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Article ; Online: Discriminative Frequencies and Temporal EEG Segmentation in the Motor Imagery Classification Approach

Dmitry Lazurenko / Igor Shepelev / Dmitry Shaposhnikov / Anton Saevskiy / Valery Kiroy

Applied Sciences, Vol 12, Iss 2736, p

2022 Volume 2736

Abstract: A linear discriminant analysis transformation-based approach to the classification of three different motor imagery types for brain–computer interfaces was considered. The study involved 16 conditionally healthy subjects (12 men, 4 women, mean age of 21 ... ...

Abstract	A linear discriminant analysis transformation-based approach to the classification of three different motor imagery types for brain–computer interfaces was considered. The study involved 16 conditionally healthy subjects (12 men, 4 women, mean age of 21.5 years). First, the search for subject-specific discriminative frequencies was conducted in the task of movement-related activity. This procedure was shown to increase the classification accuracy compared to the conditional common spatial pattern (CSP) algorithm, followed by a linear classifier considered as a baseline approach. In addition, an original approach to finding discriminative temporal segments for each motor imagery was tested. This led to a further increase in accuracy under the conditions of using Hjorth parameters and interchannel correlation coefficients as features calculated for the EEG segments. In particular, classification by the latter feature led to the best accuracy of 71.6%, averaged over all subjects (intrasubject classification), and, surprisingly, it also allowed us to obtain a comparable value of intersubject classification accuracy of 68%. Furthermore, scatter plots demonstrated that two out of three pairs of motor imagery were discriminated by the approach presented.
Keywords	EEG ; brain–computer interfaces ; motor imagery ; machine learning ; cross-correlation ; frequency power spectrum ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2022-03-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: Prevalence of lumbosacral transitional vertebra among 4816 consecutive patients with low back pain: A computed tomography, magnetic resonance imaging, and plain radiographic study with novel classification schema.

Byvaltsev, Vadim A / Kalinin, Andrei A / Shepelev, Valery V / Pestryakov, Yurii Ya / Aliyev, Marat A / Hozeev, Dmitriy V / Biryuchkov, Mikhail Y / Kundubayev, Rustem A / Riew, K Daniel

Journal of craniovertebral junction & spine

2023 Volume 14, Issue 1, Page(s) 35–43

Abstract: Study design: A retrospective single-center study.: Background: The prevalence of the lumbosacral anomalies remains controversial. The existing classification to characterize these anomalies is more complex than necessary for clinical use.: Purpose! ...

Abstract	Study design: A retrospective single-center study. Background: The prevalence of the lumbosacral anomalies remains controversial. The existing classification to characterize these anomalies is more complex than necessary for clinical use. Purpose: To assessment of the prevalence of lumbosacral transitional vertebra (LSTV) in patients with low back pain and the development of clinically relevant classification to describe these anomalies. Materials and methods: During the period from 2007 to 2017, all cases of LSTV were preoperatively verified, and classified according to Castellvi, as well as O'Driscoll. We then developed modifications of those classifications that are simpler, easier to remember, and clinically relevant. At the surgical level, this was assessed intervertebral disc and facet joint degeneration. Results: The prevalence of the LSTV was 8.1% (389/4816). The most common L5 transverse process anomaly type was fused, unilaterally or bilaterally (48%), to the sacrum and were O'Driscoll's III (40.1%) and IV (35.8%). The most common type of S1-2 disc was a lumbarized disc (75.9%), where the disc's anterior-posterior diameter was equal to the L5-S1 disc diameter. In most cases, neurological compression symptoms (85.5%) were verified to be due to spinal stenosis (41.5%) or herniated disc (39.5%). In the majority of patients without neural compression, the clinical symptoms were due to mechanical back pain (58.8%). Conclusions: LSTV is a fairly common pathology of the lumbosacral junction, occurring in 8.1% of the patients in our series (389 out of 4,816 cases). The most common types were Castellvi's type IIA (30.9%) and IIIA (34.9%) and were O'Driscoll's III (40.1%) and IV (35.8%).
Language	English
Publishing date	2023-03-13
Publishing country	India
Document type	Journal Article
ZDB-ID	2573344-8
ISSN	0976-9285 ; 0974-8237
ISSN (online)	0976-9285
ISSN	0974-8237
DOI	10.4103/jcvjs.jcvjs_149_22
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Article ; Online: The variation and evolution of complete human centromeres.

Nature

2024 Volume 629, Issue 8010, Page(s) 136–145

Abstract: Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large ... ...

Abstract	Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size
MeSH term(s)	Humans ; Centromere/genetics ; Centromere/metabolism ; Evolution, Molecular ; Animals ; Centromere Protein A/genetics ; Centromere Protein A/metabolism ; DNA, Satellite/genetics ; Genome, Human/genetics ; Pan troglodytes/genetics ; DNA Methylation/genetics ; Macaca/genetics ; Kinetochores/metabolism ; Pongo/genetics ; Genetic Variation ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosomal Proteins, Non-Histone/genetics ; Polymorphism, Single Nucleotide/genetics ; Autoantigens/genetics ; Autoantigens/metabolism
Chemical Substances	Centromere Protein A ; DNA, Satellite ; CENPA protein, human ; Chromosomal Proteins, Non-Histone ; Autoantigens
Language	English
Publishing date	2024-04-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-024-07278-3
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Article: 3D-printed cranial models simulating operative field depth for microvascular training in neurosurgery.

Byvaltsev, Vadim / Polkin, Roman / Bereznyak, Dmitry / Giers, Morgan B / Hernandez, Phillip A / Shepelev, Valery / Aliyev, Marat

Surgical neurology international

2021 Volume 12, Page(s) 213

Abstract: Background: The skills required for neurosurgical operations using microsurgical techniques in a deep operating field are difficult to master in the operating room without risk to patients. Although there are many microsurgical training models, most do ... ...

Abstract	Background: The skills required for neurosurgical operations using microsurgical techniques in a deep operating field are difficult to master in the operating room without risk to patients. Although there are many microsurgical training models, most do not use a skull model to simulate a deep field. To solve this problem, 3D models were created to provide increased training in the laboratory before the operating room, improving patient safety. Methods: A patient's head was scanned using computed tomography. The data were reconstructed and converted into a standard 3D printing file. The skull was printed with several openings to simulate common surgical approaches. These models were then used to create a deep operating field while practicing on a chicken thigh (femoral artery anastomosis) and on a rat (abdominal aortic anastomosis). Results: The advantages of practicing with the 3D printed models were clearly demonstrated by our trainees, including appropriate hand position on the skull, becoming comfortable with the depth of the anastomosis, and simulating proper skull angle and rigid fixation. One limitation is the absence of intracranial structures, which is being explored in future work. Conclusion: This neurosurgical model can improve microsurgery training by recapitulating the depth of a real operating field. Improved training can lead to increased accuracy and efficiency of surgical procedures, thereby minimizing the risk to patients.
Language	English
Publishing date	2021-05-10
Publishing country	United States
Document type	Journal Article
ISSN	2229-5097
ISSN	2229-5097
DOI	10.25259/SNI_849_2020
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Article: The variation and evolution of complete human centromeres.

Logsdon, Glennis A / Rozanski, Allison N / Ryabov, Fedor / Potapova, Tamara / Shepelev, Valery A / Mao, Yafei / Rautiainen, Mikko / Koren, Sergey / Nurk, Sergey / Porubsky, David / Lucas, Julian K / Hoekzema, Kendra / Munson, Katherine M / Gerton, Jennifer L / Phillippy, Adam M / Alexandrov, Ivan A / Eichler, Evan E

bioRxiv : the preprint server for biology

2023

Abstract: We completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find that ... ...

Abstract	We completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find that centromere single-nucleotide variation can increase by up to 4.1-fold relative to other genomic regions, with the caveat that up to 45.8% of centromeric sequence, on average, cannot be reliably aligned with current methods due to the emergence of new α-satellite higher-order repeat (HOR) structures and two to threefold differences in the length of the centromeres. The extent to which this occurs differs depending on the chromosome and haplotype. Comparing the two sets of complete human centromeres, we find that eight harbor distinctly different α-satellite HOR array structures and four contain novel α-satellite HOR variants in high abundance. DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by at least 500 kbp-a property not readily associated with novel α-satellite HORs. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan, and macaque genomes. Comparative analyses reveal nearly complete turnover of α-satellite HORs, but with idiosyncratic changes in structure characteristic to each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the p- and q-arms of human chromosomes and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
Language	English
Publishing date	2023-05-30
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.30.542849
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Article: Comparative genomics of macaques and integrated insights into genetic variation and population history.

Zhang, Shilong / Xu, Ning / Fu, Lianting / Yang, Xiangyu / Li, Yamei / Yang, Zikun / Feng, Yu / Ma, Kaiyue / Jiang, Xinrui / Han, Junmin / Hu, Ruixing / Zhang, Lu / de Gennaro, Luciana / Ryabov, Fedor / Meng, Dan / He, Yaoxi / Wu, Dongya / Yang, Chentao / Paparella, Annalisa /

Mao, Yuxiang / Bian, Xinyan / Lu, Yong / Antonacci, Francesca / Ventura, Mario / Shepelev, Valery A / Miga, Karen H / Alexandrov, Ivan A / Logsdon, Glennis A / Phillippy, Adam M / Su, Bing / Zhang, Guojie / Eichler, Evan E / Lu, Qing / Shi, Yongyong / Sun, Qiang / Mao, Yafei

bioRxiv : the preprint server for biology

2024

Abstract: The crab-eating macaques ( ...

Abstract	The crab-eating macaques (
Language	English
Publishing date	2024-04-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.07.588379
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Article: Advances in the Exon-Intron Database (EID).

Shepelev, Valery / Fedorov, Alexei

Briefings in bioinformatics

2006 Volume 7, Issue 2, Page(s) 178–185

Abstract: Investigation of exon-intron gene structures is a non-trivial task due to enormous expansions of the eukaryotic genomes, great variety of gene forms, and the imperfectness in sequence data. A number of available informational systems on various gene ... ...

Abstract	Investigation of exon-intron gene structures is a non-trivial task due to enormous expansions of the eukaryotic genomes, great variety of gene forms, and the imperfectness in sequence data. A number of available informational systems on various gene characteristics complement each other and are indispensable for many genomic studies. Among them, the Exon-Intron Database (EID) is a good choice for large-scale computational examination of exon/intron structure and splicing. It has many internal filters that control for sequence quality, consistency of gene descriptions, accordance to standards, and possible errors. New innovations in EID are described. The collection of exons and introns has been extended beyond coding regions and current versions of EID contain data on untranslated regions of gene sequences as well. Intron-less genes are included as a special part of EID. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. Examples of statistical analyses of gene sequences using EID are provided. We present the latest data on our comparison of intron positions in 11,025 orthologous genes of human, mouse and rat, and find no convincing cases of intron gain. We discuss relevant data-quality issues of genomic databases. In particular, 5% of genes in genomic databases contain internal stop codons. This fact is due to a combination of biological reasons and also to errors in sequence annotations. The EID is freely available at www.meduohio.edu/bioinfo/eid/.
MeSH term(s)	Base Sequence ; Chromosome Mapping/methods ; DNA, Recombinant/genetics ; Database Management Systems ; Databases, Genetic ; Documentation/methods ; Exons/genetics ; Information Storage and Retrieval/methods ; Introns/genetics ; Molecular Sequence Data ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; User-Computer Interface
Chemical Substances	DNA, Recombinant
Language	English
Publishing date	2006-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2068142-2
ISSN	1467-5463
ISSN	1467-5463
DOI	10.1093/bib/bbl003
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Article ; Online: The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes.

Shepelev, Valery A / Alexandrov, Alexander A / Yurov, Yuri B / Alexandrov, Ivan A

PLoS genetics

2009 Volume 5, Issue 9, Page(s) e1000641

Abstract: Alpha satellite domains that currently function as centromeres of human chromosomes are flanked by layers of older alpha satellite, thought to contain dead centromeres of primate progenitors, which lost their function and the ability to homogenize ... ...

Abstract	Alpha satellite domains that currently function as centromeres of human chromosomes are flanked by layers of older alpha satellite, thought to contain dead centromeres of primate progenitors, which lost their function and the ability to homogenize satellite repeats, upon appearance of a new centromere. Using cladistic analysis of alpha satellite monomers, we elucidated complete layer patterns on chromosomes 8, 17, and X and related them to each other and to primate alpha satellites. We show that discrete and chronologically ordered alpha satellite layers are partially symmetrical around an active centromere and their succession is partially shared in non-homologous chromosomes. The layer structure forms a visual representation of the human evolutionary lineage with layers corresponding to ancestors of living primates and to entirely fossil taxa. Surprisingly, phylogenetic comparisons suggest that alpha satellite arrays went through periods of unusual hypermutability after they became "dead" centromeres. The layer structure supports a model of centromere evolution where new variants of a satellite repeat expanded periodically in the genome by rounds of inter-chromosomal transfer/amplification. Each wave of expansion covered all or many chromosomes and corresponded to a new primate taxon. Complete elucidation of the alpha satellite phylogenetic record would give a unique opportunity to number and locate the positions of major extinct taxa in relation to human ancestors shared with extant primates. If applicable to other satellites in non-primate taxa, analysis of centromeric layers could become an invaluable tool for phylogenetic studies.
MeSH term(s)	Animals ; Centromere/genetics ; Chromosomes, Human/genetics ; DNA, Satellite ; Evolution, Molecular ; Humans ; Male ; Molecular Sequence Data ; Phylogeny ; Primates/classification ; Primates/genetics
Chemical Substances	DNA, Satellite
Language	English
Publishing date	2009-09-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1000641
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Article: Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans.

Shao, Xiang / Shepelev, Valery / Fedorov, Alexei

Bioinformatics (Oxford, England)

2006 Volume 22, Issue 6, Page(s) 692–698

Abstract: Motivation: Using bioinformatic approaches we aimed to characterize poorly understood abnormalities in splicing known as exon scrambling, exon repetition and trans-splicing.: Results: We developed a software package that allows large-scale comparison ...

Abstract	Motivation: Using bioinformatic approaches we aimed to characterize poorly understood abnormalities in splicing known as exon scrambling, exon repetition and trans-splicing. Results: We developed a software package that allows large-scale comparison of all human expressed sequence tags (EST) sequences to the entire set of human gene sequences. Among 5,992,495 EST sequences, 401 cases of exon repetition and 416 cases of exon scrambling were found. The vast majority of identified ESTs contain fragments rather than full-length repeated or scrambled exons. Their structures suggest that the scrambled or repeated exon fragments may have arisen in the process of cDNA cloning and not from splicing abnormalities. Nevertheless, we found 11 cases of full-length exon repetition showing that this phenomenon is real yet very rare. In searching for examples of trans-splicing, we looked only at reproducible events where at least two independent ESTs represent the same putative trans-splicing event. We found 15 ESTs representing five types of putative trans-splicing. However, all 15 cases were derived from human malignant tissues and could have resulted from genomic rearrangements. Our results provide support for a very rare but physiological occurrence of exon repetition, but suggest that apparent exon scrambling and trans-splicing result, respectively, from in vitro artifact and gene-level abnormalities. Availability: Exon-Intron Database (EID) is available at http://www.meduohio.edu/bioinfo/eid. Programs are available at http://www.meduohio.edu/bioinfo/software.html. The Laboratory website is available at http://www.meduohio.edu/medicine/fedorov Supplementary information: Supplementary file is available at http://www.meduohio.edu/bioinfo/software.html.
MeSH term(s)	Algorithms ; Chromosome Mapping/methods ; Computational Biology/methods ; DNA Mutational Analysis/methods ; Databases, Genetic ; Exons/genetics ; Expressed Sequence Tags ; Genetic Variation/genetics ; Genome, Human ; Humans ; Repetitive Sequences, Nucleic Acid/genetics ; Sequence Alignment/methods ; Sequence Analysis, DNA/methods ; Trans-Splicing/genetics
Language	English
Publishing date	2006-03-15
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4803
ISSN	1367-4803
DOI	10.1093/bioinformatics/bti795
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Article ; Online: Clusters of alpha satellite on human chromosome 21 are dispersed far onto the short arm and lack ancient layers.

Ziccardi, William / Zhao, Chongjian / Shepelev, Valery / Uralsky, Lev / Alexandrov, Ivan / Andreeva, Tatyana / Rogaev, Evgeny / Bun, Christopher / Miller, Emily / Putonti, Catherine / Doering, Jeffrey

Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

2016 Volume 24, Issue 3, Page(s) 421–436

Abstract: Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes ... ...

Abstract	Human alpha satellite (AS) sequence domains that currently function as centromeres are typically flanked by layers of evolutionarily older AS that presumably represent the remnants of earlier primate centromeres. Studies on several human chromosomes reveal that these older AS arrays are arranged in an age gradient, with the oldest arrays farthest from the functional centromere and arrays progressively closer to the centromere being progressively younger. The organization of AS on human chromosome 21 (HC21) has not been well-characterized. We have used newly available HC21 sequence data and an HC21p YAC map to determine the size, organization, and location of the AS arrays, and compared them to AS arrays found on other chromosomes. We find that the majority of the HC21 AS sequences are present on the p-arm of the chromosome and are organized into at least five distinct isolated clusters which are distributed over a larger distance from the functional centromere than that typically seen for AS on other chromosomes. Using both phylogenetic and L1 element age estimations, we found that all of the HC21 AS clusters outside the functional centromere are of a similar relatively recent evolutionary origin. HC21 contains none of the ancient AS layers associated with early primate evolution which is present on other chromosomes, possibly due to the fact that the p-arm of HC21 and the other acrocentric chromosomes underwent substantial reorganization about 20 million years ago.
MeSH term(s)	Base Sequence ; Centromere/genetics ; Chromosome Mapping ; Chromosomes, Artificial, Bacterial/genetics ; Chromosomes, Human, Pair 21/genetics ; DNA, Satellite/genetics ; Evolution, Molecular ; Humans ; In Situ Hybridization, Fluorescence ; Multigene Family/genetics ; Phylogeny ; Repetitive Sequences, Nucleic Acid
Chemical Substances	DNA, Satellite
Language	English
Publishing date	2016
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1161632-5
ISSN	1573-6849 ; 0967-3849
ISSN (online)	1573-6849
ISSN	0967-3849
DOI	10.1007/s10577-016-9530-z
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