Maui-VIA: a user-friendly software for visual identification, alignment, correction, and quantification of gas chromatography-mass spectrometry data

A current bottleneck in GC-MS metabolomics is the processing of raw machine data into a final datamatrix that contains the quantities of identified metabolites in each sample. While there are many bioinformatics tools available to aid the initial steps of the process, their use requires both significant technical expertise and a subsequent manual validation of identifications and alignments if high data quality is desired. The manual validation is tedious and time consuming, becoming prohibitively so as sample numbers increase. We have, therefore, developed Maui-VIA, a solution based on a visual interface that allows experts and non-experts to simultaneously and quickly process, inspect, and correct large numbers of GC-MS samples. It allows for the visual inspection of identifications and alignments, facilitating a unique and, due to its visualization and keyboard shortcuts, very fast interaction with the data. Therefore, Maui-Via fills an important niche by (1) providing functionality that optimizes the component of data processing that is currently most labor intensive to save time and (2) lowering the threshold of expertise required to process GC-MS data. Maui-VIA projects are initiated with baseline-corrected raw data, peaklists, and a database of metabolite spectra and retention indices used for identification. It provides functionality for retention index calculation, a targeted library search, the visual annotation, alignment, correction interface, and metabolite quantification, as well as the export of the final datamatrix. The high quality of data produced by Maui-VIA is illustrated by its comparison to data attained manually by an expert using vendor software on a previously published dataset concerning the response of Chlamydomonas reinhardtii to salt stress. In conclusion, Maui-VIA provides the opportunity for fast, confident, and high-quality data processing validation of large numbers of GC-MS samples by non-experts

Algebraic Systems and Pushdown Automata

The theory of algebraic power series in noncommuting variables, as we un-derstand it today, was initiated in [2] and developed in its early stages by the French school. The main motivation was the interconnection with context-free grammars: the defining equations were made to correspond to context-fre

Measurements of π±\pi^\pm, K±K^\pm, KS0K^0_S, Λ\Lambda and proton production in proton-carbon interactions at 31 GeV/cc with the NA61/SHINE spectrometer at the CERN SPS

Measurements of hadron production in p+C interactions at 31 GeV/c are performed using the NA61/ SHINE spectrometer at the CERN SPS. The analysis is based on the full set of data collected in 2009 using a graphite target with a thickness of 4% of a nuclear interaction length. Inelastic and production cross sections as well as spectra of $\pi^\pm$, $K^\pm$, p, $K^0_S$ and $\Lambda$ are measured with high precision. These measurements are essential for improved calculations of the initial neutrino fluxes in the T2K long-baseline neutrino oscillation experiment in Japan. A comparison of the NA61/SHINE measurements with predictions of several hadroproduction models is presented.Comment: v1 corresponds to the preprint CERN-PH-EP-2015-278; v2 matches the final published versio

Multiplicity and transverse momentum fluctuations in inelastic proton-proton interactions at the CERN Super Proton Synchrotron

Measurements of multiplicity and transverse momentum fluctuations of charged particles were performed in inelastic p+p interactions at 20, 31, 40, 80 and 158 GeV/c beam momentum. Results for the scaled variance of the multiplicity distribution and for three strongly intensive measures of multiplicity and transverse momentum fluctuations \$\Delta[P_{T},N]\$, \$\Sigma[P_{T},N]\$ and \$\Phi_{p_T}\$ are presented. For the first time the results on fluctuations are fully corrected for experimental biases. The results on multiplicity and transverse momentum fluctuations significantly deviate from expectations for the independent particle production. They also depend on charges of selected hadrons. The string-resonance Monte Carlo models EPOS and UrQMD do not describe the data. The scaled variance of multiplicity fluctuations is significantly higher in inelastic p+p interactions than in central Pb+Pb collisions measured by NA49 at the same energy per nucleon. This is in qualitative disagreement with the predictions of the Wounded Nucleon Model. Within the statistical framework the enhanced multiplicity fluctuations in inelastic p+p interactions can be interpreted as due to event-by-event fluctuations of the fireball energy and/or volume.Comment: 18 pages, 12 figure

Measurements of π±\pi^\pm, K±^\pm, p and pˉ\bar{\textrm{p}} spectra in proton-proton interactions at 20, 31, 40, 80 and 158 GeV/c with the NA61/SHINE spectrometer at the CERN SPS

Measurements of inclusive spectra and mean multiplicities of $\pi^\pm$, K$^\pm$, p and $\bar{\textrm{p}}$ produced in inelastic p+p interactions at incident projectile momenta of 20, 31, 40, 80 and 158 GeV/c ($\sqrt{s} =$ 6.3, 7.7, 8.8, 12.3 and 17.3 GeV, respectively) were performed at the CERN Super Proton Synchrotron using the large acceptance NA61/SHINE hadron spectrometer. Spectra are presented as function of rapidity and transverse momentum and are compared to predictions of current models. The measurements serve as the baseline in the NA61/SHINE study of the properties of the onset of deconfinement and search for the critical point of strongly interacting matter

Measurements of K0^{0}S_{S}, Λ , and Λˉ\bar{Λ} production in 120 GeV / c p + C interactions

This paper presents multiplicity measurements of K0S, Λ, and ¯Λ produced in 120  GeV/c proton-carbon interactions. The measurements were made using data collected at the NA61/SHINE experiment during two different periods. Decays of these neutral hadrons impact the measured π+, π−, p and ¯p multiplicities in the 120  GeV/c proton-carbon reaction, which are crucial inputs for long-baseline neutrino experiment predictions of neutrino beam flux. The double-differential multiplicities presented here will be used to more precisely measure charged-hadron multiplicities in this reaction, and to reweight neutral hadron production in neutrino beam Monte Carlo simulations

K∗(892)0K^{*}(892)^0 meson production in inelastic p+p interactions at 40 and 80 GeV ⁣/ ⁣c\text{ GeV }\!/\!c beam momenta measured by NA61/SHINE at the CERN SPS

Measurements of K∗(892)0 resonance production via its K+π− decay mode in inelastic p+p collisions at beam momenta 40 and 80 GeV /c (sNN−−−−√=8.8 and 12.3 GeV ) are presented. The data were recorded by the NA61/SHINE hadron spectrometer at the CERN Super Proton Synchrotron. The template method was used to extract the K∗(892)0 signal. Transverse momentum and rapidity spectra were obtained. The mean multiplicities of K∗(892)0 mesons were found to be (35.1±1.3(stat)±3.6(sys))⋅10−3 at 40 GeV /c and (58.3±1.9(stat)±4.9(sys))⋅10−3 at 80 GeV /c. The NA61/SHINE results are compared with the Epos1.99 and Hadron Resonance Gas models as well as with world data. The transverse mass spectra of K∗(892)0 mesons and other particles previously reported by NA61/SHINE were fitted within the Blast-Wave model. The transverse flow velocities are close to 0.1–0.2 of the speed of light and are significantly smaller than the ones determined in heavy nucleus-nucleus interactions at the same beam momenta

Measurement of Hadron Production in π−\pi^--C Interactions at 158 and 350 GeV/c with NA61/SHINE at the CERN SPS

We present a measurement of the momentum spectra of $\pi^\pm$, K$^\pm$, p$^\pm$, $\Lambda$, $\bar{\Lambda}$ and K$^{0}_{S}$ produced in interactions of negatively charged pions with carbon nuclei at beam momenta of 158 and 350 GeV/c. The total production cross sections are measured as well. The data were collected with the large-acceptance spectrometer of the fixed target experiment NA61/SHINE at the CERN SPS. The obtained double-differential $p$-$p_T$ spectra provide a unique reference data set with unprecedented precision and large phase-space coverage to tune models used for the simulation of particle production in extensive air showers in which pions are the most numerous projectiles