Ensemble learning-based predictor for driver synonymous mutation with sequence representation. by Chuanmei Bi, Yong Shi, Junfeng Xia, Zhen Liang, Zhiqiang Wu, Kai Xu, Na Cheng

“…In this study, we initially investigate the impact of sequence-based features, including DNA shape, physicochemical properties and one-hot encoding of nucleotides, and deep learning-derived features from pre-trained chemical molecule language models based on BERT. …”
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PreS1 deletions in genotype C HBV leads to severe hepatic inflammation and hepatocarcinogenesis via the IRE1-JNK axis by Yu-Min Choi, Junghwa Jang, Dong Hyun Kim, Ziyun Kim, Eunseo Kim, Won Hyeok Choe, Bum-Joon Kim

“…Background & Aims: Deletion of 15–21 nucleotides covering the preS1 start codon frequently occurs in patients with chronic HBV (CHB) with HBV genotype C and has been reported to be related to progression to hepatocellular carcinoma (HCC). …”
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Novel Polymorphism in a Promoter of MBL2 Gene Result in Lower MBL Expression in Chronic Infection Caused by HCV by Paywast Jamal Jalal

“…Interestingly, a new deletion of six nucleotides [AGGAAG] detected in the promoter at position -319 to -324 that succeeded by four other mutations at position -328, -336, -349 and -427 in most of the analyzed sequences. …”
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Localisation of Abundant and Organ-Specific Genes Expressed in Rosa hybrida Leaves and Flower Buds by Direct In Situ RT-PCR by Agata Jedrzejuk, Heiko Mibus, Margrethe Serek

“…We used digoxygenin-11-dUTP, biotin-11-dUTP, and fluorescein-12-dUTP-labelled nucleotides and antidig-AP/ streptavidin-fluorescein-labelled antibodies. …”
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A Canadian Isolate of Hepatitis D (delta) Virus by Véronique Poisson, Daniel B Ménard, Éric Frost, Jean-Pierre Perreault

“…Consequently, in the present study, the complete nucleotide sequence of anHDVisolated from a Canadian patient was determined. …”
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Accurate assembly of full-length consensus for viral quasispecies by Jia Tian, Ziyu Gao, Minghao Li, Ergude Bao, Jin Zhao

“…Virus genomes are typically small, often composed of only a few thousand to several hundred thousand nucleotides. While constructing a high-quality consensus of virus strains might seem feasible, most current assemblers only generated fragmented contigs. …”
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Evaluating the risk of data loss due to particle radiation damage in a DNA data storage system by Christopher N. Takahashi, David P. Ward, Carlo Cazzaniga, Christopher Frost, Paolo Rech, Kumkum Ganguly, Sean Blanchard, Steve Wender, Bichlien H. Nguyen, Jake A. Smith

“…We develop a mass action kinetics model to estimate the rate of damage accumulation in DNA strands due to neutron interactions with both nucleotides and residual water molecules, then utilize the model to evaluate the effect several design parameters of a typical DNA data storage scheme have on expected data longevity. …”
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hsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family by H. W. Cayatineto, S. T. Hakim

“…To predict the right alignments between miRNA and viral mRNA genomes, we used computational databases such as miRBase, NCBI, and Basic Alignment Search Tool–nucleotides (BLAST-n).ResultsOf the 2,600 mature miRNAs, hsa-miR-548d-3p revealed complementary sequences with the flavivirus capsid gene and bovine viral diarrhea virus (BVDV) capsid gene and was selected as a possible candidate to inhibit flaviviruses.ConclusionAlthough more detailed in vitro and in vivo studies are required to test the possible inhibitory effects of hsa-miR-548d-3p against flaviviruses, this computational study may be the first step to study further, developing a novel therapeutic for lethal viruses within the Flaviviridae family using suggested candidate miRNAs.…”
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Recent advances in adipose-derived mesenchymal stem cell-derived exosomes for regulating macrophage polarization by Zhewei Dong, Yingli Fu, Zhongming Cai, Hao Dai, Yucang He

“…Potent anti-inflammatory substances contained in exosomes include the glycoprotein MFGE8, the cytokines such as prostaglandin E2, IL-6, and IGF, as well as non-coding nucleotides (miR-451a, miR-23, miR-30d-5p, let-7, lncRNA DLEU2, circRps5, Circ-Ptpn4, and mmu_ circ_0001359). …”
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Metabolomic Analysis of the Chemical Composition of Chongjue Luohan Tea by QIAN Yuanfeng, YANG Gaozhong, XU Weilin, XU Guodong, DENG Huifang, LAN Bingying, LIN Zhi, LÜ Haipeng

“…In addition, a total of 206 secondary metabolites were identified in Luohan tea, including flavonoids (71), amino acids and their derivatives (31), organic acids (24), nucleotides and their derivatives (19), phenolic acids (16), alkaloids (12), and saccharides and their derivatives (7). …”
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Genome-wide association mapping of bruchid resistance loci in soybean. by Clever Mukuze, Ulemu M Msiska, Afang Badji, Tonny Obua, Sharon V Kweyu, Selma N Nghituwamhata, Evalyne C Rono, Mcebisi Maphosa, Faizo Kasule, Phinehas Tukamuhabwa

“…In this study, 6 multi-locus methods of the mrMLM model for genome-wide association study were used to dissect the genetic architecture of bruchid resistance on 4traits: percentage adult bruchid emergence (PBE), percentage weight loss (PWL), median development period (MDP), and Dobie susceptibility index (DSI) on 100 diverse soybean genotypes, genotyped with 14,469 single-nucleotide polymorphism (SNP) markers. Using the best linear unbiased predictors (BLUPs), 13 quantitative trait nucleotides (QTNs) were identified by the mrMLM model, of which rs16_14976250 was associated with more than 1 bruchid resistance traits. …”
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Inkjet-based oligonucleotide synthesis reagents: Formulation optimization and comparison of acetonitrile and propylene carbonate applications by Yu Xiao, Yongjin Peng, Zhen Rong, Xiaoyang He, Fei Sun, Shengqi Wang

“…When synthesizing a target sequence of 30 nucleotides, a stepwise coupling efficiency of 99.01 % was achieved. …”
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Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System by Sarel Halachmi, Michal Cohen, Raymond Szargel, Nadin Cohen

“…We found loss of heterozygocity (LOH) or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size) in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. …”
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The Expanding Family of Bone Marrow Homing Factors for Hematopoietic Stem Cells: Stromal Derived Factor 1 Is Not the Only Player in the Game by Mariusz Z. Ratajczak, ChiHwa Kim, Anna Janowska-Wieczorek, Janina Ratajczak

“…Specifically, it has been demonstrated that HSPCs respond robustly to some bioactive lipids, such as sphingosine-1-phosphate (S1P) and ceramide-1-phosphate (C1P), and migrate in response to gradients of certain extracellular nucleotides, including uridine triphosphate (UTP) and adenosine triphosphate (ATP). …”
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The Impact of Purinergic System Enzymes on Noncommunicable, Neurological, and Degenerative Diseases by Margarete Dulce Bagatini, Alessandra Antunes dos Santos, Andréia Machado Cardoso, Aline Mânica, Cristina Ruedell Reschke, Fabiano Barbosa Carvalho

“…These pathological conditions can be associated with disturbance in the signaling mediated by nucleotides and nucleosides of adenine, in expression or activity of extracellular ectonucleotidases and in activation of P2X and P2Y receptors. …”
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Synthesis of Headful Packaging Phages Through Yeast Transformation-Associated Recombination by Cheng Lu, Lan He, Yangyijun Guo, Tingting Wang, Yanrui Ye, Zhanglin Lin

“…Furthermore, we show that S4 can be synthesized from arbitrary starting nucleotides and modified with a red fluorescent protein as a reporter. …”
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Rev1, Rev3, or Rev7 siRNA Abolishes Ultraviolet Light-Induced Translesion Replication in HeLa Cells: A Comprehensive Study Using Alkaline Sucrose Density Gradient Sedimentation by Jun Takezawa, Yukio Ishimi, Naomi Aiba, Kouichi Yamada

“…When a replicative DNA polymerase stalls upon encountering a lesion on the template strand, it is relieved by other low-processivity polymerase(s), which insert nucleotide(s) opposite the lesion, extend by a few nucleotides, and dissociate from the 3′-OH. …”
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Genomic Changes in an Attenuated ZB Strain of Foot-and-Mouth Disease Virus Serotype Asia1 and Comparison with Its Virulent Parental Strain by Aiguo Xin, Mingwang Zhu, Zhenqi Peng, Qi Hu, Chenhong Shi, Defang Liao, Jihua Wang, Huachun Li

“…In addition, a total of 21 nucleotides silent mutations had been found after attenuation. …”
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The Psu protein of phage satellite P4 inhibits transcription termination factor ρ by forced hyper-oligomerization by Daniela Gjorgjevikj, Naveen Kumar, Bing Wang, Tarek Hilal, Nelly Said, Bernhard Loll, Irina Artsimovitch, Ranjan Sen, Markus C. Wahl

“…Our cryogenic electron microscopy structures of ρ-Psu complexes show that Psu dimers clamp two inactive, open ρ rings and promote their expansion to higher-oligomeric states. ATPase, nucleotide binding and nucleic acid binding studies revealed that Psu hinders ρ ring closure and traps nucleotides in their binding pockets on ρ. …”
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Genome characterization through dichotomic classes: An analysis of the whole chromosome 1 of A. thaliana by Enrico Properzi, Simone Giannerini, Diego Luis Gonzalez, Rodolfo Rosa

“…Such informational content is independent from the global proportion of nucleotides of a sequence. The present work confirms that the recent mathematical model of the genetic code is a new paradigm for understanding the management and the organization of genetic information and is an innovative tool for investigating informational aspects of error detection/correction mechanisms acting at the level of DNA replication.…”
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