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  1. Article ; Online: Computer model for the cardiovascular system: development of an e-learning tool for teaching of medical students.

    Warriner, David Roy / Bayley, Martin / Shi, Yubing / Lawford, Patricia Victoria / Narracott, Andrew / Fenner, John

    BMC medical education

    2017  Volume 17, Issue 1, Page(s) 220

    Abstract: Background: This study combined themes in cardiovascular modelling, clinical cardiology and e-learning to create an on-line environment that would assist undergraduate medical students in understanding key physiological and pathophysiological processes ... ...

    Abstract Background: This study combined themes in cardiovascular modelling, clinical cardiology and e-learning to create an on-line environment that would assist undergraduate medical students in understanding key physiological and pathophysiological processes in the cardiovascular system.
    Methods: An interactive on-line environment was developed incorporating a lumped-parameter mathematical model of the human cardiovascular system. The model outputs were used to characterise the progression of key disease processes and allowed students to classify disease severity with the aim of improving their understanding of abnormal physiology in a clinical context. Access to the on-line environment was offered to students at all stages of undergraduate training as an adjunct to routine lectures and tutorials in cardiac pathophysiology. Student feedback was collected on this novel on-line material in the course of routine audits of teaching delivery.
    Results: Medical students, irrespective of their stage of undergraduate training, reported that they found the models and the environment interesting and a positive experience. After exposure to the environment, there was a statistically significant improvement in student performance on a series of 6 questions based on cardiovascular medicine, with a 33% and 22% increase in the number of questions answered correctly, p < 0.0001 and p < 0.001 respectively.
    Conclusions: Considerable improvement was found in students' knowledge and understanding during assessment after exposure to the e-learning environment. Opportunities exist for development of similar environments in other fields of medicine, refinement of the existing environment and further engagement with student cohorts. This work combines some exciting and developing fields in medical education, but routine adoption of these types of tool will be possible only with the engagement of all stake-holders, from educationalists, clinicians, modellers to, most importantly, medical students.
    MeSH term(s) Cardiology/education ; Cardiovascular Diseases ; Cardiovascular System/physiopathology ; Computer Simulation ; Computer-Assisted Instruction ; Education, Distance ; Education, Medical, Undergraduate/methods ; Humans ; Learning ; Models, Cardiovascular ; Students, Medical ; Teaching ; United Kingdom
    Language English
    Publishing date 2017-11-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2044473-4
    ISSN 1472-6920 ; 1472-6920
    ISSN (online) 1472-6920
    ISSN 1472-6920
    DOI 10.1186/s12909-017-1058-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust.

    Colton, Hayley / Hodgson, David / Hornsby, Hailey / Brown, Rebecca / Mckenzie, Joanne / Bradley, Kirsty L / James, Cameron / Lindsey, Benjamin B / Birch, Sarah / Marsh, Louise / Wood, Steven / Bayley, Martin / Dickson, Gary / James, David C / Nicklin, Martin J / Sayers, Jon R / Zafred, Domen / Rowland-Jones, Sarah L / Kudesia, Goura /
    Kucharski, Adam / Darton, Thomas C / de Silva, Thushan I / Collini, Paul J

    Wellcome open research

    2022  Volume 6, Page(s) 220

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2022-06-10
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.17143.3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust.

    Hodgson, David / Colton, Hayley / Hornsby, Hailey / Brown, Rebecca / Mckenzie, Joanne / Bradley, Kirsty L / James, Cameron / Lindsey, Benjamin B / Birch, Sarah / Marsh, Louise / Wood, Steven / Bayley, Martin / Dickson, Gary / James, David C / Nicklin, Martin J H / Sayers, Jon R / Zafred, Domen / Rowland-Jones, Sarah L / Kudesia, Goura /
    Kucharski, Adam / Darton, Thomas C / de Silva, Thushan I / Collini, Paul J

    medRxiv : the preprint server for health sciences

    2021  

    Language English
    Publishing date 2021-07-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.07.07.21260151
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A framework for different levels of integration of computational models into web-based virtual patients.

    Kononowicz, Andrzej A / Narracott, Andrew J / Manini, Simone / Bayley, Martin J / Lawford, Patricia V / McCormack, Keith / Zary, Nabil

    Journal of medical Internet research

    2014  Volume 16, Issue 1, Page(s) e23

    Abstract: Background: Virtual patients are increasingly common tools used in health care education to foster learning of clinical reasoning skills. One potential way to expand their functionality is to augment virtual patients' interactivity by enriching them ... ...

    Abstract Background: Virtual patients are increasingly common tools used in health care education to foster learning of clinical reasoning skills. One potential way to expand their functionality is to augment virtual patients' interactivity by enriching them with computational models of physiological and pathological processes.
    Objective: The primary goal of this paper was to propose a conceptual framework for the integration of computational models within virtual patients, with particular focus on (1) characteristics to be addressed while preparing the integration, (2) the extent of the integration, (3) strategies to achieve integration, and (4) methods for evaluating the feasibility of integration. An additional goal was to pilot the first investigation of changing framework variables on altering perceptions of integration.
    Methods: The framework was constructed using an iterative process informed by Soft System Methodology. The Virtual Physiological Human (VPH) initiative has been used as a source of new computational models. The technical challenges associated with development of virtual patients enhanced by computational models are discussed from the perspectives of a number of different stakeholders. Concrete design and evaluation steps are discussed in the context of an exemplar virtual patient employing the results of the VPH ARCH project, as well as improvements for future iterations.
    Results: The proposed framework consists of four main elements. The first element is a list of feasibility features characterizing the integration process from three perspectives: the computational modelling researcher, the health care educationalist, and the virtual patient system developer. The second element included three integration levels: basic, where a single set of simulation outcomes is generated for specific nodes in the activity graph; intermediate, involving pre-generation of simulation datasets over a range of input parameters; advanced, including dynamic solution of the model. The third element is the description of four integration strategies, and the last element consisted of evaluation profiles specifying the relevant feasibility features and acceptance thresholds for specific purposes. The group of experts who evaluated the virtual patient exemplar found higher integration more interesting, but at the same time they were more concerned with the validity of the result. The observed differences were not statistically significant.
    Conclusions: This paper outlines a framework for the integration of computational models into virtual patients. The opportunities and challenges of model exploitation are discussed from a number of user perspectives, considering different levels of model integration. The long-term aim for future research is to isolate the most crucial factors in the framework and to determine their influence on the integration outcome.
    MeSH term(s) Computer Simulation ; Feasibility Studies ; Humans ; Internet ; Systems Integration ; User-Computer Interface
    Language English
    Publishing date 2014-01-23
    Publishing country Canada
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2028830-X
    ISSN 1438-8871 ; 1439-4456
    ISSN (online) 1438-8871
    ISSN 1439-4456
    DOI 10.2196/jmir.2593
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: A fourier fingerprint-based method for protein surface representation.

    Bayley, Martin J / Gardiner, Eleanor J / Willett, Peter / Artymiuk, Peter J

    Journal of chemical information and modeling

    2005  Volume 45, Issue 3, Page(s) 696–707

    Abstract: A crucial enabling technology for structural genomics is the development of algorithms that can predict the putative function of novel protein structures: the proposed functions can subsequently be experimentally tested by functional studies. Testable ... ...

    Abstract A crucial enabling technology for structural genomics is the development of algorithms that can predict the putative function of novel protein structures: the proposed functions can subsequently be experimentally tested by functional studies. Testable assignments of function can be made if it is possible to attribute a putative, or indeed probable, function on the basis of the shapes of the binding sites on the surface of a protein structure. However the comparison of the surfaces of 3D protein structures is a computationally demanding task. Here we present four surface representations that can be used locally to describe the global shape of specifically bounded local region models. The most successful of these representations is obtained by a Fourier analysis of the distribution of surface curvature on concentric spheres around a surface point and summarizes a 24 A diameter spherically clipped region of protein surface by a fingerprint of 18 Fourier amplitude values. Searching experiments using these fingerprints on a set of 366 proteins demonstrate that this provides an effective and an efficient technique for the matching of protein surfaces.
    MeSH term(s) Fourier Analysis ; Models, Molecular ; Proteins/chemistry
    Chemical Substances Proteins
    Language English
    Publishing date 2005-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 190019-5
    ISSN 1549-9596 ; 0095-2338
    ISSN 1549-9596 ; 0095-2338
    DOI 10.1021/ci049647j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Framework for Different Levels of Integration of Computational Models Into Web-Based Virtual Patients

    Kononowicz, Andrzej A / Narracott, Andrew J / Manini, Simone / Bayley, Martin J / Lawford, Patricia V / McCormack, Keith / Zary, Nabil

    Journal of Medical Internet Research, Vol 16, Iss 1, p e

    2014  Volume 23

    Abstract: BackgroundVirtual patients are increasingly common tools used in health care education to foster learning of clinical reasoning skills. One potential way to expand their functionality is to augment virtual patients’ interactivity by enriching them with ... ...

    Abstract BackgroundVirtual patients are increasingly common tools used in health care education to foster learning of clinical reasoning skills. One potential way to expand their functionality is to augment virtual patients’ interactivity by enriching them with computational models of physiological and pathological processes. ObjectiveThe primary goal of this paper was to propose a conceptual framework for the integration of computational models within virtual patients, with particular focus on (1) characteristics to be addressed while preparing the integration, (2) the extent of the integration, (3) strategies to achieve integration, and (4) methods for evaluating the feasibility of integration. An additional goal was to pilot the first investigation of changing framework variables on altering perceptions of integration. MethodsThe framework was constructed using an iterative process informed by Soft System Methodology. The Virtual Physiological Human (VPH) initiative has been used as a source of new computational models. The technical challenges associated with development of virtual patients enhanced by computational models are discussed from the perspectives of a number of different stakeholders. Concrete design and evaluation steps are discussed in the context of an exemplar virtual patient employing the results of the VPH ARCH project, as well as improvements for future iterations. ResultsThe proposed framework consists of four main elements. The first element is a list of feasibility features characterizing the integration process from three perspectives: the computational modelling researcher, the health care educationalist, and the virtual patient system developer. The second element included three integration levels: basic, where a single set of simulation outcomes is generated for specific nodes in the activity graph; intermediate, involving pre-generation of simulation datasets over a range of input parameters; advanced, including dynamic solution of the model. The third element is the description of four ...
    Keywords Computer applications to medicine. Medical informatics ; R858-859.7 ; Public aspects of medicine ; RA1-1270
    Subject code 337
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher JMIR Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Risk factors for SARS-CoV-2 seroprevalence following the first pandemic wave in UK healthcare workers in a large NHS Foundation Trust

    Colton, Hayley / Hodgson, David / Hornsby, Hailey / Brown, Rebecca / Mckenzie, Joanne / Bradley, Kirsty L / James, Cameron / Lindsey, Benjamin B / Birch, Sarah / Marsh, Louise / Wood, Steven / Bayley, Martin / Dickson, Gary / James, David C / Nicklin, Martin J.H. / Sayers, Jon R / Zafred, Domen / Rowland-Jones, Sarah L / Kudesia, Goura /
    Kucharski, Adam J / CMMID COVID-19 Working Group / Darton, Thomas C / de Silva, Thushan I / Collini, Paul J

    medRxiv

    Abstract: Background: We aimed to measure SARS-CoV-2 seroprevalence in a cohort of healthcare workers (HCWs) during the first UK wave of the COVID-19 pandemic, explore risk factors associated with infection, and investigate the impact of antibody titres on assay ... ...

    Abstract Background: We aimed to measure SARS-CoV-2 seroprevalence in a cohort of healthcare workers (HCWs) during the first UK wave of the COVID-19 pandemic, explore risk factors associated with infection, and investigate the impact of antibody titres on assay sensitivity. Methods: HCWs at Sheffield Teaching Hospitals NHS Foundation Trust (STH) were prospectively enrolled and sampled at two time points. SARS-CoV-2 antibodies were tested using an in-house assay for IgG and IgA reactivity against Spike and Nucleoprotein (sensitivity 99.47%, specificity 99.56%). Data were analysed using three statistical models: a seroprevalence model, an antibody kinetics model, and a heterogeneous sensitivity model. Findings: As of 12th June 2020, 24.4% (n=311/1275) HCWs were seropositive. Of these, 39.2% (n=122/311) were asymptomatic. The highest adjusted seroprevalence was measured in HCWs on the Acute Medical Unit (41.1%, 95% CrI 30.0-52.9) and in Physiotherapists and Occupational Therapists (39.2%, 95% CrI 24.4-56.5). Older age groups showed overall higher median antibody titres. Further modelling suggests that, for a serological assay with an overall sensitivity of 80%, antibody titres may be markedly affected by differences in age, with sensitivity estimates of 89% in those over 60 years but 61% in those ≤30 years. Interpretation: HCWs in acute medical units working closely with COVID-19 patients were at highest risk of infection, though whether these are infections acquired from patients or other staff is unknown. Current serological assays may underestimate seroprevalence in younger age groups if validated using sera from older and/or more symptomatic individuals.
    Keywords covid19
    Language English
    Publishing date 2021-07-08
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2021.07.07.21260151
    Database COVID19

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  8. Article: Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine

    Payne, Rebecca P. / Longet, Stephanie / Austin, James A. / Skelly, Donal T. / Dejnirattisai, Wanwisa / Adele, Sandra / Meardon, Naomi / Faustini, Sian / Al-Taei, Saly / Moore, Shona C. / Tipton, Tom / Hering, Luisa M. / Angyal, Adrienn / Brown, Rebecca / Nicols, Alexander R. / Gillson, Natalie / Dobson, Susan L. / Amini, Ali / Supasa, Piyada /
    Cross, Andrew / Bridges-Webb, Alice / Reyes, Laura Silva / Linder, Aline / Sandhar, Gurjinder / Kilby, Jonathan A. / Tyerman, Jessica K. / Altmann, Thomas / Hornsby, Hailey / Whitham, Rachel / Phillips, Eloise / Malone, Tom / Hargreaves, Alexander / Shields, Adrian / Saei, Ayoub / Foulkes, Sarah / Stafford, Lizzie / Johnson, Sile / Wootton, Daniel G. / Conlon, Christopher P. / Jeffery, Katie / Matthews, Philippa C. / Frater, John / Deeks, Alexandra S. / Pollard, Andrew J. / Brown, Anthony / Rowland-Jones, Sarah L. / Mongkolsapaya, Juthathip / Barnes, Eleanor / Hopkins, Susan / Hall, Victoria / Dold, Christina / Duncan, Christopher J.A. / Richter, Alex / Carroll, Miles / Screaton, Gavin / de Silva, Thushan I. / Turtle, Lance / Klenerman, Paul / Dunachie, Susanna / Abuelgasim, Hibatullah / Adland, Emily / Adlou, Syed / Akther, Hossain Delowar / Alhussni, Ahmed / Ali, Mohammad / Ansari, M. Azim / Arancibia-Cárcamo, Carolina V. / Bayley, Martin / Brown, Helen / Chalk, Jeremy / Chand, Meera / Chawla, Anu / Chinnakannan, Senthil / Cutteridge, Jospeh / de Lara, Catherine / Denly, Lucy / Diffey, Ben / Dimitriadis, Stavros / Drake, Thomas M. / Donnison, Timothy / Dupont, Maeva / Eyre, David / Fairman, Alex / Gardiner, Siobhan / Gilbert-Jarmillo, Javier / Goulder, Philip / Hackstein, Carl-Philipp / Hambleton, Sophie / Haniffa, Muzlifah / Haworth, Jenny / Holmes, Jennifer / Horner, Emily / Jämsén, Anni / Jones, Chris / Kasanyinga, Mwila / Kelly, Sinead / Kirk, Rosemary / Knight, Michael L. / Lawrie, Allan / Lee, Lian / Lett, Lauren / Lillie, Katy / Lim, Nicholas / Mehta, Hema / Mentzer, Alexander J. / O’Donnell, Denise / Ogbe, Ane / Pace, Matthew / Payne, Brendan A.I. / Platt, Gareth / Poolan, Sonia / Provine, Nicholas / Ramamurthy, Narayan / Robinson, Nichola / Romaniuk, Leigh / Rongkard, Patpong / Sampson, Oliver L. / Simmons, Beatrice / Spegarova, Jarmila S. / Stephenson, Emily / Subramaniam, Kris / Thaventhiran, James / Thomas, Sarah / Travis, Simon / Tucker, Stephanie / Turton, Helena / Watson, Adam / Watson, Lisa / Weeks, Esme / Wilson, Robert / Wood, Steven / Wright, Rachel / Xiao, Huiyuan / Zawia, Amira A.T.

    Cell. 2021 Nov. 11, v. 184, no. 23

    2021  

    Abstract: Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United ... ...

    Institution on behalf of the PITCH Consortium
    Abstract Extension of the interval between vaccine doses for the BNT162b2 mRNA vaccine was introduced in the United Kingdom to accelerate population coverage with a single dose. At this time, trial data were lacking, and we addressed this in a study of United Kingdom healthcare workers. The first vaccine dose induced protection from infection from the circulating alpha (B.1.1.7) variant over several weeks. In a substudy of 589 individuals, we show that this single dose induces severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) neutralizing antibody (NAb) responses and a sustained B and T cell response to the spike protein. NAb levels were higher after the extended dosing interval (6–14 weeks) compared with the conventional 3- to 4-week regimen, accompanied by enrichment of CD4⁺ T cells expressing interleukin-2 (IL-2). Prior SARS-CoV-2 infection amplified and accelerated the response. These data on dynamic cellular and humoral responses indicate that extension of the dosing interval is an effective immunogenic protocol.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; health services ; immunogenicity ; interleukin-2 ; vaccines ; United Kingdom
    Language English
    Dates of publication 2021-1111
    Size p. 5699-5714.e11.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2021.10.011
    Database NAL-Catalogue (AGRICOLA)

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