2,170 research outputs found
Towards a comprehensive open source platform for management and analysis of High Content Screening data
As High Content Screening (HCS) has moved into the main stream for biological and pharmaceutical investigations, a lag of well integrated pipelines for automated acquisition, management and analysis of HCS results turns out to be a bottleneck for fully leveraging the wealth of information contained in a screen and moving to higher throughput. For many applications, monolithic pipelines can not deliver the flexibility and versatility needed. Laboratories and scientific service providers instead usually look into integrating components from both, the open source world and the commercial software world into best-of-breed data pipelines. In this article, we will present two open source components that can be used as flexible and powerful building blocks for such a pipeline
Virtual Campus – Trends and Perspectives in Germany
In the last few years in Germany virtual campus initiatives have been funded considerably. In our paper we will give a review of comments and recommendations of the advisory boards in higher education policy and of the various funding schemes on the level of the federal states and the federal government. An analysis of the current program „New Media in Education” indicates trends of possible developments as well as hindrances in the virtualization of higher educationIn: A.J. Kallenberg and M.J.J.M. van de Ven (Eds), 2002, The New Educational Benefits of ICT in Higher Education: Proceedings. Rotterdam: Erasmus Plus BV, OECR
ISBN 90-9016127-
Anomalous diffusion, Localization, Aging and Sub-aging effects in trap models at very low temperature
We study in details the dynamics of the one dimensional symmetric trap model,
via a real-space renormalization procedure which becomes exact in the limit of
zero temperature. In this limit, the diffusion front in each sample consists in
two delta peaks, which are completely out of equilibrium with each other. The
statistics of the positions and weights of these delta peaks over the samples
allows to obtain explicit results for all observables in the limit .
We first compute disorder averages of one-time observables, such as the
diffusion front, the thermal width, the localization parameters, the
two-particle correlation function, and the generating function of thermal
cumulants of the position. We then study aging and sub-aging effects : our
approach reproduces very simply the two different aging exponents and yields
explicit forms for scaling functions of the various two-time correlations. We
also extend the RSRG method to include systematic corrections to the previous
zero temperature procedure via a series expansion in . We then consider the
generalized trap model with parameter and obtain that the
large scale effective model at low temperature does not depend on in
any dimension, so that the only observables sensitive to are those
that measure the `local persistence', such as the probability to remain exactly
in the same trap during a time interval. Finally, we extend our approach at a
scaling level for the trap model in and obtain the two relevant time
scales for aging properties.Comment: 33 pages, 3 eps figure
A mechanochemical model of striae distensae
Striae distensae, otherwise known as stretch marks, are common skin lesions found in a variety of clinical settings. They occur frequently during adolescence or pregnancy where there is rapid tissue expansion and in clinical situations associated with corticosteroid excess. Heralding their onset is the appearance of parallel inflammatory streaks aligned perpendicular to the direction of skin tension. Despite a considerable amount of investigative research, the pathogenesis of striae remains obscure. The interpretation of histologic samples – the major investigative tool – demonstrates an association between dermal lymphocytic inflammation, elastolysis, and a scarring response. Yet the primary causal factor in their aetiology is mechanical; either skin stretching due to underlying tissue expansion or, less frequently, a compromised dermis affected by normal loads. In this paper, we investigate the pathogenesis of striae by addressing the coupling between mechanical forces and dermal pathology. We develop a mathematical model that incorporates the mechanical properties of cutaneous fibroblasts and dermal extracellular matrix. By using linear stability analysis and numerical simulations of our governing nonlinear equations, we show that this quantitative approach may provide a realistic framework that may account for the initiating events
Mining data from 1000 genomes to identify the causal variant in regions under positive selection
The human genome contains hundreds of regions in which the patterns of genetic variation indicate recent positive natural selection, yet for most of these the underlying gene and the advantageous mutation remain unknown. We recently reported the development of a method, Composite of Multiple Signals (CMS), that combines tests for multiple signals of natural selection and increases resolution by up to 100-fold
Aging, rejuvenation and memory phenomena in spin glasses
In this paper, we review several important features of the out-of-equilibrium
dynamics of spin glasses. Starting with the simplest experiments, we discuss
the scaling laws used to describe the isothermal aging observed in spin glasses
after a quench down to the low temperature phase. We report in particular new
results on the sub-aging behaviour of spin glasses. We then discuss the
rejuvenation and memory effects observed when a spin glass is submitted to
temperature variations during aging, from the point of view of both energy
landscape pictures and of real space pictures. We highlight the fact that both
approaches point out the necessity of hierarchical processes involved in aging.
Finally, we report an investigation of the effect of small temperature
variations on aging in spin glass samples with various anisotropies which
indicates that this hierarchy depends on the spin anisotropy.Comment: submitted for the Proceedings of Stat Phys 22, Bangalore (India
Noncoding RNA, antigenic variation, and the virulence genes of Plasmodium falciparum
Long non-coding RNAs (lncRNA) are being increasingly recognized as important regulators of gene expression. A recent paper in Genome Biology reports the identification of a lncRNA family in Plasmodium falciparum, the cause of the most deadly form of malaria, that may help to explain the mechanism of antigenic variation in virulence genes of this important pathogen
Single-File Diffusion of Atomic and Colloidal Systems: Asymptotic Laws
In this work we present a general derivation of the non-Fickian behavior for
the self-diffusion of identically interacting particle systems with excluded
mutual passage. We show that the conditional probability distribution of
finding a particle at position after time , when the particle was
located at at , follows a Gaussian distribution in the long-time
limit, with variance for overdamped systems and with
variance for classical systems. The asymptotic behavior of the
mean-squared displacement, , is shown to be independent of the nature of
interactions for homogeneous systems in the fluid state. Moreover, the
long-time behavior of self-diffusion is determined by short-time and large
scale collective density fluctuations.Comment: 4 page
Interference effects in the photorecombination of argonlike Sc3+ ions: Storage-ring experiment and theory
Absolute total electron-ion recombination rate coefficients of argonlike
Sc3+(3s2 3p6) ions have been measured for relative energies between electrons
and ions ranging from 0 to 45 eV. This energy range comprises all dielectronic
recombination resonances attached to 3p -> 3d and 3p -> 4s excitations. A broad
resonance with an experimental width of 0.89 +- 0.07 eV due to the 3p5 3d2 2F
intermediate state is found at 12.31 +- 0.03 eV with a small experimental
evidence for an asymmetric line shape. From R-Matrix and perturbative
calculations we infer that the asymmetric line shape may not only be due to
quantum mechanical interference between direct and resonant recombination
channels as predicted by Gorczyca et al. [Phys. Rev. A 56, 4742 (1997)], but
may partly also be due to the interaction with an adjacent overlapping DR
resonance of the same symmetry. The overall agreement between theory and
experiment is poor. Differences between our experimental and our theoretical
resonance positions are as large as 1.4 eV. This illustrates the difficulty to
accurately describe the structure of an atomic system with an open 3d-shell
with state-of-the-art theoretical methods. Furthermore, we find that a
relativistic theoretical treatment of the system under study is mandatory since
the existence of experimentally observed strong 3p5 3d2 2D and 3p5 3d 4s 2D
resonances can only be explained when calculations beyond LS-coupling are
carried out.Comment: 11 pages, 7 figures, 3 tables, Phys. Rev. A (in print), see also:
http://www.strz.uni-giessen.de/~k
ATM and ATR protect the genome against two different types of tandem repeat instability in Fragile X premutation mice
Expansion of a tandem repeat tract is responsible for the Repeat Expansion diseases, a group of more than 20 human genetic disorders that includes those like Fragile X (FX) syndrome that result from repeat expansion in the FMR1 gene. We have previously shown that the ATM and Rad3-related (ATR) checkpoint kinase protects the genome against one type of repeat expansion in a FX premutation mouse model. By crossing the FX premutation mice to Ataxia Telangiectasia-Mutated (Atm) mutant mice, we show here that ATM also prevents repeat expansion. However, our data suggest that the ATM-sensitive mechanism is different from the ATR-sensitive one. Specifically, the effect of the ATM deficiency is more marked when the premutation allele is paternally transmitted and expansions occur more frequently in male offspring regardless of the Atm genotype of the offspring. The gender effect is most consistent with a repair event occurring in the early embryo that is more efficient in females, perhaps as a result of the action of an X-linked DNA repair gene. Our data thus support the hypothesis that two different mechanisms of FX repeat expansion exist, an ATR-sensitive mechanism seen on maternal transmission and an ATM-sensitive mechanism that shows a male expansion bias
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