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

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 $T \to 0$. 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 $T$. We then consider the generalized trap model with parameter $\alpha \in [0,1]$ and obtain that the large scale effective model at low temperature does not depend on $\alpha$ in any dimension, so that the only observables sensitive to $\alpha$ 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 $d=2$ and obtain the two relevant time scales for aging properties.Comment: 33 pages, 3 eps figure

Dynamics of Annealed Systems under External Fields: CTRW and the Fractional Fokker-Planck Equations

We consider the linear response of a system modelled by continuous-time random walks (CTRW) to an external field pulse of rectangular shape. We calculate the corresponding response function explicitely and show that it exhibits aging, i.e. that it is not translationally invariant in the time-domain. This result differs from that of systems which behave according to fractional Fokker-Planck equations

Aging in the random energy model

In this letter we announce rigorous results on the phenomenon of aging in the Glauber dynamics of the random energy model and their relation to Bouchaud's 'REM-like' trap model. We show that, below the critical temperature, if we consider a time-scale that diverges with the system size in such a way that equilibrium is almost, but not quite reached on that scale, a suitably defined autocorrelation function has the same asymptotic behaviour than its analog in the trap model.Comment: 4pp, P

1D Aging

We derive exact expressions for a number of aging functions that are scaling limits of non-equilibrium correlations, R(tw,tw+t) as tw --> infinity with t/tw --> theta, in the 1D homogenous q-state Potts model for all q with T=0 dynamics following a quench from infinite temperature. One such quantity is (the two-point, two-time correlation function) when n/sqrt(tw) --> z. Exact, closed-form expressions are also obtained when one or more interludes of infinite temperature dynamics occur. Our derivations express the scaling limit via coalescing Brownian paths and a ``Brownian space-time spanning tree,'' which also yields other aging functions, such as the persistence probability of no spin flip at 0 between tw and tw+t.Comment: 4 pages (RevTeX); 2 figures; submitted to Physical Review Letter

Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs

Fibroblasts are ubiquitous mesenchymal cells with many vital functions during development, tissue repair, and disease. Fibroblasts from different anatomic sites have distinct and characteristic gene expression patterns, but the principles that govern their molecular specialization are poorly understood. Spatial organization of cellular differentiation may be achieved by unique specification of each cell type; alternatively, organization may arise by cells interpreting their position along a coordinate system. Here we test these models by analyzing the genome-wide gene expression profiles of primary fibroblast populations from 43 unique anatomical sites spanning the human body. Large-scale differences in the gene expression programs were related to three anatomic divisions: anterior-posterior (rostral-caudal), proximal-distal, and dermal versus nondermal. A set of 337 genes that varied according to these positional divisions was able to group all 47 samples by their anatomic sites of origin. Genes involved in pattern formation, cell-cell signaling, and matrix remodeling were enriched among this minimal set of positional identifier genes. Many important features of the embryonic pattern of HOX gene expression were retained in fibroblasts and were confirmed both in vitro and in vivo. Together, these findings suggest that site-specific variations in fibroblast gene expression programs are not idiosyncratic but rather are systematically related to their positional identities relative to major anatomic axes

Fluctuation-dissipation relations in trap models

Trap models are intuitively appealing and often solvable models of glassy dynamics. In particular, they have been used to study aging and the resulting out-of-equilibrium fluctuation-dissipation relations between correlations and response functions. In this note I show briefly that one such relation, first given by Bouchaud and Dean, is valid for a general class of mean-field trap models: it relies only on the way a perturbation affects the transition rates, but is independent of the distribution of trap depths and the form of the unperturbed transition rates, and holds for all observables that are uncorrelated with the energy. The model with Glauber dynamics and an exponential distribution of trap depths, as considered by Barrat and Mezard, does not fall into this class if the perturbation is introduced in the standard way by shifting all trap energies. I show that a similar relation between response and correlation nevertheless holds for the out-of-equilibrium dynamics at low temperatures. The results point to intriguing parallels between trap models with energetic and entropic barriers.Comment: Extended introduction and discussion of relation to results of cond-mat/0303445. 13 pages, 2 figures, IOP styl

Exploratory Behavior, Trap Models and Glass Transitions

A random walk is performed on a disordered landscape composed of $N$ sites randomly and uniformly distributed inside a $d$-dimensional hypercube. The walker hops from one site to another with probability proportional to $\exp [- \beta E(D)]$, where $\beta = 1/T$ is the inverse of a formal temperature and $E(D)$ is an arbitrary cost function which depends on the hop distance $D$. Analytic results indicate that, if $E(D) = D^{d}$ and $N \to \infty$, there exists a glass transition at $\beta_d = \pi^{d/2}/\Gamma(d/2 + 1)$. Below $T_d$, the average trapping time diverges and the system falls into an out-of-equilibrium regime with aging phenomena. A L\'evy flight scenario and applications to exploratory behavior are considered.Comment: 4 pages, 1 figure, new versio

Wind Energy and the Turbulent Nature of the Atmospheric Boundary Layer

Wind turbines operate in the atmospheric boundary layer, where they are exposed to the turbulent atmospheric flows. As the response time of wind turbine is typically in the range of seconds, they are affected by the small scale intermittent properties of the turbulent wind. Consequently, basic features which are known for small-scale homogeneous isotropic turbulence, and in particular the well-known intermittency problem, have an important impact on the wind energy conversion process. We report on basic research results concerning the small-scale intermittent properties of atmospheric flows and their impact on the wind energy conversion process. The analysis of wind data shows strongly intermittent statistics of wind fluctuations. To achieve numerical modeling a data-driven superposition model is proposed. For the experimental reproduction and adjustment of intermittent flows a so-called active grid setup is presented. Its ability is shown to generate reproducible properties of atmospheric flows on the smaller scales of the laboratory conditions of a wind tunnel. As an application example the response dynamics of different anemometer types are tested. To achieve a proper understanding of the impact of intermittent turbulent inflow properties on wind turbines we present methods of numerical and stochastic modeling, and compare the results to measurement data. As a summarizing result we find that atmospheric turbulence imposes its intermittent features on the complete wind energy conversion process. Intermittent turbulence features are not only present in atmospheric wind, but are also dominant in the loads on the turbine, i.e. rotor torque and thrust, and in the electrical power output signal. We conclude that profound knowledge of turbulent statistics and the application of suitable numerical as well as experimental methods are necessary to grasp these unique features (...)Comment: Accepted by the Journal of Turbulence on May 17, 201

Chestnut wood in compression perpendicular to the grain : non-destructive correlations for test results in new and old wood

This paper addresses the evaluation of the compressive properties of chestnut wood under compression perpendicular to the grain, using destructive and non-destructive methods. Three non-destructive methods (ultrasonic testing, Resistograph and Pilodyn) are proposed and the possibility of their application is discussed based on the application of simple linear regression models. Timber specimens were tested up to failure, divided in two different groups for assessing a possible load history related degradation, namely New Chestnut Wood (NCW), never been used structurally, and Old Chestnut Wood (OCW), obtained from structural elements belonging to ancient buildings. The specimens were also divided into four groups according to the orientation of annual growth rings towards load and wave propagation direction. The results show, in general, good correlations between compression strength and stiffness with non-destructive techniques via ultrasonic testing, Resistograph and Pilodyn. However, the orientation of the loading direction with respect to the annual growth rings must be taken into account. This conclusion, and the observation that NCW and OCW shows correlations and regression models usually different, add additional complexity to the quantitative use of non-destructive evaluation techniques for the assessment of the mechanical behaviour of timber elements.Fundação para a Ciência e Tecnologia (FCT) - SFRH/BD/ 5002/200