Report on the Glasgow IR group (glair4) submission

This year's submission from the Glasgow IR group (glair4) is to the category B automatic ad hoc section. Due to pressures of time and unexpected complications, our intended application of a technique known as generalised imaging [Crestani 95] was not completed in time for the TREC deadline. Therefore, the submission is the output of an IR system running a simplistic retrieval strategy, similar to last year's submission though with some intended improvements. It would appear from comparison with other category B submissions that this strategy is relatively successful. The following sections of this report contain a description of the retrieval strategy used, a analysis of the results, and finally, a discussion of our intentions for TREC 6

Luminescence dating of wind-blown sands from the Broo Peninsula, Shetland

This report provides a temporal framework to support University of Stirling geo-archaeological investigations near Huesbreck, Broo Pennisula (Shetland), examining how the early modern population there, adapted to harsh climate conditions in the 18-19th centuries, when enhanced aeolian activity led to an influx of sand to the area, leading to adaption’s in farming practices, and abandonment of several sites. Five sediment samples were submitted to the luminescence laboratories at SUERC for dating. All samples were subjected to laboratory preparation of sand-sized quartz, and purity checked using scanning electron microscopy. Dose rates for the bulk sediment were evaluated using analyses of the uranium, thorium and potassium concentrations obtained by high resolution gamma spectrometry coupled with beta dose rate measurement using thick source beta counting, and in situ field gamma spectroscopy. Equivalent doses were determined by OSL from 32 aliquots of quartz per sample using the quartz single-aliquot-regenerative (SAR) procedure. The material exhibited good OSL sensitivity and produced acceptable SAR internal quality control performance. Radial plotting methods revealed good internal homogeneity in the dose distributions obtained for each sample. The chronology established for the sampled sands on the site spans from the mid 16th century (AD 1540 ± 40; SUTL2441) through to the early 19th century (AD 1810 ± 25), with the dates falling within three clusters - the waning stages of the Little Ice Age, the mid 18th century (AD 1730 ± 25 to 1760 ± 25) and the early 19th century (AD 1810 ± 25). In the wider region, periods of sand movement and deposition in the mid 18th century, and early to late 18th century, are documented in sediment statigraphies sectioned at the Old Scatness Broch, Scatness

The troubles with using a logical model of IR on a large collection of documents

This is a paper of two halves. First, a description of a logical model of IR known as imaging will be presented. Unfortunately due to constraints of time and computing resource this model was not implemented in time for this round of TREC. Therefore this paper's second half describes the more conventional IR model and system used to generate the Glasgow IR result set (glair1)

The Difficult Case of Crystallization and Structure Solution for the ParC55 Breakage-Reunion Domain of Topoisomerase IV from Streptococcus pneumoniae

BACKGROUND: Streptococcus pneumoniae is the major cause of community-acquired pneumonia and is also associated with bronchitis, meningitis, otitis and sinusitis. The emergence and increasing prevalence of resistance to penicillin and other antibiotics has led to interest in other anti-pneumonococcal drugs such as quinolones that target the enzymes DNA gyrase and topoisomerase IV. During crystallization and in the avenues to finding a method to determine phases for the structure of the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae, obstacles were faced at each stage of the process. These problems included: majority of the crystals being twinned, either non-diffracting or exhibiting a high mosaic spread. The crystals, which were grown under conditions that favoured diffraction, were difficult to flash-freeze without loosing diffraction. The initial structure solution by molecular replacement failed and the approach proved to be unviable due to the complexity of the problem. In the end the successful structure solution required an in-depth data analysis and a very detailed molecular replacement search. METHODOLOGY/PRINCIPAL FINDINGS: Crystal anti-twinning agents have been tested and two different methods of flash freezing have been compared. The fragility of the crystals did not allow the usual method of transferring the crystals into the heavy atom solution. Consequently, it was necessary to co-crystallize in the presence of the heavy atom compound. The multiple isomorphous replacement approach was unsuccessful because the 7 cysteine mutants which were engineered could not be successfully derivatized. Ultimately, molecular replacement was used to solve the structure by sorting through a large number of solutions in space group P1 using CNS. CONCLUSIONS/SIGNIFICANCE: The main objective of this paper is to describe the obstacles which were faced and overcome in order to acquire data sets on such difficult crystals and determine phases for successful structure solution