Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives

Comprehensive comparison of in silico MS/MS fragmentation tools of the CASMI contest: database boosting is needed to achieve 93% accuracy.

In mass spectrometry-based untargeted metabolomics, rarely more than 30% of the compounds are identified. Without the true identity of these molecules it is impossible to draw conclusions about the biological mechanisms, pathway relationships and provenance of compounds. The only way at present to address this discrepancy is to use in silico fragmentation software to identify unknown compounds by comparing and ranking theoretical MS/MS fragmentations from target structures to experimental tandem mass spectra (MS/MS). We compared the performance of four publicly available in silico fragmentation algorithms (MetFragCL, CFM-ID, MAGMa+ and MS-FINDER) that participated in the 2016 CASMI challenge. We found that optimizing the use of metadata, weighting factors and the manner of combining different tools eventually defined the ultimate outcomes of each method. We comprehensively analysed how outcomes of different tools could be combined and reached a final success rate of 93% for the training data, and 87% for the challenge data, using a combination of MAGMa+, CFM-ID and compound importance information along with MS/MS matching. Matching MS/MS spectra against the MS/MS libraries without using any in silico tool yielded 60% correct hits, showing that the use of in silico methods is still important

A runtime safety analysis concept for open adaptive systems

© Springer Nature Switzerland AG 2019. In the automotive industry, modern cyber-physical systems feature cooperation and autonomy. Such systems share information to enable collaborative functions, allowing dynamic component integration and architecture reconfiguration. Given the safety-critical nature of the applications involved, an approach for addressing safety in the context of reconfiguration impacting functional and non-functional properties at runtime is needed. In this paper, we introduce a concept for runtime safety analysis and decision input for open adaptive systems. We combine static safety analysis and evidence collected during operation to analyse, reason and provide online recommendations to minimize deviation from a system’s safe states. We illustrate our concept via an abstract vehicle platooning system use case

Stability and Evolution of Supernova Fallback Disks

We show that thin accretion disks made of Carbon or Oxygen are subject to the same thermal ionization instability as Hydrogen and Helium disks. We argue that the instability applies to disks of any metal content. The relevance of the instability to supernova fallback disks probably means that their power-law evolution breaks down when they first become neutral. We construct simple analytical models for the viscous evolution of fallback disks to show that it is possible for these disks to become neutral when they are still young (ages of a few 10^3 to 10^4 years), compact in size (a few 10^9 cm to 10^11 cm) and generally accreting at sub-Eddington rates (Mdot ~ a few 10^14 - 10^18 g/s). Based on recent results on the nature of viscosity in the disks of close binaries, we argue that this time may also correspond to the end of the disk activity period. Indeed, in the absence of a significant source of viscosity in the neutral phase, the entire disk will likely turn to dust and become passive. We discuss various applications of the evolutionary model, including anomalous X-ray pulsars and young radio pulsars. Our analysis indicates that metal-rich fallback disks around newly-born neutron stars and black holes become neutral generally inside the tidal truncation radius (Roche limit) for planets, at \~10^11 cm. Consequently, the efficiency of the planetary formation process in this context will mostly depend on the ability of the resulting disk of rocks to spread via collisions beyond the Roche limit. It appears easier for the merger product of a doubly degenerate binary, whether it is a massive white dwarf or a neutron star, to harbor planets because it can spread beyond the Roche limit before becoming neutral.[Abridged]Comment: 34 pages, 2 figures, accepted for publication in Ap

Low-latitude equinoctial spread-F occurrence at different longitude sectors under low solar activity

We present the results of a comparative study of spread-F signatures over five low-latitude sites: Chiangmai (CGM; 18.8° N, 98.9° E, mag. Lat. 8.8° N), Thailand; Tanjungsari (TNJ; 6.9° S, 107.6° E, mag. Lat. 16.9° S), Indonesia; Palmas (PAL; 10.2° S, 311.8° E, mag. Lat. 0.9° S) and São José Dos Campos (SJC; 23.2° S, 314.1° E, mag. Lat. 14.0° S), Brazil; and Tucumán (TUC; 26.9° S, 294.6° E, mag. Lat. 16.8° S), Argentina. The investigation was based on simultaneous ionograms recorded by an FMCW (frequency-modulated continuous-wave) at CGM, an IPS-71 (digital ionosonde from KEL aerospace) at TNJ, a CADI (Canadian Advanced Digital Ionosonde) at PAL and SJC, and an AIS-INGV (Advanced Ionospheric Sounder – Istituto Nazionale di Geofisica e Vulcanologia) at TUC, during the equinoctial periods March–April (R12 = 2.0 and R12 = 2.2) and September–October (R12 = 6.1 and R12 = 7.0) 2009, for very low solar activity. Spread-F signatures were categorized into two types: the range spread-F (RSF) and the frequency spread-F (FSF). The study confirms that the dynamics and the physical processes responsible for these phenomena are actually complicated. In fact, the features that arise from the investigation are different, depending on both the longitude sector and on the hemisphere. For instance, TUC, under the southern crest of the ionospheric equatorial ionization anomaly (EIA), shows a predominance of RSF signatures, while both SJC, under the southern crest of EIA but in a different longitude sector, and CGM, under the northern crest of EIA, show a predominance of FSF signatures. Moreover, the spread-F occurrence over the longitude sector that includes CGM and TNJ is significantly lower than the spread-F occurrence over the longitude sector of PAL, SJC, and TUC.Fil: Pezzopane, M.. Istituto Nazionale Di Geofisica E Vulcanologia; Italia;Fil: Zuccheretti, E.. Istituto Nazionale Di Geofisica E Vulcanologia; Italia;Fil: Abadi, P.. Indonesian National Institute of Aeronautics and Space. Space Science Center. Division of Ionosphere and Telecommunication; Indonesia;Fil: de Abreu, A. J.. Universidade do Vale do Paraíba; Brazil;Fil: de Jesus, R.. Universidade do Vale do Paraíba; Brazil;Fil: Fagundes, P. R.. Universidade do Vale do Paraíba; Brazil;Fil: Supnithi, P.. King Mongkut’s Institute of Technology Ladkrabang . Faculty of Engineering; Tailandia;Fil: Rungraengwajiake, S.. King Mongkut’s Institute of Technology Ladkrabang . Faculty of Engineering; Tailandia;Fil: Nagatsuma, T.. National Institute of Information and Communications Technology. Space Weather and Environment Informatics Laboratory; Japón;Fil: Tsugawa, T.. National Institute of Information and Communications Technology. Space Weather and Environment Informatics Laboratory; Japón;Fil: Cabrera, Miguel Angel. Universidad Nacional de Tucumán. Facultad de Ciencias Exactas y Tecnología. Departamento de Física. Laboratorio de Ionosfera; Argentina; Universidad Nacional de Tucumán. Facultad de Ciencias Exactas y Tecnología. Departamento de Electricidad, Electrónica y Computación. Laboratorio de Telecomunicaciones; Argentina; Universidad Tecnológica Nacional. Facultad Regional Tucumán. Centro de Investigación de Atmósfera Superior y Radiopropagación; Argentina;Fil: Ezquer, Rodolfo Gerardo. Universidad Tecnológica Nacional. Facultad Regional Tucumán. Centro de Investigación de Atmósfera Superior y Radiopropagación; Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina; Universidad Nacional de Tucumán. Facultad de Ciencias Exactas y Tecnología. Departamento de Física. Laboratorio de Ionosfera; Argentina

Short-period AM CVn systems as optical, X-ray and gravitational wave sources

We model the population of AM CVn systems in the Galaxy and discuss the detectability of these systems with optical, X-ray and gravitational wave detectors. We concentrate on the short period (P < 1500 s) systems, some of which are expected to be in a phase of direct impact accretion. Using a self-consistent model for the star formation history and radial distribution of stars in the Galaxy plus simple models for the emission of optical and X-ray radiation from the AM CVn systems and interstellar absorption, we derive the sample of short-period AM CVn systems that can be detected in the optical and/or X-ray bands. At the shortest periods the detectable systems are all X-ray sources, some with periods as short as three minutes. At periods above 10 minutes most detectable systems are optical sources. About one third of the X-ray sources are also detectable in the optical band. We also calculate the gravitational wave signal of the short-period AM CVn systems. We find that potentially several thousand AM CVn systems can be resolved by the gravitational wave detector LISA, comparable to the expected number of detached double white dwarfs that can be resolved. We estimate that several hundreds of the AM CVn systems resolvable by LISA, are also detectable in the optical and/or X-ray bands.Comment: Accepted for publication in MNRA

Generation and quality control of lipidomics data for the alzheimers disease neuroimaging initiative cohort.

Alzheimers disease (AD) is a major public health priority with a large socioeconomic burden and complex etiology. The Alzheimer Disease Metabolomics Consortium (ADMC) and the Alzheimer Disease Neuroimaging Initiative (ADNI) aim to gain new biological insights in the disease etiology. We report here an untargeted lipidomics of serum specimens of 806 subjects within the ADNI1 cohort (188 AD, 392 mild cognitive impairment and 226 cognitively normal subjects) along with 83 quality control samples. Lipids were detected and measured using an ultra-high-performance liquid chromatography quadruple/time-of-flight mass spectrometry (UHPLC-QTOF MS) instrument operated in both negative and positive electrospray ionization modes. The dataset includes a total 513 unique lipid species out of which 341 are known lipids. For over 95% of the detected lipids, a relative standard deviation of better than 20% was achieved in the quality control samples, indicating high technical reproducibility. Association modeling of this dataset and available clinical, metabolomics and drug-use data will provide novel insights into the AD etiology. These datasets are available at the ADNI repository at http://adni.loni.usc.edu/