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  1. Article ; Online: Impact of the Crystal Structure of Silica Nanoparticles on Rhodamine 6G Adsorption: A Molecular Dynamics Study.

    Doveiko, Daniel / Kubiak-Ossowska, Karina / Chen, Yu

    ACS omega

    2024  Volume 9, Issue 3, Page(s) 4123–4136

    Abstract: Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved ... ...

    Abstract Understanding the mechanism of adsorption of Rhodamine 6G (R6G) to various crystal structures of silica nanoparticles (SNPs) is important to elucidate the impact of dye size when measuring the size of the dye-SNP complex via the time-resolved fluorescence anisotropy method. In this work, molecular dynamics (MD) simulations were used to get an insight into the R6G adsorption process, which cannot be observed using experimental methods. It was found that at low pH, α-Cristobalite structured SNPs have a strong affinity to R6G; however, at high pH, more surface silanol groups undergo ionization when compared with α-Quartz, preventing the adsorption. Therefore, α-Quartz structured SNPs are more suitable for R6G adsorption at high pH than the α-Cristobalite ones. Furthermore, it was found that stable adsorption can occur only when the R6G xanthene core is oriented flat with respect to the SNP surface, indicating that the dye size does not contribute significantly to the measured size of the dye-SNP complex. The requirement of correct dipole moment orientation indicates that only one R6G molecule can adsorb on any sized SNP, and the R6G layer formation on SNP is not possible. Moreover, the dimerization process of R6G and its competition with the adsorption has been explored. It has been shown that the highest stable R6G aggregate is a dimer, and in this form, R6G does not adsorb to SNPs. Finally, using steered molecular dynamics (SMD) with constant-velocity pulling, the binding energies of R6G dimers and R6G complexes with both α-Quartz and α-Cristobalite SNPs of 40 Å diameter were estimated. These confirm that R6G adsorption is most stable on 40 Å α-Quartz at pH 7, although dimerization is equally possible.
    Language English
    Publishing date 2024-01-09
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.3c06657
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Asthma in elderly and coronavirus disease 2019: Results of 90-day post-hospital follow-up.

    Avdeev, Sergey N / Gaynitdinova, Viliya V / Pozdnakova, Anna A / Yu Chikina, Svetlana / Kosobokova, Karina A

    Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology

    2023  Volume 131, Issue 5, Page(s) 663–664

    MeSH term(s) Humans ; Aged ; COVID-19 ; Follow-Up Studies ; Asthma/epidemiology ; Age Factors ; Hospitals
    Language English
    Publishing date 2023-08-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1228189-x
    ISSN 1534-4436 ; 0003-4738 ; 1081-1206
    ISSN (online) 1534-4436
    ISSN 0003-4738 ; 1081-1206
    DOI 10.1016/j.anai.2023.08.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Recent advances in dental zirconia: 15 years of material and processing evolution.

    Cesar, Paulo Francisco / Miranda, Ranulfo Benedito de Paula / Santos, Karina Felix / Scherrer, Susanne S / Zhang, Yu

    Dental materials : official publication of the Academy of Dental Materials

    2024  

    Abstract: Objectives: The objective was to discuss the research on zirconia published in the past 15 years to help the dental materials community understand the key properties of the types of zirconia and their clinical applications.: Methods: A literature ... ...

    Abstract Objectives: The objective was to discuss the research on zirconia published in the past 15 years to help the dental materials community understand the key properties of the types of zirconia and their clinical applications.
    Methods: A literature search was performed in May/2023 using Web of Science Core Collection with the term "dental zirconia". The search returned 5102 articles, which were categorized into 31 groups according to the research topic.
    Results: The current approach to improving the translucency of zirconia is to decrease the alumina content while increasing the yttria content. The resulting materials (4Y-, 5Y-, and above 5 mol% PSZs) may contain more than 50% of cubic phase, with a decrease in mechanical properties. The market trend for zirconia is the production of CAD/CAM disks containing more fracture resistant 3Y-TZP at the bottom layers and more translucent 5Y-PSZ at the top. Although flaws located between layers in multilayered blocks might represent a problem, newer generations of zirconia layered blocks appear to have solved this problem with novel powder compaction technology. Significant advancements in zirconia processing technologies have been made, but there is still plenty of room for improvement, especially in the fields of high-speed sintering and additive manufacturing.
    Significance: The wide range of zirconia materials currently available in the market may cause confusion in materials selection. It is therefore imperative for dental clinicians and laboratory technicians to get the needed knowledge on zirconia material science, to follow manufacturers' instructions, and to optimize the design of the prosthetic restoration with a good understanding where to reinforce the structure with a tough and strong zirconia.
    Language English
    Publishing date 2024-03-22
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 605995-8
    ISSN 1879-0097 ; 0109-5641
    ISSN (online) 1879-0097
    ISSN 0109-5641
    DOI 10.1016/j.dental.2024.02.026
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genome sequencing and

    Suazo Tejada, Andrea Karina / Yu, Pei-Ling / Smith, Katherine E / Huguet-Tapia, Jose C / Carrillo, Joseph / Brawner, Jeremy T / Vallad, Gary E

    Microbiology resource announcements

    2023  Volume 13, Issue 1, Page(s) e0090623

    Abstract: We report a draft genome assembly ... ...

    Abstract We report a draft genome assembly of
    Language English
    Publishing date 2023-12-11
    Publishing country United States
    Document type Journal Article
    ISSN 2576-098X
    ISSN (online) 2576-098X
    DOI 10.1128/mra.00906-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: PTEN regulated PI3K-p110 and AKT isoform plasticity controls metastatic prostate cancer progression.

    Miller, Karina / Degan, Seamus / Wang, Yanqing / Cohen, Joseph / Ku, Sheng-Yu / Goodrich, David / Gelman, Irwin

    Research square

    2023  

    Abstract: ... ...

    Abstract PTEN
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2924750/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Correction: PTEN-regulated PI3K-p110 and AKT isoform plasticity controls metastatic prostate cancer progression.

    Miller, Karina A / Degan, Seamus / Wang, Yanqing / Cohen, Joseph / Ku, Sheng Yu / Goodrich, David W / Gelman, Irwin H

    Oncogene

    2023  Volume 43, Issue 1, Page(s) 76

    Language English
    Publishing date 2023-12-14
    Publishing country England
    Document type Published Erratum
    ZDB-ID 639046-8
    ISSN 1476-5594 ; 0950-9232
    ISSN (online) 1476-5594
    ISSN 0950-9232
    DOI 10.1038/s41388-023-02920-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Identification and functional characterization of the German cockroach, Blattella germanica, short interspersed nuclear elements.

    Firsov, Sergei Yu / Kosherova, Karina A / Mukha, Dmitry V

    PloS one

    2022  Volume 17, Issue 6, Page(s) e0266699

    Abstract: In recent decades, experimental data has accumulated indicating that short interspersed nuclear elements (SINEs) can play a significant functional role in the regulation of gene expression in the host genome. In addition, molecular markers based on SINE ... ...

    Abstract In recent decades, experimental data has accumulated indicating that short interspersed nuclear elements (SINEs) can play a significant functional role in the regulation of gene expression in the host genome. In addition, molecular markers based on SINE insertion polymorphisms have been developed and are widely used for genetic differentiation of populations of eukaryotic organisms. Using routine bioinformatics analysis and publicly available genomic DNA and small RNA-seq data, we first described nine SINEs in the genome of the German cockroach, Blattella germanica. All described SINEs have tRNA promoters, and the start of their transcription begins 11 bp upstream of an "A" box of these promoters. The number of copies of the described SINEs in the B. germanica genome ranges from several copies to more than a thousand copies in a SINE-specific manner. Some of the described SINEs and their degenerate copies can be localized both in the introns of genes and loci known as piRNA clusters. piRNAs originating from piRNA clusters are shown to be mapped to seven of the nine types of SINEs described, including copies of SINEs localized in gene introns. We speculate that SINEs, localized in the introns of certain genes, may regulate the level of expression of these genes by a PIWI-related molecular mechanism.
    MeSH term(s) Animals ; Blattellidae/genetics ; Evolution, Molecular ; Genome ; Phylogeny ; RNA, Small Interfering ; Sequence Analysis, DNA ; Short Interspersed Nucleotide Elements/genetics
    Chemical Substances RNA, Small Interfering
    Language English
    Publishing date 2022-06-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0266699
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Dynamics of Cations around DNA and Protein as Revealed by

    Yu, Binhan / Bien, Karina G / Pletka, Channing C / Iwahara, Junji

    Analytical chemistry

    2022  Volume 94, Issue 5, Page(s) 2444–2452

    Abstract: Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological ... ...

    Abstract Counterions are vital for the structure and function of biomolecules. However, the behavior of counterions remains elusive due to the difficulty in characterizing mobile ions. Here, we demonstrate that the dynamics of cations around biological macromolecules can be revealed by
    MeSH term(s) Cations ; DNA/chemistry ; Diffusion ; Magnetic Resonance Spectroscopy/methods ; Sodium/chemistry
    Chemical Substances Cations ; DNA (9007-49-2) ; Sodium (9NEZ333N27)
    Language English
    Publishing date 2022-01-26
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1508-8
    ISSN 1520-6882 ; 0003-2700
    ISSN (online) 1520-6882
    ISSN 0003-2700
    DOI 10.1021/acs.analchem.1c04197
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations.

    Yu, Binhan / Bien, Karina G / Wang, Tianzhi / Iwahara, Junji

    Biophysical journal

    2022  Volume 121, Issue 18, Page(s) 3562–3570

    Abstract: Counterions are important constituents for the structure and function of nucleic acids. ... ...

    Abstract Counterions are important constituents for the structure and function of nucleic acids. Using
    MeSH term(s) Cations/chemistry ; Cations, Monovalent/chemistry ; Cesium/chemistry ; DNA/chemistry ; Ions ; Lithium/chemistry ; Sodium/chemistry ; Static Electricity
    Chemical Substances Cations ; Cations, Monovalent ; Ions ; Cesium (1KSV9V4Y4I) ; DNA (9007-49-2) ; Lithium (9FN79X2M3F) ; Sodium (9NEZ333N27)
    Language English
    Publishing date 2022-06-25
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2022.06.022
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Identification and functional characterization of the German cockroach, Blattella germanica, short interspersed nuclear elements.

    Sergei Yu Firsov / Karina A Kosherova / Dmitry V Mukha

    PLoS ONE, Vol 17, Iss 6, p e

    2022  Volume 0266699

    Abstract: In recent decades, experimental data has accumulated indicating that short interspersed nuclear elements (SINEs) can play a significant functional role in the regulation of gene expression in the host genome. In addition, molecular markers based on SINE ... ...

    Abstract In recent decades, experimental data has accumulated indicating that short interspersed nuclear elements (SINEs) can play a significant functional role in the regulation of gene expression in the host genome. In addition, molecular markers based on SINE insertion polymorphisms have been developed and are widely used for genetic differentiation of populations of eukaryotic organisms. Using routine bioinformatics analysis and publicly available genomic DNA and small RNA-seq data, we first described nine SINEs in the genome of the German cockroach, Blattella germanica. All described SINEs have tRNA promoters, and the start of their transcription begins 11 bp upstream of an "A" box of these promoters. The number of copies of the described SINEs in the B. germanica genome ranges from several copies to more than a thousand copies in a SINE-specific manner. Some of the described SINEs and their degenerate copies can be localized both in the introns of genes and loci known as piRNA clusters. piRNAs originating from piRNA clusters are shown to be mapped to seven of the nine types of SINEs described, including copies of SINEs localized in gene introns. We speculate that SINEs, localized in the introns of certain genes, may regulate the level of expression of these genes by a PIWI-related molecular mechanism.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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