On the Use of Bootstrapped Topologies in Coalescent-Based Bayesian MCMC Inference: A Comparison of Estimation and Computational Efficiencies

Coalescent-based Bayesian Markov chain Monte Carlo (MCMC) inference generates estimates of evolutionary parameters and their posterior probability distributions. As the number of sequences increases, the length of time taken to complete an MCMC analysis increases as well. Here, we investigate an approach to distribute the MCMC analysis across a cluster of computers. To do this, we use bootstrapped topologies as fixed genealogies, perform a single MCMC analysis on each genealogy without topological rearrangements, and pool the results across all MCMC analyses. We show, through simulations, that although the standard MCMC performs better than the bootstrap-MCMC at estimating the effective population size (scaled by mutation rate), the bootstrap-MCMC returns better estimates of growth rates. Additionally, we find that our bootstrap-MCMC analyses are, on average, 37 times faster for equivalent effective sample sizes

Heat engines and heat pumps in a hydrostatic atmosphere: How surface pressure and temperature constrain wind power output and circulation cell size

The kinetic energy budget of the atmosphere's meridional circulation cells is analytically assessed. In the upper atmosphere kinetic energy generation grows with increasing surface temperature difference \$\Delta T_s\$ between the cold and warm ends of a circulation cell; in the lower atmosphere it declines. A requirement that kinetic energy generation is positive in the lower atmosphere limits the poleward cell extension \$L\$ of Hadley cells via a relationship between \$\Delta T_s\$ and surface pressure difference \$\Delta p_s\$: an upper limit exists when \$\Delta p_s\$ does not grow with increasing \$\Delta T_s\$. This pattern is demonstrated here using monthly data from MERRA re-analysis. Kinetic energy generation along air streamlines in the boundary layer does not exceed \$40\$~J~mol\$^{-1}\$; it declines with growing \$L\$ and reaches zero for the largest observed \$L\$ at 2~km height. The limited meridional cell size necessitates the appearance of heat pumps -- circulation cells with negative work output where the low-level air moves towards colder areas. These cells consume the positive work output of the heat engines -- cells where the low-level air moves towards the warmer areas -- and can in theory drive the global efficiency of atmospheric circulation down to zero. Relative contributions of \$\Delta p_s\$ and \$\Delta T_s\$ to kinetic energy generation are evaluated: \$\Delta T_s\$ dominates in the upper atmosphere, while \$\Delta p_s\$ dominates in the lower. Analysis and empirical evidence indicate that the net kinetic power output on Earth is dominated by surface pressure gradients, with minor net kinetic energy generation in the upper atmosphere. The role of condensation in generating surface pressure gradients is discussed.Comment: 26 pages, 9 figures, 2 tables; re-organized presentation, more discussion and a new figure (Fig. 4) added; in Fig. 3 the previously invisible dots (observations) can now be see

Approximate probabilistic verification of hybrid systems

Hybrid systems whose mode dynamics are governed by non-linear ordinary differential equations (ODEs) are often a natural model for biological processes. However such models are difficult to analyze. To address this, we develop a probabilistic analysis method by approximating the mode transitions as stochastic events. We assume that the probability of making a mode transition is proportional to the measure of the set of pairs of time points and value states at which the mode transition is enabled. To ensure a sound mathematical basis, we impose a natural continuity property on the non-linear ODEs. We also assume that the states of the system are observed at discrete time points but that the mode transitions may take place at any time between two successive discrete time points. This leads to a discrete time Markov chain as a probabilistic approximation of the hybrid system. We then show that for BLTL (bounded linear time temporal logic) specifications the hybrid system meets a specification iff its Markov chain approximation meets the same specification with probability $1$. Based on this, we formulate a sequential hypothesis testing procedure for verifying -approximately- that the Markov chain meets a BLTL specification with high probability. Our case studies on cardiac cell dynamics and the circadian rhythm indicate that our scheme can be applied in a number of realistic settings

Comparison of observed and model-computed low frequency circulation and hydrography on the New England Shelf

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 113 (2008): C09015, doi:10.1029/2007JC004394.The finite volume coastal ocean model (FVCOM) is configured to study the interannual variability of circulation in the Gulf of Maine (GoM) and Georges Bank. The FVCOM-GoM system incorporates realistic time-dependent surface forcing derived from a high-resolution mesoscale meteorological model (MM5) and assimilation of observed quantities including sea surface temperature and salinity and temperature fields on the open boundary. An evaluation of FVCOM-GoM model skill on the New England shelf is made by comparison of computed fields and data collected during the Coastal Mixing and Optics (CMO) Program (August 1996–June 1997). Model mean currents for the full CMO period compare well in both magnitude and direction in fall and winter but overpredict the westward flow in spring. The direction and ellipticity of the subtidal variability correspond but computed magnitudes are around 20% below observed, partially due to underprediction of the variability by MM5. Response of subtidal currents to wind-forcing shows the model captures the directional dependence, as well as seasonal variability of the lag. Hydrographic results show that FVCOM-GoM resolves the spatial and temporal evolution of the temperature and salinity fields. The model-computed surface salinity field compares well, except in May when there is no indication of the fresh surface layer from the Connecticut River discharge noted in the observations. Analysis of model-computed results indicates that the plume was unable to extend to the mooring location due to the presence of a westward mean model-computed flow during that time that was stronger than observed. Overall FVCOM-GoM captures well the dynamics of the mean and subtidal flow on the New England shelf.G. Cowles was supported by the Massachusetts Marine Fisheries Institute (MFI) through NOAA grants DOC/NOAA/ NA04NMF4720332 and DOC/NOAA/NA05NMF4721131, S. Lentz by the NSF Ocean Sciences Division through grants OCE-841292 and OCE- 848961, C. Chen and Q. Xu through the NSF/NOAA GLOBEC/Northwest Atlantic/Georges Bank Program under NSF grants OCE-0234545 and OCE-0227679 and NOAA grants NA-16OP2323, and R. Beardsley through NOAA grant NA-17RJ1223

High intensity interval training in a real world setting: A randomized controlled feasibility study in overweight inactive adults, measuring change in maximal oxygen uptake

Background In research clinic settings, overweight adults undertaking HIIT (high intensity interval training) improve their fitness as effectively as those undertaking conventional walking programs but can do so within a shorter time spent exercising. We undertook a randomized controlled feasibility (pilot) study aimed at extending HIIT into a real world setting by recruiting overweight/obese, inactive adults into a group based activity program, held in a community park. Methods Participants were allocated into one of three groups. The two interventions, aerobic interval training and maximal volitional interval training, were compared with an active control group undertaking walking based exercise. Supervised group sessions (36 per intervention) were held outdoors. Cardiorespiratory fitness was measured using VO2max (maximal oxygen uptake, results expressed in ml/min/kg), before and after the 12 week interventions. Results On ITT (intention to treat) analyses, baseline (N = 49) and exit (N = 39) O2 was 25.3±4.5 and 25.3±3.9, respectively. Participant allocation and baseline/exit VO2max by group was as follows: Aerobic interval training N =  16, 24.2±4.8/25.6±4.8; maximal volitional interval training N = 16, 25.0±2.8/25.2±3.4; walking N = 17, 26.5±5.3/25.2±3.6. The post intervention change in VO2max was +1.01 in the aerobic interval training, −0.06 in the maximal volitional interval training and −1.03 in the walking subgroups. The aerobic interval training subgroup increased VO2max compared to walking (p = 0.03). The actual (observed, rather than prescribed) time spent exercising (minutes per week, ITT analysis) was 74 for aerobic interval training, 45 for maximal volitional interval training and 116 for walking (p =  0.001). On descriptive analysis, the walking subgroup had the fewest adverse events. Conclusions In contrast to earlier studies, the improvement in cardiorespiratory fitness in a cohort of overweight/obese participants undertaking aerobic interval training in a real world setting was modest. The most likely reason for this finding relates to reduced adherence to the exercise program, when moving beyond the research clinic setting

Selective blockade of the discriminative stimulus effects of pentobarbital in pigeons

The ability of CNS stimulants to block the discriminative effects of pentobarbital was studied in pigeons trained to discriminate IM pentobarbital (5 mg/kg) from saline. Pentobarbital, when administered alone, consistently produced greater than 90% pentobarbital-appropriate responding. The concomitant administration of pentobarbital and increasing doses of bemegride or pentylenetetrazol resulted in a dose-related decrease in pentobarbital-appropriate responses. In contrast, picrotoxin, another CNS stimulant, had little or no effect on pentobarbital-appropriate responding produced by pentobarbital.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46426/1/213_2004_Article_BF00432447.pd

Palaeoproterozoic magnesite: lithological and isotopic evidence for playa/sabkha environments

Magnesite forms a series of 1- to 15-m-thick beds within the approximate to2.0 Ga (Palaeoproterozoic) Tulomozerskaya Formation, NW Fennoscandian Shield, Russia. Drillcore material together with natural exposures reveal that the 680-m-thick formation is composed of a stromatolite-dolomite-'red bed' sequence formed in a complex combination of shallow-marine and non-marine, evaporitic environments. Dolomite-collapse breccia, stromatolitic and micritic dolostones and sparry allochemical dolostones are the principal rocks hosting the magnesite beds. All dolomite lithologies are marked by delta C-13 values from +7.1 parts per thousand to +11.6 parts per thousand (V-PDB) and delta O-18 ranging from 17.4 parts per thousand to 26.3 parts per thousand (V-SMOW). Magnesite occurs in different forms: finely laminated micritic; stromatolitic magnesite; and structureless micritic, crystalline and coarsely crystalline magnesite. All varieties exhibit anomalously high delta C-13 values ranging from +9.0 parts per thousand to +11.6 parts per thousand and delta O-18 values of 20.0-25.7 parts per thousand. Laminated and structureless micritic magnesite forms as a secondary phase replacing dolomite during early diagenesis, and replaced dolomite before the major phase of burial. Crystalline and coarsely crystalline magnesite replacing micritic magnesite formed late in the diagenetic/metamorphic history. Magnesite apparently precipitated from sea water-derived brine, diluted by meteoric fluids. Magnesitization was accomplished under evaporitic conditions (sabkha to playa lake environment) proposed to be similar to the Coorong or Lake Walyungup coastal playa magnesite. Magnesite and host dolostones formed in evaporative and partly restricted environments; consequently, extremely high delta C-13 values reflect a combined contribution from both global and local carbon reservoirs. A C- 13-rich global carbon reservoir (delta C-13 at around +5 parts per thousand) is related to the perturbation of the carbon cycle at 2.0 Ga, whereas the local enhancement in C-13 (up to +12 parts per thousand) is associated with evaporative and restricted environments with high bioproductivity

Seepage forces, important factors in the formation of horizontal hydraulic fractures and bedding-parallel fibrous veins ('beef' and 'cone-in-cone')

International audienceBedding-parallel fibrous veins ('beef' and 'cone-in-cone') are common to a number of sedimentary basins, especially those containing black shale. The type locality is SW England. The commonest mineral in the fibres is calcite. The fibres indicate vertical opening, against the force of gravity. In the past, this has been attributed to fluid overpressure. However, a simple analysis, based on Von Terzaghi's concepts, leads to the conclusion that, for the fractures to be horizontal, either the rock must be anisotropic, or it must be subject to horizontal compression. By means of a more complete analysis, supported by physical models, we show that horizontal fractures are to be expected, even if the rock is isotropic and there are no tectonic stresses. Upward fluid flow, in response to an overpressure gradient, imparts seepage forces to all elements of the solid framework. The seepage forces counteract the weight of the rock, and even surpass it, generating a tensile effective stress. The process may lead, either to tensile hydraulic fracturing, or to dilatant shear failure. We suggest that these two failure modes, and the availability of suitable solutes, explain the frequent occurrence of 'beef' and 'cone-in-cone' respectively