Integrating metatranscriptomes and metagenomes for deconvolution of composition and expression in human gut and artificial communities

Over the last 15 years the human microbiome has received increasing attention.During this time, many studies have contributed to shed light on the complex network of interactions both between the microorganisms and their host, and within microbial communities themselves. While traditionally aiming at assessing composition, recent studies have broadened this scope to multi-dimensional aspects, using multi-omics approaches.By integrating information about genomes, transcripts, proteins and metabolites, a holistic understanding of the microbiome is now within reach.However progressive, these studies generally suffer from a lack of closure, as interpretation and integration of this data is all but straightforward. In the particular case of metatranscriptomes, species abundance and gene expression are coupled into a single readout.Consequently, normalization of this data is a crucial but poorly understood and unresolved problem. Here I present different approaches to normalise metatranscriptomes and highlight procedural concerns when obtaining this type of data. Results show that better normalization strategies are necessary when integrating multi-omics data and that controlled pilot experiments are required for a better understanding of the intricate dynamics and interactions between members of these communities. This work further exposes concerns about the interpretation of functional aspects of microbial populations, primarily driven by the many uncontrolled sources of variation herein discussed. As these new data types become more widespread, methods will certainly evolve towards better standardization and controlled procedures. This will help the microbiome field to move beyond its descriptive state into one able to provide a more detailed and mechanistic understanding

The Iray Light Transport Simulation and Rendering System

While ray tracing has become increasingly common and path tracing is well understood by now, a major challenge lies in crafting an easy-to-use and efficient system implementing these technologies. Following a purely physically-based paradigm while still allowing for artistic workflows, the Iray light transport simulation and rendering system allows for rendering complex scenes by the push of a button and thus makes accurate light transport simulation widely available. In this document we discuss the challenges and implementation choices that follow from our primary design decisions, demonstrating that such a rendering system can be made a practical, scalable, and efficient real-world application that has been adopted by various companies across many fields and is in use by many industry professionals today

Study of Hydrophobic Domains in Humic Acids

Fyzikálně-chemická povaha hydrofobních domén huminových kyselin byla studována z několika hledisek. K objasnění významu fluorescenčních spekter byly vzorky podrobeny sekvenční frakcionaci, která pomohla k částečnému objasnění vlivu vodorozpustných složek, volných a vázaných lipidů na optické vlastnosti huminových kyselin. Výsledky naznačily, že fluorescenční píky tradičně přiřazované superpozici jednotlivých struktur jsou spíše důsledkem agregačních vlastností huminových molekul tvořících vlivem hydrofobního efektu zdánlivě vysoce aromatické struktury. Dále pak bylo zjištěno, že na optických vlastnostech huminových kyselin mají podíl i molekuly, které nemají primárně fluoroforní nebo chromoforní vlastnosti. Tento pohled je v souladu s teorií supramolekulárního uspořádání huminových kyselin. Dále byly studovány agregace, konformační chování a termodynamická stabilita huminových kyselin pomocí metody vysoce rozlišovací ultrazvukové spektroskopie. Bylo prokázáno, že huminové kyseliny mají schopnost agregovat už od velmi nízkých koncentrací (The nature of hydrophobic domains in humic acids was studied from different points of view. To shed light on the meaning of fluorescent spectra, the measured samples underwent the sequential extraction which partially revealed the role of water-soluble components, free and bond lipids in optical properties of humic acids. The results indicated that the fluorescence peaks traditionally attributed to the superposition of individual chemical structures are rather a result of aggregation properties of humic molecules and hydrophobic effect driving aromatic molecules together forming aggregates apparently large molecular weight. Further, it seems that there is a significant influence of non-fluorophores and non-chromophores on the optical properties of humic acids. Results are consistent with the theory on supramolecular structure of humic acids. Next, the aggregation, conformational behaviour and thermodynamic stability of humic acids were studied by high resolution ultrasonic spectroscopy. It was demonstrated that humic molecules are able to interact and form aggregates at very low concentration (

Inflation, personal taxes, and real output: a dynamic analysis

An examination, using the overlapping-generations approach, of how the interactions between inflation and the nominal taxation of capital income affect the cyclical behavior of the U.S. economy.Inflation (Finance) ; Business cycles ; Income tax

Thermalisation of self-interacting solar flare fast electrons

Most theoretical descriptions of the production of solar flare bremsstrahlung radiation assume the collision of dilute accelerated particles with a cold, dense target plasma, neglecting interactions of the fast particles with each other. This is inadequate for situations where collisions with this background plasma are not completely dominant, as may be the case in, for example, low-density coronal sources. We aim to formulate a model of a self-interacting, entirely fast electron population in the absence of a dense background plasma, to investigate its implications for observed bremsstrahlung spectra and the flare energy budget. We derive approximate expressions for the time-dependent distribution function of the fast electrons using a Fokker-Planck approach. We use these expressions to generate synthetic bremsstrahlung X-ray spectra as would be seen from a corresponding coronal source. We find that our model qualitatively reproduces the observed behaviour of some flares. As the flare progresses, the model's initial power-law spectrum is joined by a lower energy, thermal component. The power-law component diminishes, and the growing thermal component proceeds to dominate the total emission over timescales consistent with flare observations. The power-law exhibits progressive spectral hardening, as is seen in some flare coronal sources. We also find that our model requires a factor of 7 - 10 fewer accelerated electrons than the cold, thick target model to generate an equivalent hard X-ray flux. This model forms the basis of a treatment of self-interactions among flare fast electrons, a process which affords a more efficient means to produce bremsstrahlung photons and so may reduce the efficiency requirements placed on the particle acceleration mechanism. It also provides a useful description of the thermalisation of fast electrons in coronal sources.Comment: 9 pages, 7 figures, accepted for Astronomy & Astrophysics; this version clarifies arguments around Eqs. (11) and (20

Mashing up Visual Languages and Web Mash-ups

Research on web mashups and visual languages share an interest in human-centered computing. Both research communities are concerned with supporting programming by everyday, technically inexpert users. Visual programming environments have been a focus for both communities, and we believe that there is much to be gained by further discussion between these research communities. In this paper we explore some connections between web mashups and visual languages, and try to identify what each might be able to learn from the other. Our goal is to establish a framework for a dialog between the communities, and to promote the exchange of ideas and our respective understandings of humancentered computing.published or submitted for publicationis peer reviewe

Probing expert anticipation with the temporal occlusion paradigm: Experimental investigations of some methodological issues

Copyright @ 2005 Human KineticsTwo experiments were conducted to examine whether the conclusions drawn regarding the timing of anticipatory information pick-up from temporal occlusion studies are influenced by whether (a) the viewing period is of variable or fixed duration and (b) the task is a laboratory-based one with simple responses or a natural one requiring a coupled, interceptive movement response. Skilled and novice tennis players either made pencil-and-paper predictions of service direction (Experiment 1) or attempted to hit return strokes (Experiment 2) to tennis serves while their vision was temporally occluded in either a traditional progressive mode (where more information was revealed in each subsequent occlusion condition) or a moving window mode (where the visual display was only available for a fixed duration with this window shifted to different phases of the service action). Conclusions regarding the timing of information pick-up were generally consistent across display mode and across task setting lending support to the veracity and generalisability of findings regarding perceptual expertise in existing laboratory-based progressive temporal occlusion studies.This study is funded by the Australian Institute of Sport Tennis program

Radio Spectral Evolution of an X-ray Poor Impulsive Solar Flare: Implications for Plasma Heating and Electron Acceleration

We present radio and X-ray observations of an impulsive solar flare that was moderately intense in microwaves, yet showed very meager EUV and X-ray emission. The flare occurred on 2001 Oct 24 and was well-observed at radio wavelengths by the Nobeyama Radioheliograph (NoRH), the Nobeyama Radio Polarimeters (NoRP), and by the Owens Valley Solar Array (OVSA). It was also observed in EUV and X-ray wavelength bands by the TRACE, GOES, and Yohkoh satellites. We find that the impulsive onset of the radio emission is progressively delayed with increasing frequency relative to the onset of hard X-ray emission. In contrast, the time of flux density maximum is progressively delayed with decreasing frequency. The decay phase is independent of radio frequency. The simple source morphology and the excellent spectral coverage at radio wavelengths allowed us to employ a nonlinear chi-squared minimization scheme to fit the time series of radio spectra to a source model that accounts for the observed radio emission in terms of gyrosynchrotron radiation from MeV-energy electrons in a relatively dense thermal plasma. We discuss plasma heating and electron acceleration in view of the parametric trends implied by the model fitting. We suggest that stochastic acceleration likely plays a role in accelerating the radio-emitting electrons.Comment: 22 pages, 10 figure