Quantifying similarity in animal vocal sequences: Which metric performs best?

1. Many animals communicate using sequences of discrete acoustic elements which can be complex, vary in their degree of stereotypy, and are potentially open-ended. Variation in sequences can provide important ecological, behavioural, or evolutionary information about the structure and connectivity of populations, mechanisms for vocal cultural evolution, and the underlying drivers responsible for these processes. Various mathematical techniques have been used to form a realistic approximation of sequence similarity for such tasks. 2. Here, we use both simulated and empirical datasets from animal vocal sequences (rock hyrax, Procavia capensis; humpback whale, Megaptera novaeangliae; bottlenose dolphin, Tursiops truncatus; and Carolina chickadee, Poecile carolinensis) to test which of eight sequence analysis metrics are more likely to reconstruct the information encoded in the sequences, and to test the fidelity of estimation of model parameters, when the sequences are assumed to conform to particular statistical models. 3. Results from the simulated data indicated that multiple metrics were equally successful in reconstructing the information encoded in the sequences of simulated individuals (Markov chains, n-gram models, repeat distribution, and edit distance), and data generated by different stochastic processes (entropy rate and n-grams). However, the string edit (Levenshtein) distance performed consistently and significantly better than all other tested metrics (including entropy, Markov chains, n-grams, mutual information) for all empirical datasets, despite being less commonly used in the field of animal acoustic communication. 4. The Levenshtein distance metric provides a robust analytical approach that should be considered in the comparison of animal acoustic sequences in preference to other commonly employed techniques (such as Markov chains, hidden Markov models, or Shannon entropy). The recent discovery that non-Markovian vocal sequences may be more common in animal communication than previously thought, provides a rich area for future research that requires non-Markovian based analysis techniques to investigate animal grammars and potentially the origin of human language.We thank Melinda Rekdahl, Todd Freeberg and his graduate students, Amiyaal Ilany, Elizabeth Hobson, and Jessica Crance for providing comments of on a previous version of this manuscript. We thank Mike Noad, Melinda Rekdahl, and Claire Garrigue for assistance with humpback whale song collection and initial categorisation of the song, Vincent Janik and Laela Sayigh for assistance with signature whistle collection, Todd Freeberg with chickadee recordings, and Eli Geffen and Amiyaal Ilany for assistance with hyrax song collection and analysis. E.C.G is supported by a Newton International Fellowship. Part of this work was conducted while E.C.G. was supported by a National Research Council (National Academy of Sciences) Postdoctoral Fellowship at the National Marine Mammal Laboratory, AFSC, NMFS, NOAA. The findings and conclusions in this paper are those of the authors and do not necessarily represent the views of the National Marine Fisheries Service. We would also like to thank Randall Wells and the Sarasota Dolphin Research Program for the opportunity to record the Sarasota dolphins, where data were collected under a series of National Marine Fisheries Service Scientific Research Permits issued to Randall Wells. A.K. is supported by the Herchel Smith Postdoctoral Fellowship Fund. Part of this work was conducted while A.K. was a Postdoctoral Fellow at the National Institute for Mathematical and Biological Synthesis, an Institute sponsored by the National Science Foundation through NSF Award #DBI-1300426, with additional support from The University of Tennessee, Knoxville.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1111/2041-210X.1243

Reductions in radiographic progression in early RA over 25-years: changing contribution from RF in 2 multi-centre UK inception cohorts

Objectives: To assess 5-year progression of erosions and Joint Space Narrowing (JSN), and their associations with RF status in two large, multi-centre early-RA cohorts spanning 25-years. Methods: Radiographic joint damage was recorded using the Sharp/van der Heijde (SvdH) method in the Early RA Study (ERAS) 1986-2001, and the Early RA Network (ERAN) 2002-2013. Mixed-effects negative-binomial regression estimated changes in radiographic damage over 5-years, including erosions and JSN separately. Rheumatoid Factor (RF), along with age, sex and baseline markers of disease activity were controlled for. Results: 1,216 patients from ERAS and 446 from ERAN had radiographic data. Compared to ERAS, ERAN patients had a lower mean total SvdH score at baseline (ERAN=6.2 vs. ERAS=10.5, p<0.001), and mean annual rate of change (ERAN=2.5 vs. ERAS=6.9 per year, p<0.001). 74% of ERAS and 27% of ERAN patients progressed ≥5 units. Lower scores at baseline in ERAN were largely driven by reductions in JSN (ERAS=3.9 vs. ERAN=1.2, p<0.001), along with erosions (ERAS=1.9 vs. ERAN=0.8, p<0.001). RF was associated with greater progression in each cohort, but the absolute difference in mean annual rate of change for RF positive patients was substantially higher for ERAS (RF+= 8.6 vs. RF-= 5.1, p<0.001), relative to ERAN (RF+= 2.0 vs. RF-= 1.9, p=0.855). Conclusion: Radiographic progression has significantly reduced between the two cohorts, associated with lower baseline damage and other factors, including changes in early DMARD use. The impact of RF status as a prognostic marker of clinically meaningful change in radiographic progression has markedly diminished in the context of more modern treatment. This article is protected by copyright. All rights reserved

Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone

BACKGROUND New strains of meticillin-resistant Staphylococcus aureus (MRSA) may be associated with changes in rates of disease or clinical presentation. Conventional typing techniques may not detect new clonal variants that underlie changes in epidemiology or clinical phenotype. AIM To investigate the role of clonal variants of MRSA in an outbreak of MRSA bacteraemia at a hospital in England. METHODS Bacteraemia isolates of the major UK lineages (EMRSA-15 and -16) from before and after the outbreak were analysed by whole-genome sequencing in the context of epidemiological and clinical data. For comparison, EMRSA-15 and -16 isolates from another hospital in England were sequenced. A clonal variant of EMRSA-16 was identified at the outbreak hospital and a molecular signature test designed to distinguish variant isolates among further EMRSA-16 strains. FINDINGS By whole-genome sequencing, EMRSA-16 isolates during the outbreak showed strikingly low genetic diversity (P < 1 × 10(-6), Monte Carlo test), compared with EMRSA-15 and EMRSA-16 isolates from before the outbreak or the comparator hospital, demonstrating the emergence of a clonal variant. The variant was indistinguishable from the ancestral strain by conventional typing. This clonal variant accounted for 64/72 (89%) of EMRSA-16 bacteraemia isolates at the outbreak hospital from 2006. CONCLUSIONS Evolutionary changes in epidemic MRSA strains not detected by conventional typing may be associated with changes in disease epidemiology. Rapid and affordable technologies for whole-genome sequencing are becoming available with the potential to identify and track the emergence of variants of highly clonal organisms

Atenolol versus losartan in children and young adults with Marfan's syndrome

BACKGROUND : Aortic-root dissection is the leading cause of death in Marfan's syndrome. Studies suggest that with regard to slowing aortic-root enlargement, losartan may be more effective than beta-blockers, the current standard therapy in most centers. METHODS : We conducted a randomized trial comparing losartan with atenolol in children and young adults with Marfan's syndrome. The primary outcome was the rate of aortic-root enlargement, expressed as the change in the maximum aortic-root-diameter z score indexed to body-surface area (hereafter, aortic-root z score) over a 3-year period. Secondary outcomes included the rate of change in the absolute diameter of the aortic root; the rate of change in aortic regurgitation; the time to aortic dissection, aortic-root surgery, or death; somatic growth; and the incidence of adverse events. RESULTS : From January 2007 through February 2011, a total of 21 clinical centers enrolled 608 participants, 6 months to 25 years of age (mean [+/- SD] age, 11.5 +/- 6.5 years in the atenolol group and 11.0 +/- 6.2 years in the losartan group), who had an aorticroot z score greater than 3.0. The baseline-adjusted rate of change (+/- SE) in the aortic-root z score did not differ significantly between the atenolol group and the losartan group (-0.139 +/- 0.013 and -0.107 +/- 0.013 standard-deviation units per year, respectively; P = 0.08). Both slopes were significantly less than zero, indicating a decrease in the degree of aortic-root dilatation relative to body-surface area with either treatment. The 3-year rates of aortic-root surgery, aortic dissection, death, and a composite of these events did not differ significantly between the two treatment groups. CONCLUSIONS : Among children and young adults with Marfan's syndrome who were randomly assigned to losartan or atenolol, we found no significant difference in the rate of aorticroot dilatation between the two treatment groups over a 3-year period

A quantitative theory-versus-experiment comparison for the intense laser dissociation of H2+

A detailed theory-versus-experiment comparison is worked out for H$_2^+$ intense laser dissociation, based on angularly resolved photodissociation spectra recently recorded in H.Figger's group. As opposite to other experimental setups, it is an electric discharge (and not an optical excitation) that prepares the molecular ion, with the advantage for the theoretical approach, to neglect without lost of accuracy, the otherwise important ionization-dissociation competition. Abel transformation relates the dissociation probability starting from a single ro-vibrational state, to the probability of observing a hydrogen atom at a given pixel of the detector plate. Some statistics on initial ro-vibrational distributions, together with a spatial averaging over laser focus area, lead to photofragments kinetic spectra, with well separated peaks attributed to single vibrational levels. An excellent theory-versus-experiment agreement is reached not only for the kinetic spectra, but also for the angular distributions of fragments originating from two different vibrational levels resulting into more or less alignment. Some characteristic features can be interpreted in terms of basic mechanisms such as bond softening or vibrational trapping.Comment: submitted to PRA on 21.05.200

Crystal structure, electronic, and magnetic properties of the bilayered rhodium oxide Sr3Rh2O7

The bilayered rhodium oxide Sr3Rh2O7 was synthesized by high-pressure and high-temperature heating techniques. The single-phase polycrystalline sample of Sr3Rh2O7 was characterized by measurements of magnetic susceptibility, electrical resistivity, specific heat, and thermopower. The structural characteristics were investigated by powder neutron diffraction study. The rhodium oxide Sr3Rh2O7 [Bbcb, a = 5.4744(8) A, b = 5.4716(9) A, c = 20.875(2) A] is isostructural to the metamagnetic metal Sr3Ru2O7, with five 4d electrons per Rh, which is electronically equivalent to the hypothetic bilayered ruthenium oxide, where one electron per Ru is doped into the Ru-327 unit. The present data show the rhodium oxide Sr3Rh2O7 to be metallic with enhanced paramagnetism, similar to Sr3Ru2O7. However, neither manifest contributions from spin fluctuations nor any traces of a metamagnetic transition were found within the studied range from 2 K to 390 K below 70 kOe.Comment: To be published in PR

Primary Invasive Aspergillosis of the Digestive Tract: Report of Two Cases and Review of the Literature

BACKGROUND: Disseminated aspergillosis is thought to occur as a result of vascular invasion from the lungs with subsequent bloodstream dissemination, and portals of entry other than sinuses and/or the respiratory tract remain speculative. METHODS: We report two cases of primary aspergillosis in the digestive tract and present a detailed review of eight of the 23 previously-published cases for which detailed data are available. RESULTS AND CONCLUSION: These ten cases presented with symptoms suggestive of typhlitis, with further peritonitis requiring laparotomy and small bowel segmental resection. All cases were characterized by the absence of pulmonary disease at the time of histologically-confirmed gastrointestinal involvement with vascular invasion by branched Aspergillus hyphae. These cases suggest that the digestive tract may represent a portal of entry for Aspergillus species in immunocompromised patients

Dilaton gravity approach to three dimensional Lifshitz black hole

The z=3 Lifshitz black hole is an exact black hole solution to the new massive gravity in three dimensions. In order to understand this black hole clearly, we perform a dimensional reduction to two dimensional dilaton gravity by utilizing the circular symmetry. Considering the linear dilaton, we find the same Lifshitz black hole in two dimensions. This implies that all thermodynamic quantities of the z=3 Lifshitz black hole could be obtained from its corresponding black hole in two dimensions. As a result, we derive the temperature, mass, heat capacity, Bekesnstein-Hawking entropy, and free energy.Comment: 13 pages, 1 figure, version to appear in EPJ

Star and Planet Formation with ALMA: an Overview

Submillimeter observations with ALMA will be the essential next step in our understanding of how stars and planets form. Key projects range from detailed imaging of the collapse of pre-stellar cores and measuring the accretion rate of matter onto deeply embedded protostars, to unravelling the chemistry and dynamics of high-mass star-forming clusters and high-spatial resolution studies of protoplanetary disks down to the 1 AU scale.Comment: Invited review, 8 pages, 5 figures; to appear in the proceedings of "Science with ALMA: a New Era for Astrophysics". Astrophysics & Space Science, in pres

Critical Currents of Ideal Quantum Hall Superfluids

Filling factor $\nu=1$ bilayer electron systems in the quantum Hall regime have an excitonic-condensate superfluid ground state when the layer separation $d$ is less than a critical value $d_c$. On a quantum Hall plateau current injected and removed through one of the two layers drives a dissipationless edge current that carries parallel currents, and a dissipationless bulk supercurrent that carries opposing currents in the two layers. In this paper we discuss the theory of finite supercurrent bilayer states, both in the presence and in the absence of symmetry breaking inter-layer hybridization. Solutions to the microscopic mean-field equations exist at all condensate phase winding rates for zero and sufficiently weak hybridization strengths. We find, however, that collective instabilities occur when the supercurrent exceeds a critical value determined primarily by a competition between direct and exchange inter-layer Coulomb interactions. The critical current is estimated using a local stability criterion and varies as $(d_c-d)^{1/2}$ when $d$ approaches $d_c$ from below. For large inter-layer hybridization, we find that the critical current is limited by a soliton instability of microscopic origin.Comment: 18 RevTeX pgs, 21 eps figure