Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealisations of biochemically reacting systems must be able to capture stochastic phenomena. While robust theory exists to describe such stochastic models, the computational challenges in exploring these models can be a significant burden in practice since realistic models are analytically intractable. Determining the expected behaviour and variability of a stochastic biochemical reaction network requires many probabilistic simulations of its evolution. Using a biochemical reaction network model to assist in the interpretation of time course data from a biological experiment is an even greater challenge due to the intractability of the likelihood function for determining observation probabilities. These computational challenges have been subjects of active research for over four decades. In this review, we present an accessible discussion of the major historical developments and state-of-the-art computational techniques relevant to simulation and inference problems for stochastic biochemical reaction network models. Detailed algorithms for particularly important methods are described and complemented with MATLAB implementations. As a result, this review provides a practical and accessible introduction to computational methods for stochastic models within the life sciences community

The HI Chronicles of LITTLE THINGS BCDs II: The Origin of IC 10's HI Structure

In this paper we analyze Very Large Array (VLA) telescope and Green Bank Telescope (GBT) atomic hydrogen (HI) data for the LITTLE THINGS(1) blue compact dwarf galaxy IC 10. The VLA data allow us to study the detailed HI kinematics and morphology of IC 10 at high resolution while the GBT data allow us to search the surrounding area at high sensitivity for tenuous HI. IC 10's HI appears highly disturbed in both the VLA and GBT HI maps with a kinematically distinct northern HI extension, a kinematically distinct southern plume, and several spurs in the VLA data that do not follow the general kinematics of the main disk. We discuss three possible origins of its HI structure and kinematics in detail: a current interaction with a nearby companion, an advanced merger, and accretion of intergalactic medium. We find that IC 10 is most likely an advanced merger or a galaxy undergoing accretion. 1:Local Irregulars That Trace Luminosity Extremes, The HI Nearby Galaxy Survey; https://science.nrao.edu/science/surveys/littlethingsComment: 36 pages, 17 figures, accepted for publication in The Astronomical Journa

THE CHANGES IN EFFORT DISTRIBUTION FROM NOVICE TO EXPERIENCED PERFORMERS IN THE TRIPLE JUMP

This study investigated the ratios of the three phases in triple jumping by novice (n=8) and experienced (n=5) athletes during indoor competition. Video data were analysed to determine the phase distances for 58 competitive triple jump performances. Phase ratio percentages were calculated for each of the trials. There were significant differences in the step phase percentage (

Rapid Bayesian inference for expensive stochastic models

Almost all fields of science rely upon statistical inference to estimate unknown parameters in theoretical and computational models. While the performance of modern computer hardware continues to grow, the computational requirements for the simulation of models are growing even faster. This is largely due to the increase in model complexity, often including stochastic dynamics, that is necessary to describe and characterize phenomena observed using modern, high resolution, experimental techniques. Such models are rarely analytically tractable, meaning that extremely large numbers of stochastic simulations are required for parameter inference. In such cases, parameter inference can be practically impossible. In this work, we present new computational Bayesian techniques that accelerate inference for expensive stochastic models by using computationally inexpensive approximations to inform feasible regions in parameter space, and through learning transforms that adjust the biased approximate inferences to closer represent the correct inferences under the expensive stochastic model. Using topical examples from ecology and cell biology, we demonstrate a speed improvement of an order of magnitude without any loss in accuracy. This represents a substantial improvement over current state-of-the-art methods for Bayesian computations when appropriate model approximations are available

Inbreeding ratio and genetic relationships among strains of the Western clawed frog, Xenopus tropicalis

The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts

Reducing water extractable phosphorus in poultry litter using chitosan treatment

Phosphorus (P) is an important factor in the eutrophication of freshwater, and watershed sources include effluent discharges and the landscape. Poultry litter applied to the landscape can be a potential source of P, which is dependent on rainfall, runoff and dissolution. Chitosan, the deacetylated form of the biopolymer chitin, has been shown to have an effect on reducing water extractable phosphorus (WEP) in poultry litter when applied as a powder. The intent of this study was to measure the effect that poultry litter treatment (PLT), acetic acid and incubation time have on chitosan’s ability to reduce WEP in poultry litter. The results were that (1) the presence of PLT in the litter inhibits chitosan’s ability to reduce WEP; (2) chitosan dissolved in acetic acid (0.005, 0.01, 0.02, and 0.05 g mL-1) does not decrease WEP at any point during a 7 week incubation period; and (3) chitosan in a powder form reaches its full effectiveness after three weeks of incubation. Chitosan could be an effective coamendment to poultry litter with other treatments in order to reduce WEP

VII Zw 403: H I structure in a blue compact dwarf galaxy

‘In these times, during the rise in the popularity of institutional repositories, the Society does not forbid authors from depositing their work in such repositories. However, the AAS regards the deposit of scholarly work in such repositories to be a decision of the individual scholar, as long as the individual's actions respect the diligence of the journals and their reviewers.’ Original article can be found at : http://iopscience.iop.org/ Copyright American Astronomical SocietyWe present optical (UBVJ), ultraviolet (FUV, NUV), and high-resolution atomic hydrogen (H I) observations of the nearby blue compact dwarf (BCD), VII Zw 403. We find that VII Zw 403 has a relatively high H I mass-to-light ratio for a BCD. The rotation velocity is nominally 10-15 km s(-1), but rises to similar to 20 km s(-1) after correction for the similar to 8-10 km s(-1) random motions present in the gas. The velocity field is complex, including a variation in the position angle of the major axis going from the northeast to the southwest parts of the galaxy. Our high-resolution Hi maps reveal structure in the central gas, including a large, low-density Hi depression or hole between the southern and northern halves of the galaxy, coincident with an unresolved X-ray source. Although interactions have been proposed as the triggering mechanism for the vigorous star formation occurring in BCDs, VII Zw 403 does not seem to have been tidally triggered by an external interaction, as we have found no nearby possible perturbers. It also does not appear to fall in the set of galaxies that exhibit a strong central mass density concentration, as its optical scale length is large in comparison to similar systems. However, there are some features that are compatible with an accretion event: optical/Hi axis misalignment, a change in position angle of the kinematic axis, and a complex velocity field.Peer reviewe