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  1. Book: Phase-separated biomolecular condensates

    Zhou, Huan-Xiang / Spille, Jan-Hendrik / Banerjee, Priya

    (Methods in molecular biology ; 2563 ; Springer protocols)

    2023  

    Author's details edited by Huan-Xiang Zhou, Jan-Hendrik Spille, Priya Banerjee
    Series title Methods in molecular biology ; 2563
    Springer protocols
    Collection
    Keywords Cell organelles
    Subject code 571.65
    Language English
    Size xiv, 449 Seiten, Illustrationen, 26 cm
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT021570041
    ISBN 978-1-0716-2662-7 ; 9781071626634 ; 1-0716-2662-0 ; 1071626639
    Database Catalogue ZB MED Medicine, Health

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  2. Article: Treatments associated with all-cause mortality among children with primary brain and central nervous system tumors: a retrospective cohort study from the SEER database.

    Zhou, Huan

    Translational pediatrics

    2023  Volume 12, Issue 8, Page(s) 1504–1516

    Abstract: Background: Evidence on treatment modalities and survival in childhood primary brain and central nervous system (CNS) tumors remains contradictory, with previous studies often lacking sufficient patient cohort sizes to assess the differences in ... ...

    Abstract Background: Evidence on treatment modalities and survival in childhood primary brain and central nervous system (CNS) tumors remains contradictory, with previous studies often lacking sufficient patient cohort sizes to assess the differences in histological subtypes. This cohort study based on a large population investigated the effects of various treatments on the mortality of patients with different histological types of primary brain and CNS tumors from the Surveillance, Epidemiology, and End Results (SEER) database.
    Methods: Data of demography, primary tumor site, histology, tumor grade and treatments from all pediatric patients with primary brain and CNS tumors were extracted in this retrospective cohort. The outcomes were overall, 1-, 5-, and 10-year all-cause mortality. Multivariate Cox proportional hazards models were to explore the associations of treatment with overall, 1-, 5-, and 10-year all-cause mortality, with hazard ratios (HRs) and 95% confidence intervals (CIs).
    Results: Totally 10,994 children were included, with the mean age at diagnosis of 7.3 years, and the median follow-up time of 5.0 years. Of which, 2,003 (18.2%) were diffuse astrocytoma, 3,188 (29.0%) were embryonal tumors, and 3,691 (33.5%) were malignant glioma. Then 4,333 (39.41%) children died during the follow-up. For diffuse astrocytomas and malignant gliomas, patients who received all other treatments were associated with overall, 1-, 5- and 10-year all-cause mortality compared to those only received resection. Embryonal tumors patients receiving resection with radiation only and those receiving resection with both chemotherapy and radiation were associated with lower odds of overall, 1-, 5- and 10-year all-cause mortality compared to patients who only received resection. For ependymal tumors, no surgery/only biopsy with chemotherapy, resection with chemotherapy only, resection with both chemotherapy and radiation, and other treatments had increased risks of overall all-cause mortality compared with resection. The risk of 1-year all-cause mortality increased in ependymal tumors with treatment involving resection and radiation. However, resection with both chemotherapy and radiation was not significantly associated with the 1- nor 5-year all-cause mortality.
    Conclusions: Resection may be recommended for children with diffuse astrocytoma, ependymal tumors, and malignant glioma, while resection with radiotherapy or chemoradiation may be recommended for children with embryonal tumors.
    Language English
    Publishing date 2023-08-28
    Publishing country China
    Document type Journal Article
    ZDB-ID 2901309-4
    ISSN 2224-4344 ; 2224-4344 ; 2224-4336
    ISSN (online) 2224-4344
    ISSN 2224-4344 ; 2224-4336
    DOI 10.21037/tp-23-362
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Power Law in a Bounded Range: Estimating the Lower and Upper Bounds from Sample Data.

    Zhou, Huan-Xiang

    ArXiv

    2023  

    Abstract: Power law distributions are widely observed in chemical physics, geophysics, biology, and beyond. The independent variable x of these distributions has an obligatory lower bound and in many cases also an upper bound. Estimating these bounds from sample ... ...

    Abstract Power law distributions are widely observed in chemical physics, geophysics, biology, and beyond. The independent variable x of these distributions has an obligatory lower bound and in many cases also an upper bound. Estimating these bounds from sample data is notoriously difficult, with a recent method involving O(N^3) operations, where N denotes sample size. Here I develop an approach for estimating the lower and upper bounds that involves O(N) operations. The approach centers on calculating the mean values, x_min and x_max, of the smallest x and the largest x in N-point samples. A fit of x_min or x_max as a function of N yields the estimate for the lower or upper bound. Application to synthetic data demonstrates the accuracy and reliability of this approach.
    Language English
    Publishing date 2023-03-23
    Publishing country United States
    Document type Preprint
    ISSN 2331-8422
    ISSN (online) 2331-8422
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Power law in a bounded range: Estimating the lower and upper bounds from sample data.

    Zhou, Huan-Xiang

    The Journal of chemical physics

    2022  Volume 158, Issue 19

    Abstract: Power law distributions are widely observed in chemical physics, geophysics, biology, and beyond. The independent variable x of these distributions has an obligatory lower bound and, in many cases, also an upper bound. Estimating these bounds from sample ...

    Abstract Power law distributions are widely observed in chemical physics, geophysics, biology, and beyond. The independent variable x of these distributions has an obligatory lower bound and, in many cases, also an upper bound. Estimating these bounds from sample data is notoriously difficult, with a recent method involving O(N3) operations, where N denotes sample size. Here I develop an approach for estimating the lower and upper bounds that involve O(N) operations. The approach centers on calculating the mean values, x̂min and x̂max, of the smallest x and the largest x in N-point samples. A fit of x̂min or x̂max as a function of N yields the estimate for the lower or upper bound. Application to synthetic data demonstrates the accuracy and reliability of this approach.
    Language English
    Publishing date 2022-10-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0151614
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions.

    Qin, Sanbo / Zhou, Huan-Xiang

    bioRxiv : the preprint server for biology

    2024  

    Abstract: We present a method, FMAPS(q), for calculating the structure factor, ...

    Abstract We present a method, FMAPS(q), for calculating the structure factor,
    Language English
    Publishing date 2024-03-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.27.587040
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Shape recovery of deformed biomolecular droplets: Dependence on condensate viscoelasticity.

    Zhou, Huan-Xiang

    The Journal of chemical physics

    2021  Volume 155, Issue 14, Page(s) 145102

    Abstract: A theoretical study on the shape dynamics of phase-separated biomolecular droplets is presented, highlighting the importance of condensate viscoelasticity. Previous studies on shape dynamics have modeled biomolecular condensates as purely viscous, but ... ...

    Abstract A theoretical study on the shape dynamics of phase-separated biomolecular droplets is presented, highlighting the importance of condensate viscoelasticity. Previous studies on shape dynamics have modeled biomolecular condensates as purely viscous, but recent data have shown them to be viscoelastic. Here, we present an exact analytical solution for the shape recovery dynamics of deformed biomolecular droplets. The shape recovery of viscous droplets has an exponential time dependence, with the time constant given by the "viscocapillary" ratio, i.e., viscosity over interfacial tension. In contrast, the shape recovery dynamics of viscoelastic droplets is multi-exponential, with shear relaxation yielding additional time constants. During shape recovery, viscoelastic droplets exhibit shear thickening (increase in apparent viscosity) at fast shear relaxation rates but shear thinning (decrease in apparent viscosity) at slow shear relaxation rates. These results highlight the importance of viscoelasticity and expand our understanding of how material properties affect condensate dynamics in general, including aging.
    MeSH term(s) Biomolecular Condensates/chemistry ; Elasticity ; Models, Chemical ; Surface Tension ; Viscosity
    Language English
    Publishing date 2021-09-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0064247
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Viscoelasticity of biomolecular condensates conforms to the Jeffreys model.

    Zhou, Huan-Xiang

    The Journal of chemical physics

    2021  Volume 154, Issue 4, Page(s) 41103

    Abstract: Biomolecular condensates, largely by virtue of their material properties, are revolutionizing biology, and yet, the physical understanding of these properties is lagging. Here, I show that the viscoelasticity of condensates can be captured by a simple ... ...

    Abstract Biomolecular condensates, largely by virtue of their material properties, are revolutionizing biology, and yet, the physical understanding of these properties is lagging. Here, I show that the viscoelasticity of condensates can be captured by a simple model, comprising a component where shear relaxation is an exponential function (with time constant τ
    MeSH term(s) Animals ; Caenorhabditis elegans/chemistry ; Caenorhabditis elegans Proteins/chemistry ; Models, Chemical ; Particle Size ; Potassium Chloride/chemistry ; RNA-Binding Proteins/chemistry ; Salts/chemistry ; Viscosity
    Chemical Substances Caenorhabditis elegans Proteins ; PGL-3 protein, C elegans ; RNA-Binding Proteins ; Salts ; Potassium Chloride (660YQ98I10)
    Language English
    Publishing date 2021-01-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0038916
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins.

    Qin, Sanbo / Zhou, Huan-Xiang

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Dynamics is a crucial link between sequence and function for intrinsically disordered proteins (IDPs). NMR spin relaxation is a powerful technique for characterizing the sequence-dependent backbone dynamics of IDPs. Of particular interest is ... ...

    Abstract Dynamics is a crucial link between sequence and function for intrinsically disordered proteins (IDPs). NMR spin relaxation is a powerful technique for characterizing the sequence-dependent backbone dynamics of IDPs. Of particular interest is the
    Language English
    Publishing date 2023-02-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.02.02.526886
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.

    Hu, Guodong / Zhou, Huan-Xiang

    bioRxiv : the preprint server for biology

    2023  

    Abstract: The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. ... ...

    Abstract The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg
    Language English
    Publishing date 2023-03-12
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.03.12.532287
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.

    Hu, Guodong / Zhou, Huan-Xiang

    Communications biology

    2023  Volume 6, Issue 1, Page(s) 791

    Abstract: The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. ... ...

    Abstract The SAM/SAH riboswitch binds S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) with similar affinities. Mg
    MeSH term(s) Nucleic Acid Conformation ; Riboswitch ; Magnesium ; S-Adenosylmethionine/chemistry ; S-Adenosylmethionine/metabolism ; Ligands ; RNA/chemistry ; Ions
    Chemical Substances Riboswitch ; Magnesium (I38ZP9992A) ; S-Adenosylmethionine (7LP2MPO46S) ; Ligands ; RNA (63231-63-0) ; Ions
    Language English
    Publishing date 2023-07-31
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-023-05175-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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