WaVPeak: picking NMR peaks through wavelet-based smoothing and volume-based filtering

Motivation: Nuclear magnetic resonance (NMR) has been widely used as a powerful tool to determine the 3D structures of proteins in vivo. However, the post-spectra processing stage of NMR structure determination usually involves a tremendous amount of time and expert knowledge, which includes peak picking, chemical shift assignment and structure calculation steps. Detecting accurate peaks from the NMR spectra is a prerequisite for all following steps, and thus remains a key problem in automatic NMR structure determination

Effect of water and straw management practices on methane emissions from rice fields: A review through a meta-analysis

[EN] Rice fields contribute substantially to global warming of the atmosphere through emission of methane (CH4). This article reviews the state of the art of factors affecting CH4 emissions in rice fields, focusing on soil organic matter content and water management practices. A quantitative relationship between these factors was established through a meta-analysis based on a literature survey. This relationship can be useful to update emission factors used to estimate CH4 in the National Emission Inventories. Methane emissions in rice fields can be as much as 90% higher in continuously flooded rice fields compared with other water management practices, independent from straw addition. Water management systems that involve absence of flooding in total or for part of the growing period such as midseason drainages, intermittent flooding, and percolation control, can reduce CH4 emissions substantially. Moreover, CH4 emissions increase with the amount of straw added up to 7.7 t/ha for continuously flooded soils and up to 5.1 t/ha for other water regimes. Above these levels, no further increase is produced with further addition of straw. With regard to rice straw management mitigation strategies, recommended practices are composting rice straw, straw burning under controlled conditions, recollecting rice straw for biochar production, generation of energy, to be used as a substrate, or to obtain other byproducts with added value. This review improves the understanding of the relationship between straw application rate, water regimes, and CH4 emissions from rice fields to date. This relationship can help to select the most appropriate management practices to improve current mitigation strategies to reduce atmospheric CH4. © 2012 Mary Ann Liebert, Inc.This study was financially supported by Fundacio´n Agroalimed from the Consellerı´a de Agricultura of Valencia, Spain and the Vicerrectorado de Investigacio´n of the UPV (Programa de Apoyo a la Investigacio´n y Desarrollo, PAID06-11 Program, Project No. 1950).Sanchís Jiménez, EM.; Ferrer Roglán, M.; Torres, AG.; Cambra López, M.; Calvet Sanz, S. (2012). Effect of water and straw management practices on methane emissions from rice fields: A review through a meta-analysis. Environmental Engineering Science. 29(12):1053-1062. https://doi.org/10.1089/ees.2012.0006S10531062291

Improvement of the liquid-chromatographic analysis of protein tryptic digests by the use of long-capillary monolithic columns with UV and MS detection

Optimisation of peak capacity is an important strategy in gradient liquid chromatography (LC). This can be achieved by using either long columns or columns packed with small particles. Monolithic columns allow the use of long columns at relatively low back-pressure. The gain in peak capacity using long columns was evaluated by the separation of a tryptic bovine serum albumin digest with an LC–UV–mass spectrometry (MS) system and monolithic columns of different length (150 and 750 mm). Peak capacities were determined from UV chromatograms and MS/MS data were used for Mascot database searching. Analyses with a similar gradient slope for the two columns produced ratios of the peak capacities that were close to the expected value of the square root of the column length ratio. Peak capacities of the short column were 12.6 and 25.0 with 3 and 15 min gradients, respectively, and 29.7 and 41.0 for the long column with 15 and 75 min gradients, respectively. Protein identification scores were also higher for the long column, 641 and 750 for the 3- and 15-min gradients with the short column and 1,376 and 993 for the 15- and 75-min gradients with the long column. Thus, the use of long monolithic columns provides improved peptide separation and increased reliability of protein identification

Design of analog front-ends for the RD53 demonstrator chip

The RD53 collaboration is developing a large scale pixel front-end chip, which will be a tool to evaluate the performance of 65 nm CMOS technology in view of its application to the readout of the innermost detector layers of ATLAS and CMS at the HL-LHC. Experimental results of the characterization of small prototypes will be discussed in the frame of the design work that is currently leading to the development of the large scale demonstrator chip RD53A to be submitted in early 2017. The paper is focused on the analog processors developed in the framework of the RD53 collaboration, including three time over threshold front-ends, designed by INFN Torino and Pavia, University of Bergamo and LBNL and a zero dead time front-end based on flash ADC designed by a joint collaboration between the Fermilab and INFN. The paper will also discuss the radiation tolerance features of the front-end channels, which were exposed to up to 800 Mrad of total ionizing dose to reproduce the system operation in the actual experiment

Effects of Tillage and Nitrogen Fertilizers on CH4 and CO2 Emissions and Soil Organic Carbon in Paddy Fields of Central China

Quantifying carbon (C) sequestration in paddy soils is necessary to help better understand the effect of agricultural practices on the C cycle. The objective of the present study was to assess the effects of tillage practices [conventional tillage (CT) and no-tillage (NT)] and the application of nitrogen (N) fertilizer (0 and 210 kg N ha−1) on fluxes of CH4 and CO2, and soil organic C (SOC) sequestration during the 2009 and 2010 rice growing seasons in central China. Application of N fertilizer significantly increased CH4 emissions by 13%–66% and SOC by 21%–94% irrespective of soil sampling depths, but had no effect on CO2 emissions in either year. Tillage significantly affected CH4 and CO2 emissions, where NT significantly decreased CH4 emissions by 10%–36% but increased CO2 emissions by 22%–40% in both years. The effects of tillage on the SOC varied with the depth of soil sampling. NT significantly increased the SOC by 7%–48% in the 0–5 cm layer compared with CT. However, there was no significant difference in the SOC between NT and CT across the entire 0–20 cm layer. Hence, our results suggest that the potential of SOC sequestration in NT paddy fields may be overestimated in central China if only surface soil samples are considered

Feasibility studies for the measurement of time-like proton electromagnetic form factors from p¯ p→ μ+μ- at P ¯ ANDA at FAIR

This paper reports on Monte Carlo simulation results for future measurements of the moduli of time-like proton electromagnetic form factors, | GE| and | GM| , using the p¯ p→ μ+μ- reaction at P ¯ ANDA (FAIR). The electromagnetic form factors are fundamental quantities parameterizing the electric and magnetic structure of hadrons. This work estimates the statistical and total accuracy with which the form factors can be measured at P ¯ ANDA , using an analysis of simulated data within the PandaRoot software framework. The most crucial background channel is p¯ p→ π+π-, due to the very similar behavior of muons and pions in the detector. The suppression factors are evaluated for this and all other relevant background channels at different values of antiproton beam momentum. The signal/background separation is based on a multivariate analysis, using the Boosted Decision Trees method. An expected background subtraction is included in this study, based on realistic angular distributions of the background contribution. Systematic uncertainties are considered and the relative total uncertainties of the form factor measurements are presented