Recent evidence that TADs and chromatin loops are dynamic structures.

Mammalian genomes are folded into spatial domains, which regulate gene expression by modulating enhancer-promoter contacts. Here, we review recent studies on the structure and function of Topologically Associating Domains (TADs) and chromatin loops. We discuss how loop extrusion models can explain TAD formation and evidence that TADs are formed by the ring-shaped protein complex, cohesin, and that TAD boundaries are established by the DNA-binding protein, CTCF. We discuss our recent genomic, biochemical and single-molecule imaging studies on CTCF and cohesin, which suggest that TADs and chromatin loops are dynamic structures. We highlight complementary polymer simulation studies and Hi-C studies employing acute depletion of CTCF and cohesin, which also support such a dynamic model. We discuss the limitations of each approach and conclude that in aggregate the available evidence argues against stable loops and supports a model where TADs are dynamic structures that continually form and break throughout the cell cycle

Temperature equilibration in a fully ionized plasma: electron-ion mass ratio effects

Brown, Preston, and Singleton (BPS) produced an analytic calculation for energy exchange processes for a weakly to moderately coupled plasma: the electron-ion temperature equilibration rate and the charged particle stopping power. These precise calculations are accurate to leading and next-to-leading order in the plasma coupling parameter, and to all orders for two-body quantum scattering within the plasma. Classical molecular dynamics can provide another approach that can be rigorously implemented. It is therefore useful to compare the predictions from these two methods, particularly since the former is theoretically based and the latter numerically. An agreement would provide both confidence in our theoretical machinery and in the reliability of the computer simulations. The comparisons can be made cleanly in the purely classical regime, thereby avoiding the arbitrariness associated with constructing effective potentials to mock up quantum effects. We present here the classical limit of the general result for the temperature equilibration rate presented in BPS. We examine the validity of the m_electron/m_ion --> 0 limit used in BPS to obtain a very simple analytic evaluation of the long-distance, collective effects in the background plasma.Comment: 14 pages, 4 figures, small change in titl

New State Distribution and Host Records of North American Buprestidae (Coleoptera)

The following new state records are reported for buprestid species in the eastern United States: Agrilus egeniformis Champlain and Knull and Polyceta elata LeConte from Georgia, Agrilus defectus LeConte and Agrilus vittaticollis (Randall) from Minnesota and Agrilus paramasculinus Champlain and Knull from Michigan and Indiana. Chrysobothris shawnee Wellso and Manley and Chrysobothris rugosiceps Melsheimer are reported from red oak (Quercus rubra L.) and English oak (Quercus robur L.) for the first time, after being reared from naturally infested host material collected in Michigan, USA

On the failure of subadditivity of the Wigner-Yanase entropy

It was recently shown by Hansen that the Wigner-Yanase entropy is, for general states of quantum systems, not subadditive with respect to decomposition into two subsystems, although this property is known to hold for pure states. We investigate the question whether the weaker property of subadditivity for pure states with respect to decomposition into more than two subsystems holds. This property would have interesting applications in quantum chemistry. We show, however, that it does not hold in general, and provide a counterexample.Comment: LaTeX2e, 4 page

The Impact of Simulation Sequencing on Perceived Clinical Decision Making

An emerging nursing education trend is to utilize simulated learning experiences as a means to optimize competency and decision making skills. The purpose of this study was to examine differences in students\u27 perception of clinical decision making and clinical decision making-related self-confidence and anxiety based on the sequence (order) in which they participated in a block of simulated versus hospital-based learning experiences. A quasi-experimental crossover design was used. Between and within group differences were found relative to self-confidence with the decision making process. When comparing groups, at baseline the simulation followed by hospital group had significantly higher self-confidence scores, however, at 14-weeks both groups were not significantly different. Significant within group differences were found in the simulation followed by hospital group only, demonstrating a significant decrease in clinical decision making related anxiety across the semester. Finally, there were no significant difference in; perceived clinical decision making within or between the groups at the two measurement points. Preliminary findings suggest that simulated learning experiences can be offered with alternating sequences without impacting the process, anxiety or confidence with clinical decision making. This study provides beginning evidence to guide curriculum development and allow flexibility based on student needs and available resources

Solvent fluctuations around solvophobic, solvophilic and patchy nanostructures and the accompanying solvent mediated interactions

Using classical density functional theory (DFT) we calculate the density profile $\rho({\mathbf r})$ and local compressibility $\chi({\mathbf r})$ of a simple liquid solvent in which a pair of blocks with (microscopic) rectangular cross-section are immersed. We consider blocks that are solvophobic, solvophilic and also ones that have both solvophobic and solvophilic patches. Large values of $\chi({\mathbf r})$ correspond to regions in space where the liquid density is fluctuating most strongly. We seek to elucidate how enhanced density fluctuations correlate with the solvent mediated force between the blocks, as the distance between the blocks and the chemical potential of the liquid reservoir vary. For sufficiently solvophobic blocks, at small block separations and small deviations from bulk gas-liquid coexistence, we observe a strongly attractive (near constant) force, stemming from capillary evaporation to form a low density gas-like intrusion between the blocks. The accompanying $\chi({\mathbf r})$ exhibits structure which reflects the incipient gas-liquid interfaces that develop. We argue that our model system provides a means to understanding the basic physics of solvent mediated interactions between nanostructures, and between objects such as proteins in water, that possess hydrophobic and hydrophilic patches.Comment: 19 pages, 21 figure

Hollow Heaps

We introduce the hollow heap, a very simple data structure with the same amortized efficiency as the classical Fibonacci heap. All heap operations except delete and delete-min take $O(1)$ time, worst case as well as amortized; delete and delete-min take $O(\log n)$ amortized time on a heap of $n$ items. Hollow heaps are by far the simplest structure to achieve this. Hollow heaps combine two novel ideas: the use of lazy deletion and re-insertion to do decrease-key operations, and the use of a dag (directed acyclic graph) instead of a tree or set of trees to represent a heap. Lazy deletion produces hollow nodes (nodes without items), giving the data structure its name.Comment: 27 pages, 7 figures, preliminary version appeared in ICALP 201