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  1. Article ; Online: Comment on "Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids".

    Jamieson-Lane, Alastair / Blasius, Bernd

    PLoS biology

    2021  Volume 19, Issue 12, Page(s) e3001449

    Abstract: Plasmid transfer contributes significantly to bacterial evolution, but the forces selecting such generosity are poorly understood; this Formal Comment revisits a study which examined these forces both analytically and experimentally, making a correction ... ...

    Abstract Plasmid transfer contributes significantly to bacterial evolution, but the forces selecting such generosity are poorly understood; this Formal Comment revisits a study which examined these forces both analytically and experimentally, making a correction to the algebra and reaching strikingly different results.
    MeSH term(s) Bacteria/genetics ; Plasmids/genetics
    Language English
    Publishing date 2021-12-21
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3001449
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  2. Article: Comparing optimization criteria in antibiotic allocation protocols.

    Jamieson-Lane, Alastair / Friedrich, Alexander / Blasius, Bernd

    Royal Society open science

    2022  Volume 9, Issue 3, Page(s) 220181

    Abstract: Clinicians prescribing antibiotics in a hospital context follow one of several possible 'treatment protocols'-heuristic rules designed to balance the immediate needs of patients against the long-term threat posed by the evolution of antibiotic resistance ...

    Abstract Clinicians prescribing antibiotics in a hospital context follow one of several possible 'treatment protocols'-heuristic rules designed to balance the immediate needs of patients against the long-term threat posed by the evolution of antibiotic resistance and multi-resistant bacteria. Several criteria have been proposed for assessing these protocols; unfortunately, these criteria frequently conflict with one another, each providing a different recommendation as to which treatment protocol is best. Here, we review and compare these optimization criteria. We are able to demonstrate that criteria focused primarily on slowing evolution of resistance are directly antagonistic to patient health both in the short and long term. We provide a new optimization criteria of our own, intended to more meaningfully balance the needs of the future and present. Asymptotic methods allow us to evaluate this criteria and provide insights not readily available through the numerical methods used previously in the literature. When cycling antibiotics, we find an antibiotic switching time which proves close to optimal across a wide range of modelling assumptions.
    Language English
    Publishing date 2022-03-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2787755-3
    ISSN 2054-5703
    ISSN 2054-5703
    DOI 10.1098/rsos.220181
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  3. Article ; Online: The gossip paradox: Why do bacteria share genes?

    Jamieson-Lane, Alastair D / Blasius, Bernd

    Mathematical biosciences and engineering : MBE

    2022  Volume 19, Issue 6, Page(s) 5482–5508

    Abstract: Bacteria, in contrast to eukaryotic cells, contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids, smaller loops of DNA capable of being passed from one cell to another. The sharing of plasmid genes between individual ... ...

    Abstract Bacteria, in contrast to eukaryotic cells, contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids, smaller loops of DNA capable of being passed from one cell to another. The sharing of plasmid genes between individual bacteria and between bacterial lineages has contributed vastly to bacterial evolution, allowing specialized traits to 'jump ship' between one lineage or species and the next. The benefits of this generosity from the point of view of both recipient cell and plasmid are generally understood: plasmids receive new hosts and ride out selective sweeps across the population, recipient cells gain new traits (such as antibiotic resistance). Explaining this behavior from the point of view of donor cells is substantially more difficult. Donor cells pay a fitness cost in order to share plasmids, and run the risk of sharing advantageous genes with their competition and rendering their own lineage redundant, while seemingly receiving no benefit in return. Using both compartment based models and agent based simulations we demonstrate that 'secretive' genes which restrict horizontal gene transfer are favored over a wide range of models and parameter values, even when sharing carries no direct cost. 'Generous' chromosomal genes which are more permissive of plasmid transfer are found to have neutral fitness at best, and are generally disfavored by selection. Our findings lead to a peculiar paradox: given the obvious benefits of keeping secrets, why do bacteria share information so freely?
    MeSH term(s) Bacteria/genetics ; Drug Resistance, Microbial ; Gene Transfer, Horizontal ; Phenotype ; Plasmids/genetics
    Language English
    Publishing date 2022-05-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2265126-3
    ISSN 1551-0018 ; 1551-0018
    ISSN (online) 1551-0018
    ISSN 1551-0018
    DOI 10.3934/mbe.2022257
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  4. Article ; Online: Calculation of epidemic arrival time distributions using branching processes.

    Jamieson-Lane, Alastair / Blasius, Bernd

    Physical review. E

    2020  Volume 102, Issue 4-1, Page(s) 42301

    Abstract: The rise of the World Airline Network over the past century has led to sharp changes in our notions of "distance" and "closeness"-in terms of both trade and travel, but also (less desirably) with respect to the spread of disease. When novel pathogens are ...

    Abstract The rise of the World Airline Network over the past century has led to sharp changes in our notions of "distance" and "closeness"-in terms of both trade and travel, but also (less desirably) with respect to the spread of disease. When novel pathogens are discovered, countries, cities, and hospitals are caught trying to predict how much time they have to prepare. In this paper, by considering the early stages of epidemic spread as a simple branching process, we derive the full probability distribution of arrival times. We are able to rederive a number of past arrival time results (in suitable limits) and demonstrate the robustness of our approach, both to parameter values far outside the traditionally considered regime and to errors in the parameter values used. The branching process approach provides some theoretical justification to the "effective distance" introduced by Brockmann and Helbing [Science 342, 1337 (2013)SCIEAS0036-807510.1126/science.1245200]; however, we also observe that when compared to real-world data, the predictive power of all methods in this class is significantly lower than has been previously reported.
    Keywords covid19
    Language English
    Publishing date 2020-11-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.102.042301
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  5. Article ; Online: Effects of age-targeted sequestration for COVID-19.

    Jamieson-Lane, Alastair / Cytrynbaum, Eric

    Journal of biological dynamics

    2020  Volume 14, Issue 1, Page(s) 621–632

    Abstract: We model the extent to which age-targeted protective sequestration can be used to reduce ICU admissions caused by novel coronavirus COVID-19. Using demographic data from New Zealand, we demonstrate that lowering the age threshold to 50 years of age ... ...

    Abstract We model the extent to which age-targeted protective sequestration can be used to reduce ICU admissions caused by novel coronavirus COVID-19. Using demographic data from New Zealand, we demonstrate that lowering the age threshold to 50 years of age reduces ICU admissions drastically and show that for sufficiently strict isolation protocols, sequestering one-third of the countries population for a total of 8 months is sufficient to avoid overwhelming ICU capacity throughout the entire course of the epidemic. Similar results are expected to hold for other countries, though some minor adaption will be required based on local age demographics and hospital facilities.
    MeSH term(s) Adolescent ; Adult ; Age Factors ; Aged ; Aged, 80 and over ; Betacoronavirus ; COVID-19 ; Child ; Child, Preschool ; Communicable Disease Control/methods ; Computer Simulation ; Coronavirus Infections/epidemiology ; Coronavirus Infections/prevention & control ; Coronavirus Infections/transmission ; Critical Care ; Female ; Hospitalization ; Humans ; Infant ; Infant, Newborn ; Intensive Care Units/supply & distribution ; Male ; Middle Aged ; Models, Biological ; New Zealand/epidemiology ; Pandemics/prevention & control ; Patient Isolation/methods ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/transmission ; Quarantine/methods ; Risk Factors ; SARS-CoV-2 ; Young Adult
    Keywords covid19
    Language English
    Publishing date 2020-07-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1751-3766
    ISSN (online) 1751-3766
    DOI 10.1080/17513758.2020.1795285
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  6. Article ; Online: Comment on "Indirect Fitness Benefits Enable the Spread of Host Genes Promoting Costly Transfer of Beneficial Plasmids".

    Alastair Jamieson-Lane / Bernd Blasius

    PLoS Biology, Vol 19, Iss 12, p e

    2021  Volume 3001449

    Abstract: Plasmid transfer contributes significantly to bacterial evolution, but the forces selecting such generosity are poorly understood; this Formal Comment revisits a study which examined these forces both analytically and experimentally, making a correction ... ...

    Abstract Plasmid transfer contributes significantly to bacterial evolution, but the forces selecting such generosity are poorly understood; this Formal Comment revisits a study which examined these forces both analytically and experimentally, making a correction to the algebra and reaching strikingly different results.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-12-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Pathways for socio-economic system transitions expressed as a Markov chain.

    Schweizer, Vanessa Jine / Jamieson-Lane, Alastair David / Cai, Hua / Lehner, Stephan / Smerlak, Matteo

    PloS one

    2023  Volume 18, Issue 7, Page(s) e0288928

    Abstract: Cross-impact balance (CIB) analysis provides a system-theoretical view of scenarios useful for investigating complex socio-economic systems. CIB can synthesize a variety of qualitative or quantitative inputs and return information suggestive of system ... ...

    Abstract Cross-impact balance (CIB) analysis provides a system-theoretical view of scenarios useful for investigating complex socio-economic systems. CIB can synthesize a variety of qualitative or quantitative inputs and return information suggestive of system evolution. Current software tools for CIB are limited to identifying system attractors as well as describing system evolution from only one scenario of initial conditions at a time. Through this study, we enhance CIB by developing and applying a method that considers all possible system evolutions as transitions in a Markov chain. We investigated a simple three-variable system (27 possible scenarios) of the demographic transition and were able to generally replicate the findings of traditional CIB. Through our experiments with four possible approaches to produce CIB Markov chains, we found that information about transition pathways is gained; however, information about system attractors may be lost. Through a comparison of model results to a recent literature review on human demography, we found that low-income countries are more likely to remain stuck in a demographic trap if economic development is not prioritized alongside educational gains. Future work could test our comparative methodological findings for systems comprised of more than three variables.
    MeSH term(s) Humans ; Markov Chains ; Educational Status ; Software
    Language English
    Publishing date 2023-07-31
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0288928
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  8. Article ; Online: Effects of age-targeted sequestration for COVID-19

    Alastair Jamieson-Lane / Eric Cytrynbaum

    Journal of Biological Dynamics, Vol 14, Iss 1, Pp 621-

    2020  Volume 632

    Abstract: We model the extent to which age-targeted protective sequestration can be used to reduce ICU admissions caused by novel coronavirus COVID-19. Using demographic data from New Zealand, we demonstrate that lowering the age threshold to 50 years of age ... ...

    Abstract We model the extent to which age-targeted protective sequestration can be used to reduce ICU admissions caused by novel coronavirus COVID-19. Using demographic data from New Zealand, we demonstrate that lowering the age threshold to 50 years of age reduces ICU admissions drastically and show that for sufficiently strict isolation protocols, sequestering one-third of the countries population for a total of 8 months is sufficient to avoid overwhelming ICU capacity throughout the entire course of the epidemic. Similar results are expected to hold for other countries, though some minor adaption will be required based on local age demographics and hospital facilities.
    Keywords covid-19 ; sir model ; structured population ; epidemics ; age ; Environmental sciences ; GE1-350 ; Biology (General) ; QH301-705.5 ; covid19
    Language English
    Publishing date 2020-01-01T00:00:00Z
    Publisher Taylor & Francis Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Effects of age-targeted sequestration for COVID-19

    Jamieson-Lane, Alastair / Cytrynbaum, Eric

    Journal of Biological Dynamics

    2020  Volume 14, Issue 1, Page(s) 621–632

    Keywords Ecology ; Ecology, Evolution, Behavior and Systematics ; covid19
    Language English
    Publisher Informa UK Limited
    Publishing country uk
    Document type Article ; Online
    ISSN 1751-3758
    DOI 10.1080/17513758.2020.1795285
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Epidemic Arrival Times; Theory, Discussion, and Limitations

    Jamieson-Lane, Alastair / Blasius, Bernd

    Abstract: The rise of the World Airline Network over the past century has lead to sharp changes in our notions of `distance' and `closeness' - both in terms of trade and travel, but also (less desirably) with respect to the spread of disease. Using flight data ... ...

    Abstract The rise of the World Airline Network over the past century has lead to sharp changes in our notions of `distance' and `closeness' - both in terms of trade and travel, but also (less desirably) with respect to the spread of disease. Using flight data from the WAN, along with a drastically simplified epidemic model, we are able to predict epidemic arrival times, for arbitrary initial conditions, in a computationally efficient manner. Our framework provides some theoretical justification to the `effective distance' originally introduced by Brockmann \&Helbing (2013), however we also observed that the predictive power of such heuristics is significantly lower than previously reported. Further improvements to our framework allow predictions to be made, even in parameter regimes where past methods are known to fail, and illuminate the circumstances under which this class of methods can be expected to fail.
    Keywords covid19
    Publisher ArXiv
    Document type Article
    Database COVID19

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