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Atmospheric fungal nanoparticle bursts.
Aerosol nanoparticles play an important role in the climate system by affecting cloud formation and properties, as well as in human health because of their deep reach into lungs and the circulatory system. Determining nanoparticle sources and composition is a major challenge in assessing their impacts in these areas. The sudden appearance of large numbers of atmospheric nanoparticles is commonly attributed to secondary formation from gas-phase precursors, but in many cases, the evidence for this is equivocal. We report the detection of a mode of fungal fragments with a mobility diameter of roughly 30 nm released in episodic bursts in ambient air over an agricultural area in northern Oklahoma. These events reached concentrations orders of magnitude higher than other reports of biological particles and show similarities to unclarified events reported previously in the Amazon. These particles potentially represent a large source of both cloud-forming ice nuclei and respirable allergens in a variety of ecosystems
TrAp: a Tree Approach for Fingerprinting Subclonal Tumor Composition
Revealing the clonal composition of a single tumor is essential for
identifying cell subpopulations with metastatic potential in primary tumors or
with resistance to therapies in metastatic tumors. Sequencing technologies
provide an overview of an aggregate of numerous cells, rather than
subclonal-specific quantification of aberrations such as single nucleotide
variants (SNVs). Computational approaches to de-mix a single collective signal
from the mixed cell population of a tumor sample into its individual components
are currently not available. Herein we propose a framework for deconvolving
data from a single genome-wide experiment to infer the composition, abundance
and evolutionary paths of the underlying cell subpopulations of a tumor. The
method is based on the plausible biological assumption that tumor progression
is an evolutionary process where each individual aberration event stems from a
unique subclone and is present in all its descendants subclones. We have
developed an efficient algorithm (TrAp) for solving this mixture problem. In
silico analyses show that TrAp correctly deconvolves mixed subpopulations when
the number of subpopulations and the measurement errors are moderate. We
demonstrate the applicability of the method using tumor karyotypes and somatic
hypermutation datasets. We applied TrAp to SNV frequency profile from Exome-Seq
experiment of a renal cell carcinoma tumor sample and compared the mutational
profile of the inferred subpopulations to the mutational profiles of twenty
single cells of the same tumor. Despite the large experimental noise, specific
co-occurring mutations found in clones inferred by TrAp are also present in
some of these single cells. Finally, we deconvolve Exome-Seq data from three
distinct metastases from different body compartments of one melanoma patient
and exhibit the evolutionary relationships of their subpopulations
Process algebra modelling styles for biomolecular processes
We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed
Atmospheric ice nuclei in the Eyjafjallajökull volcanic ash plume
We have sampled atmospheric ice nuclei (IN) and aerosol in Germany and in Israel during spring 2010. IN were analyzed by the static vapor diffusion chamber FRIDGE, as well as by electron microscopy. During the Eyjafjallajökull volcanic eruption of April 2010 we have measured the highest ice nucleus number concentrations (>600 l−1) in our record of 2 yr of daily IN measurements in central Germany. Even in Israel, located about 5000 km away from Iceland, IN were as high as otherwise only during desert dust storms. The fraction of aerosol activated as ice nuclei at −18 °C and 119% rhice and the corresponding area density of ice-active sites per aerosol surface were considerably higher than what we observed during an intense outbreak of Saharan dust over Europe in May 2008.
Pure volcanic ash accounts for at least 53–68% of the 239 individual ice nucleating particles that we collected in aerosol samples from the event and analyzed by electron microscopy. Volcanic ash samples that had been collected close to the eruption site were aerosolized in the laboratory and measured by FRIDGE. Our analysis confirms the relatively poor ice nucleating efficiency (at −18 °C and 119% ice-saturation) of such "fresh" volcanic ash, as it had recently been found by other workers. We find that both the fraction of the aerosol that is active as ice nuclei as well as the density of ice-active sites on the aerosol surface are three orders of magnitude larger in the samples collected from ambient air during the volcanic peaks than in the aerosolized samples from the ash collected close to the eruption site. From this we conclude that the ice-nucleating properties of volcanic ash may be altered substantially by aging and processing during long-range transport in the atmosphere, and that global volcanism deserves further attention as a potential source of atmospheric ice nuclei
Modelling the Dynamics of an Aedes albopictus Population
We present a methodology for modelling population dynamics with formal means
of computer science. This allows unambiguous description of systems and
application of analysis tools such as simulators and model checkers. In
particular, the dynamics of a population of Aedes albopictus (a species of
mosquito) and its modelling with the Stochastic Calculus of Looping Sequences
(Stochastic CLS) are considered. The use of Stochastic CLS to model population
dynamics requires an extension which allows environmental events (such as
changes in the temperature and rainfalls) to be taken into account. A simulator
for the constructed model is developed via translation into the specification
language Maude, and used to compare the dynamics obtained from the model with
real data.Comment: In Proceedings AMCA-POP 2010, arXiv:1008.314
The Algebraic View of Computation
We argue that computation is an abstract algebraic concept, and a computer is
a result of a morphism (a structure preserving map) from a finite universal
semigroup.Comment: 13 pages, final version will be published elsewher
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