Avoiding spurious feedback loops in the reconstruction of gene regulatory networks with dynamic bayesian networks

Feedback loops and recurrent structures are essential to the regulation and stable control of complex biological systems. The application of dynamic as opposed to static Bayesian networks is promising in that, in principle, these feedback loops can be learned. However, we show that the widely applied BGe score is susceptible to learning spurious feedback loops, which are a consequence of non-linear regulation and autocorrelation in the data. We propose a non-linear generalisation of the BGe model, based on a mixture model, and demonstrate that this approach successfully represses spurious feedback loops

Elastic interactions of active cells with soft materials

Anchorage-dependent cells collect information on the mechanical properties of the environment through their contractile machineries and use this information to position and orient themselves. Since the probing process is anisotropic, cellular force patterns during active mechanosensing can be modelled as anisotropic force contraction dipoles. Their build-up depends on the mechanical properties of the environment, including elastic rigidity and prestrain. In a finite sized sample, it also depends on sample geometry and boundary conditions through image strain fields. We discuss the interactions of active cells with an elastic environment and compare it to the case of physical force dipoles. Despite marked differences, both cases can be described in the same theoretical framework. We exactly solve the elastic equations for anisotropic force contraction dipoles in different geometries (full space, halfspace and sphere) and with different boundary conditions. These results are then used to predict optimal position and orientation of mechanosensing cells in soft material.Comment: Revtex, 38 pages, 8 Postscript files included; revised version, accepted for publication in Phys. Rev.

Block Toeplitz determinants, constrained KP and Gelfand-Dickey hierarchies

We propose a method for computing any Gelfand-Dickey tau function living in Segal-Wilson Grassmannian as the asymptotics of block Toeplitz determinant associated to a certain class of symbols. Also truncated block Toeplitz determinants associated to the same symbols are shown to be tau function for rational reductions of KP. Connection with Riemann-Hilbert problems is investigated both from the point of view of integrable systems and block Toeplitz operator theory. Examples of applications to algebro-geometric solutions are given.Comment: 35 pages. Typos corrected, some changes in the introductio

Natural disturbances and the physiognomy of pine savannas : A phenomenological model

Abstract. Question: The decline of the Pinus palustris ecosystems has resulted from anthropogenic influences, such as conversion to pine plantation forestry, agriculture and land development, all of which are closely related to increases in human populations. Other effects, however, have arisen from alterations in disturbance regimes that maintain the structure and function of these ecosystems. How have alterations of the disturbance regime altered the physiognomy of ‘old-growth’ stands, and what are the implications for ecosystem conservation and restoration? Methods: In contrast to models that emphasize close interactions among the vertically complex strata, we develop a conceptual phenomenological model for the physiognomic structure of Pinus palustris stands. We relate two natural disturbances (tropical storms and fire) that affect different stages of the life cycle to different aspects of the physiognomic structure. We then compare overstorey stand structure and ground cover composition of two old-growth longleaf stands near the extremes of different composite disturbance regimes: the Wade Tract (frequent hurricanes and fire) and the Boyd Tract (infrequent hurricanes and long-term fire exclusion). Results: We predict that tropical storms and fires have different effects on stand physiognomy. Tropical storms are periodic, and sometimes intense, whereas fires are more frequent and less intense. Hurricanes directly influence the overstorey via wind-caused damage and mortality, and indirectly influence the herb layer by altering the spatial distribution of shading and litter accumulation. Fire exerts direct effects on juvenile stages and indirect effects on the herb layer via fine fuel consumption and selective mortality of potential competitors of P. palustris juveniles. These differences in effects of disturbances can result in widely different physiognomies for P. palustris stands. Finally, some global climate change scenarios have suggested that changes may occur in tropical storm and fire regimes, altering frequency and severity. Such changes may greatly affect pine stands, and ultimately entire pine savanna ecosystems. Conclusions: Our phenomenological model of disturbance regimes in Pinus palustris old-growth produces very different physiognomies for different disturbances regimes that reflect natural process and human management actions. This model can be used to derive restoration strategies for pine savannas that are linked to reinstitution of important ecological processes rather than specific physiognomic states

Kaluza-Klein gravitino production with a single photon at e^+ e^- colliders

In a supersymmetric large extra dimension scenario, the production of Kaluza-Klein gravitinos accompanied by a photino at e^+ e^- colliders is studied. We assume that a bulk supersymmetry is softly broken on our brane such that the low-energy theory resembles the MSSM. Low energy supersymmetry breaking is further assumed as in GMSB, leading to sub-eV mass shift in each KK mode of the gravitino from the corresponding graviton KK mode. Since the photino decays within a detector due to its sufficiently large inclusive decay rate into a photon and a gravitino, the process e^+ e^- -> photino + gravitino yields single photon events with missing energy. Even if the total cross section can be substantial at sqrt(s)=500 GeV, the KK graviton background of e^+ e^- -> photon + graviton is kinematically advantageous and thus much larger. It is shown that the observable, sigma(e^-_L)-sigma(e^-_R), can completely eliminate the KK graviton background but retain most of the KK gravitino signal, which provides a unique and robust method to probe the supersymmetric bulk.Comment: Reference added and typos correcte

Non-Thermal Behavior in Multifragment Decay

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

Statistical Multifragmentation in Central Au+Au Collisions at 35 MeV/u

Multifragment disintegrations, measured for central Au + Au collisions at E/A = 35 MeV, are analyzed with the Statistical Multifragmentation Model. Charge distributions, mean fragment energies, and two-fragment correlation functions are well reproduced by the statistical breakup of a large, diluted and thermalized system slightly above the multifragmentation threshold.Comment: Latex file, 8 pages + 4 postscript figures available upon request from [email protected]

Multifragment production in Au+Au at 35 MeV/u

Multifragment disintegration has been measured with a high efficiency detection system for the reaction $Au + Au$ at $E/A = 35\ MeV$. From the event shape analysis and the comparison with the predictions of a many-body trajectories calculation the data, for central collisions, are compatible with a fast emission from a unique fragment source.Comment: 9 pages, LaTex file, 4 postscript figures available upon request from [email protected]. - to appear in Phys. Lett.

Assessing the Evolutionary Nature of Multifragment Decay

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

The Fueling and Evolution of AGN: Internal and External Triggers

In this chapter, I review the fueling and evolution of active galactic nuclei (AGN) under the influence of internal and external triggers, namely intrinsic properties of host galaxies (morphological or Hubble type, color, presence of bars and other non-axisymmetric features, etc) and external factors such as environment and interactions. The most daunting challenge in fueling AGN is arguably the angular momentum problem as even matter located at a radius of a few hundred pc must lose more than 99.99 % of its specific angular momentum before it is fit for consumption by a BH. I review mass accretion rates, angular momentum requirements, the effectiveness of different fueling mechanisms, and the growth and mass density of black BHs at different epochs. I discuss connections between the nuclear and larger-scale properties of AGN, both locally and at intermediate redshifts, outlining some recent results from the GEMS and GOODS HST surveys.Comment: Invited Review Chapter to appear in LNP Volume on "AGN Physics on All Scales", Chapter 6, in press. 40 pages, 12 figures. Typo in Eq 5 correcte