Bayesian inference of biochemical kinetic parameters using the linear noise approximation

Background Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the deveopment of effective statistical methods to calibrate such models against available data. Given the prevalence of stochasticity and noise in biochemical systems inference for stochastic models is of special interest. In this paper we present a simple and computationally efficient algorithm for the estimation of biochemical kinetic parameters from gene reporter data. Results We use the linear noise approximation to model biochemical reactions through a stochastic dynamic model which essentially approximates a diffusion model by an ordinary differential equation model with an appropriately defined noise process. An explicit formula for the likelihood function can be derived allowing for computationally efficient parameter estimation. The proposed algorithm is embedded in a Bayesian framework and inference is performed using Markov chain Monte Carlo. Conclusion The major advantage of the method is that in contrast to the more established diffusion approximation based methods the computationally costly methods of data augmentation are not necessary. Our approach also allows for unobserved variables and measurement error. The application of the method to both simulated and experimental data shows that the proposed methodology provides a useful alternative to diffusion approximation based methods

Putting plant resistance traits on the map: a test of the idea that plants are better defended at lower latitudes

It has long been believed that plant species from the tropics have higher levels of traits associated with resistance to herbivores than do species from higher latitudes. A meta-analysis recently showed that the published literature does not support this theory. However, the idea has never been tested using data gathered with consistent methods from a wide range of latitudes. We quantified the relationship between latitude and a broad range of chemical and physical traits across 301 species from 75 sites world-wide. Six putative resistance traits, including tannins, the concentration of lipids (an indicator of oils, waxes and resins), and leaf toughness were greater in highlatitude species. Six traits, including cyanide production and the presence of spines, were unrelated to latitude. Only ash content (an indicator of inorganic substances such as calcium oxalates and phytoliths) and the properties of species with delayed greening were higher in the tropics. Our results do not support the hypothesis that tropical plants have higher levels of resistance traits than do plants from higher latitudes. If anything, plants have higher resistance toward the poles. The greater resistance traits of high-latitude species might be explained by the greater cost of losing a given amount of leaf tissue in low-productivity environments.EEA Santa CruzFil: Moles, Angela T. The University of New South Wales. School of Biological, Earth and Environmental Sciences. Evolution & Ecology Research Centre; Australia.Fil: Moles, Angela T. Victoria University of Wellington. School of Biological Sciences; Nueva ZelandiaFil: Moles, Angela T. Australian National University. Research School of Biology; Australia.Fil: Moles, Angela T. Macquarie University. Department of Biological Sciences; Australia.Fil: Wallis, Ian R. Australian National University. Research School of Biology; Australia.Fil: Foley, William J. Australian National University. Research School of Biology; Australia.Fil: Warton, David I. The University of New South Wales. School of Mathematics and Statistics and Evolution & Ecology Research Centre; Australia.Fil: Stegen, James C. University of North Carolina. Department of Biology; Estados UnidosFil: Bisigato, Alejandro J. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina.Fil: Cella-Pizarro, Lucrecia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Nacional Patagónico; Argentina.Fil: Clark, Connie J. Woods Hole Research Center; Estados UnidosFil: Cohen, Philippe S. Stanford University. Jasper Ridge Biological Preserve; Estados UnidosFil: Cornwell, William K. University of British Columbia. Biodiversity Research Centre; Canadá.Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina.Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina.Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina.Fil: Prior, Lynda D. University of Tasmania. School of Plant Science; Australia

Evidence for Intrinsic Redshifts in Normal Spiral Galaxies

The Tully-Fisher Relationship (TFR) is utilized to identify anomalous redshifts in normal spiral galaxies. Three redshift anomalies are identified in this analysis: (1) Several clusters of galaxies are examined in which late type spirals have significant excess redshifts relative to early type spirals in the same clusters, (2) Galaxies of morphology similar to ScI galaxies are found to have a systematic excess redshift relative to the redshifts expected if the Hubble Constant is 72 km s-1 Mpc-1, (3) individual galaxies, pairs, and groups are identified which strongly deviate from the predictions of a smooth Hubble flow. These redshift deviations are significantly larger than can be explained by peculiar motions and TFR errors. It is concluded that the redshift anomalies identified in this analysis are consistent with previous claims for large non-cosmological (intrinsic) redshifts.Comment: Accepted for publication at Astrophysics&Space Science. 36 pages including 8 tables and 7 figure

In vivo alpha-V beta-3 integrin expression in human aortic atherosclerosis.

OBJECTIVES: Intraplaque angiogenesis and inflammation are key promoters of atherosclerosis and are mediated by the alpha-V beta-3 (αvβ3) integrin pathway. We investigated the applicability of the αvβ3-integrin receptor-selective positron emission tomography (PET) radiotracer 18F-fluciclatide in assessing human aortic atherosclerosis. METHODS: Vascular 18F-fluciclatide binding was evaluated using ex vivo analysis of carotid endarterectomy samples with autoradiography and immunohistochemistry, and in vivo kinetic modelling following radiotracer administration. Forty-six subjects with a spectrum of atherosclerotic disease categorised as stable (n=27) or unstable (n=19; recent myocardial infarction) underwent PET and CT imaging of the thorax after administration of 229 (IQR 217-237) MBq 18F-fluciclatide. Thoracic aortic 18F-fluciclatide uptake was quantified on fused PET-CT images and corrected for blood-pool activity using the maximum tissue-to-background ratio (TBRmax). Aortic atherosclerotic burden was quantified by CT wall thickness, plaque volume and calcium scoring. RESULTS: 18F-Fluciclatide uptake co-localised with regions of increased αvβ3 integrin expression, and markers of inflammation and angiogenesis. 18F-Fluciclatide vascular uptake was confirmed in vivo using kinetic modelling, and on static imaging correlated with measures of aortic atherosclerotic burden: wall thickness (r=0.57, p=0.001), total plaque volume (r=0.56, p=0.001) and aortic CT calcium score (r=0.37, p=0.01). Patients with recent myocardial infarction had greater aortic 18F-fluciclatide uptake than those with stable disease (TBRmax 1.29 vs 1.21, p=0.02). CONCLUSIONS: In vivo expression of αvβ3 integrin in human aortic atheroma is associated with plaque burden and is increased in patients with recent myocardial infarction. Quantification of αvβ3 integrin expression with 18F-fluciclatide PET has potential to assess plaque vulnerability and disease activity in atherosclerosis

Intrinsic Redshifts and the Tully-Fisher Distance Scale

The Tully-Fisher relationship (TFR) has been shown to have a relatively small observed scatter of ~ +/-0.35 mag implying an intrinsic scatter < +/-0.30 mag. However, when the TFR is calibrated from distances derived from the Hubble relation for field galaxies scatter is consistently found to be +/-0.64 to +/-0.84 mag. This significantly larger scatter requires that intrinsic TFR scatter is actually much larger than +/-0.30 mag, that field galaxies have an intrinsic TFR scatter much larger than cluster spirals, or that field galaxies have a velocity dispersion relative to the Hubble flow in excess of 1000 km s-1. Each of these potential explanations faces difficulties contradicted by available data and the results of previous studies. An alternative explanation is that the measured redshifts of galaxies are composed of a cosmological redshift component predicted from the value of the Hubble Constant and a superimposed intrinsic redshift component previously identified in other studies. This intrinsic redshift component may exceed 5000 km s-1 in individual galaxies. In this alternative scenario a possible value for the Hubble Constant is 55-60 km s-1 Mpc-1.Comment: 15 pages, Astrophysics&Space Science - Accepted for publicatio

The miniJPAS survey: Identification and characterization of the emission line galaxies down to z<0.35z < 0.35 in the AEGIS field

The Javalambre-Physics of the Accelerating Universe Astrophysical Survey (J-PAS) is expected to map thousands of square degrees of the northern sky with 56 narrowband filters in the upcoming years. This will make J-PAS a very competitive and unbiased emission line survey compared to spectroscopic or narrowband surveys with fewer filters. The miniJPAS survey covered 1 deg$^2$, and it used the same photometric system as J-PAS, but the observations were carried out with the pathfinder J-PAS camera. In this work, we identify and characterize the sample of emission line galaxies (ELGs) from miniJPAS with a redshift lower than $0.35$. Using a method based on artificial neural networks, we detect the ELG population and measure the equivalent width and flux of the $H\alpha$, $H\beta$, [OIII], and [NII] emission lines. We explore the ionization mechanism using the diagrams [OIII]/H$\beta$ versus [NII]/H$\alpha$ (BPT) and EW(H$\alpha$) versus [NII]/H$\alpha$ (WHAN). We identify 1787 ELGs ($83$%) from the parent sample (2154 galaxies) in the AEGIS field. For the galaxies with reliable EW values that can be placed in the WHAN diagram (2000 galaxies in total), we obtained that $72.8 \pm 0.4$%, $17.7 \pm 0.4$% , and $9.4 \pm 0.2$% are star-forming (SF), active galactic nucleus (Seyfert), and quiescent galaxies, respectively. Based on the flux of $H\alpha$ we find that the star formation main sequence is described as $\log$ SFR $[M_\mathrm{\odot} \mathrm{yr}^{-1}] = 0.90^{+ 0.02}_{-0.02} \log M_{\star} [M_\mathrm{\odot}] -8.85^{+ 0.19}_{-0.20}$ and has an intrinsic scatter of $0.20^{+ 0.01}_{-0.01}$. The cosmic evolution of the SFR density ($\rho_{\text{SFR}}$) is derived at three redshift bins: $0 < z \leq 0.15$, $0.15 < z \leq 0.25$, and $0.25 < z \leq 0.35$, which agrees with previous results that were based on measurements of the $H\alpha$ emission line.Comment: 22 pages, 19 figure

Musical events and perceptual ecologies

This paper, followed by two responses, discusses the application of ecological theory to an understanding of a number of issues in the aesthetics of music. It argues for an understanding of music as based in event perception, with an expanded conception of the sources that are specified by those events. Building on the theory of affordances, it considers the limitations of an information theoretic conception of musical complexity, discusses the importance of perceptual learning (understood as shaping by a structured environment) in understanding the affordances of music for different listeners, and raises the challenging problem of the terms in which musical materials might be appropriately described. The apparent tension between ecological and aesthetic positions—in which adaptation and accommodation seem to be at odds with a modernist aesthetic perspective which prioritizes the unsettling and defamiliarizing function of art—is confronted, before the paper concludes with some observations about different disciplinary perspectives on aesthetics, and matters of specificity and generality

A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology

This is a post-peer-review, pre-copyedit version of an article published in Cluster Computing. The final authenticated version is available online at: https://doi.org/10.1007/s10586-017-0860-1[Abstract] Metaheuristics are gaining increasing recognition in many research areas, computational systems biology among them. Recent advances in metaheuristics can be helpful in locating the vicinity of the global solution in reasonable computation times, with Differential Evolution (DE) being one of the most popular methods. However, for most realistic applications, DE still requires excessive computation times. With the advent of Cloud Computing effortless access to large number of distributed resources has become more feasible, and new distributed frameworks, like Spark, have been developed to deal with large scale computations on commodity clusters and cloud resources. In this paper we propose a parallel implementation of an enhanced DE using Spark. The proposal drastically reduces the execution time, by means of including a selected local search and exploiting the available distributed resources. The performance of the proposal has been thoroughly assessed using challenging parameter estimation problems from the domain of computational systems biology. Two different platforms have been used for the evaluation, a local cluster and the Microsoft Azure public cloud. Additionally, it has been also compared with other parallel approaches, another cloud-based solution (a MapReduce implementation) and a traditional HPC solution (a MPI implementation)Ministerio de Economía y Competitividad; DPI2014-55276-C5-2-RMinisterio de Economía y Competitividad; TIN2013-42148-PMinisterio de Economía y Competitividad; TIN2016-75845-PXunta de Galicia ; R2016/045Xunta de Galicia; GRC2013/05

Measurement of the cross-section and charge asymmetry of WW bosons produced in proton-proton collisions at s=8\sqrt{s}=8 TeV with the ATLAS detector

This paper presents measurements of the $W^+ \rightarrow \mu^+\nu$ and $W^- \rightarrow \mu^-\nu$ cross-sections and the associated charge asymmetry as a function of the absolute pseudorapidity of the decay muon. The data were collected in proton--proton collisions at a centre-of-mass energy of 8 TeV with the ATLAS experiment at the LHC and correspond to a total integrated luminosity of 20.2~\mbox{fb^{-1}}. The precision of the cross-section measurements varies between 0.8% to 1.5% as a function of the pseudorapidity, excluding the 1.9% uncertainty on the integrated luminosity. The charge asymmetry is measured with an uncertainty between 0.002 and 0.003. The results are compared with predictions based on next-to-next-to-leading-order calculations with various parton distribution functions and have the sensitivity to discriminate between them.Comment: 38 pages in total, author list starting page 22, 5 figures, 4 tables, submitted to EPJC. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2017-13

Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS

The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured