Algorithmic Discovery of Methylation “Hot Spots” in DNA from Lymphoma Patients

The computational aspects of the problem in this paper involve, firstly, selective mapping of methylated DNA clones according to methylation level and, secondly, extracting motif information from all the mapped elements in the absence of prior probability distribution. Our novel implementation of algorithms to map and maximize expectation in this setting has generated data that appear to be distinct for each lymphoma subtype examined. A “clone” represents a polymerase chain reaction (PCR) product (on average ~500 bp) which belongs to a microarray of 8544 such sequences preserving CpG-rich islands (CGIs) [1]. Accumulating evidence indicates that cancers including lymphomas demonstrate hypermethylation of CGIs “silencing” an increasing number of tumor suppressor (TS) genes which can lead to tumorigenesis

P-model v1.0: an optimality-based light use efficiency model for simulating ecosystem gross primary production

Terrestrial photosynthesis is the basis for vegetation growth and drives the land carbon cycle. Accurately simulating gross primary production (GPP, ecosystem-level apparent photosynthesis) is key for satellite monitoring and Earth System Model predictions under climate change. While robust models exist for describing leaf-level photosynthesis, predictions diverge due to uncertain photosynthetic traits and parameters which vary on multiple spatial and temporal scales. Here, we describe and evaluate a gross primary production (GPP, photosynthesis per unit ground area) model, the P-model, that combines the Farquhar-von Caemmerer-Berry model for C3 photosynthesis with an optimality principle for the carbon assimilation- transpiration trade-off, and predicts a multi-day average light use efficiency (LUE) for any climate and C3 vegetation type. The model is forced here with satellite data for the fraction of absorbed photosynthetically active radiation and site-specific meteorological data and is evaluated against GPP estimates from a globally distributed network of ecosystem flux measurements. Although the P-model requires relatively few inputs and prescribed parameters, the R2 for predicted versus observed GPP based on the full model setup is 0.75 (8-day mean, 131 sites) – better than some state-of-the-art satellite data-driven light use efficiency models. The R2 is reduced to 0.69 when not accounting for the reduction in quantum yield at low temperatures and effects of low soil moisture on LUE. The R2 for the P-model-predicted LUE is 0.37 (means by site) and 0.53 (means by vegetation type). The P-model provides a simple but powerful method for predicting – rather than prescribing light use efficiency and simulating terrestrial photosythesis across a wide range of conditions. The model is available as an R package (rpmodel)

Evidence-Based Professional Development of Science Teachers in Two Countries

The focus of this collaborative research project of King?s College London, and the Weizmann Institute, Israel. project is on investigating the ways in which teachers can demonstrate accomplished teaching in a specific domain of science and on the teacher learning that is generated through continuing professional development programs (CPD) that lead towards such practice. The interest lies in what processes and inputs are required to help secondary school science teachers develop expertise in a specific aspect of science teaching. `It focuses on the design of the CPD programmes and examines the importance of an evidence-based approach through portfolioconstruction in which professional dialogue pathes the way for teacher learning. The set of papers highlight the need to set professional challenge while tailoring CPD to teachers? needs to create the environment in which teachers can advance and transform their practice. The cross-culture perspective added to the richness of the development and enabled the researchers to examine which aspects were fundamental to the design by considering similarities and differences between the domains

Cosmic magnetic fields from velocity perturbations in the early Universe

We show, using a covariant and gauge-invariant charged multifluid perturbation scheme, that velocity perturbations of the matter-dominated dust Friedmann-Lemaitre-Robertson-Walker (FLRW) model can lead to the generation of cosmic magnetic fields. Moreover, using cosmic microwave background (CMB) constraints, it is argued that these fields can reach strengths of between 10^{-28} and 10^{-29} G at the time the dynamo mechanism sets in, making them plausible seed field candidates.Comment: 11 pages, 1 figure, IOP style, minor changes and typos correcte

Excitation-assisted inelastic processes in trapped Bose-Einstein condensates

We find that inelastic collisional processes in Bose-Einstein condensates induce local variations of the mean-field interparticle interaction and are accompanied by the creation/annihilation of elementary excitation. The physical picture is demonstrated for the case of three body recombination in a trapped condensate. For a high trap barrier the production of high energy trapped single particle excitations results in a strong increase of the loss rate of atoms from the condensate.Comment: 4 pages, no figure

Initial conditions, Discreteness and non-linear structure formation in cosmology

In this lecture we address three different but related aspects of the initial continuous fluctuation field in standard cosmological models. Firstly we discuss the properties of the so-called Harrison-Zeldovich like spectra. This power spectrum is a fundamental feature of all current standard cosmological models. In a simple classification of all stationary stochastic processes into three categories, we highlight with the name ``super-homogeneous'' the properties of the class to which models like this, with $P(0)=0$, belong. In statistical physics language they are well described as glass-like. Secondly, the initial continuous density field with such small amplitude correlated Gaussian fluctuations must be discretised in order to set up the initial particle distribution used in gravitational N-body simulations. We discuss the main issues related to the effects of discretisation, particularly concerning the effect of particle induced fluctuations on the statistical properties of the initial conditions and on the dynamical evolution of gravitational clustering.Comment: 28 pages, 1 figure, to appear in Proceedings of 9th Course on Astrofundamental Physics, International School D. Chalonge, Kluwer, eds N.G. Sanchez and Y.M. Pariiski, uses crckapb.st pages, 3 figure, ro appear in Proceedings of 9th Course on Astrofundamental Physics, International School D. Chalonge, Kluwer, Eds. N.G. Sanchez and Y.M. Pariiski, uses crckapb.st

Neutrino Masses with "Zero Sum" Condition: mν1+mν2+mν3=0m_{\nu_1} + m_{\nu_2} + m_{\nu_3} = 0

It is well known that the neutrino mass matrix contains more parameters than experimentalists can hope to measure in the foreseeable future even if we impose CP invariance. Thus, various authors have proposed ansatzes to restrict the form of the neutrino mass matrix further. Here we propose that $m_{\nu_1} + m_{\nu_2} + m_{\nu_3} = 0$; this ``zero sum'' condition can occur in certain class of models, such as models whose neutrino mass matrix can be expressed as commutator of two matrices. With this condition, the absolute neutrino mass can be obtained in terms of the mass-squared differences. When combined with the accumulated experimental data this condition predicts two types of mass hierarchies, with one of them characterized by $m_{\nu_3} \approx -2m_{\nu_1} \approx -2 m_{\nu_2} \approx 0.063$ eV, and the other by $m_{\nu_1} \approx -m_{\nu_2} \approx 0.054$ eV and $m_{\nu_3} \approx 0.0064$ eV. The mass ranges predicted is just below the cosmological upper bound of 0.23 eV from recent WMAP data and can be probed in the near future. We also point out some implications for direct laboratory measurement of neutrino masses, and the neutrino mass matrix.Comment: Latex 12 pages. No figures. New references adde

Intermittent release of transients in the slow solar wind: 2. In situ evidence

In paper 1, we showed that the Heliospheric Imager (HI) instruments on the pair of NASA STEREO spacecraft can be used to image the streamer belt and, in particular, the variability of the slow solar wind which originates near helmet streamers. The observation of intense intermittent transient outflow by HI implies that the corresponding in situ observations of the slow solar wind and corotating interaction regions (CIRs) should contain many signatures of transients. In the present paper, we compare the HI observations with in situ measurements from the STEREO and ACE spacecraft. Analysis of the solar wind ion, magnetic field, and suprathermal electron flux measurements from the STEREO spacecraft reveals the presence of both closed and partially disconnected interplanetary magnetic field lines permeating the slow solar wind. We predict that one of the transients embedded within the second CIR (CIR‐D in paper 1) should impact the near‐Earth ACE spacecraft. ACE measurements confirm the presence of a transient at the time of CIR passage; the transient signature includes helical magnetic fields and bidirectional suprathermal electrons. On the same day, a strahl electron dropout is observed at STEREO‐B, correlated with the passage of a high plasma beta structure. Unlike ACE, STEREO‐B observes the transient a few hours ahead of the CIR. STEREO‐A, STEREO‐B, and ACE spacecraft observe very different slow solar wind properties ahead of and during the CIR analyzed in this paper, which we associate with the intermittent release of transients

The Apparent Fractal Conjecture: Scaling Features in Standard Cosmologies

This paper presents an analysis of the smoothness problem in cosmology by focussing on the ambiguities originated in the simplifying hypotheses aimed at observationally verifying if the large-scale distribution of galaxies is homogeneous, and conjecturing that this distribution should follow a fractal pattern in perturbed standard cosmologies. This is due to a geometrical effect, appearing when certain types of average densities are calculated along the past light cone. The paper starts reviewing the argument concerning the possibility that the galaxy distribution follows such a scaling pattern, and the premises behind the assumption that the spatial homogeneity of standard cosmology can be observable. Next, it is argued that to discuss observable homogeneity one needs to make a clear distinction between local and average relativistic densities, and showing how the different distance definitions strongly affect them, leading the various average densities to display asymptotically opposite behaviours. Then the paper revisits Ribeiro's (1995: astro-ph/9910145) results, showing that in a fully relativistic treatment some observational average densities of the flat Friedmann model are not well defined at z ~ 0.1, implying that at this range average densities behave in a fundamentally different manner as compared to the linearity of the Hubble law, well valid for z < 1. This conclusion brings into question the widespread assumption that relativistic corrections can always be neglected at low z. It is also shown how some key features of fractal cosmologies can be found in the Friedmann models. In view of those findings, it is suggested that the so-called contradiction between the cosmological principle, and the galaxy distribution forming an unlimited fractal structure, may not exist.Comment: 30 pages, 2 figures, LaTeX. This paper is a follow-up to gr-qc/9909093. Accepted for publication in "General Relativity and Gravitation

Magnetized cosmological perturbations

A large-scale cosmic magnetic field affects not only the growth of density perturbations, but also rotational instabilities and anisotropic deformation in the density distribution. We give a fully relativistic treatment of all these effects, incorporating the magneto-curvature coupling that arises in a relativistic approach. We show that this coupling produces a small enhancement of the growing mode on superhorizon scales. The magnetic field generates new nonadiabatic constant and decaying modes, as well as nonadiabatic corrections to the standard growing and decaying modes. Magnetized isocurvature perturbations are purely decaying on superhorizon scales. On subhorizon scales before recombination, magnetized density perturbations propagate as magneto-sonic waves, leading to a small decrease in the spacing of acoustic peaks. Fluctuations in the field direction induce scale-dependent vorticity, and generate precession in the rotational vector. On small scales, magnetized density vortices propagate as Alfv\'{e}n waves during the radiation era. After recombination, they decay slower than non-magnetized vortices. Magnetic fluctuations are also an active source of anisotropic distortion in the density distribution. We derive the evolution equations for this distortion, and find a particular growing solution.Comment: Revised version, typos corrected, to appear in Phys. Rev.