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.

Uma nova abordagem branch and cut aplicada ao problema de planejamento da expansão de redes de transmissão de grande porte

Neste artigo propomos um algoritmo branch and cut com novas inequações específicas ao problema de planejamento da expansão de redes de transmissão de energia elétrica. Todas as inequações propostas neste trabalho são válidas tanto para os modelos lineares como para os modelos não lineares do problema. Os testes computacionais têm mostrado a eficiência do método proposto neste trabalho quando aplicado a subsistemas reais brasileiros e ao sistema colombiano.

Optimised polyolefin branch quantification by 13 C NMR spectroscopy

Quantitative branch determination in polyolefins by solid- and melt-state 13C NMR has been investigated. Both methods were optimised toward sensitivity per unit time. While solid-state NMR was shown to give quick albeit only qualitative results, melt-state NMR allowed highly time efficient accurate branch quantification. Comparison of spectra obtained using spectrometers operating at 300, 500 and 700 MHz 1H Larmor frequency, with 4 and 7~mm MAS probeheads, showed that the best sensitivity was achieved at 500 MHz using a 7 mm 13C-1H optimised high temperature probehead. For materials available in large quantities, static melt-state NMR, using large diameter detection coils and high coil filling at 300 MHz, was shown to produce comparable results to melt-state MAS measurements in less time. While the use of J-coupling mediated polarisation transfer techniques was shown to be possible, direct polarisation via single-pulse excitation proved to be more suitable for branch quantification in the melt-state. Artificial line broadening, introduced by FID truncation, was able to be reduced by the use of π pulse-train heteronuclear dipolar decoupling. This decoupling method, when combined with an extended duty-cycle, allowed for significant improvement in resolution. Standard setup, processing and analysis techniques were developed to minimise systematic errors contributing to the measured branch contents. The final optimised melt-state MAS NMR method was shown to allow time efficient quantification of comonomer content and distribution in both polyethylene- and polypropylene-co-α-olefins. The sensitivity of the technique was demonstrated by quantifying branch concentrations of 8 branches per 100,000 CH2 for an industrial ‘linear’ polyethylene in only 13 hours. Even lower degrees of 3–8 long-chain branches per 100,000 carbons were able to be estimated in just 24 hours for a series of γ-irradiated polypropylene homopolymers.

Cut-first branch-and-price-second for the capacitated arc-routing problem

This paper presents the first full-fledged branch-and-price (bap) algorithm for the capacitated arc-routing problem (CARP). Prior exact solution techniques either rely on cutting planes or the transformation of the CARP into a node-routing problem. The drawbacks are either models with inherent symmetry, dense underlying networks, or a formulation where edge flows in a potential solution do not allow the reconstruction of unique CARP tours. The proposed algorithm circumvents all these drawbacks by taking the beneficial ingredients from existing CARP methods and combining them in a new way. The first step is the solution of the one-index formulation of the CARP in order to produce strong cuts and an excellent lower bound. It is known that this bound is typically stronger than relaxations of a pure set-partitioning CARP model.rnSuch a set-partitioning master program results from a Dantzig-Wolfe decomposition. In the second phase, the master program is initialized with the strong cuts, CARP tours are iteratively generated by a pricing procedure, and branching is required to produce integer solutions. This is a cut-first bap-second algorithm and its main function is, in fact, the splitting of edge flows into unique CARP tours.

Laser-guided lumbar medial branch kryorhizotomy

The authors describe a modification of the medial branch kryorhizotomy technique for the treatment of lumbar facet joint syndrome using a fluoroscopy-based laser-guided method. A total of 32 patients suffering from lumbar facet joint syndrome confirmed by positive medial nerve block underwent conventional or laser-guided kryorhizotomy. The procedural time (20.6 +/- 1.0 vs 16.3 +/- 0.9 minutes, p < 0.01), fluoroscopy time (54.1 +/- 3.5 vs 28.2 +/- 2.4 seconds, p < 0.01), radiation dose (407.5 +/- 32.0 vs 224.1 +/- 20.3 cGy/cm(2), p < 0.01), and patient discomfort during the procedure (7.1 +/- 0.4 vs 5.2 +/- 0.4 on the visual analog scale, p < 0.01) were significantly reduced in the laser-guided group. There was a tendency for a better positioning accuracy when the laser guidance method was used (3.0 +/- 0.3 vs 2.2 +/- 0.3 mm of deviation from the target points, p > 0.05). No difference in the outcome was observed between the 2 groups of patients (visual analog scale score 3.5 +/- 0.2 vs 3.3 +/- 0.3, p > 0.05). This improved minimally invasive surgical technique offers advantages to conventional fluoroscopy-based kryorhizotomy.

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.

The Ink Shop Olive Branch Press, Ithaca, New York, Solo Exhibition

Solo Exhibition of prints and drawings at The Ink Shop Olive Branch Press in Ithaca, New York November 2012-January 2013

Delayed coverage in malapposed and side-branch struts with respect to well-apposed struts in drug-eluting stents: in vivo assessment with optical coherence tomography

Background—Pathology studies on fatal cases of very late stent thrombosis have described incomplete neointimal coverage as common substrate, in some cases appearing at side-branch struts. Intravascular ultrasound studies have described the association between incomplete stent apposition (ISA) and stent thrombosis, but the mechanism explaining this association remains unclear. Whether the neointimal coverage of nonapposed side-branch and ISA struts is delayed with respect to well-apposed struts is unknown. Methods and Results—Optical coherence tomography studies from 178 stents implanted in 99 patients from 2 randomized trials were analyzed at 9 to 13 months of follow-up. The sample included 38 sirolimus-eluting, 33 biolimus-eluting, 57 everolimus-eluting, and 50 zotarolimus-eluting stents. Optical coherence tomography coverage of nonapposed side-branch and ISA struts was compared with well-apposed struts of the same stent by statistical pooled analysis with a random-effects model. A total of 34 120 struts were analyzed. The risk ratio of delayed coverage was 9.00 (95% confidence interval, 6.58 to 12.32) for nonapposed side-branch versus well-apposed struts, 9.10 (95% confidence interval, 7.34 to 11.28) for ISA versus well-apposed struts, and 1.73 (95% confidence interval, 1.34 to 2.23) for ISA versus nonapposed side-branch struts. Heterogeneity of the effect was observed in the comparison of ISA versus well-apposed struts (H=1.27; I2=38.40) but not in the other comparisons. Conclusions—Coverage of ISA and nonapposed side-branch struts is delayed with respect to well-apposed struts in drug-eluting stents, as assessed by optical coherence tomography.

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.

Differences in neointimal thickness between the adluminal and the abluminal sides of malapposed and side-branch struts in a polylactide bioresorbable scaffold: evidence in vivo about the abluminal healing process

The goal of this study was to describe the neointimal healing on the abluminal side (ABL) of malapposed (ISA) struts and nonapposed side-branch (NASB) struts in terms of coverage by optical coherence tomography (OCT) and in comparison with the adluminal side (ADL).