Ms2lda.org: web-based topic modelling for substructure discovery in mass spectrometry

Motivation: We recently published MS2LDA, a method for the decomposition of sets of molecular fragment data derived from large metabolomics experiments. To make the method more widely available to the community, here we present ms2lda.org, a web application that allows users to upload their data, run MS2LDA analyses and explore the results through interactive visualisations. Results: Ms2lda.org takes tandem mass spectrometry data in many standard formats and allows the user to infer the sets of fragment and neutral loss features that co-occur together (Mass2Motifs). As an alternative workflow, the user can also decompose a dataset onto predefined Mass2Motifs. This is accomplished through the web interface or programmatically from our web service

Virtual timers in hierarchical real-time systems

Hierarchical scheduling frameworks (HSFs) provide means for composing complex real-time systems from welldefined subsystems. This paper describes an approach to provide hierarchically scheduled real-time applications with virtual event timers, motivated by the need for integrating priority processing applications in an HSF. Specifically, the paper proposes a technique to minimize the overhead of event handling in HSFs and outlines a simple implementation

General Spectral Flow Formula for Fixed Maximal Domain

We consider a continuous curve of linear elliptic formally self-adjoint differential operators of first order with smooth coefficients over a compact Riemannian manifold with boundary together with a continuous curve of global elliptic boundary value problems. We express the spectral flow of the resulting continuous family of (unbounded) self-adjoint Fredholm operators in terms of the Maslov index of two related curves of Lagrangian spaces. One curve is given by the varying domains, the other by the Cauchy data spaces. We provide rigorous definitions of the underlying concepts of spectral theory and symplectic analysis and give a full (and surprisingly short) proof of our General Spectral Flow Formula for the case of fixed maximal domain. As a side result, we establish local stability of weak inner unique continuation property (UCP) and explain its role for parameter dependent spectral theory.Comment: 22 page

Role of Nucleotide Identity in Effective CRISPR Target Escape Mutations

Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped CRISPR interference through mutations in their protospacer target site. We previously observed a trend that nucleotide-dependent mismatches between crRNA and the protospacer strongly influence the efficiency of primed CRISPR adaptation. Here we show that guanine-substitutions in the target strand of the protospacer are highly detrimental to CRISPR interference and interference-dependent priming, while cytosine-substitutions are more readily tolerated. Furthermore, we show that this effect is based on strongly decreased binding affinity of the effector complex Cascade for guanine-mismatched targets, while cytosine-mismatched targets only minimally affect target DNA binding. Structural modeling of Cascade-bound targets with mismatches shows that steric clashes of mismatched guanines lead to unfavorable conformations of the RNA-DNA duplex. This effect has strong implications for the natural selection of target site mutations that lead to effective escape from type I CRISPR–Cas systems

Magnetic-interference patterns in Josephson junctions with d+is symmetry

The magnetic interference pattern and the spontaneous flux in unconventional Josephson junctions of superconductors with d+is symmetry are calculated for different reduced junction lengths and the relative factor of the d and s wave components. This is a time reversal broken symmetry state. We study the stability of the fractional vortex and antivortex which are spontaneously formed and examine their evolution as we change the length and the relative factor of d and s wave components. The asymmetry in the field modulated diffraction pattern exists for lengths as long as L=10\lambda_J.Comment: 8 pages, 6 eps files, submitted to PR

Discovery and Observations of ASASSN-13db, an EX Lupi-Type Accretion Event on a Low-Mass T Tauri Star

We discuss ASASSN-13db, an EX Lupi-type ("EXor") accretion event on the young stellar object (YSO) SDSS J051011.01$-$032826.2 (hereafter SDSSJ0510) discovered by the All-Sky Automated Survey for SuperNovae (ASAS-SN). Using archival photometric data of SDSSJ0510 we construct a pre-outburst spectral energy distribution (SED) and find that it is consistent with a low-mass class II YSO near the Orion star forming region ($d \sim 420$ pc). We present follow-up photometric and spectroscopic observations of the source after the $\Delta V \sim-$5.4 magnitude outburst that began in September 2013 and ended in early 2014. These data indicate an increase in temperature and luminosity consistent with an accretion rate of $\sim10^{-7}$ $\rm{M}_\odot$ yr$^{-1}$, three or more orders of magnitude greater than in quiescence. Spectroscopic observations show a forest of narrow emission lines dominated by neutral metallic lines from Fe I and some low-ionization lines. The properties of ASASSN-13db are similar to those of the EXor prototype EX Lupi during its strongest observed outburst in late 2008.Comment: 14 pages, 4 figures, 1 table. Updated May 2014 to reflect changes in the final version published in ApJL. Photometric data presented in this submission are included as ancillary files. For a brief video explaining this paper, see http://youtu.be/yRCCrNJnvt

Mapping of mechanical properties of cement paste microstructures

The presented study is related to the EU 7 th Framework Programme CODICE (COmputationally Driven design of Innovative CEment-based materials). The main aim of the project is the development of a multi-scale model for the computer based simulation of mechanical and durability performance of cementitious materials. This paper reports results of micro/nano scale characterisation and mechanical property mapping of cementitious skeletons formed by the cement hydration at different ages. Using the statistical nanoindentation and micro-mechanical property mapping technique, intrinsic properties of different hydrate phases, and also the possible interaction (or overlapping) of different phases (e.g. calcium-silcate-hydrates) has been studied. Results of the mapping and statistical indentation testing appear to suggest the possible existence of more hydrate phases than the commonly reported LD and HD C-S-H and CH phase

Aerosol particles at a high-altitude site on the Southeast Tibetan Plateau, China: Implications for pollution transport from South Asia

      Bulk aerosol samples were collected from 16 July 2008 to 26 July 2009 at Lulang, a high-altitude (>3300m above sea level) site on the southeast Tibetan Plateau (TP); objectives were to determine chemical characteristics of the aerosol and identify its major sources. We report aerosol (total suspended particulate, TSP) mass levels and the concentrations of selected elements, carbonaceous species, and water-soluble inorganic ions. Significant buildup of aerosol mass and chemical species (organic carbon, element carbon, nitrate, and sulfate) occurred during the premonsoon, while lower concentrations were observed during the monsoon. Seasonal variations in aerosol and chemical species were driven by precipitation scavenging and atmospheric circulation. Two kinds of high-aerosol episodes were observed: one was enriched with dust indicators (Fe and Ca2+), and the other was enhanced with organic and elemental carbon (OC and EC), SO42−, NO3−, and Fe. The TSP loadings during the latter were 3 to 6 times those on normal days. The greatest aerosol optical depths (National Centers for Environmental Protection/National Center for Atmospheric Research reanalysis) occurred upwind, in eastern India and Bangladesh, and trajectory analysis indicates that air pollutants were transported from the southwest. Northwesterly winds brought high levels of natural emissions (Fe, Ca2+) and low levels of pollutants (SO42−, NO3−, K+, and EC); this was consistent with high aerosol optical depths over the western deserts and Gobi. Our work provides evidence that both geological and pollution aerosols from surrounding regions impact the aerosol population of the TP

Anomaly analysis of Hawking radiation from Kaluza-Klein black hole with squashed horizon

Considering gravitational and gauge anomalies at the horizon, a new method that to derive Hawking radiations from black holes has been developed by Wilczek et al. In this paper, we apply this method to non-rotating and rotating Kaluza-Klein black holes with squashed horizon, respectively. For the rotating case, we found that, after the dimensional reduction, an effective U(1) gauge field is generated by an angular isometry. The results show that the gauge current and energy-momentum tensor fluxes are exactly equivalent to Hawking radiation from the event horizon.Comment: 15 pages, no figures, the improved version, accepted by Eur. Phys. J.