Crystallization and preliminary crystallographic analysis of the DNA gyrase B protein from B-stearothermophilus

DNA gyrase B (GyrB) from B. stearothermophilus has been crystallized in the presence of the non-hydrolyzable ATP analogue, 5'-adenylpl-beta-gamma-imidodiphosphate (ADPNP), by the dialysis method. A complete native data set to 3.7 Angstrom has been collected from crystals which belonged to the cubic space group I23 with unit-cell dimension a = 250.6 Angstrom. Self-rotation function analysis indicates the position of a molecular twofold axis. Low-resolution data sets of a thimerosal and a selenomethionine derivative have also been analysed. The heavy-atom positions are consistent with one dimer in the asymmetric unit

Application of selective epitaxy to fabrication of nanometer scale wire and dot structures

The selective growth of nanometer scale GaAs wire and dot structures using metalorganic vapor phase epitaxy is demonstrated. Spectrally resolved cathodoluminescence images as well as spectra from single dots and wires are presented. A blue shifting of the GaAs peak is observed as the size scale of the wires and dots decreases

Detection of mechanical resonance of a single-electron transistor by direct current

We have suspended an Al based single-electron transistor whose island can resonate freely between the source and drain leads forming the clamps. In addition to the regular side gate, a bottom gate with a larger capacitance to the SET island is placed underneath to increase the SET coupling to mechanical motion. The device can be considered as a doubly clamped Al beam that can transduce mechanical vibrations into variations of the SET current. Our simulations based on the orthodox model, with the SET parameters estimated from the experiment, reproduce the observed transport characteristics in detail.Comment: 4 pages, 3 figure

Structural Elements Regulating AAA+ Protein Quality Control Machines

Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines

Parity effect in Al and Nb single electron transistors in a tunable environment

Two different types of Cooper pair transistors, with Al and Nb islands, have been investigated in a tunable electromagnetic environment. The device with an Al island demonstrates gate charge modulation with 2e-periodicity in a wide range of environmental impedances at bath temperatures below 340 mK. Contrary to the results of the Al sample, we were not able to detect 2e-periodicity under any conditions on similar samples with Nb island. We attribute this to the material properties of Nb.Comment: 3 pages, 3 figure

A Simple Linear Ranking Algorithm Using Query Dependent Intercept Variables

The LETOR website contains three information retrieval datasets used as a benchmark for testing machine learning ideas for ranking. Algorithms participating in the challenge are required to assign score values to search results for a collection of queries, and are measured using standard IR ranking measures (NDCG, precision, MAP) that depend only the relative score-induced order of the results. Similarly to many of the ideas proposed in the participating algorithms, we train a linear classifier. In contrast with other participating algorithms, we define an additional free variable (intercept, or benchmark) for each query. This allows expressing the fact that results for different queries are incomparable for the purpose of determining relevance. The cost of this idea is the addition of relatively few nuisance parameters. Our approach is simple, and we used a standard logistic regression library to test it. The results beat the reported participating algorithms. Hence, it seems promising to combine our approach with other more complex ideas.Comment: 5 page

MScMS-II: an innovative IR-based indoor coordinate measuring system for large-scale metrology applications

According to the current great interest concerning large-scale metrology applications in many different fields of manufacturing industry, technologies and techniques for dimensional measurement have recently shown a substantial improvement. Ease-of-use, logistic and economic issues, as well as metrological performance are assuming a more and more important role among system requirements. This paper describes the architecture and the working principles of a novel infrared (IR) optical-based system, designed to perform low-cost and easy indoor coordinate measurements of large-size objects. The system consists of a distributed network-based layout, whose modularity allows fitting differently sized and shaped working volumes by adequately increasing the number of sensing units. Differently from existing spatially distributed metrological instruments, the remote sensor devices are intended to provide embedded data elaboration capabilities, in order to share the overall computational load. The overall system functionalities, including distributed layout configuration, network self-calibration, 3D point localization, and measurement data elaboration, are discussed. A preliminary metrological characterization of system performance, based on experimental testing, is also presente