Statistical mechanics of transcription-factor binding site discovery using Hidden Markov Models

Hidden Markov Models (HMMs) are a commonly used tool for inference of transcription factor (TF) binding sites from DNA sequence data. We exploit the mathematical equivalence between HMMs for TF binding and the "inverse" statistical mechanics of hard rods in a one-dimensional disordered potential to investigate learning in HMMs. We derive analytic expressions for the Fisher information, a commonly employed measure of confidence in learned parameters, in the biologically relevant limit where the density of binding sites is low. We then use techniques from statistical mechanics to derive a scaling principle relating the specificity (binding energy) of a TF to the minimum amount of training data necessary to learn it.Comment: 25 pages, 2 figures, 1 table V2 - typos fixed and new references adde

Hospital managers' need for information in decision-making--An interview study in nine European countries.

Assessments of new health technologies in Europe are often made at the hospital level. However, the guidelines for health technology assessment (HTA), e.g. the EUnetHTA Core Model, are produced by national HTA organizations and focus on decision-making at the national level. This paper describes the results of an interview study with European hospital managers about their need for information when deciding about investments in new treatments. The study is part of the AdHopHTA project. Face-to-face, structured interviews were conducted with 53 hospital managers from nine European countries. The hospital managers identified the clinical, economic, safety and organizational aspects of new treatments as being the most relevant for decision-making. With regard to economic aspects, the hospital managers typically had a narrower focus on budget impact and reimbursement. In addition to the information included in traditional HTAs, hospital managers sometimes needed information on the political and strategic aspects of new treatments, in particular the relationship between the treatment and the strategic goals of the hospital. If further studies are able to verify our results, guidelines for hospital-based HTA should be altered to reflect the information needs of hospital managers when deciding about investments in new treatments

A study of pseudoscalar states produced centrally in pp interactions at 450 GeV/c

A study has been made of pseudoscalar mesons produced centrally in pp interactions. The results show that the eta and etaprime appear to have a similar production mechanism which differs from that of the pi0. The production properties of the eta and etaprime are not consistent with what is expected from double Pomeron exchange. In addition the production mechanism for the eta and etaprime is such that the production cross section are greatest when the azimuthal angle between the pT vectors of the two protons is 90 degrees.Comment: 11 pages, Latex, 3 Figure

A study of the centrally produced phiphi system in pp interactions at 450 GeV/c

The reaction pp to pfps(K+K-K+K-) in which the K+K-K+K- system is centrally produced has been studied at 450 GeV/c. Phi phi production has been found to dominate this reaction and is compatible with being produced by double Pomeron exchange. An angular analysis of the phi phi system favours JPC = 2++ and its dPT dependence is similar to that observed for glueball candidates.Comment: 11 pages, Latex, 4 Figure

Modeling the actinides with disordered local moments

A first-principles disordered local moment (DLM) picture within the local-spin-density and coherent potential approximations (LSDA+CPA) of the actinides is presented. The parameter free theory gives an accurate description of bond lengths and bulk modulus. The case of $\delta$-Pu is studied in particular and the calculated density of states is compared to data from photo-electron spectroscopy. The relation between the DLM description, the dynamical mean field approach and spin-polarized magnetically ordered modeling is discussed.Comment: 6 pages, 4 figure

Exploring Large Digital Library Collections Using a Map-Based Visualisation

In this paper we describe a novel approach for exploring large document collections using a map-based visualisation. We use hierarchically structured semantic concepts that are attached to the documents to create a visualisation of the semantic space that resembles a Google Map. The approach is novel in that we exploit the hierarchical structure to enable the approach to scale to large document collections and to create a map where the higher levels of spatial abstraction have semantic meaning. An informal evaluation is carried out to gather subjective feedback from users. Overall results are positive with users finding the visualisation enticing and easy to use

Partial wave analysis of J/\psi \to \gamma \phi \phi

Using $5.8 \times 10^7 J/\psi$ events collected in the BESII detector, the radiative decay $J/\psi \to \gamma \phi \phi \to \gamma K^+ K^- K^0_S K^0_L$ is studied. The $\phi\phi$ invariant mass distribution exhibits a near-threshold enhancement that peaks around 2.24 GeV/$c^{2}$. A partial wave analysis shows that the structure is dominated by a $0^{-+}$ state ($\eta(2225)$) with a mass of $2.24^{+0.03}_{-0.02}{}^{+0.03}_{-0.02}$ GeV/$c^{2}$ and a width of $0.19 \pm 0.03^{+0.06}_{-0.04}$ GeV/$c^{2}$. The product branching fraction is: $Br(J/\psi \to \gamma \eta(2225))\cdot Br(\eta(2225)\to \phi\phi) = (4.4 \pm 0.4 \pm 0.8)\times 10^{-4}$.Comment: 11 pages, 4 figures. corrected proof for journa

Search for the Rare Decays J/Psi --> Ds- e+ nu_e, J/Psi --> D- e+ nu_e, and J/Psi --> D0bar e+ e-

We report on a search for the decays J/Psi --> Ds- e+ nu_e + c.c., J/Psi --> D- e+ nu_e + c.c., and J/Psi --> D0bar e+ e- + c.c. in a sample of 5.8 * 10^7 J/Psi events collected with the BESII detector at the BEPC. No excess of signal above background is observed, and 90% confidence level upper limits on the branching fractions are set: B(J/Psi --> Ds- e+ nu_e + c.c.)<4.8*10^-5, B(J/Psi --> D- e+ nu_e + c.c.) D0bar e+ e- + c.c.)<1.1*10^-5Comment: 10 pages, 4 figure

Measurements of psi(2S) decays to octet baryon-antibaryon pairs

With a sample of 14 million psi(2S) events collected by the BESII detector at the Beijing Electron Positron Collider (BEPC), the decay channels psi(2S)->p p-bar, Lambda Lambda-bar, Sigma0 Sigma0-bar, Xi Xi-bar are measured, and their branching ratios are determined to be (3.36+-0.09+-0.24)*10E-4, (3.39+-0.20+-0.32)*10E-4, (2.35+-0.36+-0.32)*10E-4, (3.03+-0.40+-0.32)*10E-4, respectively. In the decay psi(2S)->p p-bar, the angular distribution parameter alpha is determined to be 0.82+-0.17+-0.04.Comment: 8 pages, 8 figure

Study of J/psi decays to Lambda Lambdabar and Sigma0 Sigma0bar

The branching ratios and Angular distributions for J/psi decays to Lambda Lambdabar and Sigma0 Sigma0bar are measured using BESII 58 million J/psi.Comment: 11 pages, 5 figure