Slow nonequilibrium dynamics: parallels between classical and quantum glasses and gently driven systems

We review an scenario for the non-equilibrium dynamics of glassy systems that has been motivated by the exact solution of simple models. This approach allows one to set on firmer grounds well-known phenomenological theories. The old ideas of entropy crisis, fictive temperatures, free-volume... have clear definitions within these models. Aging effects in the glass phase are also captured. One of the salient features of the analytic solution, the breakdown of the fluctuation-dissipation relations, provides a definition of a bonafide {\it effective temperature} that is measurable by a thermometer, controls heat flows, partial equilibrations, and the reaction to the external injection of heat. The effective temperature is an extremely robust concept that appears in non-equilibrium systems in the limit of small entropy production as, for instance, sheared fluids, glasses at low temperatures when quantum fluctuations are relevant, tapped or vibrated granular matter, etc. The emerging scenario is one of partial equilibrations, in which glassy systems arrange their internal degrees of freedom so that the slow ones select their own effective temperatures. It has been proven to be consistent within any perturbative resummation scheme (mode coupling, etc) and it can be challenged by experimental and numerical tests, some of which it has already passed.Comment: 15 pages, 8 figure

RNA-Seq of Human Neurons Derived from iPS Cells Reveals Candidate Long Non-Coding RNAs Involved in Neurogenesis and Neuropsychiatric Disorders

Genome-wide expression analysis using next generation sequencing (RNA-Seq) provides an opportunity for in-depth molecular profiling of fundamental biological processes, such as cellular differentiation and malignant transformation. Differentiating human neurons derived from induced pluripotent stem cells (iPSCs) provide an ideal system for RNA-Seq since defective neurogenesis caused by abnormalities in transcription factors, DNA methylation, and chromatin modifiers lie at the heart of some neuropsychiatric disorders. As a preliminary step towards applying next generation sequencing using neurons derived from patient-specific iPSCs, we have carried out an RNA-Seq analysis on control human neurons. Dramatic changes in the expression of coding genes, long non-coding RNAs (lncRNAs), pseudogenes, and splice isoforms were seen during the transition from pluripotent stem cells to early differentiating neurons. A number of genes that undergo radical changes in expression during this transition include candidates for schizophrenia (SZ), bipolar disorder (BD) and autism spectrum disorders (ASD) that function as transcription factors and chromatin modifiers, such as POU3F2 and ZNF804A, and genes coding for cell adhesion proteins implicated in these conditions including NRXN1 and NLGN1. In addition, a number of novel lncRNAs were found to undergo dramatic changes in expression, one of which is HOTAIRM1, a regulator of several HOXA genes during myelopoiesis. The increase we observed in differentiating neurons suggests a role in neurogenesis as well. Finally, several lncRNAs that map near SNPs associated with SZ in genome wide association studies also increase during neuronal differentiation, suggesting that these novel transcripts may be abnormally regulated in a subgroup of patients