Interpol: An R package for preprocessing of protein sequences

<p>Abstract</p> <p>Background</p> <p>Most machine learning techniques currently applied in the literature need a fixed dimensionality of input data. However, this requirement is frequently violated by real input data, such as DNA and protein sequences, that often differ in length due to insertions and deletions. It is also notable that performance in classification and regression is often improved by numerical encoding of amino acids, compared to the commonly used sparse encoding.</p> <p>Results</p> <p>The software "Interpol" encodes amino acid sequences as numerical descriptor vectors using a database of currently 532 descriptors (mainly from AAindex), and normalizes sequences to uniform length with one of five linear or non-linear interpolation algorithms. Interpol is distributed with open source as platform independent R-package. It is typically used for preprocessing of amino acid sequences for classification or regression.</p> <p>Conclusions</p> <p>The functionality of Interpol widens the spectrum of machine learning methods that can be applied to biological sequences, and it will in many cases improve their performance in classification and regression.</p

Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation

<p>Abstract</p> <p>Background</p> <p><it>Myxococcus xanthus </it>is a Gram negative bacterium that can differentiate into metabolically quiescent, environmentally resistant spores. Little is known about the mechanisms involved in differentiation in part because sporulation is normally initiated at the culmination of a complex starvation-induced developmental program and only inside multicellular fruiting bodies. To obtain a broad overview of the sporulation process and to identify novel genes necessary for differentiation, we instead performed global transcriptome analysis of an artificial chemically-induced sporulation process in which addition of glycerol to vegetatively growing liquid cultures of <it>M. xanthus </it>leads to rapid and synchronized differentiation of nearly all cells into myxospore-like entities.</p> <p>Results</p> <p>Our analyses identified 1 486 genes whose expression was significantly regulated at least two-fold within four hours of chemical-induced differentiation. Most of the previously identified sporulation marker genes were significantly upregulated. In contrast, most genes that are required to build starvation-induced multicellular fruiting bodies, but which are not required for sporulation <it>per se</it>, were not significantly regulated in our analysis. Analysis of functional gene categories significantly over-represented in the regulated genes, suggested large rearrangements in core metabolic pathways, and in genes involved in protein synthesis and fate. We used the microarray data to identify a novel operon of eight genes that, when mutated, rendered cells unable to produce viable chemical- or starvation-induced spores. Importantly, these mutants displayed no defects in building fruiting bodies, suggesting these genes are necessary for the core sporulation process. Furthermore, during the starvation-induced developmental program, these genes were expressed in fruiting bodies but not in peripheral rods, a subpopulation of developing cells which do not sporulate.</p> <p>Conclusions</p> <p>These results suggest that microarray analysis of chemical-induced spore formation is an excellent system to specifically identify genes necessary for the core sporulation process of a Gram negative model organism for differentiation.</p

Nonlinear eigenvalue problem for optimal resonances in optical cavities

The paper is devoted to optimization of resonances in a 1-D open optical cavity. The cavity's structure is represented by its dielectric permittivity function e(s). It is assumed that e(s) takes values in the range 1 <= e_1 <= e(s) <= e_2. The problem is to design, for a given (real) frequency, a cavity having a resonance with the minimal possible decay rate. Restricting ourselves to resonances of a given frequency, we define cavities and resonant modes with locally extremal decay rate, and then study their properties. We show that such locally extremal cavities are 1-D photonic crystals consisting of alternating layers of two materials with extreme allowed dielectric permittivities e_1 and e_2. To find thicknesses of these layers, a nonlinear eigenvalue problem for locally extremal resonant modes is derived. It occurs that coordinates of interface planes between the layers can be expressed via arg-function of corresponding modes. As a result, the question of minimization of the decay rate is reduced to a four-dimensional problem of finding the zeroes of a function of two variables.Comment: 16 page

Kink far below the Fermi level reveals new electron-magnon scattering channel in Fe

Many properties of real materials can be modeled using ab initio methods within a single-particle picture. However, for an accurate theoretical treatment of excited states, it is necessary to describe electron-electron correlations including interactions with bosons: phonons, plasmons, or magnons. In this work, by comparing spin- and momentum-resolved photoemission spectroscopy measurements to many-body calculations carried out with a newly developed first-principles method, we show that a kink in the electronic band dispersion of a ferromagnetic material can occur at much deeper binding energies than expected (E_b=1.5 eV). We demonstrate that the observed spectral signature reflects the formation of a many-body state that includes a photohole bound to a coherent superposition of renormalized spin-flip excitations. The existence of such a many-body state sheds new light on the physics of the electron-magnon interaction which is essential in fields such as spintronics and Fe-based superconductivity.Comment: 6 pages, 2 figure

Dark Matter Spin-Dependent Limits for WIMP Interactions on 19-F by PICASSO

The PICASSO experiment at SNOLAB reports new results for spin-dependent WIMP interactions on $^{19}$F using the superheated droplet technique. A new generation of detectors and new features which enable background discrimination via the rejection of non-particle induced events are described. First results are presented for a subset of two detectors with target masses of $^{19}$F of 65 g and 69 g respectively and a total exposure of 13.75 $\pm$ 0.48 kgd. No dark matter signal was found and for WIMP masses around 24 GeV/c$^2$ new limits have been obtained on the spin-dependent cross section on $^{19}$F of $\sigma_F$ = 13.9 pb (90% C.L.) which can be converted into cross section limits on protons and neutrons of $\sigma_p$ = 0.16 pb and $\sigma_n$ = 2.60 pb respectively (90% C.L). The obtained limits on protons restrict recent interpretations of the DAMA/LIBRA annual modulations in terms of spin-dependent interactions.Comment: Revised version, accepted for publication in Phys. Lett. B, 20 pages, 7 figure

Status of the PICASSO Project

The Picasso project is a dark matter search experiment based on the superheated droplet technique. Preliminary runs performed at the Picasso Lab in Montreal have showed the suitability of this detection technique to the search for weakly interacting cold dark matter particles. In July 2002, a new phase of the project started. A batch of six 1-liter detectors with an active mass of approximately 40g was installed in a gallery of the SNO observatory in Sudbury, Ontario, Canada at a depth of 6,800 feet (2,070m). We give a status report on the new experimental setup, data analysis, and preliminary limits on spin-dependent neutralino interaction cross section.Comment: 3 pages, 2 figures. To appear in the Proceedings of the TAUP 2003 conference, 5-9 September, 2003, University of Washington, Seattle, US

Averaging level control to reduce off-spec material in a continuous pharmaceutical pilot plant

The judicious use of buffering capacity is important in the development of future continuous pharmaceutical manufacturing processes. The potential benefits are investigated of using optimal-averaging level control for tanks that have buffering capacity for a section of a continuous pharmaceutical pilot plant involving two crystallizers, a combined filtration and washing stage and a buffer tank. A closed-loop dynamic model is utilized to represent the experimental operation, with the relevant model parameters and initial conditions estimated from experimental data that contained a significant disturbance and a change in setpoint of a concentration control loop. The performance of conventional proportional-integral (PI) level controllers is compared with optimal-averaging level controllers. The aim is to reduce the production of off-spec material in a tubular reactor by minimizing the variations in the outlet flow rate of its upstream buffer tank. The results show a distinct difference in behavior, with the optimal-averaging level controllers strongly outperforming the PI controllers. In general, the results stress the importance of dynamic process modeling for the design of future continuous pharmaceutical processes

A novel class of CoA-transferase involved in short-chain fatty acid metabolism in butyrate-producing human colonic bacteria

Peer reviewedPublisher PD