Aryana-bs: context-aware alignment of bisulfite-sequencing reads by Hassan Nikaein, Ali Sharifi-Zarchi, Afsoon Afzal, Saeedeh Ezzati, Farzane Rasti, Hamidreza Chitsaz, Govindarajan Kunde-Ramamoorthy

“…Many aligners that require seed sequences fail when frequent C-to-T conversions occur over short distances, resulting in reduced alignment accuracy. …”
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Diagnosis value of targeted and metagenomic sequencing in respiratory tract infection by Yukun Kuang, Yukun Kuang, Weiping Tan, Weiping Tan, Chaohui Hu, Zehan Dai, Lihong Bai, Lihong Bai, Jiyu Wang, Jiyu Wang, Huai Liao, Huai Liao, Haihong Chen, Haihong Chen, Rongling He, Rongling He, Pengyuan Zhu, Jun Liu, Canmao Xie, Canmao Xie, Zunfu Ke, Zunfu Ke, Zunfu Ke, Ke-Jing Tang, Ke-Jing Tang, Ke-Jing Tang

“…BackgroundTargeted next-generation sequencing (tNGS) has become a trending tool in the field of infection diagnosis, but concerns are also raising about its performance compared with metagenomic next-generation sequencing (mNGS). …”
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P-BERT: Toward Long Sequence Modeling by Enabling Language Representation With Prefix Sequence Compression, Soft Position Embedding, and Data Augmentation for Patent Relevance Asse... by Fei Wang, Xingchen Shi, Dongsheng Wang, Yinxia Lou

“…Because patent relevance is evaluated based on local sequence semantics, this paper proposes a patent-oriented bidirectional encoder representation from transformers (P-BERT) to enable the semantic modeling ability of long sequences. …”
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Sequence analysis of six blood pressure candidate regions in 4,178 individuals: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) targeted sequencing study. by Alanna C Morrison, Joshua C Bis, Shih-Jen Hwang, Georg B Ehret, Thomas Lumley, Kenneth Rice, Donna Muzny, Richard A Gibbs, Eric Boerwinkle, Bruce M Psaty, Aravinda Chakravarti, Daniel Levy

“…Six genes--ATP2B1, CACNB2, CYP17A1, JAG1, PLEKHA7, and SH2B3--were evaluated for sequence variation with large effects on systolic blood pressure (SBP), diastolic blood pressure (DBP), pulse pressure (PP), and mean arterial pressure (MAP).…”
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Leveraging machine learning models to evaluate immune infiltration in the ovarian cancer microenvironment: a single-cell analysis approach by Jie Liu, Baoguo Xia, Bingxin Li, Hui Liang

“…We utilized single-cell RNA sequencing data to characterize immune cell populations with unprecedented resolution. …”
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Arabic Speech Recognition Based on Encoder-Decoder Architecture of Transformer by Mohanad Sameer, Ahmed Talib, Alla Hussein, Husniza Husni

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Evaluation of genetic diversity of some Zucchini yellow mosaic virus-infected cucurbits based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, inter simple sequence repeat and start codon targeted molecular tools by Shrouk E.E. Farg, Shafik D. Ibrahim, Samir Mahgoub, Atef S. Sadik, Mamdouh H. Abdel-Ghaffar

“…The aim of this study was to evaluate the genetic diversity of some Zucchini yellow mosaic virus (ZYMV)-infected cucurbits compared to the healthy plants based on three molecular tools. …”
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Protocol for the analysis of cell-free DNA end characteristics for accurate cancer diagnosis by Xiaoyi Liu, Fanglei Gong, Huizhen Lin, Yunyun An, Kun Sun

“…Overall, we provide commands to align cfDNA whole-genome sequencing data starting from raw reads, then extract fragmentomic features, and finally build diagnostic models with performance evaluations.For complete information on the generation and use of this protocol, please refer to Ju et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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Evaluation of newly combination of Trichoderma with dimethyl disulfide fumigant to control Fusarium oxysporum, optimize soil microbial diversity and improve tomato yield by Zhaoai Shi, Min Zhang, Guangming Chen, Aocheng Cao, Qiuxia Wang, Dongdong Yan, Wensheng Fang, Yuan Li

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Evaluation of the Standard M10 MTB/NTM Molecular Test for the Rapid Identification of Tuberculous and Nontuberculous Mycobacteria in Liquid Cultures by Sara Caldrer, Alberta Carrara, Andrea Ragusa, Lavinia Nicolini, Elena Pomari, Cristina Mazzi, Fabio Formenti, Francesca Perandin

“…Nevertheless, overall, the adoption of this test could be considered for laboratory management to enable rapid and effective sample targeting for subsequent diagnostic evaluation and treatment decision-making.…”
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Investigating the probabilistic behavior of reference evapotranspiration using Vine tree sequence by Aliheidar Nasrolahi, Mohammad Nazeri Tahroudi, Yaser Sabzevari

“…The tree sequence of vine copulas including C-, D-, and R-vine was examined according to the input variables based on AIC and logarithm of likelihood evaluation criteria. …”
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NONLINEAR FILTERING OF RANDOM SEQUENCES WITH EXTENDED LEAST-SQUARE METHOD 1 by V. M. Artemiev, A. O. Naumov, L. L. Kokhan

“…For nonlinear random sequences filtering the extended least-square method is proposed. …”
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An Algorithm for Part Input Sequencing of Flexible Manufacturing Systems with Machine Disruption by Yumin He, Alexandre Dolgui, Milton Smith

“…An algorithm is proposed for FMS part input sequencing to handle machine breakage. Evaluation is performed for the proposed algorithm by simulation experiments and result analyses. …”
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Design of linear and cyclic peptide binders from protein sequence information by Qiuzhen Li, Efstathios Nikolaos Vlachos, Patrick Bryant

“…For one target protein, we demonstrate that linear and cyclic peptide binders of different lengths can be designed in a single shot, and adversarial designs can be avoided through orthogonal in silico evaluation.…”
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Detecting Anomalies in Sequences of Short Text Using Iterative Language Models by Cynthia Freeman, Ian Beaver, Abdullah Mueen

“…Empirical evaluation shows that our method achieves, on average, 31% higher max F1 scores than the baseline method of non-negative matrix factorization across three large human-annotated sequences of short texts.…”
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Next-Generation Sequencing: Key for Diagnosing Angiomyolipoma – A Case Report by José Revilla López, Rainer Enciso Chancahuana, Sayuri Meza Cruzado, Francisco Meléndez Ríos, Yashira L. Negron Abril, Daniel Sumarriva, Timothy Samec, Yasser Sullcahuaman Allende, Ivan Chávez Passiuri, Luis Casanova Marquez, Carlos Carracedo Gonzáles

“…Pathological re-evaluation confirmed the diagnosis of a metastatic retroperitoneal AML with complete response and no evidence of disease. …”
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FLAIR MR sequence in the diagnosis and follow-up of low-grade astrocytomas by Stošić-Opinćal Tatjana, Gavrilov Mihail, Stošić Srboljub, Lavrnić Slobodan, Perić Vesna, Grujičić Danica

“…Aim. To evaluate the sensitivity of fluid-attenuated inversion recovery (FLAIR) sequence in the diagnosis and follow-up of the patients with low-grade astrocytomas compared with T2-weighted (T2W) sequence. …”
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OPUS-BFactor: Predicting Protein B-Factor with Sequence and Structure Information by Yulu Yang, Ying Lv, Zhenwei Luo, Qinghua Wang, Gang Xu, Jianpeng Ma

“…Specifically, OPUS-BFactor treats pair features as a bias term, incorporating them into the attention matrix derived from the sequence-level features of each residue pair, thereby effectively merging pair features with sequence features. …”
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Optimising RNA extraction for paddy bulk soil samples for metatranscriptome sequencing by Sumitra Sivaprakasam, Tan Yee Fan, Yukgehnaish Kumarasan, Erneeza Mohd Hata, Ganesan Vadamalai, Bent Petersen, Thomas Sicheritz-Pontén, Sivachandran Parimannan, Heera Rajandas

“…The resulting RNA was subjected to metatranscriptome sequencing, de novo assembly and annotation. Results Upon evaluation, the RNA extraction protocol by Peng et al., 2018 (method B3) was optimized by incorporating 20% and 30% PEG-based precipitation to remove carry-over pigmentation. …”
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Searching for bacteria within acute cholecystitis using next-generation sequencers by Tomohiro Otsuka, Yoichi Ishizaki, Jiro Yoshimoto, Kenji Takamori, Shin Watanabe

“…Methods: We targeted patients diagnosed as having Grade I or Grade II acute cholecystitis (in accordance with the Tokyo Guidelines 2018 established by the Japanese Society of Hepato-Biliary-Pancreatic Surgery) who underwent laparoscopic cholecystectomy within 24 h of diagnosis at Juntendo University Urayasu Hospital between July 2021 and January 2024 for evaluation. We drew bile sample from the gallbladder of each patient to confirm the presence of biliary bacterial flora, using both standard bacteriology (culture test) and 16S rRNA gene sequence. …”
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