A hierarchical Bayesian framework to infer the progression level to diabetes based on deficient clinical data.

The increase in lifestyle-related diseases such as heart disease, diabetes, and high blood pressure is a challenging problem that should be resolved. The physiological mechanisms of the human body have long been studied using mathematical models. In particular, to study glucose metabolism, several models that infer insulin sensitivity and β-cell function have been developed.

Spatial distribution of selection pressure on a protein based on the hierarchical Bayesian model.

Proteins adapt to novel environments and/or gain function by substitution in amino acid sequences. Therefore, mutations in protein-coding genes are subject to selection pressure. The strength and character of selection pressure may vary among the regions of the protein.

Structural considerations in the fitness landscape of a virus.

Viral fitness is determined by replication within hosts and transmission between them. We examine how pleiotropic mutations that have antagonistic effects (i.e.

A likelihood-based index of protein protein binding affinities with application to influenza HA escape from antibodies.

In many biological systems, proteins interact with other organic molecules to produce indispensable functions, in which molecular recognition phenomena are essential. Proteins have kept or gained their functions during molecular evolution. Their functions seem to be flexible, and a few amino acid substitutions sometimes cause drastic changes in function.

Robust time estimation reconciles views of the antiquity of placental mammals.

Background: Molecular studies have reported divergence times of modern placental orders long before the Cretaceous-Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution.

Methodology/principal Findings: New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described.

Core set approach to reduce uncertainty of gene trees.

Background: A genealogy based on gene sequences within a species plays an essential role in the estimation of the character, structure, and evolutionary history of that species. Because intraspecific sequences are more closely related than interspecific ones, detailed information on the evolutionary process may be available by determining all the node sequences of trees and provide insight into functional constraints and adaptations. However, strong evolutionary correlations on a few lineages make this determination difficult as a whole, and the maximum parsimony (MP) method frequently allows a number of topologies with a same total branching length.

Fold recognition of the human immunodeficiency virus type 1 V3 loop and flexibility of its crown structure during the course of adaptation to a host.

The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of the virus, which is an important determinant of HIV pathogenesis. Hence, the information about preferred conformations of the V3-loop region and its flexibility could be a crucial tool for understanding the mechanisms of progression from an initial infection to AIDS.

Multidimensional vector space representation for convergent evolution and molecular phylogeny.

With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models can support incorrect topologies significantly because of the high signal-to-noise ratio.

Academic performance and comparative effectiveness of computer- and textbook-based self-instruction.

We intended to clarify the influence of student academic ability on the effectiveness of CAI, using data of a study to assess the effectiveness of a new type of CAI software, cyberPatient (CP), at Kochi Medical School (KMS). A total of 59 third-year students were randomly assigned to four groups: Group-1 used a textbook for self-instruction, Group-2 used CP, Group-3 used both types of learning materials, and Group-4 did not learn. Learning performance was evaluated by multiple-choice examination and OSCE.