permGPU: Using graphics processing units in RNA microarray association studies.

BACKGROUND: Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. RESULTS: We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. CONCLUSIONS: permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

Developing the Cost of Large Carnivore Conflict Rapid Response Units - A Namibian Case Study

Namibia is home to half the world’s remaining wild cheetahs and - provides critical habitat for lions, leopards, spotted and brown hyena and African Wild Dogs. Despite such ecological importance, only 5% of cheetah's, <1% of African Wild Dogs', and similar percentages of remaining habitat for other large carnivores exists on officially protected lands. As a result, human/carnivore conflict is a large problem on private lands, where 60% of surveyed farmers will shoot any large carnivore on sight. This project explores building a carnivore rapid response team equipped to mitigate human/carnivore conflict through researching the financial costs of such an endeavor, with an eye on capitalizing potential benefits to all 6 Namibian large carnivore species.

Teaching, learning and assessment in MSc. Databases units at University of Greenwich

In this paper we look at ways of delivering and assessing learning on database units offered on higher degree programmes (MSc) in the School of Computing and Mathematical Sciences at the University of Greenwich. Of critical importance is the teaching methods employed for verbal disposition, practical laboratory exercises and a careful evaluation of assessment methods and assessment tools in view of the fact that databases involve not only database design but also use of practical tools, such as database management systems (DBMSs) software, human designers, database administrators (DBA) and end users. Our goal is to clearly identify potential key success factors in delivering and assessing learning in both practical and theoretical aspects of database course units.

Réflexions sur l'appauvrissement des syntaxons aux limites chorologiques des unités phytosociologiques supérieurs et quelques-unes de leurs consequences

Con la ayuda de algunos ejemplos, se estudia el comportamiento de los sintáxones en los límites corológicos de las unidades fitosociológicas superiores; se muestra que, a medida que nos alejamos de su centro de gravedad, esas unidades pierden poco a poco sus especies y que, en sus límites corológicos, no quedan más especies características de unidades superiores para definir las comunidades. Se evocan entonces algunas consecuencias de esas observaciones: noción de combinación específica original, interpretación fitosociológica de los sintáxones, nomenclatura fitosociológica.

Drug use amongst young people attending emotional and behavioural difficulty units during adolescence: A longitudinal anlaysis

This paper reports on the findings from a longitudinal survey of the drug use behaviours of young people who were attending Emotional and Behavioural Difficulty (EBD) units from the age of 11-16 years. It forms part of the Belfast Youth Development Study, a longitudinal study of adolescent drug use. This paper presents a follow-up report to a cross-sectional paper that reported on drug use behaviours of a sample of young people attending EBD units when aged 12/13 years at school year 9 (McCrystal et al 2005a). In the present paper reported drug use and behaviours associated with increased risk of its use between the ages of 11-16 years were examined. The findings show that those attending EBD Units consistently reported higher levels of licit and illicit drug use throughout adolescence. Compared with young people in mainstream school, higher levels of behaviours associated with drug use including antisocial behaviour, disaffection with school, and poor communication with their parents/guardians were noted. These findings have implications for the development and timing of targeted prevention initiatives for young people attending EBD units at all stages of adolescent development.

Measles virus minigenomes encoding two autofluorescent proteins reveal cell-to-cell variation in reporter expression dependent on viral sequences between the transcription units.

Transcription from morbillivirus genomes commences at a single promoter in the 3' non-coding terminus, with the six genes being transcribed sequentially. The 3' and 5' untranslated regions (UTRs) of the genes (mRNA sense), together with the intergenic trinucleotide spacer, comprise the non-coding sequences (NCS) of the virus and contain the conserved gene end and gene start signals, respectively. Bicistronic minigenomes containing transcription units (TUs) encoding autofluorescent reporter proteins separated by measles virus (MV) NCS were used to give a direct estimation of gene expression in single, living cells by assessing the relative amounts of each fluorescent protein in each cell. Initially, five minigenomes containing each of the MV NCS were generated. Assays were developed to determine the amount of each fluorescent protein in cells at both cell population and single-cell levels. This revealed significant variations in gene expression between cells expressing the same NCS-containing minigenome. The minigenome containing the M/F NCS produced significantly lower amounts of fluorescent protein from the second TU (TU2), compared with the other minigenomes. A minigenome with a truncated F 5' UTR had increased expression from TU2. This UTR is 524 nt longer than the other MV 5' UTRs. Insertions into the 5' UTR of the enhanced green fluorescent protein gene in the minigenome containing the N/P NCS showed that specific sequences, rather than just the additional length of F 5' UTR, govern this decreased expression from TU2.

Rapid annulation of tropolone units via a pyrylium ylide 1,3-dipolar cycloaddition reaction

The tropolone subunit of the naturally occurring alkaloid rubrolone aglycon is synthesized via a short reaction sequence starting with a 1,3-dipolar cycloaddition of a pyrylium ylide and indenone, followed by enone oxidation, oxygen bridge elimination and finally hydroxy group oxidation.