Corrole isomers: intrinsic gas-phase shapes via traveling wave ion mobility mass spectrometry and dissociation chemistries via tandem mass spectrometry

Corrole and four of its isomers with subtle structural changes promoted by exchange of nitrogen and carbon atoms in the corrole ring have been studied by traveling wave ion mobility mass spectrometry and collision induced dissociation experiments. Significant differences in shapes and charge distributions for their protonated molecules were found to lead to contrasting gas phase mobilities, most particularly for corrorin, the most "confused" isomer. Accordingly, corrorin was predicted by B3LYP/6-31g(d,p) and collisional cross section calculations to display the most compact tri-dimensional structure, whereas NCC4 and corrole were found to be the most planar isomers. Better resolution between the corrole isomers was achieved using the more polarizable and massive CO2 as the drift gas. Sequential losses of HF molecules were found to dominate the dissociation chemistry of the protonated molecules of these corrole isomers, but their unique structures caused contrasting labilities towards CID, whereas NCC4 showed a peculiar and structurally diagnostic loss of NH3, allowing its prompt differentiation from the other isomers.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Abstract Background From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas.

The APSEL4D Monolithic Active Pixel Sensor and its Usage in a Single Electron Interference Experiment

We have realized a Data Acquisition chain for the use and characterization of APSEL4D, a 32 x 128 Monolithic Active Pixel Sensor, developed as a prototype for frontier experiments in high energy particle physics. In particular a transition board was realized for the conversion between the chip and the FPGA voltage levels and for the signal quality enhancing. A Xilinx Spartan-3 FPGA was used for real time data processing, for the chip control and the communication with a Personal Computer through a 2.0 USB port. For this purpose a firmware code, developed in VHDL language, was written. Finally a Graphical User Interface for the online system monitoring, hit display and chip control, based on windows and widgets, was realized developing a C++ code and using Qt and Qwt dedicated libraries. APSEL4D and the full acquisition chain were characterized for the first time with the electron beam of the transmission electron microscope and with 55Fe and 90Sr radioactive sources. In addition, a beam test was performed at the T9 station of the CERN PS, where hadrons of momentum of 12 GeV/c are available. The very high time resolution of APSEL4D (up to 2.5 Mfps, but used at 6 kfps) was fundamental in realizing a single electron Young experiment using nanometric double slits obtained by a FIB technique. On high statistical samples, it was possible to observe the interference and diffractions of single isolated electrons traveling inside a transmission electron microscope. For the first time, the information on the distribution of the arrival time of the single electrons has been extracted.

L'algoritmo bionomico per il Traveling Salesman Problem

In questa tesi viene presentato un nuovo metaeuristico per la risoluzione del Traveling Salesman Problem (TSP) simmetrico. Tale metodo, detto algoritmo bionomico, è una variante dell'algoritmo genetico che usa un metodo innovativo di generazione del parents set. Nella tesi vengono proposti diversi metodi di crossover specifici per il TSP ma che possono essere facilmente estesi per altri problemi di ottimizzazione combinatoria. Tali metodi sono stati sperimentati su un insieme di problemi test, i risultati computazionali mostrano l'efficienza dei metodi proposti. In particolare uno dei metodi domina gli altri sia per la miglior qualità delle soluzioni prodotte che per il minor tempo di calcolo impiegato.

Tags in the Catalogue: Insights From a Usability Study of LibraryThing for Libraries

Library of Congress Subject Headings (LCSH), the standard subject language used in library catalogues, are often criticized for their lack of currency, biased language, and atypical syndetic structure. Conversely, folksonomies (or tags), which rely on the natural language of their users, offer a flexibility often lacking in controlled vocabularies and may offer a means of augmenting more rigid controlled vocabularies such as LCSH. Content analysis studies have demonstrated the potential for folksonomies to be used as a means of enhancing subject access to materials, and libraries are beginning to integrate tagging systems into their catalogues. This study examines the utility of tags as a means of enhancing subject access to materials in library online public access catalogues (OPACs) through usability testing with the LibraryThing for Libraries catalogue enhancements. Findings indicate that while they cannot replace LCSH, tags do show promise for aiding information seeking in OPACs. In the context of information systems design, the study revealed that while folksonomies have the potential to enhance subject access to materials, that potential is severely limited by the current inability of catalogue interfaces to support tag-based searches alongside standard catalogue searches.

Quality evaluation of tandem mass spectral libraries

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

Pulse-front tilt for short-wavelength lasing by means of traveling-wave plasma-excitation

Generation of coherent short-wavelength radiation across a plasma column is dramatically improved under traveling-wave excitation (TWE). The latter is optimized when its propagation is close to the speed of light, which implies small-angle target-irradiation. Yet, short-wavelength lasing needs large irradiation angles in order to increase the optical penetration of the pump into the plasma core. Pulse-front back-tilt is considered to overcome such trade-off. In fact, the TWE speed depends on the pulse-front slope (envelope of amplitude), whereas the optical penetration depth depends on the wave-front slope (envelope of phase). Pulse-front tilt by means of compressor misalignment was found effective only if coupled with a high-magnification front-end imaging/focusing component. It is concluded that speed matching should be accomplished with minimal compressor misalignment and maximal imaging magnification.