Spatial variability of 14C reservoir effects in Tibetan Plateau lakes

Abstract HKT-ISTP 2013 B

The Genesis Solar Wind Concentrator Target: Mass Fractionation Characterised by Neon Isotopes

The concentrator on Genesis provided samples of increased fluences of solar wind ions for precise determination of the oxygen isotopic composition. The concentration process caused mass fractionation as a function of the radial target position. This fractionation was measured using Ne released by UV laser ablation and compared with modelled Ne data, obtained from ion-trajectory simulations. Measured data show that the concentrator performed as expected and indicate a radially symmetric concentration process. Measured concentration factors are up to ∼30 at the target centre. The total range of isotopic fractionation along the target radius is 3.8%/amu, with monotonically decreasing 20Ne/22Ne towards the centre, which differs from model predictions. We discuss potential reasons and propose future attempts to overcome these disagreement

Conditioning bounds for traveltime tomography in layered media

This paper revisits the problem of recovering a smooth, isotropic, layered wave speed profile from surface traveltime information. While it is classic knowledge that the diving (refracted) rays classically determine the wave speed in a weakly well-posed fashion via the Abel transform, we show in this paper that traveltimes of reflected rays do not contain enough information to recover the medium in a well-posed manner, regardless of the discretization. The counterpart of the Abel transform in the case of reflected rays is a Fredholm kernel of the first kind which is shown to have singular values that decay at least root-exponentially. Kinematically equivalent media are characterized in terms of a sequence of matching moments. This severe conditioning issue comes on top of the well-known rearrangement ambiguity due to low velocity zones. Numerical experiments in an ideal scenario show that a waveform-based model inversion code fits data accurately while converging to the wrong wave speed profile

13C labeling experiments at metabolic nonstationary conditions: An exploratory study

<p>Abstract</p> <p>Background</p> <p>Stimulus Response Experiments to unravel the regulatory properties of metabolic networks are becoming more and more popular. However, their ability to determine enzyme kinetic parameters has proven to be limited with the presently available data. In metabolic flux analysis, the use of ¹³C labeled substrates together with isotopomer modeling solved the problem of underdetermined networks and increased the accuracy of flux estimations significantly.</p> <p>Results</p> <p>In this contribution, the idea of increasing the information content of the dynamic experiment by adding ¹³C labeling is analyzed. For this purpose a small example network is studied by simulation and statistical methods. Different scenarios regarding available measurements are analyzed and compared to a non-labeled reference experiment. Sensitivity analysis revealed a specific influence of the kinetic parameters on the labeling measurements. Statistical methods based on parameter sensitivities and different measurement models are applied to assess the information gain of the labeled stimulus response experiment.</p> <p>Conclusion</p> <p>It was found that the use of a (specifically) labeled substrate will significantly increase the parameter estimation accuracy. An overall information gain of about a factor of six is observed for the example network. The information gain is achieved from the specific influence of the kinetic parameters towards the labeling measurements. This also leads to a significant decrease in correlation of the kinetic parameters compared to an experiment without ¹³C-labeled substrate.</p

Analysis of lead oxide (PbO) layers for direct conversion X-ray detection

Lead oxide (PbO) is a candidate direct conversion material for medical X-ray applications. We produced various samples and detectors with thick PbO layers. X-ray performance data such as dark current, charge generation yield and temporal behavior were evaluated on small samples. The influence of the metal contacts was studied in detail. We also covered large a-Si thin-film transistor (TFT)-plates with PbO. Imaging results from a large detector with an active area of 18 cm × 20 cm are presented. The detector has 960 × 1080 pixels with a pixel pitch of 184 ?m. The modulation transfer function at the Nyquist frequency of 2.72 linepairs/mm is 50%. Finally, a full size X-ray image is presented

Comparison of genotyping using pooled DNA samples (allelotyping) and individual genotyping using the affymetrix genome-wide human SNP array 6.0

Background: Genome-wide association studies (GWAS) using array-based genotyping technology are widely used to identify genetic loci associated with complex diseases or other phenotypes. The costs of GWAS projects based on individual genotyping are still comparatively high and increase with the size of study populations. Genotyping using pooled DNA samples, as also being referred as to allelotyping approach, offers an alternative at affordable costs. In the

An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments

<p>Abstract</p> <p>Background</p> <p>Metabolic fluxes provide invaluable insight on the integrated response of a cell to environmental stimuli or genetic modifications. Current computational methods for estimating the metabolic fluxes from ¹³<it>C </it>isotopomer measurement data rely either on manual derivation of analytic equations constraining the fluxes or on the numerical solution of a highly nonlinear system of isotopomer balance equations. In the first approach, analytic equations have to be tediously derived for each organism, substrate or labelling pattern, while in the second approach, the global nature of an optimum solution is difficult to prove and comprehensive measurements of external fluxes to augment the ¹³<it>C </it>isotopomer data are typically needed.</p> <p>Results</p> <p>We present a novel analytic framework for estimating metabolic flux ratios in the cell from ¹³<it>C </it>isotopomer measurement data. In the presented framework, equation systems constraining the fluxes are derived automatically from the model of the metabolism of an organism. The framework is designed to be applicable with all metabolic network topologies, ¹³<it>C </it>isotopomer measurement techniques, substrates and substrate labelling patterns.</p> <p>By analyzing nuclear magnetic resonance (NMR) and mass spectrometry (MS) measurement data obtained from the experiments on glucose with the model micro-organisms <it>Bacillus subtilis </it>and <it>Saccharomyces cerevisiae </it>we show that our framework is able to automatically produce the flux ratios discovered so far by the domain experts with tedious manual analysis. Furthermore, we show by <it>in silico </it>calculability analysis that our framework can rapidly produce flux ratio equations – as well as predict when the flux ratios are unobtainable by linear means – also for substrates not related to glucose.</p> <p>Conclusion</p> <p>The core of ¹³<it>C </it>metabolic flux analysis framework introduced in this article constitutes of flow and independence analysis of metabolic fragments and techniques for manipulating isotopomer measurements with vector space techniques. These methods facilitate efficient, analytic computation of the ratios between the fluxes of pathways that converge to a common junction metabolite. The framework can been seen as a generalization and formalization of existing tradition for computing metabolic flux ratios where equations constraining flux ratios are manually derived, usually without explicitly showing the formal proofs of the validity of the equations.</p

Development of a kinetic metabolic model: application to Catharanthus roseus hairy root

A kinetic metabolic model describing Catharanthus roseus hairy root growth and nutrition was developed. The metabolic network includes glycolysis, pentose-phosphate pathway, TCA cycle and the catabolic reactions leading to cell building blocks such as amino acids, organic acids, organic phosphates, lipids and structural hexoses. The central primary metabolic network was taken at pseudo-steady state and metabolic flux analysis technique allowed reducing from 31 metabolic fluxes to 20 independent pathways. Hairy root specific growth rate was described as a function of intracellular concentration in cell building blocks. Intracellular transport and accumulation kinetics for major nutrients were included. The model uses intracellular nutrients as well as energy shuttles to describe metabolic regulation. Model calibration was performed using experimental data obtained from batch and medium exchange liquid cultures of C. roseus hairy root using a minimal medium in Petri dish. The model is efficient in estimating the growth rate