3,515 research outputs found
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 J051011.01032826.2 (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 ( pc). We present
follow-up photometric and spectroscopic observations of the source after the
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 yr,
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.
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