Dynamical correlations in the escape strategy of Influenza A virus

An interesting result from Hogeweg's theories of multilevel selection (the level of selection is removed from the level of evolution). Influenza poses an apparent paradox. The virus evolves fast enough that a single host can be infected several times in its life, yet, the seasonal quasi-species is well defined enough to allow for a vaccine. [...]
May 21, 2013 0
Genotype characteristics of huSARS-CoV and pcSARS-CoV

SARS-CoV originated from bats in 1998 and may still exist in humans

Title says it all. Conclusion comes from phylogenies. The 29-nt deletion was the original justification for the civit theory. Abstract SARS-CoV is believed to originate from civets and was thought to have been eliminated as a threat after the 2003 outbreak. Here, we show that human SARS-CoV (huSARS-CoV) originated directly from bats, rather than civets, [...]
May 21, 2013 0
Earnst Haeckel's illustration of cyrtoideas

Does evolution have a goal?

Much religious history builds a hierarchy of being, usually placing man at the pinnacle of life. And above life is God, the Creator. Then came Darwin, and evolution via natural selection. Random chance does not have a direction. There is no pinnacle, no divine guidance, no goal. And yet. Clearly, life is a trend to [...]
May 18, 2013 0
Lower average age is strongly correlated with increased susceptibility to epidemic outbreak, according to the author's model.

Inferring the Structure of Social Contacts from Demographic Data in the Analysis of Infectious Diseases Spread

Estimating human mixing patterns is necessary for disease control, but hard. The authors propose a general computational approach to derive mixing patterns from routinely collected socio-demographic data. More specifically, they wish to create age-specific mixing matricies. This is done as a linear combination of four sub-matricies, Household, School, Work, and Community. These are taken from [...]
May 17, 2013 0
Dynamics of number of cherries(normalized), assortativity coefficient and Sackin's index as given by the ODE's over a range of infectivity ratio (top row), range of contact rates with no population mixing (middle row) and range of contact rates with high population mixing (bottom row).

Modeling tree shape and structure in viral phylodynamics

This paper provides a way to model the effects of population structure on a phylogenetic tree topology. Methodology and Experimental setup Three measures of tree imbalance and structure are modeled No. of cherries (Nc).  A cherry is a pair of leaves that share a direct common ancestor Sackin's index (S). A measure of topological distance [...]
May 14, 2013 0
Figure 2. PhyloTempo graphical output summarizing phylogenetic tree shape statistics. Note: A tree from the OPTIONS data set (patient p5, unique sequences) with a high TC statistic (0.7) was used.

PhyloTempo

Summary: Two new measures of tree topology are introduced: temporal clustering (TC), and staircase-ness. Several other existing statistics are also implemented for the purpose of comparison: Aldous's graphical test and likelihood test to decide if a tree fits the Yule or uniform model; Coless's and Sackin's shape statisitics under both Yule and uniform hypotheses; cherry [...]
May 14, 2013 0
Comparing Run times (h) of RAxML and FastTree on alignments (left to right in increasing order of difficultly) after they've been run through two alignment tools.

Comparing RAxML and FastTree

RAxML is one of the state-of-the-art softwares out there which infers a maximum likelihood phylogenetic tree for protein/DNA sequences. FastTree implements an approximate-maximum -likelihood algorithm which allows for very fast inference. The paper comparing RAxML and FastTree concludes that For large datasets, FastTree gives results in computationally feasible times. In such cases RAxML cannot be [...]
May 10, 2013 0

Multiple instances of ancient balancing selection shared between humans and chimpanzees

Balancing selection (BS)-- retention of (population level) diversity in the genome. Since diversity can offer protection against pathogens/parasites, known examples tend to include the immune system. Examples include the MHC and the sickle cell gene; blood groups also qualify. The authors use a genome wide cross-species scan to identify BS in the human genome [Note: [...]
April 30, 2013 0

The web of human sexual contacts

Analyzing data from a Swedish survey regarding the sexual behavior the authors concluded that the network of sexual contacts follows a power law degree distribution. This scale free network structure has many implications regarding the propagation and the persistence of a disease. A disease will persist in this structure because of the lack of an [...]
April 25, 2013 0