Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line

Background: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames (ORFs) and flanking untranslated regions. The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions.Results: We use Long Serial Analysis of Gene Expression (LongSAGE) in bursal lymphocytes and the DT40 cell line to verify the quality and completeness of the annotated transcripts. 53.6% of the more than 38,000 unique SAGE tags (unitags) match to full length bursal cDNAs, the Ensembl transcript build or the genome sequence. The majority of all matching unitags show single matches to the genome, but no matches to the genome derived Ensembl transcript build. Nevertheless, most of these tags map close to the 3' boundaries of annotated Ensembl transcripts.Conclusions: These results suggests that rather few genes are missing in the current Ensembl chicken transcript build, but that the 3' ends of many transcripts may not have been accurately predicted. The tags with no match in the transcript sequences can now be used to improve gene predictions, pinpoint the genomic location of entirely missed transcripts and optimize the accuracy of gene finder software.

Authors', Institutions' and Countries' rankings in regional and urban science : an analysis for nine top international journals from 1991 to 2000

This paper examines the most productive authors, institutions and countries in regional and urban science from 1991 to 2000 using information on published articles (and pages) from a sample of widely recognized journals in this field: ARS, JUE, JRS, IJURR, IRSR, PRS, RSUE, RS and US. We also consider the relation between the country of the institution named in articles and the country in which the journal is published, in order to know if there are a home publication bias in regional and urban science. Analysis was made for the whole decade and by subperiods, this allowed us to make a more dynamic interpretation of the results

Authors', Institutions' and Countries' rankings in regional and urban science : an analysis for nine top international journals from 1991 to 2000

This paper examines the most productive authors, institutions and countries in regional and urban science from 1991 to 2000 using information on published articles (and pages) from a sample of widely recognized journals in this field: ARS, JUE, JRS, IJURR, IRSR, PRS, RSUE, RS and US. We also consider the relation between the country of the institution named in articles and the country in which the journal is published, in order to know if there are a home publication bias in regional and urban science. Analysis was made for the whole decade and by subperiods, this allowed us to make a more dynamic interpretation of the results

Factors affecting visual analysis in single-case designs

Visual inspection remains the most frequently applied method for detecting treatment effects in single-case designs. The advantages and limitations of visual inference are here discussed in relation to other procedures for assessing intervention effectiveness. The first part of the paper reviews previous research on visual analysis, paying special attention to the validation of visual analysts" decisions, inter-judge agreement, and false alarm and omission rates. The most relevant factors affecting visual inspection (i.e., effect size, autocorrelation, data variability, and analysts" expertise) are highlighted and incorporated into an empirical simulation study with the aim of providing further evidence about the reliability of visual analysis. Our results concur with previous studies that have reported the relationship between serial dependence and increased Type I rates. Participants with greater experience appeared to be more conservative and used more consistent criteria when assessing graphed data. Nonetheless, the decisions made by both professionals and students did not match sufficiently the simulated data features, and we also found low intra-judge agreement, thus suggesting that visual inspection should be complemented by other methods when assessing treatment effectiveness.