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  1. Article ; Online: Reproducibility of COVID-era infectious disease models.

    Henderson, Alec S / Hickson, Roslyn I / Furlong, Morgan / McBryde, Emma S / Meehan, Michael T

    Epidemics

    2024  Volume 46, Page(s) 100743

    Abstract: Infectious disease modelling has been prominent throughout the COVID-19 pandemic, helping to understand the virus' transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the ... ...

    Abstract Infectious disease modelling has been prominent throughout the COVID-19 pandemic, helping to understand the virus' transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the computational reproducibility of infectious disease modelling articles from the COVID era. We found that four out of 100 randomly sampled studies released between January 2020 and August 2022 could be completely computationally reproduced using the resources provided (e.g., code, data, instructions) whilst a further eight were partially reproducible. For the 100 most highly cited articles from the same period we found that 11 were completely reproducible with a further 22 partially reproducible. Reflecting on our experience, we discuss common issues affecting computational reproducibility and how these might be addressed.
    MeSH term(s) Humans ; COVID-19/epidemiology ; Pandemics ; Reproducibility of Results ; Communicable Diseases/epidemiology
    Language English
    Publishing date 2024-01-23
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2467993-8
    ISSN 1878-0067 ; 1755-4365
    ISSN (online) 1878-0067
    ISSN 1755-4365
    DOI 10.1016/j.epidem.2024.100743
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Systematic Review of Mathematical Models of Dengue Transmission and Vector Control: 2010-2020.

    Ogunlade, Samson T / Meehan, Michael T / Adekunle, Adeshina I / McBryde, Emma S

    Viruses

    2023  Volume 15, Issue 1

    Abstract: Vector control methods are considered effective in averting dengue transmission. However, several factors may modify their impact. Of these controls, chemical methods, in the long run, may increase mosquitoes' resistance to chemicides, thereby decreasing ...

    Abstract Vector control methods are considered effective in averting dengue transmission. However, several factors may modify their impact. Of these controls, chemical methods, in the long run, may increase mosquitoes' resistance to chemicides, thereby decreasing control efficacy. The biological methods, which may be self-sustaining and very effective, could be hampered by seasonality or heatwaves (resulting in, e.g., loss of
    MeSH term(s) Animals ; Humans ; Dengue/epidemiology ; Dengue/prevention & control ; Aedes ; Mosquito Vectors ; Models, Theoretical ; Wolbachia
    Language English
    Publishing date 2023-01-16
    Publishing country Switzerland
    Document type Systematic Review ; Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v15010254
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Quantifying the impact of Wolbachia releases on dengue infection in Townsville, Australia.

    Ogunlade, Samson T / Adekunle, Adeshina I / Meehan, Michael T / McBryde, Emma S

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 14932

    Abstract: From October 2014 to February 2019, local authorities in Townsville, North Queensland, Australia continually introduced Wolbachia-infected mosquitoes to control seasonal outbreaks of dengue infection. In this study, we develop a mathematical modelling ... ...

    Abstract From October 2014 to February 2019, local authorities in Townsville, North Queensland, Australia continually introduced Wolbachia-infected mosquitoes to control seasonal outbreaks of dengue infection. In this study, we develop a mathematical modelling framework to estimate the effectiveness of this intervention as well as the relative dengue transmission rates of Wolbachia-infected and wild-type mosquitoes. We find that the transmission rate of Wolbachia-infected mosquitoes is reduced approximately by a factor of 20 relative to the uninfected wild-type population. In addition, the Townsville Wolbachia release program led to a 65% reduction in predicted dengue incidence during the release period and over 95% reduction in the 24 months that followed. Finally, to investigate the potential impact of other Wolbachia release programs, we use our estimates of relative transmissibility to calculate the relationship between the reproductive number of dengue and the proportion of Wolbachia-infected mosquitoes in the vector population.
    MeSH term(s) Animals ; Wolbachia ; Mosquito Vectors ; Australia/epidemiology ; Queensland/epidemiology ; Culicidae ; Dengue/epidemiology ; Dengue/prevention & control
    Language English
    Publishing date 2023-09-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-42336-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Modelling the ecological dynamics of mosquito populations with multiple co-circulating Wolbachia strains.

    Ogunlade, Samson T / Adekunle, Adeshina I / McBryde, Emma S / Meehan, Michael T

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 20826

    Abstract: Wolbachia intracellular bacteria successfully reduce the transmissibility of arthropod-borne viruses (arboviruses) when introduced into virus-carrying vectors such as mosquitoes. Despite the progress made by introducing Wolbachia bacteria into the Aedes ... ...

    Abstract Wolbachia intracellular bacteria successfully reduce the transmissibility of arthropod-borne viruses (arboviruses) when introduced into virus-carrying vectors such as mosquitoes. Despite the progress made by introducing Wolbachia bacteria into the Aedes aegypti wild-type population to control arboviral infections, reports suggest that heat-induced loss-of-Wolbachia-infection as a result of climate change may reverse these gains. Novel, supplemental Wolbachia strains that are more resilient to increased temperatures may circumvent these concerns, and could potentially act synergistically with existing variants. In this article, we model the ecological dynamics among three distinct mosquito (sub)populations: a wild-type population free of any Wolbachia infection; an invading population infected with a particular Wolbachia strain; and a second invading population infected with a distinct Wolbachia strain from that of the first invader. We explore how the range of possible characteristics of each Wolbachia strain impacts mosquito prevalence. Further, we analyse the differential system governing the mosquito populations and the Wolbachia infection dynamics by computing the full set of basic and invasive reproduction numbers and use these to establish stability of identified equilibria. Our results show that releasing mosquitoes with two different strains of Wolbachia did not increase their prevalence, compared with a single-strain Wolbachia-infected mosquito introduction and only delayed Wolbachia dominance.
    MeSH term(s) Animals ; Wolbachia ; Mosquito Vectors ; Aedes ; Body Temperature Regulation ; Climate Change
    Language English
    Publishing date 2022-12-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-25242-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Replicating superspreader dynamics with compartmental models.

    Meehan, Michael T / Hughes, Angus / Ragonnet, Romain R / Adekunle, Adeshina I / Trauer, James M / Jayasundara, Pavithra / McBryde, Emma S / Henderson, Alec S

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 15319

    Abstract: Infectious disease outbreaks often exhibit superspreader dynamics, where most infected people generate no, or few secondary cases, and only a small fraction of individuals are responsible for a large proportion of transmission. Although capturing this ... ...

    Abstract Infectious disease outbreaks often exhibit superspreader dynamics, where most infected people generate no, or few secondary cases, and only a small fraction of individuals are responsible for a large proportion of transmission. Although capturing this heterogeneity is critical for estimating outbreak risk and the effectiveness of group-specific interventions, it is typically neglected in compartmental models of infectious disease transmission-which constitute the most common transmission dynamic modeling framework. In this study we propose different classes of compartmental epidemic models that incorporate transmission heterogeneity, fit them to a number of real outbreak datasets, and benchmark their performance against the canonical superspreader model (i.e., the negative binomial branching process model). We find that properly constructed compartmental models can capably reproduce observed superspreader dynamics and we provide the pathogen-specific parameter settings required to do so. As a consequence, we also show that compartmental models parameterized according to a binary clinical classification have limited support.
    MeSH term(s) Humans ; Epidemiological Models ; Disease Outbreaks ; Benchmarking ; Epidemics ; Models, Statistical
    Language English
    Publishing date 2023-09-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-42567-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Mathematical analysis of a two-strain tuberculosis model in Bangladesh.

    Kuddus, Md Abdul / McBryde, Emma S / Adekunle, Adeshina I / White, Lisa J / Meehan, Michael T

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 3634

    Abstract: Tuberculosis (TB) is an airborne infectious disease that causes millions of deaths worldwide each year (1.2 million people died in 2019). Alarmingly, several strains of the causative agent, Mycobacterium tuberculosis (MTB)-including drug-susceptible (DS) ...

    Abstract Tuberculosis (TB) is an airborne infectious disease that causes millions of deaths worldwide each year (1.2 million people died in 2019). Alarmingly, several strains of the causative agent, Mycobacterium tuberculosis (MTB)-including drug-susceptible (DS) and drug-resistant (DR) variants-already circulate throughout most developing and developed countries, particularly in Bangladesh, with totally drug-resistant strains starting to emerge. In this study we develop a two-strain DS and DR TB transmission model and perform an analysis of the system properties and solutions. Both analytical and numerical results show that the prevalence of drug-resistant infection increases with an increasing drug use through amplification. Both analytic results and numerical simulations suggest that if the basic reproduction numbers of both DS ([Formula: see text]) and DR ([Formula: see text]) TB are less than one, i.e. [Formula: see text] the disease-free equilibrium is asymptotically stable, meaning that the disease naturally dies out. Furthermore, if [Formula: see text], then DS TB dies out but DR TB persists in the population, and if [Formula: see text] both DS TB and DR TB persist in the population. Further, sensitivity analysis of the model parameters found that the transmission rate of both strains had the greatest influence on DS and DR TB prevalence. We also investigated the effect of treatment rates and amplification on both DS and DR TB prevalence; results indicate that inadequate or inappropriate treatment makes co-existence more likely and increases the relative abundance of DR TB infections.
    MeSH term(s) Antitubercular Agents/therapeutic use ; Bangladesh/epidemiology ; Basic Reproduction Number ; Humans ; Mycobacterium tuberculosis ; Tuberculosis/drug therapy ; Tuberculosis/epidemiology ; Tuberculosis, Multidrug-Resistant/drug therapy
    Chemical Substances Antitubercular Agents
    Language English
    Publishing date 2022-03-07
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-07536-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Reproducibility of COVID-era infectious disease models

    Henderson, Alec S / Hickson, Roslyn I / Morgan, Morgan / McBryde, Emma S / Meehan, Michael T

    medRxiv

    Abstract: Infectious disease modelling has been prominent throughout the COVID-19 pandemic, help- ing to understand the virus9 transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the ... ...

    Abstract Infectious disease modelling has been prominent throughout the COVID-19 pandemic, help- ing to understand the virus9 transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the computational reproducibility of infectious disease modelling articles from the COVID era. We found that only four out of 100 randomly sampled studies released between January 2020 and August 2022 could be com- putationally reproduced using the resources provided (e.g., code, data, instructions). For the 100 most highly cited articles from the same period we found that only 11 were reproducible. Reflecting on our experience, we discuss common issues affecting computational reproducibility and how these might be addressed
    Keywords covid19
    Language English
    Publishing date 2023-10-12
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2023.10.11.23296911
    Database COVID19

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  8. Article ; Online: Reproducibility of COVID-era infectious disease models

    Henderson, Alec S. / Hickson, Roslyn I. / Furlong, Morgan / McBryde, Emma S. / Meehan, Michael T.

    medRxiv

    Abstract: Infectious disease modelling has been prominent throughout the COVID-19 pandemic, help- ing to understand the virus9 transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the ... ...

    Abstract Infectious disease modelling has been prominent throughout the COVID-19 pandemic, help- ing to understand the virus9 transmission dynamics and inform response policies. Given their potential importance and translational impact, we evaluated the computational reproducibility of infectious disease modelling articles from the COVID era. We found that only four out of 100 randomly sampled studies released between January 2020 and August 2022 could be com- putationally reproduced using the resources provided (e.g., code, data, instructions). For the 100 most highly cited articles from the same period we found that only 11 were reproducible. Reflecting on our experience, we discuss common issues affecting computational reproducibility and how these might be addressed
    Keywords covid19
    Language English
    Publishing date 2023-10-12
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2023.10.11.23296911
    Database COVID19

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    Inter-library loan at ZB MED

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  9. Article ; Online: Mathematical analysis of a

    Adekunle, Adeshina I / Meehan, Michael T / McBryde, Emma S

    Infectious Disease Modelling

    2019  Volume 4, Page(s) 265–285

    Abstract: Arboviral infections, especially dengue, continue to cause significant health burden in their endemic regions. One of the strategies to tackle these infections is to replace the main vector agent, ...

    Abstract Arboviral infections, especially dengue, continue to cause significant health burden in their endemic regions. One of the strategies to tackle these infections is to replace the main vector agent,
    Language English
    Publishing date 2019-10-19
    Publishing country China
    Document type Journal Article
    ZDB-ID 3015225-2
    ISSN 2468-0427 ; 2468-2152
    ISSN (online) 2468-0427
    ISSN 2468-2152
    DOI 10.1016/j.idm.2019.10.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Estimating the global burden of Epstein-Barr virus-related cancers.

    Wong, Yide / Meehan, Michael T / Burrows, Scott R / Doolan, Denise L / Miles, John J

    Journal of cancer research and clinical oncology

    2021  Volume 148, Issue 1, Page(s) 31–46

    Abstract: ... Burkitt lymphoma (BL), Diffuse large B-cell lymphoma (DLBCL) and Extranodal NK/T-cell lymphoma, Nasal type (ENKTL ...

    Abstract Background: More than 90% of the adult population globally is chronically infected by the Epstein-Barr virus (EBV). It is well established that EBV is associated with a number of malignancies, and advances in knowledge of EBV-related malignancies are being made every year. Several studies have analysed the global epidemiology and geographic distribution of EBV-related cancers. However, most have only described a single cancer type or subtype in isolation or limited their study to the three or four most common EBV-related cancers. This review will present an overview on the spectrum of cancers linked to EBV based on observations of associations and proportions in the published literature while also using these observations to estimate the incidence and mortality burden of some of these cancers.
    Method: We have reviewed the literature on defining features, distribution and outcomes across six cancers with a relatively large EBV-related case burden: Nasopharyngeal carcinoma (NPC), Gastric carcinoma (GC), Hodgkin lymphoma (HL), Burkitt lymphoma (BL), Diffuse large B-cell lymphoma (DLBCL) and Extranodal NK/T-cell lymphoma, Nasal type (ENKTL-NT). We retrieved published region-specific EBV-related case proportions for NPC, GC, HL and BL and performed meta-analyses on pooled region-specific studies of EBV-related case proportions for DLBCL and ENKTL-NT. We match these pooled proportions with their respective regional incidence and mortality numbers retrieved from a publicly available cancer database. Additionally, we also reviewed the literature on several other less common EBV-related cancers to summarize their key characteristics herein.
    Conclusion: We estimated that EBV-related cases from these six cancers accounted for 239,700-357,900 new cases and 137,900-208,700 deaths in 2020. This review highlights the significant global impact of EBV-related cancers and extends the spectrum of disease that could benefit from an EBV-specific therapeutic.
    MeSH term(s) Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Bleomycin/therapeutic use ; Burkitt Lymphoma/drug therapy ; Burkitt Lymphoma/virology ; Dacarbazine/therapeutic use ; Doxorubicin/therapeutic use ; Epstein-Barr Virus Infections/epidemiology ; Epstein-Barr Virus Infections/pathology ; Herpesvirus 4, Human/pathogenicity ; Hodgkin Disease/drug therapy ; Hodgkin Disease/virology ; Humans ; Lymphoma, Extranodal NK-T-Cell/drug therapy ; Lymphoma, Extranodal NK-T-Cell/virology ; Lymphoma, Large B-Cell, Diffuse/drug therapy ; Lymphoma, Large B-Cell, Diffuse/virology ; Nasopharyngeal Carcinoma/drug therapy ; Nasopharyngeal Carcinoma/virology ; Nasopharyngeal Neoplasms/drug therapy ; Nasopharyngeal Neoplasms/virology ; Neoplasms/drug therapy ; Neoplasms/epidemiology ; Neoplasms/virology ; Stomach Neoplasms/drug therapy ; Stomach Neoplasms/virology ; Vinblastine/therapeutic use
    Chemical Substances Bleomycin (11056-06-7) ; Vinblastine (5V9KLZ54CY) ; Dacarbazine (7GR28W0FJI) ; Doxorubicin (80168379AG)
    Language English
    Publishing date 2021-10-27
    Publishing country Germany
    Document type Journal Article ; Meta-Analysis ; Review
    ZDB-ID 134792-5
    ISSN 1432-1335 ; 0171-5216 ; 0084-5353 ; 0943-9382
    ISSN (online) 1432-1335
    ISSN 0171-5216 ; 0084-5353 ; 0943-9382
    DOI 10.1007/s00432-021-03824-y
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