Dosage Sensing, Threshold Responses, and Epigenetic Memory: A Systems Biology Perspective on Random X‐Chromosome Inactivation

X‐chromosome inactivation ensures dosage compensation between the sexes in mammals by randomly choosing one out of the two X chromosomes in females for inactivation. This process imposes a plethora of questions: How do cells count their X chromosome number and ensure that exactly one stays active? How do they randomly choose one of two identical X chromosomes for inactivation? And how do they stably maintain this state of monoallelic expression? Here, different regulatory concepts and their plausibility are evaluated in the context of theoretical studies that have investigated threshold behavior, ultrasensitivity, and bistability through mathematical modeling. It is discussed how a twofold difference between a single and a double dose of X‐linked genes might be converted to an all‐or‐nothing response and how mutually exclusive expression can be initiated and maintained. Finally, candidate factors that might mediate the proposed regulatory principles are reviewed

Quantum fluctuations in the spiral phase of the Hubbard model

We study the magnetic excitations in the spiral phase of the two--dimensional Hubbard model using a functional integral method. Spin waves are strongly renormalized and a line of near--zeros is observed in the spectrum around the spiral pitch $\pm{\bf Q}$. The possibility of disordered spiral states is examined by studying the one--loop corrections to the spiral order parameter. We also show that the spiral phase presents an intrinsic instability towards an inhomogeneous state (phase separation, CDW, ...) at weak doping. Though phase separation is suppressed by weak long--range Coulomb interactions, the CDW instability only disappears for sufficiently strong Coulomb interaction.Comment: Figures are NOW appended via uuencoded postscript fil

EU DataGRID testbed management and support at CERN

In this paper we report on the first two years of running the CERN testbed site for the EU DataGRID project. The site consists of about 120 dual-processor PCs distributed over several testbeds used for different purposes: software development, system integration, and application tests. Activities at the site included test productions of MonteCarlo data for LHC experiments, tutorials and demonstrations of GRID technologies, and support for individual users analysis. This paper focuses on node installation and configuration techniques, service management, user support in a gridified environment, and includes considerations on scalability and security issues and comparisons with "traditional" production systems, as seen from the administrator point of view.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 7 pages, LaTeX. PSN THCT00

Searching for rewards in graph-structured spaces

How do people generalize and explore structured spaces? We study human behavior on a multi-armed bandit task, where rewards are influenced by the connectivity structure of a graph. A detailed predictive model comparison shows that a Gaussian Process regression model using a diffusion kernel is able to best describe participant choices, and also predict judgments about expected reward and confidence. This model unifies psychological models of function learning with the Successor Representation used in reinforcement learning, thereby building a bridge between different models of generalization

The soft fermion dispersion relation at next-to-leading order in hot QED

We study next-to-leading order contributions to the soft static fermion dispersion relation in hot QED. We derive an expression for the complete next-to-leading order contribution to the retarded fermion self-energy. The real and imaginary parts of this expression give the next-to-leading order contributions to the mass and damping rate of the fermionic quasi-particle. Many of the terms that are expected to contribute according to the traditional power counting argument are actually subleading. We explain why the power counting method over estimates the contribution from these terms. For the electron damping rate in QED we obtain: $\gamma_{QED} = \frac{e^2 T}{4\pi}(2.70)$. We check our method by calculating the next-to-leading order contribution to the damping rate for the case of QCD with two flavours and three coulours. Our result agrees with the result obtained previously in the literature. The numerical evaluation of the nlo contribution to the mass is left to a future publication.Comment: 15 pages, 5 figure

Edge Enhancement Investigations by Means of Experiments and Simulations

Standard neutron imaging procedures are based on the “shadow” of the transmitted radiation, attenuated by the sample material. Under certain conditions significant deviations from pure transmission can be found in the form of enhancement or depression at the edges of the samples. These effects can limit the quantification process in the related regions. Otherwise, an enhancement and improvement of visibility can be achieved e.g. in defect analysis. In systematic studies we investigated the dependency of these effects on the specific material (mainly for common metals), such as the sample-to-detector distance, the beam collimation, the material thickness and the neutron energy. The beam lines ICON and BOA at PSI and ANTARES at TU München were used for these experiments due to their capability for neutron imaging with highest possible spatial resolution (6.5 to 13.5 micro-meter pixel size, respectively) and their cold beam spectrum. Next to the experimental data we used a McStas tool for the description of refraction and reflection features at edges for comparison. Even if minor contributions by coherent in-line propagation phase contrast are underlined, the major effect can be described by refraction of the neutrons at the sample-void interface. Ways to suppress and to magnify the edge effects can be derived from these findings.Fil: Lehmann, E.. Paul Scherrer Institut; SuizaFil: Schulz, M.. Technische Universitat Munchen; AlemaniaFil: Wang, Y.. China Insititute of Atomic Energy; ChinaFil: Tartaglione, Aureliano. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Coherent Resonat millenial-scale climate transitions triggered by massive meltwater pulses

The role of mean and stochastic freshwater forcing on the generation of millennial-scale climate variability in the North Atlantic is studied using a low-order coupled atmosphere–ocean–sea ice model. It is shown that millennial-scale oscillations can be excited stochastically, when the North Atlantic Ocean is fresh enough. This finding is used in order to interpret the aftermath of massive iceberg surges (Heinrich events) in the glacial North Atlantic, which are characterized by an excitation of Dansgaard–Oeschger events. Based on model results, it is hypothesized that Heinrich events trigger Dansgaard–Oeschger cycles and that furthermore the occurrence of Heinrich events is dependent on the accumulated climatic effect of a series of Dansgaard–Oeschger events. This scenario leads to a coupled ocean–ice sheet oscillation that shares many similarities with the Bond cycle. Further sensitivity experiments reveal that the timescale of the oscillations can be decomposed into stochastic, linear, and nonlinear deterministic components. A schematic bifurcation diagram is used to compare theoretical results with paleoclimatic data

CO2 perturbation experiments: similarities and differences between dissolved inorganic carbon and total alkalinity manipulations

Increasing atmospheric carbon dioxide (CO2) through human activities and invasion of anthropogenic CO2 into the surface ocean alters the seawater carbonate chemistry, increasing CO2 and bicarbonate (HCO3−) at the expense of carbonate ion (CO32−) concentrations. This redistribution in the dissolved inorganic carbon (DIC) pool decreases pH and carbonate saturation state (Ω). Several components of the carbonate system are considered potential key variables influencing for instance calcium carbonate precipitation in marine calcifiers such as coccolithophores, foraminifera, corals, mollusks and echinoderms. Unravelling the sensitivities of marine organisms and ecosystems to CO2 induced ocean acidification (OA) requires well-controlled experimental setups and accurate carbonate system manipulations. Here we describe and analyse the chemical changes involved in the two basic approaches for carbonate chemistry manipulation, i.e. changing DIC at constant total alkalinity (TA) and changing TA at constant DIC. Furthermore, we briefly introduce several methods to experimentally manipulate DIC and TA. Finally, we examine responses obtained with both approaches using published results for the coccolithophore Emiliania huxleyi. We conclude that under most experimental conditions in the context of ocean acidification DIC and TA manipulations yield similar changes in all parameters of the carbonate system, which implies direct comparability of data obtained with the two basic approaches for CO2 perturbation