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

Porous silica-pillared MXenes with controllable interlayer distances for long-life Na-ion batteries

MXenes are a recently discovered class of two-dimensional materials that have shown great potential as electrodes in electrochemical energy storage devices. Despite their promise in this area, MXenes can still suffer limitations in the form of restricted ion accessibility between the closely spaced multistacked MXene layers, causing low capacities and poor cycle life. Pillaring, a strategy where a secondary species is inserted between layers, has been used to increase interlayer spacings in clays with great success, but has had limited application in MXenes. We report a new amine-assisted pillaring methodology that successfully intercalates silica-based pillars between Ti3C2 layers. Using this technique, the interlayer spacing can be controlled with the choice of amine and calcination temperature, up to a maximum of 3.2 nm, the largest interlayer spacing reported for an MXene. Another effect of the pillaring is a dramatic increase in surface area, achieving BET surface areas of 235 m2 g-1, a sixty-fold increase over the unpillared material and the highest reported for MXenes using an intercalation-based method. The intercalation mechanism was revealed by different characterisation techniques, allowing the surface chemistry to be optimised for the pillaring process. The porous MXene was tested for Na-ion battery applications, and showed superior capacity, rate capability and remarkable stability compared with non-pillared materials, retaining 98.5% capacity between the 50th and 100th cycles. These results demonstrate the applicability and promise of pillaring techniques applied to MXenes, providing a new approach to optimising their properties for a range of applications. Porous MXenes are very promising materials for a range of applications including energy storage, conversion, catalysis and gas separations

A Pivotal Role of Lumbar Spinothalamic Cells in the Regulation of Ejaculation via Intraspinal Connections

Introduction.  A population of lumbar spinothalamic cells (LSt cells) has been demonstrated to play a pivotal role in ejaculatory behavior and comprise a critical component of the spinal ejaculation generator. LSt cells are hypothesized to regulate ejaculation via their projections to autonomic and motor neurons in the lumbosacral spinal cord. Aim.  The current study tested the hypothesis that ejaculatory reflexes are dependent on LSt cells via projections within the lumbosacral spinal cord. Methods.  Male rats received intraspinal injections of neurotoxin saporin conjugated to substance P analog, previously shown to selectively lesion LSt cells. Two weeks later, males were anesthetized and spinal cords were transected. Subsequently, males were subjected to ejaculatory reflex paradigms, including stimulation of the dorsal penile nerve (DPN), urethrogenital stimulation or administration of D3 agonist 7‐OH‐DPAT. Electromyographic recordings of the bulbocavernosus muscle (BCM) were analyzed for rhythmic bursting characteristic of the expulsion phase of ejaculation. In addition, a fourth commonly used paradigm for ejaculation and erections in unanesthetized, spinal‐intact male rats was utilized: the ex copula reflex paradigm. Main Outcome Measures.  LSt cell lesions were predicted to prevent rhythmic bursting of BCM following DPN, urethral, or pharmacological stimulation, and emissions in the ex copula paradigm. In contrast, LSt cell lesions were not expected to abolish erectile function as measured in the ex copula paradigm. Results.  LSt cell lesions prevented rhythmic contractions of the BCM induced by any of the ejaculatory reflex paradigms in spinalized rats. However, LSt cell lesions did not affect erectile function nor emissions determined in the ex copula reflex paradigm. Conclusions.  These data demonstrate that LSt cells are essential for ejaculatory, but not erectile reflexes, as previously reported for mating animals. Moreover, LSt cells mediate ejaculation via projections within the spinal cord, presumably to autonomic and motor neurons. Staudt MD, Truitt WA, McKenna KE, de Oliveira CVR, Lehman MN, and Coolen LM. A pivotal role of lumbar spinothalamic cells in the regulation of ejaculation via intraspinal connections. J Sex Med 2012;9:2256–2265.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93690/1/j.1743-6109.2011.02574.x.pd

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Measurement of the polarisation of W bosons produced with large transverse momentum in pp collisions at sqrt(s) = 7 TeV with the ATLAS experiment

This paper describes an analysis of the angular distribution of W->enu and W->munu decays, using data from pp collisions at sqrt(s) = 7 TeV recorded with the ATLAS detector at the LHC in 2010, corresponding to an integrated luminosity of about 35 pb^-1. Using the decay lepton transverse momentum and the missing transverse energy, the W decay angular distribution projected onto the transverse plane is obtained and analysed in terms of helicity fractions f0, fL and fR over two ranges of W transverse momentum (ptw): 35 < ptw < 50 GeV and ptw > 50 GeV. Good agreement is found with theoretical predictions. For ptw > 50 GeV, the values of f0 and fL-fR, averaged over charge and lepton flavour, are measured to be : f0 = 0.127 +/- 0.030 +/- 0.108 and fL-fR = 0.252 +/- 0.017 +/- 0.030, where the first uncertainties are statistical, and the second include all systematic effects.Comment: 19 pages plus author list (34 pages total), 9 figures, 11 tables, revised author list, matches European Journal of Physics C versio

Observation of a new chi_b state in radiative transitions to Upsilon(1S) and Upsilon(2S) at ATLAS

The chi_b(nP) quarkonium states are produced in proton-proton collisions at the Large Hadron Collider (LHC) at sqrt(s) = 7 TeV and recorded by the ATLAS detector. Using a data sample corresponding to an integrated luminosity of 4.4 fb^-1, these states are reconstructed through their radiative decays to Upsilon(1S,2S) with Upsilon->mu+mu-. In addition to the mass peaks corresponding to the decay modes chi_b(1P,2P)->Upsilon(1S)gamma, a new structure centered at a mass of 10.530+/-0.005 (stat.)+/-0.009 (syst.) GeV is also observed, in both the Upsilon(1S)gamma and Upsilon(2S)gamma decay modes. This is interpreted as the chi_b(3P) system.Comment: 5 pages plus author list (18 pages total), 2 figures, 1 table, corrected author list, matches final version in Physical Review Letter

Search for displaced vertices arising from decays of new heavy particles in 7 TeV pp collisions at ATLAS

We present the results of a search for new, heavy particles that decay at a significant distance from their production point into a final state containing charged hadrons in association with a high-momentum muon. The search is conducted in a pp-collision data sample with a center-of-mass energy of 7 TeV and an integrated luminosity of 33 pb^-1 collected in 2010 by the ATLAS detector operating at the Large Hadron Collider. Production of such particles is expected in various scenarios of physics beyond the standard model. We observe no signal and place limits on the production cross-section of supersymmetric particles in an R-parity-violating scenario as a function of the neutralino lifetime. Limits are presented for different squark and neutralino masses, enabling extension of the limits to a variety of other models.Comment: 8 pages plus author list (20 pages total), 8 figures, 1 table, final version to appear in Physics Letters