Epithelial–mesenchymal transition (EMT) plays a critical role in promoting cancer metastasis. In this study, cancer EMT is considered as an overall structural change in the gene regulatory network (GRN), and its essential features are elucidated by the network biology approach. We first defined the state space of GRN as a set of all possible activation patterns of GRN, and then introduced t…

Network or edge biomarkers area reliable form to characterize phenotypes or diseases.However, obtaining edges or correlations between molecules for an individual requires measurement ofmultiple samples of that individual,which are generally unavailable in clinical practice. Thus, it is strongly demanded to diagnose a disease by edge or network biomarkers in one-sample-for-one-individual context…

Tumors are the result of accumulated genomic alterations that cooperate synergistically to produce uncontrollable cell growth. Although identifying recurrent alterations among large collections of tumors provides a way to pinpoint genes that endow a selective advantage in oncogenesis and progression, it fails to address the genetic interactions behind this selection process. A non-random pat…

Displacements and stress-field changes associated with earthquakes, volcanoes, landslides and human activity are often simulated using numerical models in an attempt to understand the underlying processes and their governing physics. The application of elastic dislocation theory to these problems, however, may be biased because of numerical instabilities in the calculations. Here, we present a…

Ribosomes are among the most fundamental molecular machines in all cells, as they are required for protein synthesis. Most structural rRNA components are generated in the nucleolus and assembled into pre-ribosomal particles. Here we show Apak, a previously identified p53 inhibitor, as a novel ribosomal stress response protein. In unstressed cells, Apak is bound to the deSUMOylase SENP1 in the n…

We present an extension of the nodal discontinuous Galerkin method for elastic wave propagation to high interpolation orders and arbitrary heterogeneous media. The high-order lagrangian interpolation is based on a set of nodes with excellent interpolation properties in the standard triangular element. In order to take into account highly variable geological media, another set of suitable quadra…

Histone deacetylase 1(HDAC1) is an important epigenetic controller involvedin transcriptional regulation throughmodification of chromatin structure. Genetic and epigenetic changes and deregulation of signal transduction pathways have been implicated in the development of breast cancer. Downregulation of estrogen receptor a (ERa) expression is one of the mechanisms behind the acquisition of e…

Pten controls a signaling axis that is implicated to regulate cell proliferation, growth, survival, migration, and metabolism. The molecular mechanisms underlying the specificity of Pten responses to such diverse cellular functions are currently poorly understood. Herewe report the control of Pten activity and signaling specificity during the cell cycle by Ndfip1 regulation of Pten spatial dist…

The DNA damage response helps to maintain genome integrity, suppress tumorigenesis, and mediate the effects of radiotherapy and chemotherapy. Our previous studies have shown that Smad1 is upregulated and activated by Atm in DNA damage response, which can further bind to p53 and promote p53 stabilization. Herewe report another aspect of the interplay between p53 and Smad1. Comparison of recta…

A new effective model is presented to compute horizontal-to-vertical spectral ratios (HVSR) relative to ambient vibrations, under the assumption that these are originated by a distribution of spatially correlated random surface sources. The major novelty of this model lies in the description of both ground displacement and sources as stochastic fields defined on the Earth’s surface, stationar…