ABCtoolbox: a versatile toolkit for approximate Bayesian computations

Background The estimation of demographic parameters from genetic data often requires the computation of likelihoods. However, the likelihood function is computationally intractable for many realistic evolutionary models, and the use of Bayesian inference has therefore been limited to very simple models. The situation changed recently with the advent of Approximate Bayesian Computation (ABC) algorithms allowing one to obtain parameter posterior distributions based on simulations not requiring likelihood computations. Results Here we present ABCtoolbox, a series of open source programs to perform Approximate Bayesian Computations (ABC). It implements various ABC algorithms including rejection sampling, MCMC without likelihood, a Particle-based sampler and ABC-GLM. ABCtoolbox is bundled with, but not limited to, a program that allows parameter inference in a population genetics context and the simultaneous use of different types of markers with different ploidy levels. In addition, ABCtoolbox can also interact with most simulation and summary statistics computation programs. The usability of the ABCtoolbox is demonstrated by inferring the evolutionary history of two evolutionary lineages of Microtus arvalis. Using nuclear microsatellites and mitochondrial sequence data in the same estimation procedure enabled us to infer sex-specific population sizes and migration rates and to find that males show smaller population sizes but much higher levels of migration than females. Conclusion ABCtoolbox allows a user to perform all the necessary steps of a full ABC analysis, from parameter sampling from prior distributions, data simulations, computation of summary statistics, estimation of posterior distributions, model choice, validation of the estimation procedure, and visualization of the results.

Computations of Vector-Valued Siegel Modular Forms

We carry out some computations of vector-valued Siegel modular forms of degree two, weight (k, 2) and level one, and highlight three experimental results: (1) we identify a rational eigenform in a three-dimensional space of cusp forms; (2) we observe that non-cuspidal eigenforms of level one are not always rational; (3) we verify a number of cases of conjectures about congruences between classical modular forms and Siegel modular forms. Our approach is based on Satoh's description of the module of vector-valued Siegel modular forms of weight (k, 2) and an explicit description of the Hecke action on Fourier expansions. (C) 2013 Elsevier Inc. All rights reserved.

DISTRIBUTED REPRODUCIBLE RESEARCH USING CACHED COMPUTATIONS

The ability to make scientific findings reproducible is increasingly important in areas where substantive results are the product of complex statistical computations. Reproducibility can allow others to verify the published findings and conduct alternate analyses of the same data. A question that arises naturally is how can one conduct and distribute reproducible research? This question is relevant from the point of view of both the authors who want to make their research reproducible and readers who want to reproduce relevant findings reported in the scientific literature. We present a framework in which reproducible research can be conducted and distributed via cached computations and describe specific tools for both authors and readers. As a prototype implementation we introduce three software packages written in the R language. The cacheSweave and stashR packages together provide tools for caching computational results in a key-value style database which can be published to a public repository for readers to download. The SRPM package provides tools for generating and interacting with "shared reproducibility packages" (SRPs) which can facilitate the distribution of the data and code. As a case study we demonstrate the use of the toolkit on a national study of air pollution exposure and mortality.

Synthesis of computations and experiments for obtaining pulsatile gas flow rates from dynamic pressure difference measurements across an orifice-plate meter

The use of conventional orifice-plate meter is typically restricted to measurements of steady flows. This study proposes a new and effective computational-experimental approach for measuring the time-varying (but steady-in-the-mean) nature of turbulent pulsatile gas flows. Low Mach number (effectively constant density) steady-in-the-mean gas flows with large amplitude fluctuations (whose highest significant frequency is characterized by the value fF) are termed pulsatile if the fluctuations have a direct correlation with the time-varying signature of the imposed dynamic pressure difference and, furthermore, they have fluctuation amplitudes that are significantly larger than those associated with turbulence or random acoustic wave signatures. The experimental aspect of the proposed calibration approach is based on use of Coriolis-meters (whose oscillating arm frequency fcoriolis >> fF) which are capable of effectively measuring the mean flow rate of the pulsatile flows. Together with the experimental measurements of the mean mass flow rate of these pulsatile flows, the computational approach presented here is shown to be effective in converting the dynamic pressure difference signal into the desired dynamic flow rate signal. The proposed approach is reliable because the time-varying flow rate predictions obtained for two different orifice-plate meters exhibit the approximately same qualitative, dominant features of the pulsatile flow.

Coreleased orexin and glutamate evoke nonredundant spike outputs and computations in histamine neurons.

Stable wakefulness requires orexin/hypocretin neurons (OHNs) and OHR2 receptors. OHNs sense diverse environmental cues and control arousal accordingly. For unknown reasons, OHNs contain multiple excitatory transmitters, including OH peptides and glutamate. To analyze their cotransmission within computational frameworks for control, we optogenetically stimulated OHNs and examined resulting outputs (spike patterns) in a downstream arousal regulator, the histamine neurons (HANs). OHR2s were essential for sustained HAN outputs. OHR2-dependent HAN output increased linearly during constant OHN input, suggesting that the OHN→HAN(OHR2) module may function as an integral controller. OHN stimulation evoked OHR2-dependent slow postsynaptic currents, similar to midnanomolar OH concentrations. Conversely, glutamate-dependent output transiently communicated OHN input onset, peaking rapidly then decaying alongside OHN→HAN glutamate currents. Blocking glutamate-driven spiking did not affect OH-driven spiking and vice versa, suggesting isolation (low cross-modulation) of outputs. Therefore, in arousal regulators, cotransmitters may translate distinct features of OHN activity into parallel, nonredundant control signals for downstream effectors.

Towards the continuum limit in transport coefficient computations

The analytic continuation needed for the extraction of transport coefficients necessitates in principle a continuous function of the Euclidean time variable. We report on progress towards achieving the continuum limit for 2-point correlator measurements in thermal SU(3) gauge theory, with specific attention paid to scale setting. In particular, we improve upon the determination of the critical lattice coupling and the critical temperature of pure SU(3) gauge theory, estimating r0Tc ≃ 0.7470(7) after a continuum extrapolation. As an application the determination of the heavy quark momentum diffusion coefficient from a correlator of colour-electric fields attached to a Polyakov loop is discussed.

Accurate computations of the structures and binding energies of the imidazole ... benzene and pyrrole ... benzene complexes

Using explicitly-correlated coupled-cluster theory with single and double excitations, the intermolecular distances and interaction energies of the T-shaped imidazole⋯⋯benzene and pyrrole⋯⋯benzene complexes have been computed in a large augmented correlation-consistent quadruple-zeta basis set, adding also corrections for connected triple excitations and remaining basis-set-superposition errors. The results of these computations are used to assess other methods such as Møller–Plesset perturbation theory (MP2), spin-component-scaled MP2 theory, dispersion-weighted MP2 theory, interference-corrected explicitly-correlated MP2 theory, dispersion-corrected double-hybrid density-functional theory (DFT), DFT-based symmetry-adapted perturbation theory, the random-phase approximation, explicitly-correlated ring-coupled-cluster-doubles theory, and double-hybrid DFT with a correlation energy computed in the random-phase approximation.

Influence of Surface Oceanographic Variability on Abundance of the Western Winter-Spring Cohort of Neon Flying Squid Ommastrephes Bartramii in the Nw Pacific Ocean

Abundance of the Ommastrephes bartramii winter-spring cohort fluctuated greatly from 1995 to 2004. To understand how abundance was influenced by sea surface conditions, we examined the variations in the proportion of thermal habitats with favourable sea surface temperature (SST). The SST data of both the spawning and feeding grounds were used to calculate the monthly proportion of favourable-SST areas (PFSSTA). Catch per fishing day per fishing boat (catch per unit effort, CPUE) of the Chinese mainland squid-jigging fleet was used as squid abundance index. The relationships between CPUE and monthly PFSSTA at spawning and feeding grounds were analyzed, and the relationship between CPUE and selected PFSSTA was quantified with a multiple linear regression model. Results showed that February PFSSTA at the spawning ground and August to November PFSSTA at the feeding ground could account for about 60% of the variability in O. bartramii abundance between 1995 and 2004, that February was the most important period influencing squid recruitment during the spawning season, and that feeding ground PFSSTA during the fishing season would influence CPUE by causing squid to aggregate. Our forecast model was found to perform well when we compared the model-predicted CPUEs and the average CPUEs observed during August to November in 2005 and 2006 from the Chinese squid-jigging fishery.

Physical-Biological Oceanographic Coupling Influencing Phytoplankton and Primary Production in the South China Sea

Two cruises were carried out in the summer and winter of 1998 to study coupled physical-chemical-biological processes in the South China Sea and their effects on phytoplankton stock and production. The results clearly show that the seasonal distributions of phytoplankton were closely related to the coupled processes driven by the East Asian Monsoon. Summer southwesterly monsoon induced upwelling along the China and Vietnam coasts. Several mesoscale cyclonic cold eddies and anticyclonic warm pools were identified in both seasons. In the summer, the upwelling and cold eddies, both associated with rich nutrients, low dissolved oxygen ( DO), high chlorophyll a (Chl a) and primary production ( PP), were found in the areas off the coast of central Vietnam, southeast of Hainan Island and north of the Sunda shelf, whereas in the winter they form a cold trough over the deep basin aligning from southwest to northeast. The warm pools with poor nutrients, high DO, low Chl a, and PP were found in the areas southeast of Vietnam, east of Hainan, and west of Luzon during the summer, and a northwestward warm jet from the Sulu Sea with properties similar to the warm pools was encountered during the winter. The phytoplankton stock and primary production were lower in summer due to nutrient depletion near the surface, particularly PO4. This phosphorus depletion resulted in phytoplankton species succession from diatoms to dinoflagellates and cyanophytes. A strong subsurface Chl a maximum, dominated by photosynthetic picoplankton, was found to contribute significantly to phytoplankton stocks and production.

The Nurturing of Seagliders By the National Oceanographic Partnership Program

The National Oceanographic Partnership Program provided critical support to the development of Seaglider long-range autonomous underwater vehicles. This support enabled: (1) development and integration of chemical and biological sensors, (2) transition to low-power, bi-directional satellite communication, and (3) software upgrades to enhance capability and reliability. Sponsored improvements led to setting the mission endurance and range records for autonomous underwater vehicles, wide use by the oceanographic community and licensing for commercialization.