Clinical and molecular analysis of JCPyV and BKPyV infection and associated risk of urothelial carcinoma development in the upper tract by Chun-Nun Chao, Chi-Feng Hung, Wei‑Hong Lai, Chun-Liang Tung, Wan-Yun Yeh, Kai-Wu Yang, Meilin Wang, Ya-Yan Lai, Pei-Lain Chen, Cheng-Huang Shen

“…Nested polymerase chain reaction and DNA sequencing were used to detect viral DNA and genotypes. …”
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Joint fluid multi-omics improves diagnostic confidence during evaluation of children with presumed septic arthritis by Yolanda Peña-López, Naureen G. Tareen, Bo Zhang, Indu Raman, Carlos A. Arana, Chengsong Zhu, Yang Liu, Pratibha Selvakumar, Nicolai S. C. van Oers, Simrat Morris, Lora V. Hooper, Lawson A. B. Copley, Prithvi Raj

“…The combination of 16S DNA sequencing (p = 0.006), cytokine assays (p = 0.009) and autoantibody profiling (p = 0.02) were significantly distinct between those children with and without infections. …”
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A new Lactobacillus gasseri strain HMV18 inhibits the growth of pathogenic bacteria by Xiang Gao, Zixuan Wang, Xiang Li, Xiaoling Zhang, Shengqiang Du, Miaomiao Jia, Dailun Hu, Xianxian Jia, Bin Cong, Yan Zhang, Chunling Ma, Song Zhou, Jun Zhang

“…The new isolate was identified as L. gasseri by the colony morphology, Gram staining, biochemical reactions and confirmed by the 16S rDNA sequencing. The HMV18 strain inhibited the growth of food-borne pathogens such as E. coli, S. aureus and K. oxytoca. …”
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The mutational landscape of ARMC5 in Primary Bilateral Macronodular Adrenal Hyperplasia: an update by Lucas Bouys, Anna Vaczlavik, Isadora P. Cavalcante, Florian Violon, Anne Jouinot, Annabel Berthon, Patricia Vaduva, Stéphanie Espiard, Karine Perlemoine, Peter Kamenicky, Marie-Christine Vantyghem, Antoine Tabarin, Gérald Raverot, Cristina L. Ronchi, Ulrich Dischinger, Martin Reincke, Maria C. Fragoso, Constantine A. Stratakis, Albain Chansavang, Eric Pasmant, Bruno Ragazzon, Jérôme Bertherat, for the COMETE and ENSAT Networks

“…The pathogenicity of ARMC5 variants is established on the basis of their frequency in the general population, in silico predictions, familial segregation and tumor DNA sequencing. Conclusions This is the first extensive review of ARMC5 pathogenic variants. …”
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Exploring the Role of C-C Motif Chemokine Ligand-2 Single Nucleotide Polymorphism in Pulmonary Tuberculosis: A Genetic Association Study from North India by Sanjay K. Biswas, Mayank Mittal, Ekata Sinha, Vandana Singh, Nidhi Arela, Bharat Bajaj, Pramod K. Tiwari, Vishwa M. Katoch, Keshar K. Mohanty

“…The genotyping was carried out in 373 participants with pulmonary TB (PTB) and 248 healthy controls (HCs) for CCL2-2518 A>G and -362 G>C polymorphisms by PCR-RFLP and by melting curve analysis using fluorescence-labeled hybridization fluorescent resonance energy transfer (FRET) probes, respectively, followed by DNA sequencing in a few representative samples. Genotype and allele frequencies were compared by the chi-squared test and crude and Mantel-Haenszel (M-H) odds ratio (OR). …”
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Comprehensive genomic and transcriptomic profiling of pulmonary nodules in synchronous multiple primary lung cancer by Xingsheng Liu, Kun Qian, Lei Su, Xiaoru Tian, Xin Zhao, Tengteng Wang, Li Han, Zhenzhen Li, Peilong Zhang, Ruotian Wang, Baodong Liu, Yuanbo Li, Xiaogang Tan, Yi Zhang

“…Methods We performed targeted DNA sequencing on tumor specimens and conducted bulk RNA transcriptome analysis on 53 multiple nodules originating from 26 lung cancer patients. …”
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Characteristics and spatiotemporal changes in phenotypes and genotypes of extended-spectrum β-lactamases in Escherichia coli isolated from bloodstream infections in China from 2014... by Sayyed Salman, Hao Xu, Yunbo Chen, Jinru Ji, Zhiying Liu, Yonghong Xiao

“…The genetic type was determined using polymerase chain reaction (PCR) followed by DNA sequencing. Results Between 2014 and 2021, the prevalence of ESBL-positive E. coli steadily decreased from 61.2 to 49.6%. …”
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Disproportionate Distribution of HBV Genotypes A and D and the Recombinant Genotype D/E in the High and Low HBV Endemic Regions of Uganda: A Wake-Up Call for Regional Specific HBV... by Hussein Mukasa Kafeero, Dorothy Ndagire, Ponsiano Ocama, Charles Drago Kato, Eddie Wampande, Henry Kajumbula, David Kateete, Abdul Walusansa, Ali Kudamba, Kigozi Edgar, Fred Ashaba Katabazi, Maria Magdalene Namaganda, Jamilu E. Ssenku, Hakim Sendagire

“…Purification of nested PCR products was performed using Purelink PCR product purification kit (Life Technologies, USA). Automated DNA sequencing was performed using BigDye Terminator v3.1 Cycle Sequencing Kit on 3130 Genetic Analyzer (Applied Biosystems, USA). …”
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Enterotype Bacteroides Is Associated with a High Risk in Patients with Diabetes: A Pilot Study by Jiajia Wang, Wenjuan Li, Chuan Wang, Lingshu Wang, Tianyi He, Huiqing Hu, Jia Song, Chen Cui, Jingting Qiao, Li Qing, Lili Li, Nan Zang, Kewei Wang, Chuanlong Wu, Lin Qi, Aixia Ma, Huizhen Zheng, Xinguo Hou, Fuqiang Liu, Li Chen

“…Fecal samples of each subject were also collected and were processed for 16S rDNA sequencing. Multiple logistic regression analysis was used to determine the associations of enterotypes with type 2 diabetes. …”
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Phase II trial of nab-paclitaxel plus ramucirumab in combination with nivolumab for unresectable advanced or recurrent gastric cancer after progression on first-line treatment incl... by Hidekazu Hirano, Naoki Takahashi, Yusuke Amanuma, Nobumi Suzuki, Daisuke Takahari, Takeshi Kawakami, Chie Kudo-Saito, Kengo Nagashima, Narikazu Boku, Ken Kato, Hirokazu Shoji

“…., flow cytometry, DNA sequencing [DNAseq]/RNA sequencing [RNAseq]). Recruitment started in November 2022. …”
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Relationship between mucin gene polymorphisms and different types of gallbladder stones by Gongqing Ren, Yongmao Fan, Ruizi Zhong, Gang Zou, Xiaojun Huang, Yue Zhang

“…We amplified SNP sites by polymerase chain reaction (PCR) using specific primer sets followed by DNA sequencing. Results The frequencies of MUC2 rs2856111 C/T genotype (OR = 3.81, 95%CI: 1.06–13.68) was higher than the control group. …”
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Clinical utility and predictive value of cerebrospinal fluid cell-free DNA profiling in non-small cell lung cancer patients with leptomeningeal metastasis by Sheng-Kai Liang, Wei-Yu Liao, Jin-Yuan Shih, Chia-Lin Hsu, Ching-Yao Yang, Shang-Gin Wu, Yen-Ting Lin, Yueh-Feng Wen, Lun-Che Chen, Yen-Fu Chen, Ya-Fang Chen, Yen-Heng Lin, Chong-Jen Yu

“…Among 25 enrolled patients, 22 (88.0 %) had EGFR mutations, while three (12.0 %) had EML4-ALK fusion, KIF5B-RET fusion, and ERBB2 A775_G776insSVMA. CSF cfDNA sequencing of 27 samples (from 25 patients) all confirmed their original driver mutations. …”
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Oral-Delivery Lactococcus lactis expressing cherry fusion lactoferrin peptides against infection of avian pathogenic Escherichia coli in chickens by Zhuoran Li, Xueying Wang, Dianzhong Zheng, Fuzhen Han, Yue Li, Han Zhou, Jiaxuan Li, Wen Cui, Yanping Jiang, Xiaona Wang, Weichun Xie, Lijie Tang

“…Additionally, 16S rDNA sequencing data revealed that LL-EFLmC was able to restore the intestinal flora that had been disrupted by APEC-O78. …”
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Development and characterization of orthotopic patient-derived xenograft models of peritoneal metastatic mucinous appendiceal adenocarcinoma by I. Ito, V.K. Pattalachinti, A.M.G. Yousef, S. Chowdhury, M.M. Fanaeian, E. Haque, B.B. Gunes, M. Yousef, E.R. Salle, M.A. Zeineddine, S. Ji, R. Li, W. Wang, B.A. Helmink, M.W. Taggart, M.G. White, K.F. Fournier, N.W. Fowlkes, J.P. Shen

“…Comparison of histological, immunohistochemical, and molecular analyses including both RNA and DNA sequencing revealed that the PDX models recreate many of the features of metastatic AAs, but also displayed several differences between paired PDX and human tumors, highlighting the intratumoral heterogeneity of AAs within each patient. …”
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Therapeutic Potential of <i>Cajanus cajan</i> (L.) <i>Millsp</i>. Leaf Extract in Modulating Gut Microbiota and Immune Response for the Treatment of Inflammatory Bowel Disease by Mingzhang Lin, Linghua Piao, Zhendong Zhao, Li Liao, Dayong Wang, Haiwen Zhang, Xiande Liu

“…Subsequently, flow cytometry was employed to analyze the populations of various immune cells within the spleen, thereby assessing the impact of the CCLE on the systemic immune homeostasis of IBD mice. Finally, 16S rDNA sequencing was conducted to examine the composition and relative abundance of gut microbiota across different experimental groups. …”
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Characterization of CO1 and 18S rDNA genes from Indonesian native ornamental shrimp Caridina boehmei cultured in Jakarta by Ekky Ilham Romadhona, Novi Megawati, Handang Widantara, Sutanti Sutanti, Arif Rahman Ardiansyah, Kiki Mariya Dewi, Annisa Fitri Larassagita, Aditia Firman, Moh Risky, Rahmat Rahmat, Ayub Ayub

“…The CO1 sequencing produced fragments consisting of 25.84% adenine, 20.95% cytosine, 19.11% guanine, and 34.10% thymine. The 18S rDNA sequencing produced fragments consisting of 24.47% adenine, 26.05% cytosine, 28.16% guanine, and 21.32% thymine. …”
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Assessing microbial biodiversity in oil palm seedlings using oil palm waste compost mixed media by Siti Suliza Salamat, Mohd Zulkhairi Mohd Yusoff, Mohd Ali Hassan Hassan, Mohd Huzairi Mohd Zainuddin, Yoshihito Shirai, Ahmad Husni Mohd Hanif, Mohd Shahkhirat Norizan, Fatini Mat Arisah, Mohammed Abdillah Ahmad Farid, Toshinari Maeda, Mohd Noor Mat Isa, Mohd Faizal Abu Bakar

“…Method: The study compared microbial biodiversity in soil media with compost amendments by employing DNA sequencing to assess microbial communities. The analysis focused on bacterial species richness and the prevalence of key phyla, including Proteobacteria, Actinobacteria, Acidobacteria, and others. …”
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Microbial community dynamics in shallow-water grass-type lakes: Habitat succession of microbial ecological assembly and coexistence mechanisms by Chen Feng, Junping Lu, Tingxi Liu, Xiaohong Shi, Shengnan Zhao, Chunjian Lv, Yujiao Shi, Zixuan Zhang, Yuqi Jin, Jiaqi Pang, Aojie Sun

“…Second-generation DNA sequencing was applied to reveal the spatial dynamics of the bacterial community structure and distribution across two environmental media in this nutrient-rich shallow grassland lake and to elucidate the characteristics of the co-occurrence network. …”
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Basic Molecular Biology, Metabolic and Immunological Mechanisms of Fecal Microbiota Transplantation by O. V. Goloshchapov, A. V. Beynarovich, A. B. Chukhlovin, R. V. Klementeva, A. A. Shcherbakov, E. A. Bakin, I. K. Golubovskaya, N. D. Ventslovayte, O. S. Yudintseva, M. V. Gorchakova, V. E. Karev, M. A. Kucher, M. A. Suvorova, E. V. Svetkina, G. G. Rodionov, V. V. Gostev, S. V. Sidorenko, I. S. Moiseev, A. D. Kulagin

“…To monitor the basic effects of FMT, we performed targeted DNA sequencing of 16S rRNA gene (V3–V4) using MiSeq platform as well as multiplex real-time PCR, MS/gas chromatography technique, immunophenotyping of blood lymphocytes, histological and immunohistochemical techniques.Clinical case. …”
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Clinical and genetic drivers of oligo-metastatic disease in colon cancer by Alessandro Ottaiano, Mariachiara Santorsola, Roberto Sirica, Annabella Di Mauro, Antonella Di Carlo, Monica Ianniello, Francesco Sabbatino, Rosa Castiello, Francesca Del Peschio, Marco Cascella, Francesco Perri, Maurizio Capuozzo, Nicola Martucci, Edoardo Mercadante, Valentina Borzillo, Rossella Di Franco, Francesco Izzo, Vincenza Granata, Carmine Picone, Antonella Petrillo, Massimiliano Berretta, Salvatore Stilo, Luca Tarotto, Anna Chiara Carratù, Gerardo Ferrara, Madhura Tathode, Alessia Maria Cossu, Marco Bocchetti, Michele Caraglia, Guglielmo Nasti, Giovanni Savarese

“…OMD was defined as ≤3 lesions per organ, each with a total diameter <70 mm and none exceeding 25 mm. Tumor DNA sequencing by NGS utilized the TruSight Oncology 500 kit. …”
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