Proteome coverage prediction with infinite Markov models

Motivation: Liquid chromatography tandem mass spectrometry (LC-MS/MS) is the predominant method to comprehensively characterize complex protein mixtures such as samples from prefractionated or complete proteomes. In order to maximize proteome coverage for the studied sample, i.e. identify as many traceable proteins as possible, LC-MS/MS experiments are typically repeated extensively and the results combined. Proteome coverage prediction is the task of estimating the number of peptide discoveries of future LC-MS/MS experiments. Proteome coverage prediction is important to enhance the design of efficient proteomics studies. To date, there does not exist any method to reliably estimate the increase of proteome coverage at an early stage. Results: We propose an extended infinite Markov model DiriSim to extrapolate the progression of proteome coverage based on a small number of already performed LC-MS/MS experiments. The method explicitly accounts for the uncertainty of peptide identifications. We tested DiriSim on a set of 37 LC-MS/MS experiments of a complete proteome sample and demonstrated that DiriSim correctly predicts the coverage progression already from a small subset of experiments. The predicted progression enabled us to specify maximal coverage for the test sample. We demonstrated that quality requirements on the final proteome map impose an upper bound on the number of useful experiment repetitions and limit the achievable proteome coverage. Contact: [email protected]; [email protected]

Power sums of Coxeter exponents

Consider an irreducible finite Coxeter system. We show that for any nonnegative integer n the sum of the nth powers of the Coxeter exponents can be written uniformly as a polynomial in four parameters: h (the Coxeter number), r (the rank), and two further parameters.Comment: 14 page

Bounds for the adiabatic approximation with applications to quantum computation

We present straightforward proofs of estimates used in the adiabatic approximation. The gap dependence is analyzed explicitly. We apply the result to interpolating Hamiltonians of interest in quantum computing.Comment: 15 pages, one figure. Two comments added in Secs. 2 and

The influence of coronal EUV irradiance on the emission in the He I 10830 A and D3 multiplets

Two of the most attractive spectral windows for spectropolarimetric investigations of the physical properties of the plasma structures in the solar chromosphere and corona are the ones provided by the spectral lines of the He I 10830 A and 5876 A (or D3) multiplets, whose polarization signals are sensitive to the Hanle and Zeeman effects. However, in order to be able to carry out reliable diagnostics, it is crucial to have a good physical understanding of the sensitivity of the observed spectral line radiation to the various competing driving mechanisms. Here we report a series of off-the-limb non-LTE calculations of the He I D3 and 10830 A emission profiles, focusing our investigation on their sensitivity to the EUV coronal irradiation and the model atmosphere used in the calculations. We show in particular that the intensity ratio of the blue to the red components in the emission profiles of the He I 10830 A multiplet turns out to be a good candidate as a diagnostic tool for the coronal irradiance. Measurements of this observable as a function of the distance to the limb and its confrontation with radiative transfer modeling might give us valuable information on the physical properties of the solar atmosphere and on the amount of EUV radiation at relevant wavelengths penetrating the chromosphere from above.Comment: 19 pages, 11 figures (pre-print format). Accepted for publication in Ap

Phosphorylation-based signaling networks mediate the effect of ligand affinity of the activation of naive primary T-cells

Comunicaciones a congreso

Observation and modeling of anomalous CN polarization profiles produced by the molecular Paschen-Back effect in sunspots

We report novel spectropolarimetric observations of sunspots carried out with the Tenerife Infrared Polarimeter (TIP) in a near-IR spectral region around 15410 A, which is known to contain two groups of prominent OH lines that show circular polarization signals of opposite polarity. Surrounding these well-known OH lines, we have discovered the presence of CN lines of the $\Delta v=1$ band which show anomalous polarization profiles. Although the Stokes V signals of the OH lines are antisymmetric and with a sizable amplitude, the CN lines show almost negligible circular polarization. On the contrary, the linear polarization signals turn out to be much stronger in the CN lines than in the OH lines. Interestingly, these CN lines present striking antisymmetric linear polarization profiles, which we are able to explain and model via the Paschen-Back effect theory for diatomic molecules. The presence of such peculiar CN lines in the same spectral region of the OH lines may be useful to improve our empirical knowledge of solar magnetic fields via the simultaneous observation and modeling of the transverse and longitudinal Zeeman effects in two different molecular species.Comment: 11 pages, 3 figures, published in ApJ 623, L57 (2005

Dynamic Substance Flow Analysis as a Valuable Risk Evaluation Tool – A Case Study for Brominated Flame Retardants as an Example of Potential Endocrine Disrupters

Most studies of potentially hazardous substances focus on aspects of their occurrence and fate in the environment (monitoring and modelling studies) to estimate the environmental impact and the potential exposure of humans. In order to evaluate emission sources, to recognise environmental impacts at an early stage, and to take efficient legislative or technical measures, it is essential to know their behaviour in the anthroposphere as a function of time. So far, only very few investigations of this type exist for chemicals. In regular risk assessments, only rather limited knowledge is available concerning the behaviour of chemicals in the anthroposphere (production data, substance quantities in products, recycling rates, emissions occurring during use, etc.) or their lifecycle, and no information at all about their behaviour as a function of time. For this reason, it is these aspects that were investigated in a case study within the framework of the national research programme NRP50 for selected brominated flame retardants with endocrine-disrupting potential (pentabromodiphenyl ether, hexabromocyclododecane) or the potential to degrade to such substances (decabromodiphenyl ether). A dynamic substance flow analysis (SFA) model was performed for Switzerland for the time period 1980–2020. In this review paper (a) we present a summary of typical results (system overview, consumption trends/application patterns, anthropogenic stocks and their changes, emission trends including major sources and environmental fate), (b) we summarize the effectiveness of recent risk-reduction measures in Switzerland and (c) we indicate serious remaining data gaps and recommend further important measures for risk reduction. For the future, we suggest improving the knowledge of the lifecycle of chemicals such as brominated flame retardants by applying SFA as a suitable tool to weight the effect of substance flows with respect to environmental emissions, and to serve as the basis for planning actions and measures to reduce such emissions. This is in line with one major conclusion of the NRP50 consensus platform 'Brominated Flame Retardants'

Analysis of the volatile components of five Turkish Rhododendron species by headspace solid-phase microextraction and GC-MS (HS-SPME-GC-MS)

Volatile constituents of various solvent extracts (n-hexane, CH2Cl2, H2O) of 15 different organs (leaves, flowers, fruits) of five Rhododendron species (Ericaceae) growing in Turkey were trapped with headspace solid-phase microextraction (HS-SPME) technique and analyzed by GC-MS. A total of 200 compounds were detected and identified from organic extracts, while the water extracts contained only traces of few volatiles. The CH2Cl2 extract of the R. luteum flowers was found to exhibit the most diverse composition: 34 compounds were identified, with benzyl alcohol (16.6%), limonene (14.6%) and p-cymene (8.4%) being the major compounds. The CH2Cl2-solubles of R. x sochadzeae leaves contained only phenyl ethyl alcohol. This study indicated appreciable intra-specific variations in volatile compositions within the genus. Different anatomical parts also showed altered volatile profiles. This is the first application of HS-SPME-GC-MS on the volatiles of Rhododendron species

Quantum affine Cartan matrices, Poincare series of binary polyhedral groups, and reflection representations

We first review some invariant theoretic results about the finite subgroups of SU(2) in a quick algebraic way by using the McKay correspondence and quantum affine Cartan matrices. By the way it turns out that some parameters (a,b,h;p,q,r) that one usually associates with such a group and hence with a simply-laced Coxeter-Dynkin diagram have a meaningful definition for the non-simply-laced diagrams, too, and as a byproduct we extend Saito's formula for the determinant of the Cartan matrix to all cases. Returning to invariant theory we show that for each irreducible representation i of a binary tetrahedral, octahedral, or icosahedral group one can find a homomorphism into a finite complex reflection group whose defining reflection representation restricts to i.Comment: 19 page