …”
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Predicting the Most Deleterious Missense Nonsynonymous Single-Nucleotide Polymorphisms of Hennekam Syndrome-Causing CCBE1 Gene, In Silico Analysis by Khyber Shinwari, Liu Guojun, Svetlana S. Deryabina, Mikhail A. Bolkov, Irina A. Tuzankina, Valery A. Chereshnev

“…Hennekam lymphangiectasia-lymphedema syndrome has been linked to single-nucleotide polymorphisms in the CCBE1 (collagen and calcium-binding EGF domains 1) gene. Several bioinformatics methods were used to find the most dangerous nsSNPs that could affect CCBE1 structure and function. …”
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RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…The relative role of NR3C2 were further predicted through bioinformatics methods and receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of NR3C2 in colon cancer. …”
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Increased TSPO alleviates neuropathic pain by preventing pyroptosis via the AMPK-PGC-1α pathway by Baolong Li, Kaiming Yu, Xiongyao Zhou, Jialu Sun, Le Qi, Weiye Li, Tuo Yang, Weizhen Li, Ningning Wang, Xiaosong Gu, Shusen Cui, Rangjuan Cao

“…Abstract Neuropathic pain poses a significant clinical challenge, largely due to the incomplete understanding of its molecular mechanisms, particularly the role of mitochondrial dysfunction. Bioinformatics analysis revealed that pyroptosis and inflammatory responses induced by spared nerve injury (SNI) in the spinal dorsal horn play a critical role in the initiation and persistence of neuropathic pain. …”
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Genes related to neural tube defects and glioblastoma by Rui Cao, Yurong Liu, Kaixin Wei, Ning Jin, Yuxiang Liang, Ruifang Ao, Weiwei Pan, Xiang Wang, Xiuwei Wang, Li Zhang, Jun Xie

“…To obtain genes related to both NTDs and GBM, as well as small molecule drugs with potential clinical application value. We performed bioinformatics analysis on transcriptome sequencing data of retinoic acid (RA)-induced NTDs mice, human NTDs samples and GBM samples. …”
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Intelligent Electrochemical Sensing: A New Frontier in On-the-Fly Coffee Quality Assessment by Simone Grasso, Maria Vittoria Di Loreto, Alessandro Zompanti, Davide Ciarrocchi, Laura De Gara, Giorgio Pennazza, Luca Vollero, Marco Santonico

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Pathogenicity and Whole Genome Sequence Analysis of a Pseudorabies Virus Strain FJ-2012 Isolated from Fujian, Southern China by Xue-min Wu, Qiu-yong Chen, Ru-jing Chen, Yong-liang Che, Long-bai Wang, Chen-yan Wang, Shan Yan, Yu-tao Liu, Jin-sheng Xiu, Lun-jiang Zhou

“…We then conducted a few downstream bioinformatics analyses including phylogenetic analysis and pathogenic analysis and used the virus to infect 6 pseudorabies virus-free piglets. …”
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Genomic insights into multidrug-resistant Acinetobacter baumannii strains isolated from Dhaka, Bangladesh by Sadia Ferdous, K M Shayerul Abedin Shayer, Afia Anjum, Sabbir R. Shuvo, Ishrat Jabeen, Kristi Paul Hridi, A.K.M. Imrul Hassan, Md Imran Khan, Mohammad Fazle Alam Rabbi, Mahmud Hossain, Kazi Nadim Hasan, Sohidul Islam

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Unraveling nitrogen metabolism, cold and stress adaptation in polar Bosea sp. PAMC26642 through comparative genome analysis by Anamika Khanal, Anamika Khanal, So-Ra Han, So-Ra Han, So-Ra Han, Jun Hyuck Lee, Tae-Jin Oh, Tae-Jin Oh, Tae-Jin Oh, Tae-Jin Oh

“…Comparative genomic analysis was performed using various bioinformatics tools to compare Bosea sp. PAMC26642 with other strains of the same genus, emphasizing nitrogen metabolism and stress adaptability. …”
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Single nucleotide polymorphism rs110861313 in the intergenic region of chromosome 23 is associated with the development of leukosis in the Russian Black Pied cattle by R. B. Aitnazarov, E. V. Ignatieva, T. A. Agarkova, N. G. Dvoeglazov, N. A. Osipova, V. V. Khramtsov, N. S. Yudin

“…In this case, asymptomatic virus carriers can be considered a more suitable control than healthy animals that have not been in contact with the virus. According to bioinformatics analysis, resistance to BLV can be due to the presence of the transcription factor FOXM1 binding site in the region of rs110861313. …”
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The genome sequence of the Montseny horsehair worm, Gordionus montsenyensis sp. nov., a key resource to investigate Ecdysozoa evolution by Eleftheriadi, Klara, Guiglielmoni, Nadège, Salces-Ortiz, Judit, Vargas-Chavez, Carlos, Martínez-Redondo, Gemma I., Gut, Marta, Flot, Jean-François, Schmidt-Rhaesa, Andreas, Fernández, Rosa

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LURAP1L-AS1 long noncoding RNA promotes breast cancer progression and associates with poor prognosis by Radhakrishnan Vishnubalaji, Dania Awata, Nehad M. Alajez

“…RNA sequencing of LURAP1L-AS1-depleted cells revealed dysregulation of pathways related to cell proliferation, apoptosis, migration, and RNA processing. Bioinformatics analysis predicted LURAP1L-AS1 to function as a competitive endogenous RNA (ceRNA), sponging key microRNAs, such as miR-7a-5p, miR-101-3p, miR-181a-5p, and miR-27a-3p, thereby modulating oncogenes including EZH2, MCL1, and KRAS, which are linked to increased cancer cell survival, proliferation, and metastasis.In addition to its role in TNBC, correlation analysis using breast cancer patient datasets revealed a significant association between LURAP1L-AS1 and ESR1 expression, suggesting its broader impact across breast cancer subtypes. …”
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Comprehensive analysis of α2,3-sialyltransferases as prognostic biomarkers and immunotherapy targets in kidney renal clear cell carcinoma by Yuli Jian, Kangkang Yang, Jinjing Li, Ling Tang, Guang Zeng, Xiaoxin Sun, Xiao Yu, Abdullah Al-danakh, Qiwei Chen, Deyong Yang, Shujing Wang

“…In the study, through systematic bioinformatics analysis and experimental verification, we demonstrated that ST3Gal5 expression was elevated in tumor tissues of KIRC patients, correlating with poor prognosis, and ST3Gal1 was downregulated and associated with a better prognosis. …”
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<i>Botrytis cinerea</i> PMT4 Is Involved in <i>O</i>-Glycosylation, Cell Wall Organization, Membrane Integrity, and Virulence by Verónica Plaza, Alice Pasten, Luz A. López-Ramírez, Héctor M. Mora-Montes, Julia Rubio-Astudillo, Evelyn Silva-Moreno, Luis Castillo

“…The <i>PMT</i> family is grouped into <i>PMT1</i>, <i>PMT2</i>, and <i>PMT4</i> subfamilies. Using bioinformatics analysis within the <i>Botrytis cinerea</i> genome database, an ortholog to <i>Saccharomyces cerevisiae</i> Pmt4 and other fungal species was identified. …”
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Collection of microorganisms of ICG SB RAS as a genetic resource for biotechnology by A. V. Bryanskaya, Y. E. Uvarova, A. S. Rozanov, N. M. Slynko, V. N. Shlyakhtun, K. V. Starostin, E. A. Demidov, E. V. Lazareva, O. P. Taran, S. E. Peltek

“…The value of the collection of microorganisms of the FRC ICG SB RAS as a genetic resource for biotechnology and bioengineering is determined not only by the species diversity of its strains, but also by a wide range of their area isolation and by the depth of their characterization using the widest arsenal of both classical and modern methods (including methods of genomics, proteomics, transcriptomics and bioinformatics).…”
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Evaluation of recombinant proteins <i>T. pallidum</i> Тр0163 and Тр0971 as antigens for the diagnosis of syphilis using enzyme immunoassay by Natalia V. Arbuzova, Marina V. Shpilevaya, Georgii L. Katunin, Oleg E. Kuznetsov, Nikita Yu. Nosov, Viсtoria S. Solomka

“…With the deciphering of the T. pallidum genome and the application of bioinformatics and immunoproteomics, many recombinant T. pallidum proteins have emerged that have been evaluated for their diagnostic value, some of which are used as diagnostic antigens in commercial tests. …”
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Integrated analyses uncover new features of atypical memory B cells and novel targets for intervention by Fuli Fan, Shubei Liu, Bin Wang, Xiaojian Song, Wei Wang

“…Functional characterization of AMB was performed with bioinformatics and CyTOF-based phenotyping. Alternation of AMB in systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and Sjögren's syndrome (SjS) was evaluated via bioinformatic approaches. …”
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TGFβ1-Induced Differentiation of Human Bone Marrow-Derived MSCs Is Mediated by Changes to the Actin Cytoskeleton by Mona Elsafadi, Muthurangan Manikandan, Sami Almalki, Mohammad Mobarak, Muhammad Atteya, Zafar Iqbal, Jamil Amjad Hashmi, Sameerah Shaheen, Nehad Alajez, Musaad Alfayez, Moustapha Kassem, Raed Abu Dawud, Amer Mahmood

“…In total, 1932 genes were upregulated, and 1298 genes were downregulated. Bioinformatics analysis revealed that TGFβl treatment was associated with an enrichment of genes in the skeletal and extracellular matrix categories and the regulation of the actin cytoskeleton. …”
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