The Complexity of Computing the Size of an Interval

Given a p-order A over a universe of strings (i.e., a transitive, reflexive, antisymmetric relation such that if (x, y) is an element of A then |x| is polynomially bounded by |y|), an interval size function of A returns, for each string x in the universe, the number of strings in the interval between strings b(x) and t(x) (with respect to A), where b(x) and t(x) are functions that are polynomial-time computable in the length of x. By choosing sets of interval size functions based on feasibility requirements for their underlying p-orders, we obtain new characterizations of complexity classes. We prove that the set of all interval size functions whose underlying p-orders are polynomial-time decidable is exactly #P. We show that the interval size functions for orders with polynomial-time adjacency checks are closely related to the class FPSPACE(poly). Indeed, FPSPACE(poly) is exactly the class of all nonnegative functions that are an interval size function minus a polynomial-time computable function. We study two important functions in relation to interval size functions. The function #DIV maps each natural number n to the number of nontrivial divisors of n. We show that #DIV is an interval size function of a polynomial-time decidable partial p-order with polynomial-time adjacency checks. The function #MONSAT maps each monotone boolean formula F to the number of satisfying assignments of F. We show that #MONSAT is an interval size function of a polynomial-time decidable total p-order with polynomial-time adjacency checks. Finally, we explore the related notion of cluster computation.Comment: This revision fixes a problem in the proof of Theorem 9.

Deconvolution of pro- and antiviral genomic responses in Zika virus-infected and bystander macrophages.

Genome-wide investigations of host-pathogen interactions are often limited by analyses of mixed populations of infected and uninfected cells, which lower sensitivity and accuracy. To overcome these obstacles and identify key mechanisms by which Zika virus (ZIKV) manipulates host responses, we developed a system that enables simultaneous characterization of genome-wide transcriptional and epigenetic changes in ZIKV-infected and neighboring uninfected primary human macrophages. We demonstrate that transcriptional responses in ZIKV-infected macrophages differed radically from those in uninfected neighbors and that studying the cell population as a whole produces misleading results. Notably, the uninfected population of macrophages exhibits the most rapid and extensive changes in gene expression, related to type I IFN signaling. In contrast, infected macrophages exhibit a delayed and attenuated transcriptional response distinguished by preferential expression of IFNB1 at late time points. Biochemical and genomic studies of infected macrophages indicate that ZIKV infection causes both a targeted defect in the type I IFN response due to degradation of STAT2 and reduces RNA polymerase II protein levels and DNA occupancy, particularly at genes required for macrophage identity. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected macrophages thereby reveals the coincident evolution of dominant proviral or antiviral mechanisms, respectively, that determine the outcome of ZIKV exposure

Recovering a lost seismic disaster. The destruction of El Castillejo and the discovery of the earliest historic earthquake affecting the Granada region (Spain)

This paper discusses recent archaeological fieldwork conducted at El Castillejo, a medieval Islamic settlement in Los Guájares, Granada, southern Spain. Results from combined archaeological excavation and archaeoseismological assessment of standing structures suggest that the site was affected by a destructive earthquake during its occupation. Radiocarbon samples and OSL analysis point to a seismic event in the period CE 1224–1266. The earthquake occurred within an area marked by a ‘seismological gap’ in terms of historic seismicity and the causative fault has been tentatively identified in the Nigüelas-Padul Fault System which lies north of the settlement. This event is not recorded by national or European seismic catalogues and represents the oldest historic earthquake in the Granada area. Our work stresses the significant impact that targeted archaeological investigations can generate in our understanding of the local historic seismicity, thus providing clear implications for seismic disaster prevention and reduction

Brown Dwarfs in Young Moving Groups from Pan-STARRS1. I. AB Doradus

Substellar members of young ($\lesssim$150 Myr) moving groups are valuable benchmarks to empirically define brown dwarf evolution with age and to study the low-mass end of the initial mass function. We have combined Pan-STARRS1 (PS1) proper motions with optical$-$IR photometry from PS1, 2MASS and $\textit{WISE}$ to search for substellar members of the AB Dor Moving Group within $\approx$50 pc and with spectral types of late-M to early-L, corresponding to masses down to $\approx$30 M$_{Jup}$ at the age of the group ($\approx$125 Myr). Including both photometry and proper motions allows us to better select candidates by excluding field dwarfs whose colors are similar to young AB~Dor Moving Group members. Our near-IR spectroscopy has identified six ultracool dwarfs (M6$-$L4; $\approx$30$-$100 M$_{Jup}$) with intermediate surface gravities (INT-G) as candidate members of the AB Dor Moving Group. We find another two candidate members with spectra showing hints of youth but consistent with field gravities. We also find four field brown dwarfs unassociated with the AB Dor Moving Group, three of which have INT-G gravity classification. While signatures of youth are present in the spectra of our $\approx$125 Myr objects, neither their $J-K$ nor $W1-W2$ colors are significantly redder than field dwarfs with the same spectral types, unlike younger ultracool dwarfs. We also determined PS1 parallaxes for eight of our candidates and one previously identified AB Dor Moving Group candidate. Although radial velocities (and parallaxes, for some) are still needed to fully assess membership, these new objects provide valuable insight into the spectral characteristics and evolution of young brown dwarfs.Comment: ApJ, accepte

Imaging the coordination of multiple signaling activities in living cells

Cellular signal transduction occurs in complex and redundant interaction networks that are best examined at the level of single cells by simultaneously monitoring the activation dynamics of multiple components. Recent advances in biosensor technology have made it possible to visualize and quantify the activation of multiple network nodes in the same living cell. The precision and scope of this approach has been greatly extended by novel computational approaches to determine the relationships between different networks, studied in separate cells