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

Global glacier volume projections under high-end climate change scenarios

The Paris agreement aims to hold global warming to well below 2°C and to pursue efforts to limit it to 1.5°C relative to the pre-industrial period. Recent estimates based on population growth and intended carbon emissions from participant countries, suggest global warming may exceed this ambitious target. Here we present glacier volume projections for the end of this century, under a range of high-end climate change scenarios, defined as exceeding +2°C global average warming relative to the preindustrial period. Glacier volume is modelled by developing an elevation-dependent mass balance model for the Joint UK Land Environmental Simulator (JULES). To do this, we modify JULES to include glaciated and un-glaciated surfaces that can exist at multiple heights within a single grid-box. Present day mass balance is calibrated by tuning albedo, wind speed, precipitation and temperature lapse rates to obtain the best agreement with observed mass balance profiles. JULES is forced with an ensemble of six Coupled Model Intercomparison Project Phase 5 (CMIP5) models which were downscaled using the high resolution HadGEM3-A atmosphere only global climate model. The ensemble mean volume loss at the end of the century plus/minus one standard deviation is, minus;64±5% for all glaciers excluding those on the peripheral of the Antarctic ice sheet. The uncertainty in the multi-model mean is rather small and caused by the sensitivity of HadGEM3-A to the boundary conditions supplied by the CMIP5 models. The regions which lose more than 75% of their initial volume by the end of the century are; Alaska, Western Canada and US, Iceland, Scandinavia, Russian Arctic, Central Europe, Caucasus, High Mountain Asia, Low Latitudes, Southern Andes and New Zealand. The ensemble mean ice loss expressed in sea-level equivalent contribution is 215.2±21.3mm. The largest contributors to sea level rise are Alaska (44.6±1.1mm), Arctic Canada North and South (34.9±3.0mm), Russian Arctic (33.3±4.8mm), Greenland (20.1±4.4), High Mountain Asia (combined Central Asia, South Asia East and West), (18.0±0.8mm), Southern Andes (14.4±0.1mm) and Svalbard (17.0±4.6mm). Including parametric uncertainty in the calibrated mass balance parameters, gives an upper bound global volume loss of 247.3mm, sea-level equivalent by the end of the century. Such large ice losses will have inevitable consequences for sea-level rise and for water supply in glacier-fed river systems

Studies of group velocity reduction and pulse regeneration with and without the adiabatic approximation

We present a detailed semiclassical study on the propagation of a pair of optical fields in resonant media with and without adiabatic approximation. In the case of near and on resonance excitation, we show detailed calculation, both analytically and numerically, on the extremely slowly propagating probe pulse and the subsequent regeneration of a pulse via a coupling laser. Further discussions on the adiabatic approximation provide many subtle understandings of the process including the effect on the band width of the regenerated optical field. Indeed, all features of the optical pulse regeneration and most of the intricate details of the process can be obtained with the present treatment without invoke a full field theoretical method. For very far off resonance excitation, we show that the analytical solution is nearly detuning independent, a surprising result that is vigorously tested and compared to numerical calculations with very good agreement.Comment: 13 pages, 15 figures, submitted to Phys. Rev.

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

Century-scale simulations of the response of the West Antarctic Ice Sheet to a warming climate

We use the BISICLES adaptive mesh ice sheet model to carry out one, two, and three century simulations of the fast-flowing ice streams of the West Antarctic Ice Sheet, deploying sub-kilometer resolution around the grounding line since coarser resolution results in substantial underestimation of the response. Each of the simulations begins with a geometry and velocity close to present-day observations, and evolves according to variation in meteoric ice accumulation rates and oceanic ice shelf melt rates. Future changes in accumulation and melt rates range from no change, through anomalies computed by atmosphere and ocean models driven by the E1 and A1B emissions scenarios, to spatially uniform melt rate anomalies that remove most of the ice shelves over a few centuries. We find that variation in the resulting ice dynamics is dominated by the choice of initial conditions and ice shelf melt rate and mesh resolution, although ice accumulation affects the net change in volume above flotation to a similar degree. Given sufficient melt rates, we compute grounding line retreat over hundreds of kilometers in every major ice stream, but the ocean models do not predict such melt rates outside of the Amundsen Sea Embayment until after 2100. Within the Amundsen Sea Embayment the largest single source of variability is the onset of sustained retreat in Thwaites Glacier, which can triple the rate of eustatic sea level rise

Enhanced basal lubrication and the contribution of the Greenland ice sheet to future sea-level rise

We assess the effect of enhanced basal sliding on the flow and mass budget of the Greenland ice sheet, using a newly developed parameterization of the relation between meltwater runoff and ice flow. A wide range of observations suggest that water generated by melt at the surface of the ice sheet reaches its bed by both fracture and drainage through moulins. Once at the bed, this water is likely to affect lubrication, although current observations are insufficient to determine whether changes in subglacial hydraulics will limit the potential for the speedup of flow. An uncertainty analysis based on our best-fit parameterization admits both possibilities: continuously increasing or bounded lubrication. We apply the parameterization to four higher-order ice-sheet models in a series of experiments forced by changes in both lubrication and surface mass budget and determine the additional mass loss brought about by lubrication in comparison with experiments forced only by changes in surface mass balance. We use forcing from a regional climate model, itself forced by output from the European Centre Hamburg Model (ECHAM5) global climate model run under scenario A1B. Although changes in lubrication generate widespread effects on the flow and form of the ice sheet, they do not affect substantial net mass loss; increase in the ice sheet’s contribution to sea-level rise from basal lubrication is projected by all models to be no more than 5% of the contribution from surface mass budget forcing alone

Suppression of Jahn-Teller distortion by chromium and magnesium doping in spinel LiMn2O4: A first-principles study using GGA and GGA+U

The effect of doping spinel LiMn2O4 with chromium and magnesium has been studied using the first-principles spin density functional theory within GGA (generalized gradient approximation) and GGA+U. We find that GGA and GGA+U give different ground states for pristine LiMn2O4 and same ground state for doped systems. For LiMn2O4 the body centered tetragonal phase was found to be the ground state structure using GGA and face centered orthorhombic using GGA+U, while for LiM0.5Mn1.5O4 (M= Cr or Mg) it was base centered monoclinic and for LiMMnO4 (M= Cr or Mg) it was body centered orthorhombic in both GGA and GGA+U. We find that GGA predicts the pristine LiMn2O4 to be metallic while GGA+U predicts it to be the insulating which is in accordance with the experimental observations. For doped spinels, GGA predicts the ground state to be half metallic while GGA+U predicts it to be insulating or metallic depending on the doping concentration. GGA+U predicts insulator-metal-insulator transition as a function of doping in case of Cr and in case of Mg the ground state is found to go from insulating to a half metallic state as a function of doping. Analysis of the charge density and the density of states suggest a charge transfer from the dopants to the neighboring oxygen atoms and manganese atoms. We have calculated the Jahn-Teller active mode displacement Q3 for doped compounds using GGA and GGA+U. The bond lengths calculated from GGA+U are found to be in better agreement with the experimental bond lengths. Based on the bond lengths of metal and oxygen, we have also estimated the average oxidation states of the dopants.Comment: 26 pages, 8 figure

Prospective evaluation of methylated SEPT9 in plasma for detection of asymptomatic colorectal cancer

As screening methods for colorectal cancer (CRC) are limited by uptake and adherence, further options are sought. A blood test might increase both, but none has yet been tested in a screening setting

STAT3 gain-of-function mutations connect leukemia with autoimmune disease by pathological NKG2Dhi CD8+T cell dysregulation and accumulation

The association between cancer and autoimmune disease is unexplained, exemplified by T cell large granular lymphocytic leukemia (T-LGL) where gain-of-function (GOF) somatic STAT3 mutations correlate with co -exist-ing autoimmunity. To investigate whether these mutations are the cause or consequence of CD8+ T cell clonal expansions and autoimmunity, we analyzed patients and mice with germline STAT3 GOF mutations. STAT3 GOF mutations drove the accumulation of effector CD8+ T cell clones highly expressing NKG2D, the receptor for stress-induced MHC-class-I-related molecules. This subset also expressed genes for granzymes, perforin, interferon-y, and Ccl5/Rantes and required NKG2D and the IL-15/IL-2 receptor IL2RB for maximal accumula-tion. Leukocyte-restricted STAT3 GOF was sufficient and CD8+ T cells were essential for lethal pathology in mice. These results demonstrate that STAT3 GOF mutations cause effector CD8+ T cell oligoclonal accumu-lation and that these rogue cells contribute to autoimmune pathology, supporting the hypothesis that somatic mutations in leukemia/lymphoma driver genes contribute to autoimmune disease.Peer reviewe