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  1. Book ; Online: The Transition from Seed to Seedling

    Smolikova, Galina / Medvedev, Sergei

    2022  

    Keywords Research & information: general ; Biology, life sciences ; desiccation tolerance ; DNA methylation ; epigenetics ; germination ; histone modification ; hormonal regulation ; miRNA ; post-germination ; seeds ; acceleration ; imbibition ; biological activity ; indexes ; germination measurements ; seed physiology ; soybean ; velocity ; V. vinifera ; grape seeds ; seed germination ; seedling formation ; seed longevity ; genetics ; quantitative trait loci ; candidate genes ; genebanks ; germinative process ; seedling establishment ; molecular tools ; gene expression ; RNA-seq ; Pisum sativum L. ; transcriptome ; seed
    Language 0|e
    Size 1 electronic resource (132 pages)
    Publisher MDPI - Multidisciplinary Digital Publishing Institute
    Publishing place Basel
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021621754
    ISBN 9783036555997 ; 3036555994
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article: Theoretical Analysis of Sequencing Bioinformatics Algorithms and Beyond.

    Medvedev, Paul

    Communications of the ACM

    2023  Volume 66, Issue 7, Page(s) 118–125

    Language English
    Publishing date 2023-06-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2004542-6
    ISSN 1557-7317 ; 0001-0782
    ISSN (online) 1557-7317
    ISSN 0001-0782
    DOI 10.1145/3571723
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Random walk model of mobility in glass formers.

    Medvedev, Grigori A

    Physical review. E

    2023  Volume 107, Issue 3-1, Page(s) 34122

    Abstract: A mechanism responsible for the generic features of the mean squared displacement and the decay of the orientational autocorrelator of a molecule in a glass forming liquid is poorly understood, where such a mechanism would be critical for creating the ... ...

    Abstract A mechanism responsible for the generic features of the mean squared displacement and the decay of the orientational autocorrelator of a molecule in a glass forming liquid is poorly understood, where such a mechanism would be critical for creating the theory of glass transition. A discrete random walk model is proposed where, instead of a straight line, a walk is along a tortuous path consisting of blocks of switchback ramps. Subdiffusive regime, short-term dynamic heterogeneity, and existence of the α- and β-relaxation processes emerge naturally from the model. The model suggests that slowing of the rate of relaxation may be due to an increase in the number of the switchback ramps per block rather than due to growth of an energy barrier as typically assumed.
    Language English
    Publishing date 2023-04-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.107.034122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Electronic nonequilibrium effect in ultrafast-laser-irradiated solids

    Medvedev, Nikita

    2023  

    Abstract: This paper describes the effects of electronic nonequilibrium in a simulation of ultrafast laser irradiation of materials. The simulation scheme based on tight-binding molecular dynamics, in which the electronic populations are traced with a combined ... ...

    Abstract This paper describes the effects of electronic nonequilibrium in a simulation of ultrafast laser irradiation of materials. The simulation scheme based on tight-binding molecular dynamics, in which the electronic populations are traced with a combined Monte Carlo and Boltzmann equation, enables the modeling of nonequilibrium, nonthermal, and nonadiabatic (electron-phonon coupling) effects simultaneously. The electron-electron thermalization is described within the relaxation-time approximation, which automatically restores various known limits such as instantaneous thermalization (the thermalization time ${\tau}_{e-e} \rightarrow 0$) and Born-Oppenheimer approximation (${\tau}_{e-e} \rightarrow \infty$). The results of the simulation suggest that the non-equilibrium state of the electronic system slows down electron-phonon coupling with respect to the electronic equilibrium case in all studied materials: metals, semiconductors, and insulators. In semiconductors and insulators, it also alters the damage threshold of ultrafast nonthermal phase transitions induced by modification of the interatomic potential due to electronic excitation. It is demonstrated that the models that exclude electron-electron thermalization (using the assumption of ${\tau}_{e-e} \rightarrow \infty$, such as BO or Ehrenfest approximations) may produce qualitatively different results, and a reliable model should include all three effects: electronic nonequilibrium, nonadiabatic electron-ion coupling, and nonthermal evolution of interatomic potential.
    Keywords Condensed Matter - Materials Science
    Subject code 541
    Publishing date 2023-02-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: Materials under XUV irradiation

    Medvedev, Nikita

    effects of structure, size, and temperature

    2023  

    Abstract: This proceeding discusses the impact of XUV/X-ray irradiation on materials, and how their response is affected by temperature, size, and structure. When materials are exposed to intense XUV/X-ray irradiation, they undergo a series of processes ultimately ...

    Abstract This proceeding discusses the impact of XUV/X-ray irradiation on materials, and how their response is affected by temperature, size, and structure. When materials are exposed to intense XUV/X-ray irradiation, they undergo a series of processes ultimately leading to observable structure modification and damage. These effects were studied with a hybrid simulation tool XTANT-3. The code combines several methods in one interconnected model: the photon absorption and electron cascades are simulated with transport Monte Carlo; nonequilibrium kinetics of slow electrons (in the valence and the bottom of the conduction band) is traced with the Boltzmann equation; modeling evolution of the electronic structure and interatomic potential is done with the transferable tight binding method; and the response of the atomic system is simulated with the molecular dynamics. Combining these methods enabled the tracing of the essential effects of irradiation. This brief review summarizes the recent results obtained with this simulation tool.

    Comment: Conference proceeding (to be submitted)
    Keywords Condensed Matter - Materials Science ; Condensed Matter - Other Condensed Matter
    Subject code 530
    Publishing date 2023-03-21
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  6. Article ; Online: Assessment of Cognitive Reserve using Near Infrared Spectroscopy.

    Medvedev, Andrei V

    Journal of analytical techniques and research

    2022  Volume 4, Issue 2, Page(s) 89–101

    Abstract: Cognitive reserve (CR) is the ability to preserve cognitive functions in the presence of brain pathology. In the context of Alzheimer's disease (AD), patients with higher CR show better cognitive performance relative to brain damage therefore higher CR ... ...

    Abstract Cognitive reserve (CR) is the ability to preserve cognitive functions in the presence of brain pathology. In the context of Alzheimer's disease (AD), patients with higher CR show better cognitive performance relative to brain damage therefore higher CR reduces the risk of dementia. There is a strong need to develop a neurophysiological biomarker of CR given the growing interest in understanding protective brain mechanisms in AD. FMRI studies indicate that frontoparietal network plays an important role in cognitive reserve. We calculated intraregional functional connectivity of lateral prefrontal cortex (FC LPFC) using functional near infrared spectroscopy (fNIRS) in the resting state of 13 healthy individuals who were also assessed for IQ and motoric skills (the Purdue Pegboard test, PPT). FC LPFC was found to positively correlate with IQ (a proxy measure of cognitive reserve) while showing a lack of or negative correlation with the PPT scores. The results demonstrate that the cost-effective, noninvasive and widely applicable fNIRS technology can be used to evaluate cognitive reserve in individuals at risk for and patients with AD with possible numerous applications in the context of healthy aging and other age-related cognitive disorders.
    Language English
    Publishing date 2022-05-19
    Publishing country United States
    Document type Journal Article
    ISSN 2687-8038
    ISSN (online) 2687-8038
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Ubiquitin Carboxyl-Terminal Hydrolase L1 and Its Role in Parkinson's Disease.

    Buneeva, Olga / Medvedev, Alexei

    International journal of molecular sciences

    2024  Volume 25, Issue 2

    Abstract: Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson's disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin-proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. ...

    Abstract Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson's disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin-proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson's disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein-protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein-protein interactions, which still need better characterization.
    MeSH term(s) Mice ; Animals ; Parkinson Disease/genetics ; Parkinson Disease/metabolism ; Ubiquitin Thiolesterase/metabolism ; Ubiquitin/metabolism ; Protein Processing, Post-Translational ; Ubiquitins/metabolism
    Chemical Substances Ubiquitin Thiolesterase (EC 3.4.19.12) ; Ubiquitin ; Ubiquitins
    Language English
    Publishing date 2024-01-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25021303
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: The detection of absence seizures using cross-frequency coupling analysis with a deep learning network.

    Medvedev, Andrei V / Lehmann, Bar

    Research square

    2024  

    Abstract: High frequency oscillations are important novel biomarkers of epileptogenic tissue. The interaction of oscillations across different time scales is revealed as cross-frequency coupling (CFC) representing a high-order structure in the functional ... ...

    Abstract High frequency oscillations are important novel biomarkers of epileptogenic tissue. The interaction of oscillations across different time scales is revealed as cross-frequency coupling (CFC) representing a high-order structure in the functional organization of brain rhythms. New artificial intelligence methods such as deep learning neural networks can provide powerful tools for automated analysis of EEG. Here we present a Stacked Sparse Autoencoder (SSAE) trained to recognize absence seizure activity based on the cross-frequency patterns within scalp EEG. We used EEG records from the Temple University Hospital database. Absence seizures (n = 94) from 12 patients were taken into analysis along with segments of background activity. Half of the records were selected randomly for network training and the second half were used for testing. Power-to-power coupling was calculated between all frequencies 2-120 Hz pairwise using the EEGLAB toolbox. The resulting CFC matrices were used as training or testing inputs to the autoencoder. The trained network was able to recognize background and seizure segments (not used in training) with a sensitivity of 96.3%, specificity of 99.8% and overall accuracy of 98.5%. Our results provide evidence that the SSAE neural networks can be used for automated detection of absence seizures within scalp EEG.
    Language English
    Publishing date 2024-04-10
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-4178484/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: ESKEMAP: exact sketch-based read mapping.

    Schulz, Tizian / Medvedev, Paul

    Algorithms for molecular biology : AMB

    2024  Volume 19, Issue 1, Page(s) 19

    Abstract: Background: Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a "similar sequence". Traditionally, "similar sequence" was defined as having a high alignment score and read mappers were ... ...

    Abstract Background: Given a sequencing read, the broad goal of read mapping is to find the location(s) in the reference genome that have a "similar sequence". Traditionally, "similar sequence" was defined as having a high alignment score and read mappers were viewed as heuristic solutions to this well-defined problem. For sketch-based mappers, however, there has not been a problem formulation to capture what problem an exact sketch-based mapping algorithm should solve. Moreover, there is no sketch-based method that can find all possible mapping positions for a read above a certain score threshold.
    Results: In this paper, we formulate the problem of read mapping at the level of sequence sketches. We give an exact dynamic programming algorithm that finds all hits above a given similarity threshold. It runs in
    Language English
    Publishing date 2024-05-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2224970-9
    ISSN 1748-7188
    ISSN 1748-7188
    DOI 10.1186/s13015-024-00261-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Worldwide divergence of values.

    Jackson, Joshua Conrad / Medvedev, Danila

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2650

    Abstract: Social scientists have long debated the nature of cultural change in a modernizing and globalizing world. Some scholars predicted that national cultures would converge by adopting social values typical of Western democracies. Others predicted that ... ...

    Abstract Social scientists have long debated the nature of cultural change in a modernizing and globalizing world. Some scholars predicted that national cultures would converge by adopting social values typical of Western democracies. Others predicted that cultural differences in values would persist or even increase over time. We test these competing predictions by analyzing survey data from 1981 to 2022 (n = 406,185) from 76 national cultures. We find evidence of global value divergence. Values emphasizing tolerance and self-expression have diverged most sharply, especially between high-income Western countries and the rest of the world. We also find that countries with similar per-capita GDP levels have held similar values over the last 40 years. Over time, however, geographic proximity has emerged as an increasingly strong correlate of value similarity, indicating that values have diverged globally but converged regionally.
    Language English
    Publishing date 2024-04-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46581-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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