Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Diversity-induced resonance in a system of globally coupled linear oscillators

The purpose of this paper to analyze in some detail the arguably simplest case of diversity-induced reseonance: that of a system of globally-coupled linear oscillators subjected to a periodic forcing. Diversity appears as the parameters characterizing each oscillator, namely its mass, internal frequency and damping coefficient are drawn from a probability distribution. The main ingredients for the diversity-induced-resonance phenomenon are present in this system as the oscillators display a variability in the individual responses but are induced, by the coupling, to synchronize their responses. A steady state solution for this model is obtained. We also determine the conditions under which it is possible to find a resonance effect.Comment: Reported at the XI International Workshop "Instabilities and Nonequilibrium Structures" Vina del Mar (Chile

Prospects of Detecting Baryon and Quark Superfluidity from Cooling Neutron Stars

Baryon and quark superfluidity in the cooling of neutron stars are investigated. Observations could constrain combinations of the neutron or Lambda-hyperon pairing gaps and the star's mass. However, in a hybrid star with a mixed phase of hadrons and quarks, quark gaps larger than a few tenths of an MeV render quark matter virtually invisible for cooling. If the quark gap is smaller, quark superfluidity could be important, but its effects will be nearly impossible to distinguish from those of other baryonic constituents.Comment: 4 pages, 3 ps figures, uses RevTex(aps,prl). Submitted to Phys. Rev. Let

Rapid Cooling of the Neutron Star in Cassiopeia A Triggered by Neutron Superfluidity in Dense Matter

We propose that the observed cooling of the neutron star in Cassiopeia A is due to enhanced neutrino emission from the recent onset of the breaking and formation of neutron Cooper pairs in the 3P2 channel. We find that the critical temperature for this superfluid transition is ~0.5x10^9 K. The observed rapidity of the cooling implies that protons were already in a superconducting state with a larger critical temperature. Our prediction that this cooling will continue for several decades at the present rate can be tested by continuous monitoring of this neutron star.Comment: Revised version, to be published in Phys. Rev. Let

Rotavirus genetic diversity, disease association, and temporal change in hospitalized rural Kenyan children

Background. The effectiveness of rotavirus vaccines will be dependent on the immunity conferred against prevalent and emergent variants causing severe diarrheal disease. Longitudinal surveillance of disease-causing strains is a prerequisite to intervention. Methods. Molecular characterization was conducted on rotavirus-positive stool samples from children admitted with diarrhea to a rural district hospital during 2002-2004. Extracted viral RNA was separated by polyacrylamide gel electrophoresis, and rotavirus VP4 (P types) and VP7 (G types) specificities were determined. Results. Among 558 investigated cases, the predominant genotype was P[8]G1 (42%), followed by P[8]G9 (15%), P[4]G8 (7%), P[6]G8 (6%), and P[8]G8 (4%), with 10% mixed strains. Overall, there were 6 different P types and 7 G types. No association was identified between genotype and child age, sex, or severity of diarrhea. The P and G genotypes and polyacrylamide gel electropherotypes showed significant temporal variation in frequency: P[8]G1 decreased from 51% (95% confidence interval [CI], 43%-58%) in 2002 to 30% (95% CI, 24%-37%) in 2004, and P[4]G8 increased from 2% (95% CI, 0%-5%) in 2002 to 13% (95% CI, 9%-19%). Quarterly data revealed seasonally endemic and emergence and/or decay patterns. Conclusions. Our study of rotavirus strains causing severe diarrhea in rural Kenyan children showed a predominance of P[8]G1 and confirms the importance of G8 and G9 strains in sub-Saharan Africa. Considerable genetic diversity of rotavirus strains was observed, including substantial mixed and unusual types, coupled with significant temporal strain variation and emergence. These results warn of variable vaccine efficacy and the need for long-term surveillance of circulating rotavirus genotypes

Susskind's Challenge to the Hartle-Hawking No-Boundary Proposal and Possible Resolutions

Given the observed cosmic acceleration, Leonard Susskind has presented the following argument against the Hartle-Hawking no-boundary proposal for the quantum state of the universe: It should most likely lead to a nearly empty large de Sitter universe, rather than to early rapid inflation. Even if one adds the condition of observers, they are most likely to form by quantum fluctuations in de Sitter and therefore not see the structure that we observe. Here I present my own amplified version of this argument and consider possible resolutions, one of which seems to imply that inflation expands the universe to be larger than 10^{10^{10^{122}}} Mpc.Comment: 24 pages, LaTeX, 8 references added and a distinction between Linde's and Vilenkin's tunneling proposal

No-Bang Quantum State of the Cosmos

A quantum state of the entire cosmos (universe or multiverse) is proposed which is the equal mixture of the Giddings-Marolf states that are asymptotically single de Sitter spacetimes in both past and future and are regular on the throat or neck of minimal three-volume. That is, states are excluded that have a big bang or big crunch or which split into multiple asymptotic de Sitter spacetimes. (For simplicity, transitions between different values of the cosmological constant are assumed not to occur, though different positive values are allowed.) The entropy of this mixed state appears to be of the order of the three-fourths power of the Bekenstein-Hawking A/4 entropy of de Sitter spacetime. Most of the component pure states do not have rapid inflation, but when an inflaton is present and the states are weighted by the volume at the end of inflation, a much smaller number of states may dominate and give a large amount of inflation and hence may agree with observations.Comment: 18 pages, LaTeX, updated with a few new qualifications and reference

Survival of patients with small cell lung cancer undergoing lung resection in England, 1998–2009

Introduction: Chemotherapy or chemoradiotherapy is the recommended treatment for small cell lung cancer (SCLC), except in stage I disease where clinical guidelines state there may be a role for surgery based on favourable outcomes in case series. Evidence supporting adjuvant chemotherapy in resected SCLC is limited but this is widely offered. Methods: Data on 359 873 patients who were diagnosed with a first primary lung cancer in England between 1998 and 2009 were grouped according to histology (SCLC or non-SCLC (NSCLC)) and whether they underwent a surgical resection. We explored their survival using Kaplan-Meier analysis and Cox regression, adjusting for age, sex, comorbidity and socioeconomic status. Results: The survival of 465 patients with resected SCLC was lower than patients with resected NSCLC (5-year survival 31% and 45%, respectively), but much higher than patients of either group who were not resected (3%). The difference between resected SCLC and NSCLC diminished with time after surgery. Survival was superior for the subgroup of 198 'elective' SCLC cases where the diagnosis was most likely known before resection than for the subgroup of 267 'incidental' cases where the SCLC diagnosis was likely to have been made after resection. Conclusions: These data serve as a natural experiment testing the survival after surgical management of SCLC according to NSCLC principles. Patients with SCLC treated surgically for early stage disease may have survival outcomes that approach those of NSCLC, supporting the emerging clinical practice of offering surgical resection to selected patients with SCLC

Positivity of Entropy in the Semi-Classical Theory of Black Holes and Radiation

Quantum stress-energy tensors of fields renormalized on a Schwarzschild background violate the classical energy conditions near the black hole. Nevertheless, the associated equilibrium thermodynamical entropy $\Delta S$ by which such fields augment the usual black hole entropy is found to be positive. More precisely, the derivative of $\Delta S$ with respect to radius, at fixed black hole mass, is found to vanish at the horizon for {\it all} regular renormalized stress-energy quantum tensors. For the cases of conformal scalar fields and U(1) gauge fields, the corresponding second derivative is positive, indicating that $\Delta S$ has a local minimum there. Explicit calculation shows that indeed $\Delta S$ increases monotonically for increasing radius and is positive. (The same conclusions hold for a massless spin 1/2 field, but the accuracy of the stress-energy tensor we employ has not been confirmed, in contrast to the scalar and vector cases). None of these results would hold if the back-reaction of the radiation on the spacetime geometry were ignored; consequently, one must regard $\Delta S$ as arising from both the radiation fields and their effects on the gravitational field. The back-reaction, no matter how "small",Comment: 19 pages, RevTe

Effective Potential of a Black Hole in Thermal Equilibrium with Quantum Fields

Expectation values of one-loop renormalized thermal equilibrium stress-energy tensors of free conformal scalars, spin-${1 \over 2}$ fermions and U(1) gauge fields on a Schwarzschild black hole background are used as sources in the semi-classical Einstein equation. The back-reaction and new equilibrium metric are solved for at $O({\hbar})$ for each spin field. The nature of the modified black hole spacetime is revealed through calculations of the effective potential for null and timelike orbits. Significant novel features affecting the motions of both massive and massless test particles show up at lowest order in $\epsilon= (M_{Pl}/M)^2 < 1$, where $M$ is the renormalized black hole mass, and $M_{Pl}$ is the Planck mass. Specifically, we find the tendency for \underline{stable} circular photon orbits, an increase in the black hole capture cross sections, and the existence of a gravitationally repulsive region associated with the black hole which is generated from the U(1) back-reaction. We also consider the back-reaction arising from multiple fields, which will be useful for treating a black hole in thermal equilibrium with field ensembles belonging to gauge theories.Comment: 25 pages (not including seven figures), VAND-TH-93-6. Typed in Latex, uses RevTex macro