A conserved metalloprotease mediates ecdysis in Caenorhabditis elegans

Molting is required for progression between larval stages in the life cycle of nematodes. We have identified four mutant alleles of a <i>Caenorhabditis elegans</i> metalloprotease gene, <i>nas-37</i>, that cause incomplete ecdysis. At each molt the cuticle fails to open sufficiently at the anterior end and the partially shed cuticle is dragged behind the animal. The gene is expressed in hypodermal cells 4 hours before ecdysis during all larval stages. The <i>NAS-37</i> protein accumulates in the anterior cuticle and is shed in the cuticle after ecdysis. This pattern of protein accumulation places NAS- 37 in the right place and at the right time to degrade the cuticle to facilitate ecdysis. The nas-37 gene has orthologs in other nematode species, including parasitic nematodes, and they undergo a similar shedding process. For example, <i>Haemonchus contortus</i> molts by digesting a ring of cuticle at the tip of the nose. Incubating <i>Haemonchus</i> larvae in extracted exsheathing fluids causes a refractile ring of digested cuticle to form at the tip of the nose. When <i>Haemonchus</i> cuticles are incubated with purified NAS-37, a similar refractile ring forms. NAS-37 degradation of the <i>Haemonchus</i> cuticle suggests that the metalloproteases and the cuticle substrates involved in exsheathment of parasitic nematodes are conserved in free-living nematodes

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Quantum Radiation from a 5-Dimensional Rotating Black Hole

We study a massless scalar field propagating in the background of a five-dimensional rotating black hole. We showed that in the Myers-Perry metric describing such a black hole the massless field equation allows the separation of variables. The obtained angular equation is a generalization of the equation for spheroidal functions. The radial equation is similar to the radial Teukolsky equation for the 4-dimensional Kerr metric. We use these results to quantize the massless scalar field in the space-time of the 5-dimensional rotating black hole and to derive expressions for energy and angular momentum fluxes from such a black hole.Comment: references added, accepted for publication in Physical Review

Primordial black holes in braneworld cosmologies: astrophysical constraints

In two recent papers we explored the modifications to primordial black hole physics when one moves to the simplest braneworld model, Randall--Sundrum type II. Both the evaporation law and the cosmological evolution of the population can be modified, and additionally accretion of energy from the background can be dominant over evaporation at high energies. In this paper we present a detailed study of how this impacts upon various astrophysical constraints, analyzing constraints from the present density, from the present high-energy photon background radiation, from distortion of the microwave background spectrum, and from processes affecting light element abundances both during and after nucleosynthesis. Typically, the constraints on the formation rate of primordial black holes weaken as compared to the standard cosmology if black hole accretion is unimportant at high energies, but can be strengthened in the case of efficient accretion.Comment: 17 pages RevTeX4 file with three figures incorporated; final paper in series astro-ph/0205149 and astro-ph/0208299. Minor changes to match version accepted by Physical Review

Some general properties of the renormalized stress-energy tensor for static quantum states on (n+1)-dimensional spherically symmetric black holes

We study the renormalized stress-energy tensor (RSET) for static quantum states on (n+1)-dimensional, static, spherically symmetric black holes. By solving the conservation equations, we are able to write the stress-energy tensor in terms of a single unknown function of the radial co-ordinate, plus two arbitrary constants. Conditions for the stress-energy tensor to be regular at event horizons (including the extremal and ``ultra-extremal'' cases) are then derived using generalized Kruskal-like co-ordinates. These results should be useful for future calculations of the RSET for static quantum states on spherically symmetric black hole geometries in any number of space-time dimensions.Comment: 9 pages, no figures, RevTeX4, references added, accepted for publication in General Relativity and Gravitatio

The Refederalization of American Health Care

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69090/2/10.1177_107755878704400103.pd

Black Hole Spin via Continuum Fitting and the Role of Spin in Powering Transient Jets

The spins of ten stellar black holes have been measured using the continuum-fitting method. These black holes are located in two distinct classes of X-ray binary systems, one that is persistently X-ray bright and another that is transient. Both the persistent and transient black holes remain for long periods in a state where their spectra are dominated by a thermal accretion disk component. The spin of a black hole of known mass and distance can be measured by fitting this thermal continuum spectrum to the thin-disk model of Novikov and Thorne; the key fit parameter is the radius of the inner edge of the black hole's accretion disk. Strong observational and theoretical evidence links the inner-disk radius to the radius of the innermost stable circular orbit, which is trivially related to the dimensionless spin parameter a_* of the black hole (|a_*| < 1). The ten spins that have so far been measured by this continuum-fitting method range widely from a_* \approx 0 to a_* > 0.95. The robustness of the method is demonstrated by the dozens or hundreds of independent and consistent measurements of spin that have been obtained for several black holes, and through careful consideration of many sources of systematic error. Among the results discussed is a dichotomy between the transient and persistent black holes; the latter have higher spins and larger masses. Also discussed is recently discovered evidence in the transient sources for a correlation between the power of ballistic jets and black hole spin.Comment: 30 pages. Accepted for publication in Space Science Reviews. Also to appear in hard cover in the Space Sciences Series of ISSI "The Physics of Accretion onto Black Holes" (Springer Publisher). Changes to Sections 5.2, 6.1 and 7.4. Section 7.4 responds to Russell et al. 2013 (MNRAS, 431, 405) who find no evidence for a correlation between the power of ballistic jets and black hole spi

Many body physics from a quantum information perspective

The quantum information approach to many body physics has been very successful in giving new insight and novel numerical methods. In these lecture notes we take a vertical view of the subject, starting from general concepts and at each step delving into applications or consequences of a particular topic. We first review some general quantum information concepts like entanglement and entanglement measures, which leads us to entanglement area laws. We then continue with one of the most famous examples of area-law abiding states: matrix product states, and tensor product states in general. Of these, we choose one example (classical superposition states) to introduce recent developments on a novel quantum many body approach: quantum kinetic Ising models. We conclude with a brief outlook of the field.Comment: Lectures from the Les Houches School on "Modern theories of correlated electron systems". Improved version new references adde

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

Plasma matrix metalloproteinases in neonates having surgery for congenital heart disease

During cardiopulmonary-bypass matrix-metalloproteinases released may contribute to ventricular dysfunction. This study was to determine plasma matrix-metalloproteinases in neonates after cardiopulmonary-bypass and their relation to post-operative course. A prospective observational study included 18 neonates having cardiac surgery. Plasma matrix-metalloproteinases-2 and 9 activities were measured by gelatin-zymography pre-operatively, on starting cardiopulmonarybypass, 7–8 min after aortic cross-clamp release, and 1h, 4h, 24h, and 3d after cardiopulmonary-bypass. Plasma concentrations of their tissue inhibitors 1 and 2 were determined by enzyme-linked immunosorbent assay. Cardiac function was assessed by serial echocardiography. Paired t-tests and Wilcoxon tests were used to assess temporal changes, and linear correlation with simultaneous clinical and cardiac function parameters were assessed using Pearson's product-moment correlation coefficient. Plasma matrix-metalloproteinases activities and their tissue inhibitor concentrations decreased during cardiopulmonary-bypass. Matrix-metalloproteinase-2 plasma activity increased progressively starting 1h after cardiopulmonarybypass and returned to pre-operative levels at 24h. Matrix-metalloproteinase-9 plasma activity increased significantly after release of aortic cross-clamp, peaked 7–8min later, and returned to baseline at 24h. Plasma tissueinhibitor 1 and 2 concentrations increased 1h after cardiopulmonary-bypass. Cardiac function improved from 4h to 3d after surgery (p<0.05). There was no evidence of significant correlations between matrix-metalloproteinases or their inhibitors and cardiac function, inotrope scores, organ dysfunction scores, ventilation days, or hospital days. The temporal profile of plasma matrix-metalloproteinases and their inhibitors after cardiopulmonary-bypass in neonates are similar to adults. In neonates, further study should determine whether circulating matrix-metalloproteinases are useful biomarkers of disease activity locally within the myocardium, and hence of clinical outcomes