The Yellowstone Permutation

Define a sequence of positive integers by the rule that a(n) = n for 1 <= n = 4, a(n) is the smallest number not already in the sequence which has a common factor with a(n-2) and is relatively prime to a(n-1). We show that this is a permutation of the positive integers. The remarkable graph of this sequence consists of runs of alternating even and odd numbers, interrupted by small downward spikes followed by large upward spikes, suggesting the eruption of geysers in Yellowstone National Park. On a larger scale the points appear to lie on infinitely many distinct curves. There are several unanswered questions concerning the locations of these spikes and the equations for these curves.Comment: 10 pages, 6 figures. Mar 7 2015: mostly stylistic change

Thermal origin of neutron star magnetic fields

It is proposed that magnetic field arises naturally in neutron stars as a consequence of thermal effects occurring in their outer crusts. The heat flux through the crust, which is carried mainly by degenerate electrons, can give rise to a possible thermoelectric instability in the solid crust which causes horizontal magnetic field components to grow exponentially with time. However, in order for the thermally driven growth to exceed ohmic decay, either the electron collision time must exceed existing estimates by a factor ∼ 3 or the surface layers comprise helium. A second instability is possible if the liquid phase that lies above the solid crust also contains a horizontal magnetic field. The heat flux will drive circulation which should amplify the field strength provided that there is a seed field in excess of ∼ 10^8 G. If either of these two instabilities develops the field will quickly grow to a strength of ∼ 10^(12) G, where the instabilities become non-linear. Further growth will saturate when either the magnetic stress exceeds the lattice yield stress or the temperature perturbations become non-linear, both of which occur at a subsurface field strength of ∼ 10^(14) G; the corresponding surface field strength is ∼ 10^(12) G. Further evolution of the magnetic field should lead to long-range order and yield neutron star magnetic dipole moments ∼ 10^(30) G cm^3, comparable with those observed. Newly-formed neutron stars should be able to develop their dipole moments in a hundred thousand years and maintain them for as long as heat flows through the crust. Thereafter, the dipole moment should decay in several million years, as observed in the case of most radio pulsars. Neutron stars that are formed spinning rapidly, like that in the Crab Nebula, should be able to grow magnetic fields far more rapidly since their rotational energy can also be tapped to drive thermoelectric currents. The interiors of neutron stars in binary systems may be heated by the energy released by accreting matter. The resulting heat flux may cause the production of magnetic fields in these objects. Binary pulsars, with their unusually low and persistent fields, have probably passed through this phase

Mutant enrichment by filtration concentration: a variation for the selection of temperature-conditional heterocaryons

Mutant enrichment by filtration concentration: a variation for the selection of temperature-conditional heterocaryon

Multiple shRNA combinations for near-complete coverage of all HIV-1 strains

<p>Abstract</p> <p>Background</p> <p>Combinatorial RNA interference (co-RNAi) approaches are needed to account for viral variability in treating HIV-1 with RNAi, as single short hairpin RNAs (shRNA) are rapidly rendered ineffective by resistant strains. Current work suggests that 4 simultaneously expressed shRNAs may prevent the emergence of resistant strains.</p> <p>Results</p> <p>In this study we assembled combinations of highly-conserved shRNAs to target as many HIV-1 strains as possible. We analyzed intersecting conservations of 10 shRNAs to find combinations with 4+ matching the maximum number of strains using 1220+ HIV-1 sequences from the Los Alamos National Laboratory (LANL). We built 26 combinations of 2 to 7 shRNAs with up to 87% coverage for all known strains and 100% coverage of clade B subtypes, and characterized their intrinsic suppressive activities in transient expression assays. We found that all combinations had high combined suppressive activities, though there were also large changes in the individual activities of the component shRNAs in our multiple expression cassette configurations.</p> <p>Conclusion</p> <p>By considering the intersecting conservations of shRNA combinations we have shown that it is possible to assemble combinations of 6 and 7 highly active, highly conserved shRNAs such that there is always at least 4 shRNAs within each combination covering all currently known variants of entire HIV-1 subtypes. By extension, it may be possible to combine several combinations for complete global coverage of HIV-1 variants.</p

Large Scale Inhomogeneities from the QCD Phase Transition

We examine the first-order cosmological QCD phase transition for a large class of parameter values, previously considered unlikely. We find that the hadron bubbles can nucleate at very large distance scales, they can grow as detonations as well as deflagrations, and that the phase transition may be completed without reheating to the critical temperature. For a subset of the parameter values studied, the inhomogeneities generated at the QCD phase transition might have a noticeable effect on nucleosynthesis.Comment: 15 LaTeX pages + 6 PostScript figures appended at the end of the file, HU-TFT-94-1

Peaks above the Harrison-Zel'dovich spectrum due to the Quark-Gluon to Hadron Transition

The quark-gluon to hadron transition affects the evolution of cosmological perturbations. If the phase transition is first order, the sound speed vanishes during the transition, and density perturbations fall freely. This distorts the primordial Harrison-Zel'dovich spectrum of density fluctuations below the Hubble scale at the transition. Peaks are produced, which grow at most linearly in wavenumber, both for the hadron-photon-lepton fluid and for cold dark matter. For cold dark matter which is kinetically decoupled well before the QCD transition clumps of masses below $10^{-10} M_\odot$ are produced.Comment: Extended version, including evolution of density perturbations for a bag model and for a lattice QCD fit (3 new figures). Spectrum for bag model (old figure) is available in astro-ph/9611186. 9 pages RevTeX, uses epsf.sty, 3 PS figure

Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.Comment: 15 page

Finite temperature effects on cosmological baryon diffusion and inhomogeneous Big-Bang nucleosynthesis

We have studied finite temperature corrections to the baryon transport cross sections and diffusion coefficients. These corrections are based upon the recently computed renormalized electron mass and the modified state density due to the background thermal bath in the early universe. It is found that the optimum nucleosynthesis yields computed using our diffusion coefficients shift to longer distance scales by a factor of about 3. We also find that the minimum value of $^4 He$ abundance decreases by $\Delta Y_p \simeq 0.01$ while $D$ and $^7 Li$ increase. Effects of these results on constraints from primordial nucleosynthesis are discussed. In particular, we find that a large baryonic contribution to the closure density (\Omega_b h_{50}^{2} \lsim 0.4) may be allowed in inhomogeneous models corrected for finite temperature.Comment: 7 pages, 6 figures, submitted to Phys. Rev.

Baryon number segregation at the end of the cosmological quark-hadron transition

One of the most interesting questions regarding a possible first order cosmological quark--hadron phase transition concerns the final fate of the baryon number contained within the disconnected quark regions at the end of the transition. We here present a detailed investigation of the hydrodynamical evolution of an evaporating quark drop, using a multi-component fluid description to follow the mechanisms of baryon number segregation. With this approach, we are able to take account of the simultaneous effects of baryon number flux suppression at the phase interface, entropy extraction by means of particles having long mean-free-paths, and baryon number diffusion. A range of computations has been performed to investigate the permitted parameter-space and this has shown that significant baryon number concentrations, perhaps even up to densities above that of nuclear matter, represent an inevitable outcome within this scenario.Comment: 33 pages, Latex file, 6 postscript figures included in the text (psfig.tex). To appear in Phys. Rev. D1

Ventilator-associated pneumonia in PICU – how are we doing?

Introduction. Ventilator-associated pneumonia (VAP) is a common hospital-acquired infection in children, leading to an increase in morbidity and mortality. A previous study in 2013 showed that VAP rates decreased dramatically after implementation of a VAP bundle and appointing a VAP coordinator. As part of a ‘Plan, Do, Study, Act’ cycle, it was necessary to evaluate the efficacy of these interventions. Objective. To evaluate the VAP rate in the paediatric intensive care unit (PICU) over 2 years (2017 - 2018), and to describe the causative organisms and antibiotic sensitivity/resistance patterns during this period. Methods. This was a retrospective, descriptive study using the existing PICU VAP database as well as clinical folders. Results. Over the 2 years, 31 VAP cases were identified. The VAP rate for 2017 was 4.0/1 000 ventilator days and 5.4/1 000 ventilator days for 2018. Compliance with the VAP bundle was 68% in 2017 and 70% in 2018. The median (interquartile range (IQR)) duration of ventilation in 2017 was 9 (6 -12) days and 15 (11 - 28) days in 2018. The median (IQR) length of PICU stay in 2017 was 11 (8 - 22) days and 25 (17 - 37) days in 2018. The most common cultured organism was an extended-spectrum beta-lactamase (ESBL) Klebsiella pneumoniae sensitive to amikacin and carbapenems. Conclusion. Our VAP rate has not decreased since 2013. It is imperative that we improve compliance with the VAP bundle, in order to reduce VAP rates. K. pneumoniae and Pseudomonas aeruginosa were the most common organisms causing VAPs and empiric use of piptazobactam and amikacin is still appropriate