BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories.

Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical datasets. Concurrently, our ability to perform long-timescale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially.

Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates.

In this report, we propose a novel mathematical model of the origin and evolution of sex determination in vertebrates that is based on the stochastic epigenetic modification (SEM) mechanism. We have previously shown that SEM, with rates consistent with experimental observation, can both increase the rate of gene fixation and decrease pseudogenization, thus dramatically improving the efficacy of evolution. Here, we present a conjectural model of the origin and evolution of sex determination wherein the SEM mechanism alone is sufficient to parsimoniously trigger and guide the evolution of heteromorphic sex chromosomes from the initial homomorphic chromosome configuration, without presupposing any allele frequency differences.

Systems profiling reveals recurrently dysregulated cytokine signaling responses in ER+ breast cancer patients' blood.

Cytokines operate in concert to maintain immune homeostasis and coordinate immune responses. In cases of ER breast cancer, peripheral immune cells exhibit altered responses to several cytokines, and these alterations are correlated strongly with patient outcomes. To develop a systems-level understanding of this dysregulation, we measured a panel of cytokine responses and receptor abundances in the peripheral blood of healthy controls and ER breast cancer patients across immune cell types.

Estimation of the Structure of Hydrophobic Surfaces Using the Cassie-Baxter Equation.

The effect of extreme water repellency, called the lotus effect, is caused by the formation of a Cassie-Baxter state in which only a small portion of the wetting liquid droplet is in contact with the surface. The rest of the bottom of the droplet is in contact with air pockets. Instrumental methods are often used to determine the textural features that cause this effect-scanning electron and atomic force microscopies, profilometry, etc.