TREEOME: A framework for epigenetic and transcriptomic data integration to explore regulatory interactions controlling transcription

Motivation: Predictive modelling of gene expression is a powerful framework for the in silico exploration of transcriptional regulatory interactions through the integration of high-throughput -omics data. A major limitation of previous approaches is their inability to handle conditional and synergistic interactions that emerge when collectively analysing genes subject to different regulatory mechanisms. This limitation reduces overall predictive power and thus the reliability of downstream biological inference. Results: We introduce an analytical modelling framework (TREEOME: tree of models of expression) that integrates epigenetic and transcriptomic data by separating genes into putative regulatory classes. Current predictive modelling approaches have found both DNA methylation and histone modification epigenetic data to provide little or no improvement in accuracy of prediction of transcript abundance despite, for example, distinct anti-correlation between mRNA levels and promoter-localised DNA methylation. To improve on this, in TREEOME we evaluate four possible methods of formulating gene-level DNA methylation metrics, which provide a foundation for identifying gene-level methylation events and subsequent differential analysis, whereas most previous techniques operate at the level of individual CpG dinucleotides. We demonstrate TREEOME by integrating gene-level DNA methylation (bisulfite-seq) and histone modification (ChIP-seq) data to accurately predict genome-wide mRNA transcript abundance (RNA-seq) for H1-hESC and GM12878 cell lines. Availability: TREEOME is implemented using open-source software and made available as a pre-configured bootable reference environment. All scripts and data presented in this study are available online at http://sourceforge.net/projects/budden2015treeome/.Comment: 14 pages, 6 figure

Electromagnetic modes of Maxwell fisheye lens

We provide an analysis of the radial structure of TE and TM modes of the Maxwell fisheye lens, by means of Maxwell equations as applied to the fisheye case. Choosing a lens of size R = 1 cm, we plot some of the modes in the infrared range.Comment: 2+6 pages in Latex, 3 figures to be found in the published referenc

RoboCup 2D Soccer Simulation League: Evaluation Challenges

We summarise the results of RoboCup 2D Soccer Simulation League in 2016 (Leipzig), including the main competition and the evaluation round. The evaluation round held in Leipzig confirmed the strength of RoboCup-2015 champion (WrightEagle, i.e. WE2015) in the League, with only eventual finalists of 2016 competition capable of defeating WE2015. An extended, post-Leipzig, round-robin tournament which included the top 8 teams of 2016, as well as WE2015, with over 1000 games played for each pair, placed WE2015 third behind the champion team (Gliders2016) and the runner-up (HELIOS2016). This establishes WE2015 as a stable benchmark for the 2D Simulation League. We then contrast two ranking methods and suggest two options for future evaluation challenges. The first one, "The Champions Simulation League", is proposed to include 6 previous champions, directly competing against each other in a round-robin tournament, with the view to systematically trace the advancements in the League. The second proposal, "The Global Challenge", is aimed to increase the realism of the environmental conditions during the simulated games, by simulating specific features of different participating countries.Comment: 12 pages, RoboCup-2017, Nagoya, Japan, July 201

Theory of the propagation of coupled waves in arbitrarily-inhomogeneous stratified media

We generalize the invariant imbedding theory of the wave propagation and derive new invariant imbedding equations for the propagation of arbitrary number of coupled waves of any kind in arbitrarily-inhomogeneous stratified media, where the wave equations are effectively one-dimensional. By doing this, we transform the original boundary value problem of coupled second-order differential equations to an initial value problem of coupled first-order differential equations, which makes the numerical solution of the coupled wave equations much easier. Using the invariant imbedding equations, we are able to calculate the matrix reflection and transmission coefficients and the wave amplitudes inside the inhomogeneous media exactly and efficiently. We establish the validity and the usefulness of our results by applying them to the propagation of circularly-polarized electromagnetic waves in one-dimensional photonic crystals made of isotropic chiral media. We find that there are three kinds of bandgaps in these structures and clarify the nature of these bandgaps by exact calculations.Comment: 7 pages, 1 figure, to appear in Europhys. Let

Monitoring Selenium Bioaccumulation In False Map Turtles (Graptemys pseudogeographica)

Selenium is an element that becomes bioactivated in aquatic environments. Selenium bioaccumulation may threaten a South Dakota state-threatened species, the False Map Turtle (Graptemys pseudogeographica). Invertebrate filter feeder species like zebra mussels (Dreissena polymorpha) uptake selenium via exposure. Previous laboratory work has found that False Map Turtles consume large amounts of zebra mussels throughout the summer, leading to selenium bioaccumulation from selenium transfer from prey to predator. A myriad of adverse effects, like selenosis, reproductive infertility, and death, are associated with high selenium concentrations. Sampling was completed on False Map Turtles in the summer of 2022. Samples were taken once a month from July to September. A blood sample and several morphometric measurements were collected from each turtle. Data were collected from 15 male and 38 female False Map Turtles. The average selenium concentration present during each month appeared to peak in July with an average concentration of 0.94 ug/g and a maximum concentration of 6.24 ug/g. The relationship between sex and the average selenium concentration per month showed relatively equal concentrations among males and females, with similar concentrations during August and September. Yet, during the peak month of July, male turtles had a much higher selenium concentration (1.37 ug/g) than their female counterparts (0.73 ug/g). Further work needs to be done to determine why this difference exists. Differences in overall size might alter prey selection, where males are more likely to consume the smaller zebra mussels. Additionally, detoxification systems in the turtles themselves might differ between the sexes. Regardless, these findings highlight the importance of understanding the role of invasive zebra mussels in contaminant distribution in aquatic ecosystems

Relativity principles in 1+1 dimensions and differential aging reversal

We study the behavior of clocks in 1+1 spacetime assuming the relativity principle, the principle of constancy of the speed of light and the clock hypothesis. These requirements are satisfied by a class of Finslerian theories parametrized by a real coefficient $\beta$, special relativity being recovered for $\beta=0$. The effect of differential aging is studied for the different values of $\beta$. Below the critical values $|\beta| =1/c$ the differential aging has the usual direction - after a round trip the accelerated observer returns younger than the twin at rest in the inertial frame - while above the critical values the differential aging changes sign. The non-relativistic case is treated by introducing a formal analogy with thermodynamics.Comment: 12 pages, no figures. Previous title "Parity violating terms in clocks' behavior and differential aging reversal". v2: shortened introduction, some sections removed, pointed out the relation with Finsler metrics. Submitted to Found. Phys. Let

Falsification Of The Atmospheric CO2 Greenhouse Effects Within The Frame Of Physics

The atmospheric greenhouse effect, an idea that many authors trace back to the traditional works of Fourier (1824), Tyndall (1861), and Arrhenius (1896), and which is still supported in global climatology, essentially describes a fictitious mechanism, in which a planetary atmosphere acts as a heat pump driven by an environment that is radiatively interacting with but radiatively equilibrated to the atmospheric system. According to the second law of thermodynamics such a planetary machine can never exist. Nevertheless, in almost all texts of global climatology and in a widespread secondary literature it is taken for granted that such mechanism is real and stands on a firm scientific foundation. In this paper the popular conjecture is analyzed and the underlying physical principles are clarified. By showing that (a) there are no common physical laws between the warming phenomenon in glass houses and the fictitious atmospheric greenhouse effects, (b) there are no calculations to determine an average surface temperature of a planet, (c) the frequently mentioned difference of 33 degrees Celsius is a meaningless number calculated wrongly, (d) the formulas of cavity radiation are used inappropriately, (e) the assumption of a radiative balance is unphysical, (f) thermal conductivity and friction must not be set to zero, the atmospheric greenhouse conjecture is falsified.Comment: 115 pages, 32 figures, 13 tables (some typos corrected