Reply on the comment on the paper "Superconducting transition in Nb nanowires fabricated using focused ion beam"

In this communication we present our response to the recent comment of A. Engel regarding our paper on FIB- fabricated Nb nanowires (see Vol. 20 (2009) Pag. 465302). After further analysis and additional experimental evidence, we conclude that our interpretation of the experimental results in light of QPS theory is still valid when compared with the alternative proximity-based model as proposed by A. Engel.Comment: 3 pages, 1 figure, accepted by Nanotechnolog

Lack of conservation of bacterial type promoters in plastids of Streptophyta

<p>Abstract</p> <p/> <p>We demonstrate the scarcity of conserved bacterial-type promoters in plastids of Streptophyta and report widely conserved promoters only for genes <it>psaA, psbA, psbB, psbE, rbcL</it>. Among the reasonable explanations are: evolutionary changes of sigma subunit paralogs and phage-type RNA polymerases possibly entailing the loss of corresponding nuclear genes, <it>de novo </it>emergence of the promoters, their loss together with plastome genes; functional substitution of the promoter boxes by transcription activation factor binding sites.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Arcady Mushegian, and by Dr. Alexander Bolshoy and Dr. Yuri Wolf (both nominated by Dr. Purificación López-García).</p

Modeling RNA polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level

<p>Abstract</p> <p>Background</p> <p>Modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. Among such processes is transcription in the presence of competing RNA polymerases. This process involves RNA polymerases collision followed by transcription termination.</p> <p>Results</p> <p>A mathematical and computer simulation model is developed to describe the competition of RNA polymerases during genes transcription on complementary DNA strands. E.g., in the barley <it>Hordeum vulgare </it>the polymerase competition occurs in the locus containing plastome genes <it>psbA</it>, <it>rpl23</it>, <it>rpl2 </it>and four bacterial type promoters. In heat shock experiments on isolated chloroplasts, a twofold decrease of <it>psbA </it>transcripts and even larger increase of <it>rpl23</it>-<it>rpl2 </it>transcripts were observed, which is well reproduced in the model. The model predictions are in good agreement with virtually all relevant experimental data (knockout, heat shock, chromatogram data, etc.). The model allows to hypothesize a mechanism of cell response to knockout and heat shock, as well as a mechanism of gene expression regulation in presence of RNA polymerase competition. The model is implemented for multiprocessor platforms with MPI and supported on Linux and MS Windows. The source code written in C++ is available under the GNU General Public License from the laboratory website. A user-friendly GUI version is also provided at <url>http://lab6.iitp.ru/en/rivals</url>.</p> <p>Conclusions</p> <p>The developed model is in good agreement with virtually all relevant experimental data. The model can be applied to estimate intensities of binding of the holoenzyme and phage type RNA polymerase to their promoters using data on gene transcription levels, as well as to predict characteristics of RNA polymerases and the transcription process that are difficult to measure directly, e.g., the intensity (frequency) of holoenzyme binding to the promoter in correlation to its nucleotide composition and the type of σ-subunit, the amount of transcription initiation aborts, etc. The model can be used to make functional predictions, e.g., heat shock response in isolated chloroplasts and changes of gene transcription levels under knockout of different σ-subunits or RNA polymerases or due to gene expression regulation.</p> <p>Reviewers</p> <p>This article was reviewed by Dr. Anthony Almudevar, Dr. Aniko Szabo, Dr. Yuri Wolf (nominated by Dr. Peter Olofsson) and Prof. Marek Kimmel.</p

Modeling of Crystallographic Texture Formation in Hot-rolled Sheets of Ferritic Steel

It is known that hot rolling of ferritic steel leads to formation of texture inhomogeneous through sheet thickness [1-3]. For analysis of processes, which induce formation of texture inhomogeneity, finite element method simulation of hot rolling was carried out at macro- and mesoscopic levels. Crystallographic texture is a sensitive indicator of plastic deformation process so it is possible to use it to assess the quality of the simulation. Simulated orientation distribution functions are in a good agreement with experimental result in central part of sheet (middle in thickness), but does not substantially correspond with it in outer layer. Reasons of these inconsistencies were analyzed and following were singled out: disconnection of texture with mechanical properties, possible operation of some other mechanism of deformation apart from crystallographic slip

Incentives for independent anti-corruption experts of normative legal acts and their projects

The article is devoted to the problem of incentives for independent anti-corruption experts conducting examination of normative legal acts and their project

Mediation as an alternative dispute resolution: world experience

The present paper is devoted to the application of mediation as an alternative dispute resolution procedure. It defines features of the legal regulation of mediation procedures in different countries and legal systems, such as United States, European Union, China, and Russian Federation. In addition, the main principles of mediation and their implementation in different legal systems are analyzed in this pape

Creation of pure non-crystalline diamond nanostructures via room-temperature ion irradiation and subsequent thermal annealing

Carbon exhibits a remarkable range of structural forms, due to the availability of sp3, sp2 and sp1 chemical bonds. Contrarily to other group IV elements such as silicon and germanium, the formation of an amorphous phase based exclusively on sp3 bonds is extremely challenging due to the strongly favored formation of graphitic-like structures at room 19 temperature and pressure. As such, the formation of a fully sp3-bonded carbon phase requires 20 an extremely careful (and largely unexplored) definition of the pressure and temperature across the phase diagram. Here, we report on the possibility of creating full-sp3 amorphous nanostructures within the bulk crystal of diamond with room-temperature ion-beam irradiation, followed by an annealing process that does not involve the application of any external mechanical pressure. As confirmed by numerical simulations, the (previously unreported) radiation-damage-induced formation of an amorphous sp2-free phase in diamond is determined by the buildup of extremely high internal stresses from the surrounding lattice, which (in the case of nanometer-scale regions) fully prevent the graphitization process. Besides the relevance of understanding the formation of exotic carbon phases, the use of focused/collimated ion beams discloses appealing perspectives for the direct fabrication of such nanostructures in complex three-dimensional geometries