MarVis-Filter: Ranking, Filtering, Adduct and Isotope Correction of Mass Spectrometry Data

Statistical ranking, filtering, adduct detection, isotope correction, and molecular formula calculation are essential tasks in processing mass spectrometry data in metabolomics studies. In order to obtain high-quality data sets, a framework which incorporates all these methods is required. We present the MarVis-Filter software, which provides well-established and specialized methods for processing mass spectrometry data. For the task of ranking and filtering multivariate intensity profiles, MarVis-Filter provides the ANOVA and Kruskal-Wallis tests with adjustment for multiple hypothesis testing. Adduct and isotope correction are based on a novel algorithm which takes the similarity of intensity profiles into account and allows user-defined ionization rules. The molecular formula calculation utilizes the results of the adduct and isotope correction. For a comprehensive analysis, MarVis-Filter provides an interactive interface to combine data sets deriving from positive and negative ionization mode. The software is exemplarily applied in a metabolic case study, where octadecanoids could be identified as markers for wounding in plants

Characterisation of batteries by electrochemical impedance spectroscopy

In the pursuit of batteries with higher energy density and lower cost, central to advancement of the technology is the ability to prolong cycle life. Techniques are sought which can elucidate information on battery degradation without significantly disrupting the performance of cells. Electrochemical impedance spectroscopy (EIS) offers a non-destructive route to in-situ analysis of the dynamic processes occurring inside a battery. The technique is relatively easy to use, but meaningful data analysis requires assignment of spectroscopic features to battery impedance components. Three-electrode cell configurations afford a way to potentially disentangle the impedance components. This paper examines a number of three-electrode cell designs reported in the literature, and compares their advantages and limitations. EIS results obtained using a novel in-house, three-electrode pouch cell are reported and the results compared with those obtained from conventional two-terminal impedance complex plane plots. In this way, the separate contributions of anodic and cathodic impedances can be assessed

Lithium-ion battery separator membranes based on poly(L-lactic acid) biopolymer

Sustainable materials are increasingly needed in lithium ion batteries in order to reduce their environmental impact and improve their recyclability. This work reports on the production of separators using poly (L-lactic acid) (PLLA) for lithium ion battery applications. PLLA separators were obtained by solvent casting technique, by varying polymer concentration in solution between 8 wt.% and 12 wt.% in order to evaluate their morphology, thermal, electrical and electrochemical properties. It is verified that morphology and porosity can be tuned by varying polymer concentration and that the separators are thermally stable up to 250 ºC. The best ionic conductivity of 1.6 mS/cm was obtained for the PLLA separator prepared from 10 wt.% polymer concentration in solution, due to the synergistic effect of the morphology and electrolyte uptake. For this membrane, a high discharge capacity value of 93 mAh.g-1 was obtained at the rate of 1C. In this work, it is demonstrated that PLLA is a good candidate for the development of separator membranes, in order to produce greener and environmentally friendly batteries in a circular economy context.Work supported by the Portuguese Foundation for Science and Technology (FCT) undes strategic funding UID/FIS/04650/2020 and UID/QUI/0686/2020, project PTDC/FISMAC/28157/2017, and Grants SFRH/BD/140842/2018 (J.C.B.), SFRH/BPD/121526/2016 (D.M.C), CEECIND/00833/2017 (R.G.) and SFRH/BPD/112547/2015 (C.M.C.). Financial support from the Basque Government Industry Department under the ELKARTEK and HAZITEK programs is also acknowledged. Technical and human support provided by SGIker (UPV/EHU, MICINN, GV/EJ, EGEF and ESF) is gratefully acknowledge

Tortuosity of Battery Electrodes: Validation of Impedance-Derived Values and Critical Comparison with 3D Tomography

Tortuosity values of porous battery electrodes determined using electrochemical impedance spectroscopy in symmetric cells with a non-intercalating electrolyte are typically higher than those values based on numerical analysis of 3D tomographic reconstructions. The electrochemical approach assumes that the electronic resistance in the porous coating is negligible and that the tortuosity of the porous electrode can be calculated from the ionic resistance determined by fitting a transmission line equivalent circuit model to the experimental data. In this work, we validate the assumptions behind the electrochemical approach. First, we experimentally and theoretically investigate the influence of the electronic resistance of the porous electrode on the extracted ionic resistances using a general transmission line model, and provide a convenient method to determine whether the electronic resistance is sufficiently low for the model to be correctly applied. Second, using a macroscopic setup with known tortuosity, we prove that the ionic resistance quantified by the transmission line model indeed yields the true tortuosity of a porous medium. Based on our findings, we analyze the tortuosities of porous electrodes using both X-ray tomography and electrochemical impedance spectroscopy on electrodes from the same coating and conclude that the distribution of the polymeric binder phase, which is not imaged in most tomographic experiments, is a key reason for the underestimated tortuosity values calculated from 3D reconstructions of electrode microstructures.ISSN:0013-4651ISSN:1945-711

Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software

State of the art high-throughput technologies allow comprehensive experimental studies of organism metabolism and induce the need for a convenient presentation of large heterogeneous datasets. Especially, the combined analysis and visualization of data from different high-throughput technologies remains a key challenge in bioinformatics. We present here the MarVis-Graph software for integrative analysis of metabolic and transcriptomic data. All experimental data is investigated in terms of the full metabolic network obtained from a reference database. The reactions of the network are scored based on the associated data, and sub-networks, according to connected high-scoring reactions, are identified. Finally, MarVis-Graph scores the detected sub-networks, evaluates them by means of a random permutation test and presents them as a ranked list. Furthermore, MarVis-Graph features an interactive network visualization that provides researchers with a convenient view on the results. The key advantage of MarVis-Graph is the analysis of reactions detached from their pathways so that it is possible to identify new pathways or to connect known pathways by previously unrelated reactions. The MarVis-Graph software is freely available for academic use and can be downloaded at: http://marvis.gobics.de/marvis-graph

Breaking the Silence: Protein Stabilization Uncovers Silenced Biosynthetic Gene Clusters in the Fungus Aspergillus nidulans

The genomes of filamentous fungi comprise numerous putative gene clusters coding for the biosynthesis of chemically and structurally diverse secondary metabolites (SMs), which are rarely expressed under laboratory conditions. Previous approaches to activate these genes were based primarily on artificially targeting the cellular protein synthesis apparatus. Here, we applied an alternative approach of genetically impairing the protein degradation apparatus of the model fungus Aspergillus nidulans by deleting the conserved eukaryotic csnE/CSN5 deneddylase subunit of the COP9 signalosome. This defect in protein degradation results in the activation of a previously silenced gene cluster comprising a polyketide synthase gene producing the antibiotic 2,4- dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde (DHMBA). The csnE/CSN5 gene is highly conserved in fungi, and therefore, the deletion is a feasible approach for the identification of new SMs

Big Data analysis to improve care for people living with serious illness: The potential to use new emerging technology in palliative care.

<p>The table contains the high-ranking pathways from enrichment analysis of data set M1 based on the Kolmogorov-Smirnov (KS) and rank-sum test. The pathways are sorted according to the restandardized p-values derived from the rank-sum test. The last two columns comprise the false discovery rates calculated from the restandardized p-values.</p