Biology subjects

Jones, J. H.

Publications and source records attributed to Jones, J. H..

3 recordsLinked to original sources

bioRxiv2018

Genome-wide patterns of gene expression in a wild primate indicate species-specific mechanisms associated with tolerance to natural simian immunodeficiency virus infection

Over 40 species of nonhuman primates host simian immunodeficiency viruses (SIVs). In natural hosts, infection is generally assumed to be nonpathogenic due to a long coevolutionary history between host and virus, although pathogenicity is difficult to study in wild nonhuman primates. We used whole-blood RNA-seq and SIV prevalence from 29 wild Ugandan red colobus (Piliocolobus tephrosceles) to assess the effects of SIV infection on host gene expression in wild, naturally SIV-infected primates. We found no evidence for chronic immune activation in infected individuals, suggesting that SIV is not immunocompromising in this species, in contrast to HIV in humans. Notably, an immunosuppressive gene, CD101, was upregulated in infected individuals. This gene has not been previously described in the context of nonpathogenic SIV infection. This expands the known variation associated with SIV infection in natural hosts, and may suggest a novel mechanism for tolerance of SIV infection in the Ugandan red colobus.

genomics↗

bioRxiv2017

A general goodness-of-fit test for survival analysis

Existing goodness-of-fit tests for survival data are either exclusively graphical in nature or only test specific model assumptions, such as the proportional hazards assumption. We describe a flexible, parameter-free goodness-of-fit test that provides a simple numerical assessment of a models suitability regardless of the structure of the underlying model. Intuitively, the goodness-of-fit test utilizes the fact that for a good model early event occurrence is predicted to be just as likely as late event occurrence, whereas a bad model has a bias towards early or late events. Formally, the goodness-of-fit test is based on a novel generalized Martingale residual which we call the martingale survival residual. The martingale survival residual has a uniform probability density function defined on the interval -0.5 to +0.5 if censoring is either absent or accounted for as one outcome in a competing hazards framework. For a good model, the set of calculated residuals is statistically indistinguishable from the uniform distribution, which is tested using the Kolmogorov-Smirnov statistic.

epidemiology↗

bioRxiv2016

Hierarchical Evolutionary Preferences Explain Discrepancies in Expected Utility Theory

The standard axiomatic theory of rationality posits that agents order preferences according to the average utilities associated with different choices. Expected Utility Theory has repeatedly failed as a predictive theory of choice behavior, as reflected in a growing literature in behavioral economics. Evolutionary theorists have suggested that seemingly irrational behaviors in contemporary contexts may have once served important functions, but there has been little attempt to formalize the relationship between evolutionary fitness and choice behavior. Biological agents should optimize fitness, but fitness itself is not a reasonable value function for decision-making since its time-scale exceeds the lifespan of the decision-maker. Consequently, organisms use proximate motivational systems that work on appropriate time-scales and are amenable to feedback and learning. We develop an evolutionary principal-agent model in which individuals maximize a set of proximal choice variables (age-specific demographic rates), the interests of which are aligned with fitness. The solution to our model yields pessimistic probability weightings compatible with the Rank-Dependent Expected Utility family of choice models. The pessimistic probability weighting characteristic of these models emerges naturally in an evolutionary framework because of extreme intolerance to zeros in multiplicative growth processes.

evolutionary biology↗