Ideas of distance kernels - to parameterise
Susceptibility / transmissibility

General direction -
	- reproduce statistics of epidemics ?
	- infer distance kernel, assume kernel ?
	- infer parameters ?
	- ?

Make sparse ?!

Keeling Rohani Gridding method
Selki construction

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Vector causes evolutionary pressure to lower CpG
Alpha don’t care about lymph nodes particularly
Check CpG and C+G at different genes after alignment

Lower eta => immune evasion => rubella wants to be detected

Recalc eta for various viruses ?
Arg a big part of rubella genome ? If so, induces high C+G and CpG

DiffEq ( ODE, PDE )
Analysis ( real, complex, vector, matrix, functional )
LinAlg
Numerical Analysis
Bifurcation theory
Fourier analysis

Augment Jess’s file :
	- C
	- G
	- C+G per sequence
	- CpG
	- gene chunk ID

Plots :
	- Alignment DONE
	- change in C, G, C+G, CpG PER CHUNK DONE
	- Map of average C+G, CpG, C, G 
	- Video ?

Text :
	- Significance of CpG, C+G

7742 - 8619
9642 - 10582

FIVE FOUR CLUB
EXP0XA25CHK

INTRO

Context :

Histopathology evaluates the state of the organ

Sheep :

Population dynamics demonstrating crashes

“Gross pathology” applied - Gulland, Parasitology, 1992. “Post-mortem findings in…”, “The liver was friable, …”; Graham et al
No histology !

Interesting question : cause of death ? Immunosuppression —> worms ?

Nutrition - potential cause of death. If we want to evaluate potential link between nutrition and histology - automate, blah.
Want to be able to use histo as a quantitative variable 

1. Method to get histo as a quantitative variable, not user biased. Humans impossible to standardise, reproducibility zero

PRIOR INFORMATION :
- Sheep have worms
- Sheep with high protein levels are more likely to survive
- Liver state is a good indicator of malnutrition

INFERENCE :
IF we find a positive correlation between liver and proteins
THEN high protein levels => healthy liver => cause of death probably not malnutrition

IF we find no correlation
THEN high protein levels =/=> healthy liver => can’t say anything about CoD

WANT TO SEPARATE 

Parasites / immunity or nutrition

Histo : gives us information that allows this distinction to be made

Motivation :

Proposal :

METHODS