Diagnostic challenges and treatment breakthroughs in Malassezia restricta-induced meningoencephalitis: a real-world analysis of early mNGS applications by Jian Wang, Lin Tao

“…Metagenomic next-generation sequencing (mNGS) of CSF confirmed Malassezia restricta infection in all cases, enabling prompt diagnosis. …”
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TNFRSF12A expression in stomach adenocarcinoma and its preliminary role in predicting immunotherapy response by Lin-De Sun, Lin-Lin Zhang, Zheng Wan, Xiao-Dong Yang, Jing Yao, Ze-Long Yang, Lin Liu, Jun-Yan Liu

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Changes of intestinal microbiome and its relationship with painful diabetic neuropathy in rats by Shuaiying Jia, Haiqi Mi, Yao Su, Yuning Liu, Zhi Ming, Jingyan Lin

“…Glucose metabolism and insulin sensitivity were evaluated using intraperitoneal glucose tolerance tests and insulin tolerance tests. …”
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Effect of electromagnetic field radiation on transcriptomic profile and DNA methylation level in pig conceptuses during the peri-implantation period by Anita Franczak, Agata Zmijewska, Ewa Monika Drzewiecka, Wiktoria Kozlowska, Pawel Wydorski, Lukasz Paukszto, Tiziana L. Brevini

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Adrenocortical carcinoma with circulating tumor DNA analysis at post-operative recurrence: a case report with review of literature by Daisuke Aono, Toshiaki Kato, Akina Morisawa, Sakuya Kimata, Seigo Konishi, Mitsuhiro Kometani, Takashi Yoneda, Kazuyoshi Hosomichi, Shigehiro Karashima

“…In conclusion, monitoring the ctDNA allelic ratio may be useful for evaluating disease progression in advanced ACC.…”
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Antigenic Divergence from the Seasonal Vaccine of the Influenza Virus Strains Circulating in Romania During Three Successive Seasons (2021–2024) by Ovidiu Vlaicu, Leontina Banica, Robert Hohan, Marius Surleac, Dragoş Florea, Victor Daniel Miron, Andreea Tudor, Oana Săndulescu, Anca Cristina Drăgănescu, Dan Oțelea, Simona Paraschiv

“…All the available sequences collected between August 2021 and June 2024 were analyzed by using phylogenetic analysis and the P_epitope model to predict vaccine efficacy. …”
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Longitudinal detection of somatic mutations in the saliva of head and neck squamous cell carcinoma–affected patients: a pilot study by Chiara Dal Secco, Alessandro Tel, Lorenzo Allegri, Federica Baldan, Francesco Curcio, Francesco Curcio, Salvatore Sembronio, Salvatore Sembronio, Flavio Faletra, Massimo Robiony, Massimo Robiony, Giuseppe Damante, Giuseppe Damante, Catia Mio

“…Salivary DNA (sDNA) was extracted, and a 52-gene next generation sequencing (NGS)-based panel was used for somatic variants detection.Results41.2% of samples collected before surgery bore a deleterious variant (n=7/17). …”
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Molecular investigation on measles cases rise and variants co-circulation in the Lazio region, Italy by Cesare Ernesto Maria Gruber, Silvia Gioacchini, Lavinia Fabeni, Martina Rueca, Licia Bordi, Eleonora Lalle, Melissa Baggieri, Paola Bucci, Raoul Fioravanti, Roberto Giuseppetti, Eliana Specchiarello, Pietro Giorgio Spezia, Giulia Berno, Fabrizio Carletti, Gabriella De Carli, Maria Concetta Fusco, Alessandra Barca, Paola Scognamiglio, Antonella Marchi, Emilio D’Ugo, Enrico Girardi, Francesco Vairo, Fabio Magurano, Fabrizio Maggi

“…Methods We tested samples collected through routine measles and rubella surveillance for IgM, IgG and Real-Time PCR. We sequenced positive samples with higher viral titers using an amplicon-based whole-genome next-generation sequencing (WG-NGS) approach and performed mutational and phylogenetic analysis. …”
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Antioxidant functionalized double-net/TA dynamic hydrogel promotes cartilage regeneration through stabilization of chondrocyte phenotype by Xu Wu, Honglei Wang, Chenlong Li, Yaying Zhu, Qixuan Wang, Tianyu Zhang, Yaoyao Fu, Aijuan He

“…Nonetheless, how metabolic patterns shift during in vitro expansion, and whether metabolic modulation can stabilize the chondrocyte phenotype, remain insufficiently explored.To address these questions, we first utilized single-cell RNA sequencing combined with bulk transcriptomic analysis to profile the metabolic reprogramming of chondrocytes during in vitro expansion. …”
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Co-occurrence of entomopathogenic nematodes and earthworms enhances enduring biocontrol activity and microbial diversity in a naturalized plant-soil system by Maryam Chelkha, Rubén Blanco-Pérez, David Labarga, María de Toro, Jorge Dueñas-Hernani, Kyle Wickings, Raquel Campos-Herrera

“…Assessments included plant growth, EPN infectivity, soil properties, and bacterial profiling via 16S rRNA gene sequencing. Results showed no significant impact on plant growth. …”
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The Effects of Sampling Sites, Collection Time, and Refrigerated Storage Duration on Microbiota of Raw Milk From a Chinese Dairy Farm: An Exploratory Study by Han Lu, Chongshu Dang, Ruonan Liu, Shufei Zhang, Yuling Xue, Lili Feng, Yaoguang Zhang, Yan Wu, Shijie Wang

“…The microbiota were evaluated by 16S rRNA sequencing. The results identified Pseudomonas, Lactobacillus, and Prevotella as the predominant bacterial genera across all sampling conditions. …”
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Improved Quantification of Circulating Tumor DNA in Translocation‐Associated Myxoid Liposarcoma by Simultaneous Detection of Breakpoints and Single Nucleotide Variants by A. Schmid, U. Lausch, A. Runkel, J. Kiefer, T. Pauli, M. Boerries, B. Bogner, S. U. Eisenhardt, D. Braig

“…However, due to the often very low tumor fraction, distinguishing actual tumor variants from sequencing artifacts remains a key challenge. Methods Using MLS as a model for translocation‐driven tumors, this study evaluates a refined analytical approach for detecting both single nucleotide variants (SNVs) and structural variants (SVs) with the highest possible sensitivity and specificity. …”
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Genome-wide association and transcriptomic analysis and the identification of growth-related genes in Macrobrachium nipponense by Zijian Gao, Wenyi Zhang, Sufei Jiang, Hui Qiao, Yiwei Xiong, Shubo Jin, Hongtuo Fu

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Developing a disease-specific accessible transcriptional signature as a biomarker for ataxia with oculomotor apraxia type 2 by Kathie J. Ngo, Darice Y. Wong, Alden Y. Huang, Hane Lee, Stanley F. Nelson, Brent L. Fogel

“…Methods Here we utilize Weighted Gene Co-expression Network Analysis (WGCNA) from patient blood to construct an AOA2-specific transcriptomic signature as a biomarker to evaluate SETX variants in patients clinically suspected of having AOA2. …”
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Tumor microenvironment-preserving gliosarcoma organoids as an in vitro preclinical platform: a comparative analysis with glioblastoma models by Junseong Park, Dokyeong Kim, Hyeon-Chun Park, Minyoung Park, Songzi Zhang, Okcho Na, Youn Soo Lee, Minho Lee, Stephen Ahn, Yeun-Jun Chung

“…Histological, molecular, and functional properties were evaluated using H&E staining, immunohistochemistry, whole-exome sequencing, 3D invasion assays, and single-cell RNA sequencing (scRNA-seq). …”
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Assessing concordance between RNA-Seq and NanoString technologies in Ebola-infected nonhuman primates using machine learning by Mostafa Rezapour, Aarthi Narayanan, Wyatt H. Mowery, Metin Nafi Gurcan

“…Abstract This study evaluates the concordance between RNA sequencing (RNA-Seq) and NanoString technologies for gene expression analysis in non-human primates (NHPs) infected with Ebola virus (EBOV). …”
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Oral bacterial community dynamics during induction of gingival inflammation by Bart J. F. Keijser, Bart J. F. Keijser, Tim J. van den Broek, Michelle van der Wurff, Remon Dulos, Ferry Jagers, Jolanda Kool, Martijn Rosema, Elena A. Nicu, Wim Crielaard, Bruno G. Loos, Bernd W. Brandt, Egija Zaura

“…Samples from saliva and five oral niches (tongue, keratinized gingiva, supragingival, subgingival, and interproximal dental plaque) were collected and analyzed using 16S rRNA gene sequencing. Multivariate statistical analyses were applied to evaluate microbial dynamics and their associations with clinical outcomes.ResultsThe study revealed pronounced microbial changes, particularly in supragingival plaque, where Leptotrichia and Prevotella increased while Streptococcus decreased. …”
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Utility of a Novel High‐Sensitivity Multiplex Companion Diagnostic Test Using Formalin‐Fixed Paraffin‐Embedded Cell Block Materials of Non‐small Cell Lung Cancer by Yoshiki Shinomiya, Yuko Ishida, Kanako C. Hatanaka, Mamiko Yamamoto, Ayae Nange, Asami Okumura, Yumi Wada, Mitsuharu Abiko, Tomohiro Shimizu, Ryoko Watanabe, Yamato Hashimoto, Yoshiharu Sato, Jun Sakakibara‐Konishi, Tatsuya Kato, Shinya Tanaka, Yutaka Hatanaka

“…This study aimed to evaluate the utility of cPANEL using FFPE cell block (CB) with a low TC. …”
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First De Novo genome assembly and characterization of Gaultheria prostrata by Yan-Jun Lin, Xiao-Ya Ding, Yi-Wei Huang, Yi-Wei Huang, Lu Lu

“…In this study, we preliminarily obtained the genome of G. prostrata through next-generation sequencing methods. Utilizing 47.94 Gb of high-quality sequence data (108.95× coverage), assembled into 114,436 scaffolds, with an N50 length of 33,667 bp. …”
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<p><strong>Target-site insensitivity to some acaricides in a field population of <em>Tetranychus urticae</em> Koch (</strong><strong>Acari: Tetranychidae) from Egypt</strong></p> by Haggag Zein, Abdallah M. Afifi, Fatma S. Ali, El-Sayed Shaurub, Mahmoud Ahmed

“…Also, the nucleotide sequences were aligned, megablasted, and compared for similarity with the corresponding genes in different databases such as NCBI nucleotide collection (nr/nt). …”
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