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Journal articles on the topic 'Non coding variations'

Author: Grafiati

Published: 19 October 2024

Last updated: 31 July 2025

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1

Pan, Qi, Yue-Juan Liu, Xue-Feng Bai, et al. "VARAdb: a comprehensive variation annotation database for human." Nucleic Acids Research 49, no. D1 (2020): D1431—D1444. http://dx.doi.org/10.1093/nar/gkaa922.

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Abstract With the study of human diseases and biological processes increasing, a large number of non-coding variants have been identified and facilitated. The rapid accumulation of genetic and epigenomic information has resulted in an urgent need to collect and process data to explore the regulation of non-coding variants. Here, we developed a comprehensive variation annotation database for human (VARAdb, http://www.licpathway.net/VARAdb/), which specifically considers non-coding variants. VARAdb provides annotation information for 577,283,813 variations and novel variants, prioritizes variati

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Laurent, Jon M., Sudarshan Pinglay, Leslie Mitchell, and Ran Brosh. "Probing the dark matter of the human genome with big DNA." Biochemist 41, no. 3 (2019): 46–48. http://dx.doi.org/10.1042/bio04103046.

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Less than 2% of our genome is protein-coding DNA. The vast expanses of non-coding DNA make up the genome's “dark matter”, where introns, repetitive and regulatory elements reside. Variation between individuals in non-coding regulatory DNA is emerging as a major factor in the genetics of numerous diseases and traits, yet very little is known about how such variations contribute to disease risk. Studying the genetics of regulatory variation is technically challenging as regulatory elements can affect genes located tens of thousands of base pairs away, and often, multiple distal regulatory variat

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Sedláková, V., P. Sedlák, D. Zeka, J. Domkářová, P. Doležal, and P. Vejl. "Evaluation of variations in plastid DNA non-coding regions in selected species of the genus Solanum." Czech Journal of Genetics and Plant Breeding 53, No. 3 (2017): 127–31. http://dx.doi.org/10.17221/76/2015-cjgpb.

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The diversity of three non-coding plastid DNA loci (trnL/trnF spacer, trnV/16SrRNA spacer, trnL/trnL intron) was assessed in 16 Solanum L. species (135 individuals). Polymorphisms were detected by denaturing gradient gel electrophoresis (DGGE) and verified by direct sequencing. No intraspecific diversity and only poor interspecific diversity was detected. Unique S. mochiquense Ochoa specific length polymorphism at the trnL/trnL locus represented by duplication of an 18 bp segment was discovered. The detected DGGE interspecific trnL/trnF locus polymorphism did not specifically associate with si

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Meerschaut, Ilse, Sarah Vergult, Annelies Dheedene, et al. "A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome." Genes 12, no. 7 (2021): 1048. http://dx.doi.org/10.3390/genes12071048.

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Copy number variations (CNVs) can modulate phenotypes by affecting protein-coding sequences directly or through interference of gene expression. Recent studies in cancer and limb defects pinpointed the relevance of non-coding gene regulatory elements such as long non-coding RNAs (lncRNAs) and topologically associated domain (TAD)-related gene-enhancer interactions. The contribution of such non-coding elements is largely unexplored in congenital heart defects (CHD). We performed a retrospective analysis of CNVs reported in a cohort of 270 CHD patients. We reviewed the diagnostic yield of pathog

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Bhartiya, Deeksha, and Vinod Scaria. "Genomic variations in non-coding RNAs: Structure, function and regulation." Genomics 107, no. 2-3 (2016): 59–68. http://dx.doi.org/10.1016/j.ygeno.2016.01.005.

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Bozgeyik, Esra, and Ibrahim Bozgeyik. "Non-coding RNA variations in oral cancers: A comprehensive review." Gene 851 (January 2023): 147012. http://dx.doi.org/10.1016/j.gene.2022.147012.

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7

Scarpa, Aldo, and Andrea Mafficini. "Non-coding regulatory variations: the dark matter of pancreatic cancer genomics." Gut 67, no. 3 (2017): 399–400. http://dx.doi.org/10.1136/gutjnl-2017-314310.

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Haas, Jan, Stefan Mester, Alan Lai, et al. "Genomic structural variations lead to dysregulation of important coding and non‐coding RNA species in dilated cardiomyopathy." EMBO Molecular Medicine 10, no. 1 (2017): 107–20. http://dx.doi.org/10.15252/emmm.201707838.

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9

Mattick, John S. "The central role of RNA in the genetic programming of complex organisms." Anais da Academia Brasileira de Ciências 82, no. 4 (2010): 933–39. http://dx.doi.org/10.1590/s0001-37652010000400016.

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Notwithstanding lineage-specific variations, the number and type of protein-coding genes remain relatively static across the animal kingdom. By contrast there has been a massive expansion in the extent of genomic non-proteincoding sequences with increasing developmental complexity. These non-coding sequences are, in fact, transcribed in a regulated manner to produce large numbers of large and small non-protein-coding RNAs that control gene expression at many levels including chromatin architecture, post-transcriptional processing and translation. Moreover, many RNAs are edited, especially in t

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Sedano, Melina J., Alana L. Harrison, Mina Zilaie, et al. "Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs." International Journal of Molecular Sciences 21, no. 10 (2020): 3711. http://dx.doi.org/10.3390/ijms21103711.

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Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on

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Labani, Mahdieh, Amin Beheshti, Ahmadreza Argha, and Hamid Alinejad-Rokny. "A Comprehensive Investigation of Genomic Variants in Prostate Cancer Reveals 30 Putative Regulatory Variants." International Journal of Molecular Sciences 24, no. 3 (2023): 2472. http://dx.doi.org/10.3390/ijms24032472.

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Prostate cancer (PC) is the most frequently diagnosed non-skin cancer in the world. Previous studies have shown that genomic alterations represent the most common mechanism for molecular alterations responsible for the development and progression of PC. This highlights the importance of identifying functional genomic variants for early detection in high-risk PC individuals. Great efforts have been made to identify common protein-coding genetic variations; however, the impact of non-coding variations, including regulatory genetic variants, is not well understood. Identification of these variant

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Kim, Eun Jin, Hyun Jin Yu, and Dong Wook Kim. "Sequence Variations in the Non-Coding Sequence of CTX Phages in Vibrio cholerae." Journal of Microbiology and Biotechnology 26, no. 8 (2016): 1473–80. http://dx.doi.org/10.4014/jmb.1604.04022.

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Lange, Marios, Rodiola Begolli, and Antonis Giakountis. "Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine." Non-Coding RNA 7, no. 3 (2021): 47. http://dx.doi.org/10.3390/ncrna7030047.

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The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise t

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Tsilimigras, Diamantis I., Sofia-Iris Bibli, Gerasimos Siasos, et al. "Regulation of Long Non-Coding RNAs by Statins in Atherosclerosis." Biomolecules 11, no. 5 (2021): 623. http://dx.doi.org/10.3390/biom11050623.

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Despite increased public health awareness, atherosclerosis remains a leading cause of mortality worldwide. Significant variations in response to statin treatment have been noted among different populations suggesting that the efficacy of statins may be altered by both genetic and environmental factors. The existing literature suggests that certain long noncoding RNAs (lncRNAs) might be up- or downregulated among patients with atherosclerosis. LncRNA may act on multiple levels (cholesterol homeostasis, vascular inflammation, and plaque destabilization) and exert atheroprotective or atherogenic

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Yarahmadi, Elham, Parnaz Borjian Boroujeni, Mehdi Totonchi, and Hamid Gourabi. "Genotyping of the EIF1AY Gene in Iranian Patients with Non-Obstructive Azoospermia." Current Urology 13, no. 1 (2019): 46–50. http://dx.doi.org/10.1159/000499295.

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Background: EIF1AY is one of the genes essential for normal spermatogenesis and is located in azoospermic factors region. Objective: The present study was designed to investigate the EIF1AY gene nucleotide variations, and correlate it with spermatogenic maturation arrest and azoospermia in Iranian population. Methods: A total number of 30 Iranian idiopathic non-obstructive azoospermic patients were selected as case group and 30 fertile men served as a control group who had at least 1 child. Nucleotide variation was analyzed in exon 3 and exon 5 in EIF1AY gene of both groups. DNA extraction fro

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Yasmin, Tahirah. "In silico comprehensive analysis of coding and non-coding SNPs in human mTOR protein." PLOS ONE 17, no. 7 (2022): e0270919. http://dx.doi.org/10.1371/journal.pone.0270919.

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The mammalian/mechanistic target of rapamycin (mTOR) protein is an important growth regulator and has been linked with multiple diseases including cancer and diabetes. Non-synonymous mutations of this gene have already been found in patients with renal clear cell carcinoma, melanoma, and acute lymphoid leukemia among many others. Such mutations can potentially affect a protein’s structure and hence its functions. In this study, therefore, the most deleterious SNPs of mTOR protein have been determined to identify potential biomarkers for various disease treatments. The aim is to generate a stru

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Song, Jiaming, Xin Zhao, Bo Lin, et al. "Single Nucleotide Polymorphisms and Insertion/Deletion Variation Analysis of Octoploid and Decaploid Tropical Oil Tea Camellia Populations Based on Whole-Genome Resequencing." Plants 13, no. 21 (2024): 2955. http://dx.doi.org/10.3390/plants13212955.

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Oil tea camellia (Camellia spp.) is an important woody oil crop with a high nutritional and economic value. Whole-genome resequencing (WGR) technology can provide an in-depth understanding of the genetic background of this plant as well as a reference for breeding research, germplasm resource conservation, and genetic modification. In this study, we analyzed SNP and InDel variations in 49 individual oil tea camellia germplasm samples collected from five populations located in three provinces of China: Hainan, Guangdong and Guangxi. The samples were analyzed through WGR after the ploidy of the

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18

Wilson, Claire, and Aditi Kanhere. "8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer." International Journal of Molecular Sciences 22, no. 3 (2021): 1094. http://dx.doi.org/10.3390/ijms22031094.

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The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated. One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have been identified to play a range of roles in transcription and translation. While the clinical importance of the majority of lncRNAs have yet to be identified, it is puzzling that a large number of disease-associated genetic variations are seen in lncRNA genes. The 8q24.21 locus is rich in lncRNAs and very few protein-coding genes are located in this

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Uvarova, Aksinya N., Elena A. Tkachenko, Ekaterina M. Stasevich, Elina A. Zheremyan, Kirill V. Korneev, and Dmitry V. Kuprash. "Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome." Biochemistry (Moscow) 89, no. 6 (2024): 1002–13. http://dx.doi.org/10.1134/s0006297924060026.

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Abstract Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide Association Studies. Majority of the clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain influence of the non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating molecular mechanisms underlying dependence of the disease pathogenesis o

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Uvarova, A. N., E. A. Tkachenko, E. M. Stasevich, E. A. Zheremyan, K. V. Korneev, and D. V. Kuprash. "Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome (Review)." Biohimiâ 89, no. 6 (2024): 982–95. https://doi.org/10.31857/s0320972524060023.

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Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through Genome-Wide Association Studies. The majority of clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain the influence of non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating the molecular mechanisms underlying the dependence of disease pathogenesis on specifi

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21

Prodan-Bărbulescu, Cătălin, Edward Paul Şeclăman, Virgil Enătescu, et al. "Evaluating the Connection between MicroRNAs and Long Non-Coding RNAs for the Establishment of the Major Depressive Disorder Diagnosis." Biomedicines 12, no. 3 (2024): 516. http://dx.doi.org/10.3390/biomedicines12030516.

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The most prevalent mental illness worldwide and the main contributor to suicide and disability is major depressive disorder. Major depressive disorder is now diagnosed and treated based on the patient’s statement of symptoms, mental status tests, and clinical behavioral observations. The central element of this review is the increased need for an accurate diagnostic method. In this context, the present research aims to investigate the potential role of two non-coding RNA species (microRNA and long non-coding RNA) in peripheral blood samples and brain tissue biopsy from patients with major depr

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22

Allen, Ethan J., and Roberta K. Weber. "An Exploration of Indexed and Non-Indexed Open Access Journals: Identifying Metadata Coding Variations." Journal of Web Librarianship 9, no. 2-3 (2015): 65–84. http://dx.doi.org/10.1080/19322909.2015.1020185.

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23

Torgersen, H., T. Skern, and D. Blaas. "Typing of Human Rhinoviruses Based on Sequence Variations in the 5' Non-coding Region." Journal of General Virology 70, no. 11 (1989): 3111–16. http://dx.doi.org/10.1099/0022-1317-70-11-3111.

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24

Williams, Sarah M., Joon Yong An, Janette Edson, et al. "An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder." Molecular Psychiatry 24, no. 11 (2018): 1707–19. http://dx.doi.org/10.1038/s41380-018-0049-x.

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Begum, Ghausia, Ammar Albanna, Asma Bankapur, et al. "Long-Read Sequencing Improves the Detection of Structural Variations Impacting Complex Non-Coding Elements of the Genome." International Journal of Molecular Sciences 22, no. 4 (2021): 2060. http://dx.doi.org/10.3390/ijms22042060.

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The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases. For autism spectrum disorders (ASD) cases where pathogenic variants fail to be found in the protein-coding genic regions along chromosomes, we proposed a scalable workflow to characterize the risk factor of SVs impacting non-coding elements of the genome. We applied whole-genome sequencing on an Emirati family having three children with ASD using long and short-read sequencing technology. A series of analytical pipelines were established to identif

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Tan, Fengxiao, Weixi Li, Hui Feng, Yelin Huang, and Achyut Kumar Banerjee. "Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)—insights from comparative analysis of complete chloroplast genome." PeerJ 11 (June 26, 2023): e15527. http://dx.doi.org/10.7717/peerj.15527.

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The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species s

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Chawla, Anjali, Corina Nagy, and Gustavo Turecki. "Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits." International Journal of Molecular Sciences 22, no. 14 (2021): 7612. http://dx.doi.org/10.3390/ijms22147612.

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The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it re

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Olufunmilayo, Edward O., and R. M. Damian Holsinger. "Roles of Non-Coding RNA in Alzheimer’s Disease Pathophysiology." International Journal of Molecular Sciences 24, no. 15 (2023): 12498. http://dx.doi.org/10.3390/ijms241512498.

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Alzheimer’s disease (AD) is a chronic neurodegenerative disorder that is accompanied by deficits in memory and cognitive functions. The disease is pathologically characterised by the accumulation and aggregation of an extracellular peptide referred to as amyloid-β (Aβ) in the form of amyloid plaques and the intracellular aggregation of a hyperphosphorelated protein tau in the form of neurofibrillary tangles (NFTs) that cause neuroinflammation, synaptic dysfunction, and oxidative stress. The search for pathomechanisms leading to disease onset and progression has identified many key players that

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Perović, Vladimir, Branislava Gemović, Veljko Veljković, Sanja Glišić, and Nevena Veljković. "Annotation of the functional impact of coding genetic variants." Biologia Serbica 39, no. 1 (2017): 74–82. https://doi.org/10.5281/zenodo.826908.

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<strong>Summary.</strong> Coding genetic variants can have profound effects on protein function. Computational tools for the prediction of these effects are used to complement and guide experimental biological studies. Phylogenetic analyses that determine the evolutionary relationship among related sequences are commonly used to distinguish between functionally significant and insignificant gene variations. Here, we have reviewed applications of the non-alignment sequence analyses method for phylogenetic analyses, ISTREE. Furthermore, we assessed how an unsupervised ISTREE-d3 method based on t

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Shapiro, James A. "Biological action in Read–Write genome evolution." Interface Focus 7, no. 5 (2017): 20160115. http://dx.doi.org/10.1098/rsfs.2016.0115.

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Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations

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Policarpo, Rafaela, and Constantin d’Ydewalle. "Missing lnc(RNAs) in Alzheimer’s Disease?" Genes 13, no. 1 (2021): 39. http://dx.doi.org/10.3390/genes13010039.

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With the ongoing demographic shift towards increasingly elderly populations, it is estimated that approximately 150 million people will live with Alzheimer’s disease (AD) by 2050. By then, AD will be one of the most burdensome diseases of this and potentially next centuries. Although its exact etiology remains elusive, both environmental and genetic factors play crucial roles in the mechanisms underlying AD neuropathology. Genome-wide association studies (GWAS) identified genetic variants associated with AD susceptibility in more than 40 different genomic loci. Most of these disease-associated

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Pinjou Tsai, Becky, Liang Li, Min Li, et al. "Development Of t-MDS In Patients Undergoing Autologous Transplantation For Lymphoma Is Not Associated With Increased Frequency Of Mitochondrial DNA Mutations." Blood 122, no. 21 (2013): 1535. http://dx.doi.org/10.1182/blood.v122.21.1535.1535.

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Abstract Therapy-related myelodysplasia/acute myeloid leukemia (t-MDS) is a lethal complication of cytotoxic cancer treatment. The incidence of t-MDS is particularly high in patients undergoing autologous hematopoietic cell transplantation (aHCT) for Hodgkin lymphoma (HL) or non-Hodgkin lymphoma (NHL). To better understand pathogenetic mechanisms underlying development of t-MDS we are prospectively following a cohort of patients undergoing aHCT for lymphoma at our center. In previous studies using samples from this cohort we identified altered expression of genes related to mitochondrial funct

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Cao, Ting, ShuangYang Zhang, Qian Chen, et al. "Long non-coding RNAs in schizophrenia: Genetic variations, treatment markers and potential targeted signaling pathways." Schizophrenia Research 260 (October 2023): 12–22. http://dx.doi.org/10.1016/j.schres.2023.07.027.

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Hazem, M. El-Hageen, M. Alatwi Aadel, and Nabih Zaki Rashed Ahmed. "Advanced modulation coding schemes for an optical transceiver systems–based OWC communication channel model." Bulletin of Electrical Engineering and Informatics 10, no. 2 (2021): 767~775. https://doi.org/10.11591/eei.v10i2.2433.

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This paper examines advanced modulation coding schemes for an optical transceiver systems–based optical wireless communication (OWC) channel model. These modulation techniquesinclude On-Off keying and return to zero (RZ)/non–return to zero (NRZ) coding. The signal power level against time and frequency spectral variations are measured. The max. Q factor and min. bit error rate (BER) are estimated and clarified for each modulation code scheme by using an optisystem simulation model. Transmission bit rates of up to 40 Gb/s can be achieved for possible distances up to 500 km with acce

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Calin, George A. "Abstract IA025: About motifs, non-codingRNAs and metastases." Cancer Research 83, no. 2_Supplement_2 (2023): IA025. http://dx.doi.org/10.1158/1538-7445.metastasis22-ia025.

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Abstract MicroRNA and other short or long non-codingRNAs alterations are involved in the initiation, progression and metastases of human cancer. The main molecular alterations are represented by variations in gene expression, usually mild and with consequences for a vast number of target protein coding genes. The causes of the widespread differential expression of non-codingRNAs in malignant compared with normal cells can be explained by the location of these genes in cancer-associated genomic regions, by epigenetic mechanisms and by alterations in the processing machinery. MicroRNA and other

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Hussain, Manal A., Noha M. Elemam, and Iman M. Talaat. "Androgen Receptor and Non-Coding RNAs’ Interaction in Renal Cell Carcinoma." Non-Coding RNA 10, no. 6 (2024): 56. http://dx.doi.org/10.3390/ncrna10060056.

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Renal cell carcinoma (RCC), the most prevalent among the urogenital cancers, accounts for around 3% of new cancer cases worldwide. Significantly, the incidence of RCC has doubled in developed world countries, ranking it as the sixth most common cancer in males, who represent two-thirds of RCC cases. Males with RCC exhibit a higher mortality rate and tend to develop a more aggressive form of the disease than females. Sex-related risk factors, including lifestyle and biological variations, explain this difference. The androgen receptor (AR) oncogenic signaling pathway has been extensively studie

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Huo, Yan, Han Yang, Wenjie Ding, Zhaohe Yuan, and Zunling Zhu. "Exploring the Relationship between Genomic Variation and Phenotype in Ornamental Pomegranate: A Study of Single and Double-Petal Varieties." Horticulturae 9, no. 3 (2023): 361. http://dx.doi.org/10.3390/horticulturae9030361.

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The double-petal varieties of ornamental pomegranate have higher ornamental value and garden development potential than the single-petal varieties but there has been no study on the genomic variation between them. This study aimed to determine the genomic variation between the two kinds of varieties and the relationship between the variation and phenotype by identifying the DNA variation of three single-petal varieties and three double-petal varieties using re-sequencing technology. The results showed that the variation number of each variety was in the order of single nucleotide polymorphisms

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El-Hageen, Hazem M., Aadel M. Alatwi, and Ahmed Nabih Zaki Rashed. "Advanced modulation coding schemes for an optical transceiver systems–based OWC communication channel model." Bulletin of Electrical Engineering and Informatics 10, no. 2 (2021): 767–75. http://dx.doi.org/10.11591/eei.v10i2.2433.

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This paper examines advanced modulation coding schemes for an optical transceiver systems–based optical wireless communication (OWC) channel model. These modulation techniquesinclude On-Off keying and return to zero (RZ)/non–return to zero (NRZ) coding. The signal power level against time and frequency spectral variations are measured. The max. Q factor and min. bit error rate (BER) are estimated and clarified for each modulation code scheme by using an optisystem simulation model. Transmission bit rates of up to 40 Gb/s can be achieved for possible distances up to 500 km with acceptable Q fac

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Bui, Linh T., Heini M. Natri, Lance M. Peter, et al. "Abstract 5780: Functions of genetic variation on gene expression and survival in multiple myeloma." Cancer Research 82, no. 12_Supplement (2022): 5780. http://dx.doi.org/10.1158/1538-7445.am2022-5780.

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Abstract Multiple myeloma (MM) is a malignancy of plasma cells in the bone marrow and the second most common hematological malignancy. MM is characterized by a high degree of heterogeneity and has a hereditary genetic component with relatives of MM patients having a higher risk of disease development. Additionally, MM displays a disparity in occurrence and mortality among sexes with males having a higher risk than females. Although new therapies have significantly improved survival rates, MM remains incurable as most patients experience relapses. Therefore, understanding the genetic control un

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Su, Yi, Xi Yang, Hai Yi, et al. "Identification and Characterization of EBV Genome in NKT Cell Lymphoma." Blood 132, Supplement 1 (2018): 5304. http://dx.doi.org/10.1182/blood-2018-99-118710.

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Abstract Background: Epstein-Barr virus (EBV) is closely related to (Natural Killer/T) NKT cell lymphoma. However, the genomic characteristics of EBV genome in NKT cell lymphoma are poorly understood. Methods: We targeted the EBV gene sequence of 5 samples of NKT cell lymphoma tissue and identified the genomic variation of EBV in NKT cell lymphoma, and compared with other EBV strains by bioinformatics. Results: The EBV genome was successfully retrieved from 5 samples and the variation was detected. We found a total of 3220 mutations in 5 cases of NKT cell lymphoma, including 2996 substitutions

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Hong, Thanh Phuoc, and Ling Guan. "A Scale and Rotational Invariant Key-point Detector based on Sparse Coding." ACM Transactions on Intelligent Systems and Technology 12, no. 3 (2021): 1–19. http://dx.doi.org/10.1145/3452009.

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Most popular hand-crafted key-point detectors such as Harris corner, SIFT, SURF aim to detect corners, blobs, junctions, or other human-defined structures in images. Though being robust with some geometric transformations, unintended scenarios or non-uniform lighting variations could significantly degrade their performance. Hence, a new detector that is flexible with context change and simultaneously robust with both geometric and non-uniform illumination variations is very desirable. In this article, we propose a solution to this challenging problem by incorporating Scale and Rotation Invaria

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Tang, Jianmin, Rong Zou, Taiguo Chen, et al. "Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications." Forests 14, no. 10 (2023): 2069. http://dx.doi.org/10.3390/f14102069.

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Cycas (family Cycadaceae), which spread throughout tropical and subtropical regions, is crucial in conservation biology. Due to subtle morphological variations between species, a solid species-level phylogeny for Cycas is lacking. In the present study, we assembled and analyzed the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide diversity. The Cycas chloroplast genome spans from 162,038 to 162,159 bp and contains 131 genes, including 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparati

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Moutsopoulos, Ilias, Lukas Maischak, Elze Lauzikaite, et al. "noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise." Nucleic Acids Research 49, no. 14 (2021): e83-e83. http://dx.doi.org/10.1093/nar/gkab433.

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Abstract High-throughput sequencing enables an unprecedented resolution in transcript quantification, at the cost of magnifying the impact of technical noise. The consistent reduction of random background noise to capture functionally meaningful biological signals is still challenging. Intrinsic sequencing variability introducing low-level expression variations can obscure patterns in downstream analyses. We introduce noisyR, a comprehensive noise filter to assess the variation in signal distribution and achieve an optimal information-consistency across replicates and samples; this selection a

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ALKANLI, Nevra, and Arzu AY. "Kanser Gelişimi ve Progresyonunda miRNA’LAR VE miRNA Gen Varyasyonları." Gevher Nesibe Journal IESDR 6, no. 13 (2021): 38–45. http://dx.doi.org/10.46648/gnj.226.

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MicroRNAs (miRNAs) are short non-coding RNA class and perform regulatory functions at the post transcriptional level as tumor suppressors or oncogenes. miRNAs are effective in cell differentiation, cell proliferation and apoptosis regulation in normal development processes. miRNA gene variations associated with gene silencing mechanisms, , pri-miRNA, pre-miRNA, mat-miRNA gene variations, genetic cariations in target sites of miRNAs have been identified. Significant changes may occur in miRNA expression levels as a result of genetic variations defined in miRNA genes. Therefore, it is thought th

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Baumgart, Simon J., Ekaterina Nevedomskaya, and Bernard Haendler. "Dysregulated Transcriptional Control in Prostate Cancer." International Journal of Molecular Sciences 20, no. 12 (2019): 2883. http://dx.doi.org/10.3390/ijms20122883.

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Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enh

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Hawkins, Gregory A., David J. Friedman, Lingyi Lu, et al. "Re-Sequencing of the APOL1-APOL4 and MYH9 Gene Regions in African Americans Does Not Identify Additional Risks for CKD Progression." American Journal of Nephrology 42, no. 2 (2015): 99–106. http://dx.doi.org/10.1159/000439448.

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Background: In African Americans (AAs), APOL1 G1 and G2 nephropathy risk variants are associated with non-diabetic end-stage kidney disease (ESKD) in an autosomal recessive pattern. Additional risk and protective genetic variants may be present near the APOL1 loci, since earlier age ESKD is observed in some AAs with one APOL1 renal-risk variant, and because the adjacent gene MYH9 is associated with nephropathy in populations lacking G1 and G2 variants. Methods: Re-sequencing was performed across a ∼275 kb region encompassing the APOL1-APOL4 and MYH9 genes in 154 AA cases with non-diabetic ESKD

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Shi, Ying, Yuan Wan, Xinjian Wang, and Huanhuan Li. "Incorporation of Histogram Intersection and Semantic Information into Non-Negative Local Laplacian Sparse Coding for Image Classification." Mathematics 13, no. 2 (2025): 219. https://doi.org/10.3390/math13020219.

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Traditional sparse coding has proven to be an effective method for image feature representation in recent years, yielding promising results in image classification. However, it faces several challenges, such as sensitivity to feature variations, code instability, and inadequate distance measures. Additionally, image representation and classification often operate independently, potentially resulting in the loss of semantic relationships. To address these issues, a new method is proposed, called Histogram intersection and Semantic information-based Non-negativity Local Laplacian Sparse Coding (

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Amirkhah, Raheleh, Hojjat Naderi-Meshkin, Jaynish Shah, Philip Dunne, and Ulf Schmitz. "The Intricate Interplay between Epigenetic Events, Alternative Splicing and Noncoding RNA Deregulation in Colorectal Cancer." Cells 8, no. 8 (2019): 929. http://dx.doi.org/10.3390/cells8080929.

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Colorectal cancer (CRC) results from a transformation of colonic epithelial cells into adenocarcinoma cells due to genetic and epigenetic instabilities, alongside remodelling of the surrounding stromal tumour microenvironment. Epithelial-specific epigenetic variations escorting this process include chromatin remodelling, histone modifications and aberrant DNA methylation, which influence gene expression, alternative splicing and function of non-coding RNA. In this review, we first highlight epigenetic modulators, modifiers and mediators in CRC, then we elaborate on causes and consequences of e

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Norman, Jane E., Matthew L. Jones, Neil V. Morgan, et al. "Functional Variations In Genes Encoding Platelet G-Protein Coupled Receptors In Unselected and Platelet Function Disorder Populations." Blood 122, no. 21 (2013): 3511. http://dx.doi.org/10.1182/blood.v122.21.3511.3511.

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Abstract Introduction G-protein coupled receptors (GPCRs) are critical mediators of platelet responses to stimulatory and inhibitory agonists. In rare families with mild bleeding, it is recognised that heterozygous loss of function variations in platelet GPCR genes may diminish platelet agonist responses. However, the population prevalence of loss of function variations in these genes is unknown. We have utilised population databases and next generation sequencing from patients with inherited platelet function disorders (IPFD) to describe the extent of genetic variation in the major platelet G

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Sami, Amtul Jamil. "Variations in the Bubaline Growth Hormone Gene in the Coding and Non-Coding Regions." Pakistan Journal of Zoology, 2021. http://dx.doi.org/10.17582/journal.pjz/20191006161054.

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