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  1. Article ; Online: Inverted Meckel Diverticulum in a 13-Year-Old Boy.

    Özbey, Hüseyin / Morozov, Dmitry Anatolievich

    Journal of pediatric gastroenterology and nutrition

    2023  Volume 77, Issue 2, Page(s) e48

    MeSH term(s) Male ; Humans ; Adolescent ; Meckel Diverticulum/complications ; Meckel Diverticulum/diagnosis ; Meckel Diverticulum/surgery ; Diverticulum ; Intussusception
    Language English
    Publishing date 2023-04-28
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 603201-1
    ISSN 1536-4801 ; 0277-2116
    ISSN (online) 1536-4801
    ISSN 0277-2116
    DOI 10.1097/MPG.0000000000003820
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1728: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  2. Article ; Online: Abdominal pain as the presentation of imperforate hymen in a teenage girl.

    Özbey, Hüseyin / Morozov, Dmitry / Morozov, Dmitry Anatolievich

    Pediatrics international : official journal of the Japan Pediatric Society

    2022  Volume 64, Issue 1, Page(s) e15168

    MeSH term(s) Abdominal Pain/diagnosis ; Abdominal Pain/etiology ; Adolescent ; Congenital Abnormalities ; Female ; Humans ; Hymen/abnormalities ; Hymen/surgery ; Ultrasonography
    Language English
    Publishing date 2022-04-22
    Publishing country Australia
    Document type Journal Article
    ZDB-ID 1470376-2
    ISSN 1442-200X ; 1328-8067
    ISSN (online) 1442-200X
    ISSN 1328-8067
    DOI 10.1111/ped.15168
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    Zs.A 848: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  3. Book ; Online: Cross-Domain Robustness of Transformer-based Keyphrase Generation

    Glazkova, Anna / Morozov, Dmitry

    2023  

    Abstract: Modern models for text generation show state-of-the-art results in many natural language processing tasks. In this work, we explore the effectiveness of abstractive text summarization models for keyphrase selection. A list of keyphrases is an important ... ...

    Abstract Modern models for text generation show state-of-the-art results in many natural language processing tasks. In this work, we explore the effectiveness of abstractive text summarization models for keyphrase selection. A list of keyphrases is an important element of a text in databases and repositories of electronic documents. In our experiments, abstractive text summarization models fine-tuned for keyphrase generation show quite high results for a target text corpus. However, in most cases, the zero-shot performance on other corpora and domains is significantly lower. We investigate cross-domain limitations of abstractive text summarization models for keyphrase generation. We present an evaluation of the fine-tuned BART models for the keyphrase selection task across six benchmark corpora for keyphrase extraction including scientific texts from two domains and news texts. We explore the role of transfer learning between different domains to improve the BART model performance on small text corpora. Our experiments show that preliminary fine-tuning on out-of-domain corpora can be effective under conditions of a limited number of samples.

    Comment: Presented at the XXV International Conference "Data Analytics and Management in Data Intensive Domains" (DAMDID/RCDL), October 2023
    Keywords Computer Science - Computation and Language ; Computer Science - Artificial Intelligence ; Computer Science - Machine Learning ; 68T50 ; I.2.7 ; I.7.m ; H.3.3
    Publishing date 2023-12-17
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Hypospadias surgery, erectile dysfunction and the distal ligament.

    Özbey, Hüseyin / Morozov, Dmitry

    Journal of pediatric urology

    2021  Volume 17, Issue 4, Page(s) 592–593

    MeSH term(s) Erectile Dysfunction/etiology ; Humans ; Hypospadias/surgery ; Ligaments ; Male ; Urethral Stricture/surgery ; Urologic Surgical Procedures, Male
    Language English
    Publishing date 2021-06-09
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 2237683-5
    ISSN 1873-4898 ; 1477-5131
    ISSN (online) 1873-4898
    ISSN 1477-5131
    DOI 10.1016/j.jpurol.2021.06.003
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    Zs.A 6387: Show issues Location:
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  5. Book ; Online: Applying Transformer-based Text Summarization for Keyphrase Generation

    Glazkova, Anna / Morozov, Dmitry

    2022  

    Abstract: Keyphrases are crucial for searching and systematizing scholarly documents. Most current methods for keyphrase extraction are aimed at the extraction of the most significant words in the text. But in practice, the list of keyphrases often includes words ... ...

    Abstract Keyphrases are crucial for searching and systematizing scholarly documents. Most current methods for keyphrase extraction are aimed at the extraction of the most significant words in the text. But in practice, the list of keyphrases often includes words that do not appear in the text explicitly. In this case, the list of keyphrases represents an abstractive summary of the source text. In this paper, we experiment with popular transformer-based models for abstractive text summarization using four benchmark datasets for keyphrase extraction. We compare the results obtained with the results of common unsupervised and supervised methods for keyphrase extraction. Our evaluation shows that summarization models are quite effective in generating keyphrases in the terms of the full-match F1-score and BERTScore. However, they produce a lot of words that are absent in the author's list of keyphrases, which makes summarization models ineffective in terms of ROUGE-1. We also investigate several ordering strategies to concatenate target keyphrases. The results showed that the choice of strategy affects the performance of keyphrase generation.

    Comment: 15 pages, 4 figures. DAMDID-2022
    Keywords Computer Science - Computation and Language ; Computer Science - Artificial Intelligence ; Computer Science - Machine Learning ; 68T50 ; I.2.7 ; I.7.m ; H.3.3
    Subject code 410
    Publishing date 2022-09-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: The Photocycle of Bacteriophytochrome Is Initiated by Counterclockwise Chromophore Isomerization.

    Morozov, Dmitry / Modi, Vaibhav / Mironov, Vladimir / Groenhof, Gerrit

    The journal of physical chemistry letters

    2022  Volume 13, Issue 20, Page(s) 4538–4542

    Abstract: Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics ... ...

    Abstract Photoactivation of bacteriophytochrome involves a cis-trans photoisomerization of a biliverdin chromophore, but neither the precise sequence of events nor the direction of the isomerization is known. Here, we used nonadiabatic molecular dynamics simulations on the photosensory protein dimer to resolve the isomerization mechanism in atomic detail. In our simulations the photoisomerization of the D ring occurs in the counterclockwise direction. On a subpicosecond time scale, the photoexcited chromophore adopts a short-lived intermediate with a highly twisted configuration stabilized by an extended hydrogen-bonding network. Within tens of picoseconds, these hydrogen bonds break, allowing the chromophore to adopt a more planar configuration, which we assign to the early Lumi-R state. The isomerization process is completed via helix inversion of the biliverdin chromophore to form the late Lumi-R state. The mechanistic insights into the photoisomerization process are essential to understand how bacteriophytochrome has evolved to mediate photoactivation and to engineer this protein for new applications.
    MeSH term(s) Bacterial Proteins/chemistry ; Biliverdine/chemistry ; Biliverdine/metabolism ; Hydrogen Bonding ; Isomerism ; Molecular Dynamics Simulation
    Chemical Substances Bacterial Proteins ; Biliverdine (O9MIA842K9)
    Language English
    Publishing date 2022-05-16
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.2c00899
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Book ; Online: Protein-protein docking using a tensor train black-box optimization method

    Morozov, Dmitry / Melnikov, Artem / Shete, Vishal / Perelshtein, Michael

    2023  

    Abstract: Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with various ligands. ... ...

    Abstract Black-box optimization methods play an important role in many fields of computational simulation. In particular, such methods are often used in the design and modelling of biological systems, including proteins and their complexes with various ligands. This work is mainly focused on the protein-protein docking that plays a key role in modern drug-design workflows. We develop a black-box approach for such docking problems using a novel technique based on the tensor-train decomposition of high-dimensional interaction functions. Our method shows an advantage in terms of the discovered global minima and has a high potential for further implementation on a wide range of devices, including graphical processing units and quantum processing units.

    Comment: 6 pages, 3 figures, 1 table
    Keywords Quantitative Biology - Biomolecules ; Physics - Biological Physics ; J.2 ; J.3 ; I.6.3
    Publishing date 2023-02-07
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Multi-scale molecular dynamics simulations of enhanced energy transfer in organic molecules under strong coupling.

    Sokolovskii, Ilia / Tichauer, Ruth H / Morozov, Dmitry / Feist, Johannes / Groenhof, Gerrit

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6613

    Abstract: Exciton transport can be enhanced in the strong coupling regime where excitons hybridize with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments ... ...

    Abstract Exciton transport can be enhanced in the strong coupling regime where excitons hybridize with confined light modes to form polaritons. Because polaritons have group velocity, their propagation should be ballistic and long-ranged. However, experiments indicate that organic polaritons propagate in a diffusive manner and more slowly than their group velocity. Here, we resolve this controversy by means of molecular dynamics simulations of Rhodamine molecules in a Fabry-Pérot cavity. Our results suggest that polariton propagation is limited by the cavity lifetime and appears diffusive due to reversible population transfers between polaritonic states that propagate ballistically at their group velocity, and dark states that are stationary. Furthermore, because long-lived dark states transiently trap the excitation, propagation is observed on timescales beyond the intrinsic polariton lifetime. These insights not only help to better understand and interpret experimental observations, but also pave the way towards rational design of molecule-cavity systems for coherent exciton transport.
    Language English
    Publishing date 2023-10-19
    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/s41467-023-42067-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Predicting Mutation-Induced Changes in the Electronic Properties of Photosynthetic Proteins from First Principles: The Fenna-Matthews-Olson Complex Example.

    Kim, Yongbin / Mitchell, Zach / Lawrence, Jack / Morozov, Dmitry / Savikhin, Sergei / Slipchenko, Lyudmila V

    The journal of physical chemistry letters

    2023  Volume 14, Issue 31, Page(s) 7038–7044

    Abstract: Multiscale molecular modeling is utilized to predict optical absorption and circular dichroism spectra of two single-point mutants of the Fenna-Matthews-Olson photosynthetic pigment-protein complex. The modeling approach combines classical molecular ... ...

    Abstract Multiscale molecular modeling is utilized to predict optical absorption and circular dichroism spectra of two single-point mutants of the Fenna-Matthews-Olson photosynthetic pigment-protein complex. The modeling approach combines classical molecular dynamics simulations with structural refinement of photosynthetic pigments and calculations of their excited states in a polarizable protein environment. The only experimental input to the modeling protocol is the X-ray structure of the wild-type protein. The first-principles modeling reproduces changes in the experimental optical spectra of the considered mutants, Y16F and Q198V. Interestingly, the Q198V mutation has a negligible effect on the electronic properties of the targeted bacteriochlorophyll
    MeSH term(s) Light-Harvesting Protein Complexes/chemistry ; Bacterial Proteins/chemistry ; Photosynthetic Reaction Center Complex Proteins/chemistry ; Molecular Dynamics Simulation ; Mutation
    Chemical Substances Light-Harvesting Protein Complexes ; Bacterial Proteins ; Photosynthetic Reaction Center Complex Proteins
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.3c01461
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Renovation of former industrial areas by BREEAM in city of London

    Telichenko Valery / Benuzh Andrey / Morozov Dmitry

    E3S Web of Conferences, Vol 97, p

    2019  Volume 01030

    Abstract: The main focus at this article on BREEAM Community scheme which planning of large-scale developments taking into account the use of former industrial areas. Construction on such lands of new modern areas is beneficial for both the developer and the city. ...

    Abstract The main focus at this article on BREEAM Community scheme which planning of large-scale developments taking into account the use of former industrial areas. Construction on such lands of new modern areas is beneficial for both the developer and the city. In this case, it is ideally possible to show the use of “green” technologies and standards with aim of increasing the environmental situation of the areas, the creation of reactionary zones. The article describes three steps involved in the assessment of sustainability at the masterplanning level and five assessment categories which are considered through appropriate criteria. Was made a diagram of division into types of reconstructed objects and their inherent functions after reconstruction. Considered an example of Renovation of former industrial areas by BREEAM at King’s Cross in London.
    Keywords Environmental sciences ; GE1-350
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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