search

JoRussell-IDM / updated_infection_and_immunity

malaria_two_pt_oh
0 stars 0 forks source link

Catalog of considerations #31

Open JoRussell-IDM opened 5 years ago

JoRussell-IDM commented 5 years ago

An ever expanding list of considerations to keep in mind for extended model development.

JoRussell-IDM commented 5 years ago

Edward expressed some concern with global/probabilistic calculation of immune modification and TMs for the specific reason that when we try to simulate infections/transmission with genetic specificity. I think my takeaway from this is that successfully handling the use cases of genetically explicit within host modeling will require multiple layers of bespoke logic (how do you carefully handle complex infections and exchange of multi-locus resistance markers...)

JoRussell-IDM commented 5 years ago

From Lerch 2019

In some children the dominant clone remains dominant over the observation period (Fig. 2A), whereas in others switch-over between minority clone and dominant clone was observed (Fig. 2B).

JoRussell-IDM commented 5 years ago

For converting 18S rRNA copy number, I cite the figure of 10^4 copies/ring stage parasite from Sean Murphys work: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284350/

JoRussell-IDM commented 5 years ago

Should MFI have differential effect for different cumulative exposures? In other words, does the waning of humoral/cellular memory differ from single exposure individuals, and from serially exposed individuals? By how much?

JoRussell-IDM commented 5 years ago

How do you initialize a population with the right level of cumulative exposure properties, recent exposure properties, malaria free-intervals?

Seems like you have to calculate at the start of individual initialization a proxy/default/starting value that is drawn from a distribution given the annualEIR in that setting?

Initialization of recent exposure and malaria free interval should be conditioned on the start day relative to any seasonality in transmission.

JoRussell-IDM commented 4 years ago

Nonmalarial Fever and co-incident parasitemia

Adhere to WHO case definitions and their intersection with modeling

Huge discrepencies when it comes to country data/interactions

JoRussell-IDM commented 4 years ago

Malaria in Pregnancy

JoRussell-IDM commented 4 years ago

Sickle Cell Trait and Anti-parasite and anti-disease immunity

JoRussell-IDM commented 4 years ago

Still subject to the Max Allowed Infections logic???

config param: "Max_Individual_Infections": 20,

We should figure out where max_individual_infections is still having an impart on malaria 2 logic

JoRussell-IDM commented 4 years ago

Make the sigma value of the gaussian shape configurable (was 2, then 1, now 0.6?)

Logic at Line 268 in InfectionMalaria2

Resolved: Turned into an issue.

JoRussell-IDM commented 4 years ago

Separate as Issues to actually deal with