Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set

System f2lp – computing answer sets of first-order formulas

Abstract. We present an implementation of the general language of stable models proposed by Ferraris, Lee and Lifschitz. Under certain conditions, system f2lp turns a first-order theory under the stable model semantics into an answer set program, so that existing answer set solvers can be used for computing the general language. Quantifiers are first eliminated and then the resulting quantifier-free formulas are turned into rules. Based on the relationship between stable models and circumscription, f2lp can also serve as a reasoning engine for general circumscriptive theories. We illustrate how to use f2lp to compute the circumscriptive event calculus.

Impact of wild-type and genetically modified Pseudomonas fluorescens on soil enzyme activities and microbial population structure in the rhizosphere of pea

The definitive version is available at www.blackwell-synergy.com. Copyright Blackwell Publishing DOI : 10.1046/j.1365-294x.1998.00367.xThe aim of this work was to determine the impact of wild type along with functionally and non-functionally modified Pseudomonas fluorescens strains in the rhizosphere. The wild type F113 strain carried a gene encoding the production of the antibiotic 2,4 diacetylphloroglucinol (DAPG) useful in plant disease control, and was marked with a lacZY gene cassette. The first modified strain was a functional modification of strain F113 with repressed production of DAPG, creating the DAPG negative strain F113 G22. The second paired comparison was a non-functional modification of wild type (unmarked) strain SBW25, constructed to carry marker genes only, creating strain SBW25 EeZY-6KX. Significant perturbations were found in the indigenous bacterial population structure, with the F113, (DAPG+) strain causing a shift towards slower growing colonies (K strategists) compared with the non-antibiotic producing derivative (F113 G22) and the SBW25 strains. The DAPG+ strain also significantly reduced, in comparison with the other inocula, the total Pseudomonas populations but did not affect the total microbial populations. The survival of F113 and F113 G22 were an order of magnitude lower than the SBW 25 strains. The DAPG+ strain caused a significant decrease in the shoot to root ratio in comparison to the control and other inoculants, indicating plant stress. F113 increased soil alkaline phosphatase, phosphodiesterase and aryl sulphatase activities compared to the other inocula, which themselves reduced the same enzyme activities compared to the control. In contrast to this, the -glucosidase, -galactosidase and N-acetyl glucosaminidase activities decreased with the inoculation of the DAPG+ strain. These results indicate that soil enzymes are sensitive to the impact of GMM inoculation.Peer reviewe

SU(3) breaking in hyperon transition vector form factors

We present a calculation of the SU(3)-breaking corrections to the hyperon transition vector form factors to $\mathcal{O}(p^4)$ in heavy baryon chiral perturbation theory with finite-range regularisation. Both octet and decuplet degrees of freedom are included. We formulate a chiral expansion at the kinematic point $Q^2=-(M_{B_1}-M_{B_2})^2$, which can be conveniently accessed in lattice QCD. The two unknown low-energy constants at this point are constrained by lattice QCD simulation results for the $\Sigma^-\rightarrow n$ and $\Xi^0\rightarrow \Sigma^+$ transition form factors. Hence we determine lattice-informed values of $f_1$ at the physical point. This work constitutes progress towards the precise determination of $|V_{us}|$ from hyperon semileptonic decays

The Deformation of an Elastic Substrate by a Three-Phase Contact Line

Young's classic analysis of the equilibrium of a three-phase contact line ignores the out-of-plane component of the liquid-vapor surface tension. While it has long been appreciated that this unresolved force must be balanced by elastic deformation of the solid substrate, a definitive analysis has remained elusive because conventional idealizations of the substrate imply a divergence of stress at the contact line. While a number of theories of have been presented to cut off the divergence, none of them have provided reasonable agreement with experimental data. We measure surface and bulk deformation of a thin elastic film near a three-phase contact line using fluorescence confocal microscopy. The out-of-plane deformation is well fit by a linear elastic theory incorporating an out-of-plane restoring force due to the surface tension of the gel. This theory predicts that the deformation profile near the contact line is scale-free and independent of the substrate elastic modulus.Comment: 4 pages, 3 figure

A systematic review of modelling approaches in economic evaluations of health interventions for drug and alcohol problems

© 2016 Hoang et al. Background: The overarching goal of health policies is to maximize health and societal benefits. Economic evaluations can play a vital role in assessing whether or not such benefits occur. This paper reviews the application of modelling techniques in economic evaluations of drug and alcohol interventions with regard to (i) modelling paradigms themselves; (ii) perspectives of costs and benefits and (iii) time frame. Methods: Papers that use modelling approaches for economic evaluations of drug and alcohol interventions were identified by carrying out searches of major databases. Results: Thirty eight papers met the inclusion criteria. Overall, the cohort Markov models remain the most popular approach, followed by decision trees, Individual based model and System dynamics model (SD). Most of the papers adopted a long term time frame to reflect the long term costs and benefits of health interventions. However, it was fairly common among the reviewed papers to adopt a narrow perspective that only takes into account costs and benefits borne by the health care sector. Conclusions: This review paper informs policy makers about the availability of modelling techniques that can be used to enhance the quality of economic evaluations for drug and alcohol treatment interventions

Cohomology of Line Bundles: Applications

Massless modes of both heterotic and Type II string compactifications on compact manifolds are determined by vector bundle valued cohomology classes. Various applications of our recent algorithm for the computation of line bundle valued cohomology classes over toric varieties are presented. For the heterotic string, the prime examples are so-called monad constructions on Calabi-Yau manifolds. In the context of Type II orientifolds, one often needs to compute equivariant cohomology for line bundles, necessitating us to generalize our algorithm to this case. Moreover, we exemplify that the different terms in Batyrev's formula and its generalizations can be given a one-to-one cohomological interpretation. This paper is considered the third in the row of arXiv:1003.5217 and arXiv:1006.2392.Comment: 56 pages, 8 tables, cohomCalg incl. Koszul extension available at http://wwwth.mppmu.mpg.de/members/blumenha/cohomcalg