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  1. Article ; Online: Medical Assistance in Dying and Organ Donation, the Ultimate Gift: Have We Got the Ethics Right?

    Ramsay, Michael A / Wall, Anji E

    Annals of surgery

    2023  Volume 277, Issue 5, Page(s) 719–720

    MeSH term(s) Humans ; Tissue and Organ Procurement ; Tissue Donors ; Organ Transplantation ; Cognition ; Medical Assistance
    Language English
    Publishing date 2023-01-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 340-2
    ISSN 1528-1140 ; 0003-4932
    ISSN (online) 1528-1140
    ISSN 0003-4932
    DOI 10.1097/SLA.0000000000005806
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Uk I Zs.35/1: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Molecular-dynamics simulations of macromolecular diffraction, part II: Analysis of protein crystal simulations.

    Wych, David C / Wall, Michael E

    Methods in enzymology

    2023  Volume 688, Page(s) 115–143

    Abstract: Molecular-dynamics (MD) simulations have contributed substantially to our understanding of protein structure and dynamics, yielding insights into many biological processes including protein folding, drug binding, and mechanisms of protein-protein ... ...

    Abstract Molecular-dynamics (MD) simulations have contributed substantially to our understanding of protein structure and dynamics, yielding insights into many biological processes including protein folding, drug binding, and mechanisms of protein-protein interactions. Much of what is known about protein structure comes from macromolecular crystallography (MX) experiments. MD simulations of protein crystals are useful in the study of MX because the simulations can be analyzed to calculate almost any crystallographic observable of interest, from atomic coordinates to structure factors and densities, B-factors, multiple conformations and their populations/occupancies, and diffuse scattering intensities. Computing resources and software to support crystalline MD simulations are now readily available to many researchers studying protein structure and dynamics and who may be interested in advanced interpretation of MX data, including diffuse scattering. In this work, we outline methods of analyzing MD simulations of protein crystals and provide accompanying Jupyter notebooks as practical resources for researchers wishing to perform similar analyses on their own systems of interest.
    MeSH term(s) Crystallography ; Macromolecular Substances ; Molecular Dynamics Simulation ; Protein Folding ; Software
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2023-08-18
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2023.06.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Molecular-dynamics simulations of macromolecular diffraction, part I: Preparation of protein crystal simulations.

    Wych, David C / Wall, Michael E

    Methods in enzymology

    2023  Volume 688, Page(s) 87–114

    Abstract: Molecular-dynamics (MD) simulations of protein crystals enable the prediction of structural and dynamical features of both the protein and the solvent components of macromolecular crystals, which can be validated against diffraction data from X-ray ... ...

    Abstract Molecular-dynamics (MD) simulations of protein crystals enable the prediction of structural and dynamical features of both the protein and the solvent components of macromolecular crystals, which can be validated against diffraction data from X-ray crystallographic experiments. The simulations have been useful for studying and predicting both Bragg and diffuse scattering in protein crystallography; however, the preparation is not yet automated and includes choices and tradeoffs that can impact the results. Here we examine some of the intricacies and consequences of the choices involved in setting up MD simulations of protein crystals for the study of diffraction data, and provide a recipe for preparing the simulations, packaged in an accompanying Jupyter notebook. This article and the accompanying notebook are intended to serve as practical resources for researchers wishing to put these models to work.
    MeSH term(s) Proteins/chemistry ; Molecular Dynamics Simulation ; Crystallography, X-Ray ; Solvents/chemistry ; X-Ray Diffraction
    Chemical Substances Proteins ; Solvents
    Language English
    Publishing date 2023-08-17
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1557-7988
    ISSN (online) 1557-7988
    DOI 10.1016/bs.mie.2023.06.008
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  4. Article ; Online: Current state of dietetic services for inflammatory bowel disease patients in New Zealand: an observational study.

    McCarthy, Nicky E / Schultz, Michael / Wall, Catherine L

    Nutrition & dietetics: the journal of the Dietitians Association of Australia

    2023  Volume 80, Issue 5, Page(s) 538–545

    Abstract: Aim: Nutritional therapies for inflammatory bowel disease are increasingly recommended. This study aimed to gain insight from patients, dietitians and gastroenterologists into inflammatory bowel disease dietetic care in New Zealand.: Methods: Mixed- ... ...

    Abstract Aim: Nutritional therapies for inflammatory bowel disease are increasingly recommended. This study aimed to gain insight from patients, dietitians and gastroenterologists into inflammatory bowel disease dietetic care in New Zealand.
    Methods: Mixed-methods surveys were developed and then distributed online to patients with inflammatory bowel disease and dietitians and gastroenterologists that care for patients with inflammatory bowel disease. Quantitative survey data were analysed using nonparametric statistical tests. Qualitative survey data were analysed using thematic analysis.
    Results: Responses were received from 406 inflammatory bowel disease patients, 79 dietitians and 40 gastroenterologists. Half of the patients (52%) had seen a dietitian for nutrition advice. Patients more likely to have seen a dietitian were/had: Crohn's disease (p = 0.001), previous bowel surgery (p < 0.001), younger (p < 0.001) or receiving biologic therapy (p = 0.005). Two-thirds (66%) of patients found the dietitian advice at least moderately useful. A common theme from patient comments was that dietitians needed better knowledge of inflammatory bowel disease. Almost all (97%) gastroenterologists reported that their inflammatory bowel disease patients ask about nutrition; 57% reported that there were inadequate dietitians to meet patient needs. Over 50% of dietitians saw inflammatory bowel disease patients infrequently and 39% were not confident that their knowledge of the nutritional management of inflammatory bowel disease was current. Dietitians desired greater links with the inflammatory bowel disease multidisciplinary team.
    Conclusion: Current inflammatory bowel disease dietetic services in New Zealand are inadequate. Standardised care, increased resourcing, dietitian training in inflammatory bowel disease, and stronger links with the multidisciplinary team are suggested to improve services.
    MeSH term(s) Humans ; Dietetics ; New Zealand ; Dietary Services ; Nutritional Status ; Inflammatory Bowel Diseases/therapy
    Language English
    Publishing date 2023-04-13
    Publishing country Australia
    Document type Observational Study ; Journal Article
    ZDB-ID 2082047-1
    ISSN 1747-0080 ; 1446-6368
    ISSN (online) 1747-0080
    ISSN 1446-6368
    DOI 10.1111/1747-0080.12811
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    In stock of ZB MED Bonn / Germany

    Z 2720: Show issues

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  5. Article: Interactions that know no boundaries.

    Wall, Michael E

    IUCrJ

    2018  Volume 5, Issue Pt 2, Page(s) 120–121

    Abstract: Diffuse scattering provides evidence that variations are correlated across molecular boundaries in macromolecular crystals. ...

    Abstract Diffuse scattering provides evidence that variations are correlated across molecular boundaries in macromolecular crystals.
    Language English
    Publishing date 2018-02-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252518002713
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  6. Article: Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering.

    Wall, Michael E

    IUCrJ

    2018  Volume 5, Issue Pt 2, Page(s) 172–181

    Abstract: Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the ... ...

    Abstract Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.
    Language English
    Publishing date 2018-01-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252518000519
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  7. Article ; Online: Graph-based quantum response theory and shadow Born-Oppenheimer molecular dynamics.

    Negre, Christian F A / Wall, Michael E / Niklasson, Anders M N

    The Journal of chemical physics

    2023  Volume 158, Issue 7, Page(s) 74108

    Abstract: Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian ...

    Abstract Graph-based linear scaling electronic structure theory for quantum-mechanical molecular dynamics simulations [A. M. N. Niklasson et al., J. Chem. Phys. 144, 234101 (2016)] is adapted to the most recent shadow potential formulations of extended Lagrangian Born-Oppenheimer molecular dynamics, including fractional molecular-orbital occupation numbers [A. M. N. Niklasson, J. Chem. Phys. 152, 104103 (2020) and A. M. N. Niklasson, Eur. Phys. J. B 94, 164 (2021)], which enables stable simulations of sensitive complex chemical systems with unsteady charge solutions. The proposed formulation includes a preconditioned Krylov subspace approximation for the integration of the extended electronic degrees of freedom, which requires quantum response calculations for electronic states with fractional occupation numbers. For the response calculations, we introduce a graph-based canonical quantum perturbation theory that can be performed with the same natural parallelism and linear scaling complexity as the graph-based electronic structure calculations for the unperturbed ground state. The proposed techniques are particularly well-suited for semi-empirical electronic structure theory, and the methods are demonstrated using self-consistent charge density-functional tight-binding theory both for the acceleration of self-consistent field calculations and for quantum-mechanical molecular dynamics simulations. Graph-based techniques combined with the semi-empirical theory enable stable simulations of large, complex chemical systems, including tens-of-thousands of atoms.
    Language English
    Publishing date 2023-02-22
    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 10.1063/5.0137119
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    In stock of ZB MED Bonn / Germany

    Z 4' 49/16: Show issues

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  8. Article: Quantum crystallographic charge density of urea.

    Wall, Michael E

    IUCrJ

    2016  Volume 3, Issue Pt 4, Page(s) 237–246

    Abstract: Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density ... ...

    Abstract Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the data is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. The results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.
    Language English
    Publishing date 2016-06-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2754953-7
    ISSN 2052-2525
    ISSN 2052-2525
    DOI 10.1107/S2052252516006242
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  9. Article ; Online: Interactions that know no boundaries

    Michael E. Wall

    IUCrJ, Vol 5, Iss 2, Pp 120-

    2018  Volume 121

    Keywords diffuse scattering ; intermolecular correlations ; LLM models ; Science ; Q
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher International Union of Crystallography
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Internal protein motions in molecular-dynamics simulations of Bragg and diffuse X-ray scattering

    Michael E. Wall

    IUCrJ, Vol 5, Iss 2, Pp 172-

    2018  Volume 181

    Abstract: Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the ... ...

    Abstract Molecular-dynamics (MD) simulations of Bragg and diffuse X-ray scattering provide a means of obtaining experimentally validated models of protein conformational ensembles. This paper shows that compared with a single periodic unit-cell model, the accuracy of simulating diffuse scattering is increased when the crystal is modeled as a periodic supercell consisting of a 2 × 2 × 2 layout of eight unit cells. The MD simulations capture the general dependence of correlations on the separation of atoms. There is substantial agreement between the simulated Bragg reflections and the crystal structure; there are local deviations, however, indicating both the limitation of using a single structure to model disordered regions of the protein and local deviations of the average structure away from the crystal structure. Although it was anticipated that a simulation of longer duration might be required to achieve maximal agreement of the diffuse scattering calculation with the data using the supercell model, only a microsecond is required, the same as for the unit cell. Rigid protein motions only account for a minority fraction of the variation in atom positions from the simulation. The results indicate that protein crystal dynamics may be dominated by internal motions rather than packing interactions, and that MD simulations can be combined with Bragg and diffuse X-ray scattering to model the protein conformational ensemble.
    Keywords diffuse scattering ; protein crystallography ; X-ray diffraction ; molecular-dynamics simulation ; protein conformational ensemble ; staphylococcal nuclease ; X-ray crystallography ; molecular crystals ; molecular simulation ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2018-03-01T00:00:00Z
    Publisher International Union of Crystallography
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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