Site testing

Geophysical imaging methods provide solutions to a wide range of environmental and engineering problems: protection of soil and groundwater from contamination; safe disposal of chemical and nuclear waste; geotechnical site testing for underground vaults, subways, dams, ...

Discovering single nucleotide polymorphisms (SNPs) in specific genes in a heterozygous polyploid plant species, such as sugarcane, is challenging because of the presence of a large number of homologues. To discover SNPs for mapping genes of interest, 454 sequencing of 307 polymerase chain reaction (PCR) amplicons (> 59 kb of sequence) was undertaken. One region of a four-gasket sequencing run, on a 454 Genome Sequencer FLX, was used for pooled PCR products amplified from each parent of a quantitative trait locus (QTL) mapping population (IJ76-514 × Q165). The sequencing yielded 96 755 (IJ76-514) and 86 241 (Q165) sequences with perfect matches to a PCR primer used in amplification, with an average sequence depth of approximately 300 and an average read length of 220 bases. Further analysis was carried out on amplicons whose sequences clustered into a single contig using an identity of 80% with the program cap3. In the more polymorphic sugarcane parent (Q165), 94% of amplicons (227/242) had evidence of a reliable SNP – an average of one every 35 bases. Significantly fewer SNPs were found in the pure Saccharum officinarum parent – with one SNP every 58 bases and SNPs in 86% (213/247) of amplicons. Using automatic SNP detection, 1632 SNPs were detected in Q165 sequences and 1013 in IJ76-514. From 225 candidate SNP sites tested, 209 (93%) were validated as polymorphic using the Sequenom MassARRAY system. Amplicon re-sequencing using the 454 system enables cost-effective SNP discovery that can be targeted to genes of interest and is able to perform in the highly challenging area of polyploid genomes.

We examine the historical development of astrophysical science in Antarctica from the early 20th century until today. We find three temporally overlapping eras with each having a rather distinct beginning. These are the astrogeological era of meteorite discovery the high energy era of particle detectors and the photon astronomy era of microwave sub-mm and infrared telescopes sidelined by a few optical niche experiments. The favourable atmospheric and geophysical conditions are briefly examined followed by an account of the major experiments and a summary of their results. A scientific effectiveness analysis of the various projects is presented quantitatively and we conclude with an outlook of what is to come in the 21st century

Background: Saliva is an alternative biologic matrix for drugs-of-abuse testing that offers the advantages of noninvasive, rapid, and easy sampling. We studied the excretion profile of 3,4-methylenedioxymethamphet- amine (MDMA) and its metabolites in both saliva and plasma, as well the effect of the drug on salivary pH. Methods: Saliva and plasma samples were obtained from eight healthy MDMA consumers after

Rapid advances in biosensors have recently been reported. This has been possible due to rapid growth in the development of new biomaterials such as conducting polymers, copolymers and sol gels etc and the reported improvements in sensing techniques. Biosensors are miniaturized devices employing biochemical molecular recognition as the basis for a selective analysis. The response generated as a result of biochemical reaction is detected by a transducer to give a signal (optical/electrical/thermal) that can be used with or without amplification for the estimation of the concentration of an analyte in a given test sample. Among the various biosensors, electrochemical sensors, especially amperometric biosensors presently hold a leading position.Due to specificity, portability, simplicity, high sensitivity, potential ability for real-time and on-site analysis coupled with the speed and low cost, biosensors have been projected to have applications in food analysis, environment control, clinical detection, drug and agriculture industries etc. Besides this, biosensors offer exciting opportunities for numerous decentralized clinical applications, ranging from emergency room screening, home self testing and alternative site testing, continuous and real-time in vivo monitoring. New generation of biosensors combining new bioreceptors with the ever-growing number of transducers is emerging. The present paper highlights some of the recent advances in the area of biosensors contributed by our laboratory.

The effects of management intensification on the size, activity and structure of soil microbial communities in botanically diverse haymeadows were examined. Paired traditionally managed and intensively managed haymeadows, at three submontane regions in northern England and north Wales, were sampled over four seasons. Management intensification had no significant effect on soil nutrient status, soil microbial biomass and soil microbial activity.

Drugged drivers pose a serious threat to other people in traffic as well as to themselves. Reliable oral fluid screening devices for on-site screening of drugged drivers would be both a useful and convenient means for traffic control. In this study we evaluated the appropriateness of Drugwipe 5 and Drugwipe Benzodiazepines oral fluid on-site tests for roadside drug screening. Drivers suspected of driving under the influence of drugs were screened with the Drugwipe tests. Oral fluid and whole blood samples were collected from the drivers and tested for amphetamine-type stimulant drugs, cannabis, opiates, cocaine and benzodiazepines by immunological methods, GC and GC–MS. The performance evaluations of the tests were made by comparing the results of the Drugwipe tests with laboratory GC–MS confirmation results of oral fluid or whole blood. In addition to the performance evaluations of the Drugwipe tests based on laboratory results, a questionnaire on the practical aspects of the tests was written for the police officers who performed the tests. The aim of the questionnaire was to obtain user comments on the practicality of the tests as well as the advantages and weak points of the tests.The results of the performance evaluations were: for oral fluid (sensitivity; specificity; accuracy) amphetamines (95.5%; 92.9%; 95.3%), cannabis (52.2%; 91.2%; 85.1%), cocaine (50.0%; 99.3%; 98.6%), opiates (100%; 95.8%; 95.9%), benzodiazepines (74.4%; 84.2%; 79.2%) and for whole blood accordingly, amphetamines (97.7%; 86.7%; 95.9%), cannabis (68.3%; 87.9%; 84.9%), cocaine (50.0%; 98.5%; 97.7%), opiates (87.5%; 96.9%; 96.6%) and benzodiazepines (66.7%; 87.0%; 74.4%). Although the Drugwipe 5 successfully detected amphetamine-type stimulant drugs and the police officers were quite pleased with the current features of the Drugwipe tests, improvements must still be made regarding the detection of cannabis and benzodiazepines.

The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. However, the use of high throughput experimental methods, such as ChIP-chip and ChIP-sequencing, is limited by their high cost and strong dependence on cellular type and context. We developed a computational method for the genome-wide identification of functional transcription factor binding

We apply the sky brightness modelling technique introduced and developed by Roy Garstang to high-resolution DMSP-OLS satellite measurements of upward artificial light flux and to GTOPO30 digital elevation data in order to predict the brightness distribution of the night sky at a given site in the primary astronomical photometric bands for a range of atmospheric aerosol contents. This method, based on global data and accounting for elevation, Earth curvature and mountain screening, allows the evaluation of sky glow conditions over the entire sky for any site in the World, to evaluate its evolution, to disentangle the contribution of individual sources in the surrounding territory, and to identify main contributing sources. Sky brightness, naked eye stellar visibility and telescope limiting magnitude are produced as 3-dimensional arrays whose axes are the position on the sky and the atmospheric clarity. We compared our results to available measurements.

We used this photometric data set to derive site statistics for Dome A and to search for variable stars. Thanks to the nearly-uninterrupted synoptic coverage, we find 6 times as many variables as previous surveys with similar magnitude limits. We detected 157 variable stars, of which 55% are unclassified, 27% are likely binaries and 17% are likely pulsating stars. The latter category includes delta Scuti, gamma Doradus and RR Lyrae variables. One variable may be a transiting exoplanet.

Determining brain regions in which neuroleptic drugs of different types produce similar effects, especially where these effects are not shared with drugs lacking antipsychotic efficacy, provides evidence as to how and where the clinical effects of neuroleptic drugs are mediated. For this study, the pattern of expression of the protein Fos, a marker of cellular activation, was compared after administration of the typical neuroleptic haloperidol, the antipsychotic drug clozapine, and the atypical neuroleptic olanzapine, as well as the sedative drug diphenhydramine and the anxiolytic lorazepam. Animals (Sprague-Dawley rats, three per cohort) received intraperitoneal injections of haloperidol (1 mg/kg), clozapine (20 mg/kg), olanzapine (5 mg/kg), diphenhydramine hydrochloride (1 mg/kg), lorazepam (5 mg/kg) or vehicle (2% lactic acid, 1 ml/kg). Two hours after drug administration, animals were killed. Patterns of activated cells were observed by immunohistochemistry for Fos-like antibodi...