Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions

This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using a combination of 5' rapid amplification of cDNA ends (RACE) and high-density resolution tiling arrays. We identified previously unannotated and often tissue- or cell-line-specific transcribed fragments (RACEfrags), both 5' distal to the annotated 5' terminus and internal to the annotated gene bounds for the vast majority (81.5%) of the tested genes. Half of the distal RACEfrags span large segments of genomic sequences away from the main portion of the coding transcript and often overlap with the upstream-annotated gene(s). Notably, at least 20% of the resultant novel transcripts have changes in their open reading frames (ORFs), most of them fusing ORFs of adjacent transcripts. A significant fraction of distal RACEfrags show expression levels comparable to those of known exons of the same locus, suggesting that they are not part of very minority splice forms. These results have significant implications concerning (1) our current understanding of the architecture of protein-coding genes; (2) our views on locations of regulatory regions in the genome; and (3) the interpretation of sequence polymorphisms mapping to regions hitherto considered to be "noncoding," ultimately relating to the identification of disease-related sequence alterations.

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.

On an upper bound for the arithmetic self-intersection number of the dualizing sheaf on arithmetic surfaces

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On the number of limit cycles bifurcating from a non-global degenerated center

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Price competition under cost uncertainty: A laboratory analysis

We study the relation between the number of firms and price-cost margins under price competition with uncertainty about competitors' costs. We present results of an experiment in which two, three and four identical firms repeatedly interact in this environment. In line with the theoretical prediction, market prices decrease with the number of firms, but on average stay above marginal costs. Pricing is less aggressive in duopolies than in triopolies and tetrapolies. However, independently from the number of firms, pricing is more aggressive than in the theoretical equilibrium. Both the absolute and the relative surpluses increase with the number of firms. Total surplus is close to the equilibrium level, since enhanced consumer surplus through lower prices is counteracted by occasional displacements of the most efficient firm in production.

Stable condorcet rules

We consider the following allocation problem: A fixed number of public facilities must be located on a line. Society is composed of $N$ agents, who must be allocated to one and only one of these facilities. Agents have single peaked preferences over the possible location of the facilities they are assigned to, and do not care about the location of the rest of facilities. There is no congestion. In this context, we observe that if a public decision is a Condorcet winner, then it satisfies nice properties of internal and external stability. Though in many contexts and for some preference profiles there may be no Condorcet winners, we study the extent to which stability can be made compatible with the requirement of choosing Condorcet winners whenever they exist.

Endogenous population subgroups: the best population partition and optimal number of groups

The aim of this paper is to suggest a method to find endogenously the points that group the individuals of a given distribution in k clusters, where k is endogenously determined. These points are the cut-points. Thus, we need to determine a partition of the N individuals into a number k of groups, in such way that individuals in the same group are as alike as possible, but as distinct as possible from individuals in other groups. This method can be applied to endogenously identify k groups in income distributions: possible applications can be poverty

Lower bounds for the number of limit cycles of trigonometric Abel equations

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On the upper bound of the number of limit cycles obtained by the second order averaging method I

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On the upper bound of the number of limit cycles obtained by the second order averaging method II

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On the number of K3,3-minor-free and maximal K3,3-minor-free graphs

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Las relaciones públicas: ¿below the line?

Amb freqüència s’associen les “Relacions Públiques” amb el “below the line”, qüestió que cal ser estudiada observant tant el punt de vista del propi sector de les relacions públiques com el del marketing i la comunicació publicitària, creadors aquests dos últims de la expressió i la categoria below the line. En plena “Era de la comunicació”, és imprescindible analitzar l’esmentada relació, tenint en compte el paper que juguen els nous mitjans emergents en el desenvolupament de les relacions públiques. Ens trobem en un nou entorn on desenvolupar aquesta professió únicament a través dels mitjans tradicionals poc té a veure amb la realitat del present. Avui les noves tecnologies i mitjans emergents ens porten a una “nova generació de la comunicació” on els professionals s’enfronten a nous conceptes que qüestionen l’antiga classificació de mitjans i disciplines above i below the line.

Experimental investigation of transient natural convection cooling of high prandtl number fluid with variable viscosity

Report for the scientific sojourn at the James Cook University, Australia, between June to December 2007. Free convection in enclosed spaces is found widely in natural and industrial systems. It is a topic of primary interest because in many systems it provides the largest resistance to the heat transfer in comparison with other heat transfer modes. In such systems the convection is driven by a density gradient within the fluid, which, usually, is produced by a temperature difference between the fluid and surrounding walls. In the oil industry, the oil, which has High Prandtl, usually is stored and transported in large tanks at temperatures high enough to keep its viscosity and, thus the pumping requirements, to a reasonable level. A temperature difference between the fluid and the walls of the container may give rise to the unsteady buoyancy force and hence the unsteady natural convection. In the initial period of cooling the natural convection regime dominates over the conduction contribution. As the oil cools down it typically becomes more viscous and this increase of viscosity inhibits the convection. At this point the oil viscosity becomes very large and unloading of the tank becomes very difficult. For this reason it is of primary interest to be able to predict the cooling rate of the oil. The general objective of this work is to develop and validate a simulation tool able to predict the cooling rates of high Prandtl fluid considering the variable viscosity effects.

Computation of an integral basis of a quartic number field

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