Sequence of therapy impact on older women with comorbidities and triple-negative or HER2-positive breast cancer by Nina Tamirisa, Wenli Dong, Yu Shen, Heather Lin, Simona F. Shaitelman, Gildy Babiera, Isabelle Bedrosian

“…Abstract We sought to determine whether sequencing of treatment impacted outcomes in older, comorbid patients. …”
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Isoform analysis of heterozygous putative splicing variants at the allele level using nanopore long-read sequencing by Kokoro Ozaki, Takashi Irioka, Shohei Noma, Akira Machida, Moe Fukunaga, Tatsuro Murano, Chitose Takahashi, Michihira Tagami, Tsugumi Kawashima, Tomoko Hirata, Yuki Yasuoka, Hiroya Kuwahara, Toshiyuki Araki, Ken Yagi, Hidehiro Mizusawa, Kinya Ishikawa, Yasushi Okazaki, Takanori Yokota

“…Furthermore, we uncovered the effects of a novel pathogenic splicing variant in PYGM on isoforms in a compound-heterozygous case of McArdle disease using nanopore cDNA amplicon and targeted genomic sequencing. This study demonstrates the utility of nanopore long-read sequencing for isoform analysis at the allele level, providing a valuable approach to evaluating the direct consequences of heterozygous splicing variants in individuals.…”
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Mobile Toolbox sequences task: development and validation of a remote, smartphone-based working memory test by Jerry Slotkin, Aaron J. Kaat, Stephanie Ruth Young, Elizabeth M. Dworak, Miriam A. Novack, Yusuke Shono, Hubert Adam, Cindy J. Nowinski, Sarah Pila, Zahra Hosseinian, Maria Varela Diaz, Anyelo Almonte-Correa, Keith Alperin, Monica R. Camacho, Monica R. Camacho, Bernard Landavazo, Bernard Landavazo, Rachel L. Nosheny, Rachel L. Nosheny, Michael W. Weiner, Michael W. Weiner, Richard C. Gershon

“…The Sequences measure was evaluated for usability and feasibility across two pilot studies and then assessed in this validation study (which included a total sample size of N = 1,246). …”
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Single-cell RNA sequencing highlights the influence of innate and adaptive immune response mechanisms in psoriatic arthritis by Melanie R. Nielsen, Marie Skougaard, Marie Skougaard, Marie Skougaard, Clara Drachmann, Zara R. Stisen, Sisse B. Ditlev, Leon E. Jessen, Lars Erik Kristensen, Lars Erik Kristensen

“…The secondary aim was to describe the transcriptional patterns in PsA patients compared with healthy controls.MethodsThe study applied single-cell RNA sequencing (scRNAseq) using the BD Rhapsody™ Single-Cell Analysis System to evaluate peripheral blood mononuclear cells (PBMCs) from 70 PsA patients and 10 healthy controls. …”
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Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing by Jianxia Niu, Wenxi Wang, Zihao Wang, Zhe Chen, Xiaoyu Zhang, Zhen Qin, Lingfeng Miao, Zhengzhao Yang, Chaojie Xie, Mingming Xin, Huiru Peng, Yingyin Yao, Jie Liu, Zhongfu Ni, Qixin Sun, Weilong Guo

“…Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. …”
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Generating Efficient Instruction Sequence for Software-Based Self-Testing of Processor Cores Using Reinforcement Learning by Jongseon Seo, Hyungmin Cho

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RNA degradation patterns in cardiac tissues kept at different time intervals and temperatures before RNA sequencing. by Stine Bøttcher Jacobsen, Jacob Tfelt-Hansen, Morten Holdgaard Smerup, Niels Morling, Jeppe Dyrberg Andersen

“…Storage times and temperature may influence the integrity of the tissue and thereby affect the results of gene expression analyses. To evaluate the effect of storage time at different temperatures, we performed whole transcriptome sequencing of human right atrial appendage tissues stored at either 4°C or 22°C for zero, one, seven, 14, or 28 days. …”
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Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data by Marco Stock, Corinna Losert, Matteo Zambon, Niclas Popp, Gabriele Lubatti, Eva Hörmanseder, Matthias Heinig, Antonio Scialdone

“…Abstract Many studies have used single-cell RNA sequencing (scRNA-seq) to infer gene regulatory networks (GRNs), which are crucial for understanding complex cellular regulation. …”
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Metagenomic next-generation sequencing assisted in the successful treatment of pneumonia caused by Talaromyces marneffei in an immunocompetent patient by Ling-Yan Ye, Xu-Ling Zhao, Jia-Jia Qin, Jian Lin

“…Results: Patient’s condition improved rapidly after voriconazole treatment, and he was evaluated as a HIV-negative case of T. marneffei infection with normal immune function. …”
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Multi-analyte approach combining cfDNA sequencing and protein testing for early ovarian cancer detection by Fenfen Wang, Lingfang Wang, Ziyu Xing, Lingjia Lu, Zhuoqun Lin, Senmi Qian, Tao Zhu, Zhuyan Shao, Lingjun Zhao, Jie Dong, Fangfang Qian, Yang Li, Xiaojing Chen, Siqi Yang, Xiaodong Cheng

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Transcriptome dynamics in mouse amygdala under acute and chronic stress revealed by thiol-labeled RNA sequencing by Dan Zhao, Lu Zhang, Yang Yang

“…To overcome the difficulties in detecting subtle stress-induced changes by evaluating total RNA using classic RNA sequencing, we conducted thiol-labeled RNA sequencing (SLAM-seq). …”
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Comprehensive analysis of prognosis markers with molecular features derived from pan-cancer whole-genome sequences by Mamoru Kato, Jo Nishino, Momoko Nagai, Hirofumi Rokutan, Daichi Narushima, Hanako Ono, Takanori Hasegawa, Seiya Imoto, Shigeyuki Matsui, Tatsuhiko Tsunoda, Tatsuhiro Shibata

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Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant by He-Xu Chen, Zhen-Dong Liu, Xin Bai, Bo Wu, Rong Song, Hui-Cong Yao, Ying Chen, Wei Chi, Qian Hua, Liang Cheng, Chuan-Le Xiao

“…Abstract Nanopore sequencing enables comprehensive detection of 5-methylcytosine (5mC), particularly in repeat regions. …”
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A Phylogenetic Analysis Based on Whole Genome Re-Sequencing of 41 <i>Dendrobium</i> Species by Feng-Ping Zhang, Xue-Wei Fu, Han-Run Li, Shi-Bao Zhang

“…Here, we generated an extensive single nucleotide polymorphism (SNP) dataset through whole genome re-sequencing (WGRS) of 41 <i>Dendrobium</i> species to evaluate its effectiveness in species identification. …”
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Diagnostic impact of whole exome sequencing in neurometabolic disorders in Syrian children: a single center experience by Rawan Al Khudari, Sameer Baqla, Diana Al Asmar

“…This study evaluates the diagnostic utility of WES in Syrian patients with neurological and metabolic disorders, marking the first report of WES outcomes in this context. …”
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Clinical application of nanopore sequencing for haplotype linkage analysis in preimplantation genetic testing for Duchenne muscular dystrophy by Qiuping Xia, Tianli Chang, Taoli Ding, Zhen Liu, Jiaqi Liu, Yanping Li, Zhongyuan Yao

“…This study was designed to evaluate the feasibility of using nanopore sequencing as an effective PGT-M technique for DMD, particularly in cases involving de novo mutations or incomplete pedigrees that cannot be analyzed using second-generation sequencing (SGS) alone. …”
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Targeted long-read sequencing analysis and antifungal susceptibility profiles of Sporothrix schenckii isolates from Thailand. by Nattapong Langsiri, Wijit Banlunara, Oranong Klaychontee, Navaporn Worasilchai, Regielly Cognialli, Flavio de Queiroz-Telles, Bram Spruijtenburg, Theun de Groot, Eelco F J Meijer, Ariya Chindamporn

“…While the Internal Transcribed Spacer (ITS) region is the universal fungal barcode, the calmodulin gene offers higher resolution for phylogenetic classification of Sporothrix using Sanger sequencing. This study evaluated the ability of long-read nanopore sequencing of calmodulin and ITS to identify species level and allow phylogenetic analysis of Sporothrix strains isolated from humans and felines in Thailand. …”
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A pragmatic pipeline for drug resistance and lineage identification in Mycobacterium tuberculosis using whole genome sequencing. by Linzy Elton, Alp Aydin, Neil Stoker, Sylvia Rofael, Letícia Muraro Wildner, Jabar Babatunde Pacome Agbo Achimi Abdul, John Tembo, Muzamil Abdel Hamid, Mfoutou Mapanguy Claujens Chastel, Julio Ortiz Canseco, Ronan Doyle, Giovanni Satta, Justin O'Grady, Adam Witney, Francine Ntoumi, Alimuddin Zumla, Timothy D McHugh

“…Software for basecalling and analysis were evaluated to find the most accurate resistance SNP and lineage predictor. …”
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Localization of mobile robot in prior 3D LiDAR maps using stereo image sequence by I.V. Belkin, A.A. Abramenko, V.D. Bezuglyi, D.A. Yudin

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Image First or Text First? Optimising the Sequencing of Modalities in Large Language Model Prompting and Reasoning Tasks by Grant Wardle, Teo Sušnjak

“…Our study investigates how the sequencing of text and image inputs within multi-modal prompts affects the reasoning performance of Large Language Models (LLMs). …”
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