AntiHunter 2.0: increased speed and sensitivity in searching BLAST output for EST antisense transcripts

An increasing number of eukaryotic and prokaryotic genes are being found to have natural antisense transcripts (NATs). There is also growing evidence to suggest that antisense transcription could play a key role in many human diseases. Consequently, there have been several recent attempts to set up computational procedures aimed at identifying novel NATs. Our group has developed the AntiHunter program for the identification of expressed sequence tag (EST) antisense transcripts from BLAST output. In order to perform an analysis, the program requires a genomic sequence plus an associated list of transcript names and coordinates of the genomic region. After masking the repeated regions, the program carries out a BLASTN search of this sequence in the selected EST database, reporting via email the EST entries that reveal an antisense transcript according to the user-supplied list. Here, we present the newly developed version 2.0 of the AntiHunter tool. Several improvements have been added to this version of the program in order to increase its ability to detect a larger number of antisense ESTs. As a result, AntiHunter can now detect, on average, >45% more antisense ESTs with little or no increase in the percentage of the false positives. We also raised the maximum query size to 3 Mb (previously 1 Mb). Moreover, we found that a reasonable trade-off between the program search sensitivity and the maximum allowed size of the input-query sequence could be obtained by querying the database with the MEGABLAST program, rather than by using the BLAST one. We now offer this new opportunity to users, i.e. if choosing the MEGABLAST option, users can input a query sequence up to 30 Mb long, thus considerably improving the possibility to analyze longer query regions. The AntiHunter tool is freely available at

El conflicto entre cristianos y musulmanes en las relaciones de sucesos : la liberación de Buda

Este trabajo propone el análisis de una selección de textos escritos en romance sobre la derrota turca y la toma de la ciudad de Buda en 1686, que denuncian la exultante acogida popular de la noticia de las gestas cristianas en Centroeuropa, la percepción del eterno conflicto entre Oriente y Occidente y la proyección del imaginario colectivo del siglo xvii acerca de la lucha contra los infieles.This paper offers the analysis of a selection of texts, written in Romance languages, about the Turkish defeat and the conquest of the city of Buda in 1686, which provide evidence of the popular exultation at the news of the Christian achievements in Central Europe, the perception of the eternal conflict between East and West, and the projection of the seventeenth-century collective imagination regarding the struggle against the infidel

Testing of human papillomavirus in lung cancer and non-tumor lung tissue

Abstract Background Risk factors for lung cancer, such as cigarette smoking, environmental pollution, asbestos, and genetic determinants, are well-known, whereas involvement of the human papillomavirus (HPV) is still unclear. Methods We examined a series of 100 lung cancer patients from Italy and the UK for the presence of HPV DNA in both lung tumor specimens and adjacent non-tumoral specimens from the same patients. Thirty-five of the most clinically relevant HPV types were assayed using PCR amplification of the highly conserved L1 region of the viral genome followed by hybridization with specific probes. Results No HPV was detected in tumor specimens nor in normal lung tissue of any patient. Conclusions These data indicate that, in this Western series, HPV is not associated with the risk of lung cancer. Our findings will help refine estimates of lung cancer risk in patients affected by a common viral infection involved in other types of human cancer.</p

Development and assessment of a method to determine the angle of attack on an operating wind turbine by matching onboard pressure measurements with panel method simulations

Wind Energy is substantially growing in recent years and is now one of the most competitive renewable energy sources on the market. To further foster the growth of this energy source, increasing effort is put into building accurate numerical models. Most models compute the loads acting on the turbine as a dependence of some sort to the angle of attack (AoA). Accurate AoA measurements would allow for comparison with experiments and would be of great benefit for the improvement of numerical models and the investigations of aerodynamic phenomena such as stall delay. However, the determination of the angle of attack during operation is troublesome to the present day. In addition to what was already mentioned, the AoA is key to evaluate loads acting on the wind turbine and assessing experiments, computational models, and aeroelastic models. This paper proposes a simple comparative method to estimate the AoA based on pressure distributions. The proposed method is tested using data from different numbers of pressure taps placed on the Berlin Research Turbine (BeRT) at the Hermann Föttinger Institut of the Technische Universität Berlin. The predicted results are in line with those from other methods while the operating conditions to which the model can be applied are improved