Artificial intelligence-powered prediction of AIM-2 inflammasome sequences using transformers and graph attention networks in periodontal inflammation by Pradeep Kumar Yadalam, Deepavalli Arumuganainar, Prabhu Manickam Natarajan, Carlos M. Ardila

“…Peptide sequence prediction methods were evaluated using a transformer, RNN-CNN, and GAT models. …”
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Draft genome sequences of multidrug resistant Staphylococcus arlettae isolated from cow nasal swab at Kelantan Malaysia Farm by Puteri Nazurah Megat Zakaria, Suhaili Zarizal, Noor Muzamil Mohamad, Soo Sum Lean, Mohd Nasir Mohd Desa, Erkihun Aklilu, Chew Chieng Yeo

“…Subsequent identification with matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) confirmed the isolate as Staphylococcus arlettae, with a score value of 2.09. Whole genome sequencing was conducted using the Illumina MiSeq system, with raw read quality evaluated through QUAST and genome assembly performed using SPAdes v3.12.0. …”
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Dynamic magnetic resonance imaging of the cerebrospinal fluid flow within the cerebral aqueduct by different FISIP 2D sequences by Lučić Miloš A., Koprivšek Katarina M., Till Viktor, Vesić Zoran

“…Sixty eight volunteers underwent brain MRI on 1.5T MR imager with additionally performed ECG retrospectively gated FISP 2D sequences (first one, as the part of the standard software package, with following technical parameters: TR 40, TE 12, FA 17, Matrix: 192 × 256, Acq 1, and the second one, experimentally developed by our investigation team: TR 30, TE 12, FA 70, Matrix: 192 × 256, Acq 1) respectively at two fixed slice positions - midsagittal and perpendicular to cerebral aqueduct, displayed and evaluated by multiplegated images in a closed-loop cinematographic (CINE) format. …”
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Effects of Diverse Crop Rotation Sequences on Rice Growth, Yield, and Soil Properties: A Field Study in Gewu Station by Ruiping Yang, Yu Shen, Xiangyi Kong, Baoming Ge, Xiaoping Sun, Mingchang Cao

“…This long-term field study conducted in Yancheng, China, evaluated the effects of diverse crop rotation sequences on rice growth, yield, and soil properties. …”
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Microbiome Diversity in Seafood Factories via Next-Generation Sequencing for Food Safety Management System (FSMS) Certifications in Malaysia by Shuping Kuan, Nyuk Ling Chin, Tuan Poy Tee, Noor Zafira Noor Hasnan

“…Next-Generation Sequencing (NGS) technology was applied to evaluate Food Safety Management System (FSMS) performance in seafood-processing factories by exploring microbiome diversity alongside traditional methods for detecting foodborne pathogens. …”
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Genotype–Phenotype Correlation in Children With Congenital Adrenal Hyperplasia due to 21‐Hydroxylase Deficiency Using Next Generation Sequencing by Nurgul Atas, Murat Karaoglan, Gülper Nacarkahya

“…CYP21A2 genotyping was performed by sequence‐specific primer and sequenced with next generation sequencing (NGS), and the expected phenotypes were compared to the observed phenotypes. …”
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In vitro callus induction and identification of DNA variation in Etlingera elatior using Inter-simple sequence repeat (ISSR) markers by Norsalsabila Mohd Rosli, Muhamad Fahmi Yunus, Tamil Chelvan Meenakshi Sundram, Zarina Zainuddin, Mohd Razik Midin, Md Hoirul Azri Ponari

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Integration of whole genome resequencing and transcriptome sequencing to identify candidate genes for tall and short traits in Baicheng Fatty chickens by Jiaqi Li, Kaixu Chen, Mengting Zhu, Jingdong Bi, Honggang Tang, Weiyi Gao

“…The tall and short traits of chickens are significant indicators for evaluating their growth and development. Tall chickens have longer growth cycles, allowing them to accumulate sufficient nutrients and resulting in superior meat quality. …”
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Designing New Chimeric Proline-Rich Antimicrobial Peptides to Enhance Efficacy Toward the ESKAPE+E: Beyond Sequence Extension by Adriana Di Stasi, Luigi de Pascale, Martino Morici, Daniel N. Wilson, Marco Scocchi, Mario Mardirossian

“…This study aimed to enhance B7-005’s potency by extending it with 6 or 11 amino acids derived from the C-terminal sequences of cetacean Tur1A and Lip1 PrAMPs, as well as bovine Bac7(1-35). …”
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Detecting cell-type-specific allelic expression imbalance by integrative analysis of bulk and single-cell RNA sequencing data. by Jiaxin Fan, Xuran Wang, Rui Xiao, Mingyao Li

“…Although this can be achieved by single-cell RNA sequencing (scRNA-seq), it requires full-length transcript to be sequenced in single cells of a large number of individuals, which are still cost prohibitive to generate. …”
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Integrating single-cell and bulk RNA sequencing data to characterize the heterogeneity of glycan-lipid metabolism polarization in hepatocellular carcinoma by Peng Lin, Qiong Qin, Xiang-yu Gan, Jin-shu Pang, Rong Wen, Yun He, Hong Yang

“…Gene signature, radiomics, contrast-enhanced ultrasound (CEUS), serum biomarkers were tested as potential surrogate methods for high throughput technology-based subtyping. Single-cell RNA sequencing analyses were employed to evaluate the immune characteristics changes between subtypes. …”
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How useful is Nanopore adaptive sampling for sequencing Schistosoma mansoni miracidia? [version 1; peer review: 2 approved] by Andrina Barungi, Moses Arinaitwe, Thomas Crellen, Amy B. Pedersen, Arne Jacobs, Rivka M. Lim, Poppy H.L. Lamberton, Joanne P. Webster, Thomas M. Arme

“…Background Whole-genome sequencing (WGS) is now widely used in Schistosoma genomics. …”
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Exploring changes in metabolites and fecal microbiota of advanced gastric cancer based on plasma metabolomics and 16S rDNA sequencing by Xinyi Feng, Yu Zhang, Jun Feng, Zhongjun Li, Zhi Zhang, Lin Zhu, Ruoyu Zhou, Haibo Wang, Xiaojun Dai, Yanqing Liu

“…Objective: Based on plasma metabolomics and 16S rDNA sequencing to evaluate the changes in metabolites and fecal microbiota of advanced gastric cancer. …”
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Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium. by Joshua C Bis, Anita DeStefano, Xiaoming Liu, Jennifer A Brody, Seung Hoan Choi, Benjamin F J Verhaaren, Stéphanie Debette, M Arfan Ikram, Eyal Shahar, Kenneth R Butler, Rebecca F Gottesman, Donna Muzny, Christie L Kovar, Bruce M Psaty, Albert Hofman, Thomas Lumley, Mayetri Gupta, Philip A Wolf, Cornelia van Duijn, Richard A Gibbs, Thomas H Mosley, W T Longstreth, Eric Boerwinkle, Sudha Seshadri, Myriam Fornage

“…Here, we sought to fine-map functional variants in the region and evaluate the contribution of rare variants to ischemic stroke risk.…”
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Multi-sequence MRI-based nomogram for prediction of human epidermal growth factor receptor 2 expression in breast cancer by Mengyi Shen, Li Zhang, Dingyi Zhang, Xin He, Nian Liu, Xiaohua Huang

“…The performance was mainly evaluated via the area under the receiver operating characteristic curve (AUC). …”
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Whole genome sequencing of 378 prostate cancer metastases reveals tissue selectivity for mismatch deficiency with potential therapeutic implications by Daniel J. Vis, Sander A. L. Palit, Marie Corradi, Edwin Cuppen, Niven Mehra, Martijn P. Lolkema, Lodewyk F. A. Wessels, Michiel S. van der Heijden, Wilbert Zwart, Andries M. Bergman

“…Methods Patients with mCRPC were prospectively included in the CPCT-02 metastatic site biopsy study. We evaluated whole genome sequencing (WGS) of 378 mCRPC metastases to understand the genetic traits that affect metastatic site distribution. …”
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Highly sensitive molecular assay based on Identical Multi-Repeat Sequence (IMRS) algorithm for the detection of Trichomonas vaginalis infection. by Clement Shiluli, Shwetha Kamath, Bernard N Kanoi, Racheal Kimani, Bernard Oduor, Hussein M Abkallo, Michael Maina, Harrison Waweru, Moses Kamita, Nicole Pamme, Joshua Dupaty, Catherine M Klapperich, Srinivasa Raju Lolabattu, Jesse Gitaka

“…This study aimed to evaluate the use of identical multi-repeat sequences (IMRS) as amplification primers for developing ultrasensitive diagnostic for T. vaginalis.…”
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Diversity, functionality, and stability: shaping ecosystem multifunctionality in the successional sequences of alpine meadows and alpine steppes on the Qinghai-Tibet Plateau by Xin Jin, Abby Deng, Yuejun Fan, Kun Ma, Yangan Zhao, Yingcheng Wang, Kaifu Zheng, Xueli Zhou, Guangxin Lu

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Integrating Machine Learning Workflow into Numerical Simulation for Optimizing Oil Recovery in Sand-Shale Sequences and Highly Heterogeneous Reservoir by Dung Bui, Abdul-Muaizz Koray, Emmanuel Appiah Kubi, Adewale Amosu, William Ampomah

“…This paper aims to evaluate the efficiency of various machine learning algorithms integrating with numerical simulations in optimizing oil production for a highly heterogeneous reservoir. …”
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Integrated single cell and bulk RNA sequencing analyses reveal the impact of tryptophan metabolism on prognosis and immunotherapy in colon cancer by Yanyan Hu, Ximo Xu, Hao Zhong, Chengshen Ding, Sen zhang, Wei Qin, Enkui Zhang, Duohuo Shu, Mengqin Yu, Naijipu Abuduaini, Xiao Yang, Bo Feng, Jianwen Li

“…Transcriptomic sequencing findings were corroborated by single-cell sequencing from Shanghai Ruijin Hospital. …”
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