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.

Comparative analysis of cancer genes in the human and chimpanzee genomes

Background: Cancer is a major medical problem in modern societies. However, the incidence of this disease in non-human primates is very low. To study whether genetic differences between human and chimpanzee could contribute to their distinct cancer susceptibility, we have examined in the chimpanzee genome the orthologous genes of a set of 333 human cancer genes. Results: This analysis has revealed that all examined human cancer genes are present in chimpanzee, contain intact open reading frames and show a high degree of conservation between both species. However, detailed analysis of this set of genes has shown some differences in genes of special relevance for human cancer. Thus, the chimpanzee gene encoding p53 contains a Pro residue at codon 72, while this codon is polymorphic in humans and can code for Arg or Pro, generating isoforms with different ability to induce apoptosis or interact with p73. Moreover, sequencing of the BRCA1 gene has shown an 8 Kb deletion in the chimpanzee sequence that prematurely truncates the co-regulated NBR2 gene. Conclusion: These data suggest that small differences in cancer genes, as those found in tumor suppressor genes, might influence the differences in cancer susceptibility between human and chimpanzee. Nevertheless, further analysis will be required to determine the exact contribution of the genetic changes identified in this study to the different cancer incidence in non-human primates.

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.

Frames and games

Decision-makers are sometimes influenced by the way in which choice situations are presented to them or "framed" This can be seen as an important challenge to the social sciences, since strong and pervasive framing effects would make it difficult to study human behavior in a synthetic or theoretic manner. We present results from experiments with dilemma games designed to shed light on the effects of several frame variations. We study, among others, the particular public bad frame used by Andreoni (1995) and two more naturalistic frames involving stories. Our results show that none of the frame manipulations have a significant effect on average behavior, but we do find some effects on extreme behavior. We also find that incentives do matter where frames do not matter.

Reading Ng Kim Chew: Malaysian-Chineseness and memory in contemporary Malaysian Chinese literature in taiwan

The idea of Chineseness as a geographic, cultural-specific and ethnically-charged concept, and the pivotal role assumed by memory linger throughout the writings of most authors hailing from Chinese community in Southeast Asia. Among these communities, being the Malaysian Chinese the more prolific in terms of number of writers and pieces of literature produced, this paper deals specifically with it. Its focus is put on the literature produced by Malaysian Chinese authors residing in Taiwan, which topic constitutes an important part of the first chapter, and on one of its main representatives, Ng Kim Chew, to whom chapter two and three are fully dedicated. A literary analysis of one of his short stories, Huo yu tu, will allow the reader to have a first-hand experience, through excerpts from the original text, of the importance of Chineseness and memory in the literary production of Ng and of many authors sharing with him similar life and literary experiences. I started this research from the assumption that these authors make large use of their own memories and memories from their own community in their writing as a way to re-tie themselves to the Chineseness they left in their places of origin. However in the case of Ng Kim Chew, the analysis of his works led be to theorizing that the identity he is imbued with, if there is one, is not Chinese, nor Malaysian, but purely and distinctively Malaysian-Chinese. This paper can also serve as an introduction for the general public to the field of Sinophone literature from Southeast Asia and to promote wider and innovative paths of research within the realm of Chinese studies that go beyond China proper.

Eye tracking for on-screen reading

A medida que avanza la tecnolog a, cada vez son m as comunes los libros digitales. Por eso, existen varias formas de mejorar la experiencia de lectura del usuario, como mostrar la de nici on de una palabra que resulte dif cil, o resaltar lo importante del texto cuando se pasa la vista por encima. En este proyecto, se ha investigado la base de esto con la ayuda de un Eye Tracker. Se ha implementado una clasi caci on en palabras f aciles y dif ciles dependiendo de c omo una persona lee, y una forma de saber si se est a leyendo el texto o pasando la vista por encima.

Fermat's treatise on quadrature: A new reading

The Treatise on Quadrature of Fermat (c. 1659), besides containing the first known proof of the computation of the area under a higher parabola, R x+m/n dx, or under a higher hyperbola, R x-m/n dx with the appropriate limits of integration in each case , has a second part which was not understood by Fermat s contemporaries. This second part of the Treatise is obscure and difficult to read and even the great Huygens described it as'published with many mistakes and it is so obscure (with proofs redolent of error) that I have been unable to make any sense of it'. Far from the confusion that Huygens attributes to it, in this paper we try to prove that Fermat, in writing the Treatise, had a very clear goal in mind and he managed to attain it by means of a simple and original method. Fermat reduced the quadrature of a great number of algebraic curves to the quadrature of known curves: the higher parabolas and hyperbolas of the first part of the paper. Others, he reduced to the quadrature of the circle. We shall see how the clever use of two procedures, quite novel at the time: the change of variables and a particular case of the formulaof integration by parts, provide Fermat with the necessary tools to square very easily curves as well-known as the folium of Descartes, the cissoid of Diocles or the witch of Agnesi.

Some critical reflections on Michel Foucault's reading of Plutarch's Eroticus (Amatorius)

This aim of this article is to reflect on Michel Foucault's reading of Plutarch's Eroticus in his Histoire de la sexualité, putting emphasis on the fact that, against what it is affirmed by the French thinker, the real debate is not, in the author's opinion, about true pleasure, that obtained by the erastés from his erómenos or that obtained by husbands from their wives, but the need to assign also love and friendship (éros kaì philia) to the conjugal love.

Leaving the cave in search of life (A Platonic reading of R. Sirera's La caverna (The Cave)

The aim of this article is to show how a contemporary playwright thinks once more of the Platonic image of the cave in order to reflect on the necessary existential journey of men and women as in the case of a Bildungsroman. Sooner or later men and women must abandon the protection that any sort of cavern such as home, the family garden or family itself can offer. In spite of writing from a by no means idealistic or metaphysical point of view, thanks to R. Sirera and to the very applicability of Platonic images, Plato becomes once again a classical reference which is both useful and even unavoidable if one bears in mind the Platonic origin of all the literary caverns.

Patriarchal Hauntings: Re-reading Villainy and Gender in Daphne du Maurier's Rebecca

Criticism of Daphne du Maurier’s popular classic Rebecca (1938) can be divided into two mainstream interpretations. On the one hand, it was traditionally marketed as a gothic romance where the hero and the heroine conquered the evil women that separated them. On the other, certain feminist critics have recently provided a very diff erent view of the story, aligning it with gothic narratives that deal with the dangers women suff er under the patriarchal control of their husbands. Th is would imply that du Maurier’s novel should not be read as a traditional romance that promotes patriarchy, as the former interpretation suggested. In this article, I propose, through a Gothic Studies and a Gender Studies reading, that villainy in this novel is not exclusively linked to gender and, therefore, the victim and abuser statuses cannot be equated to femininity and masculinity, respectively. Instead, I argue that villainy in the novel is inextricably connected to being in a powerful position within patriarchy, and that it is the desire to maintain this position and perpetuate the patriarchal system that leads the main characters (men and women) to commit acts of villainy.

Frames of War: When is Life Grievable?

La tesis principal de Butler en Frames of War es que los marcos interpretativos por medio de los cuales nos es posible entender la violencia son parte material y esencial del propio acto de librar una guerra. Del mismo modo que un contenido y su envoltorio a veces no pueden separarse, lo que entendemos como"contenido" (el hecho bélico) está necesariamente enmarcado y no es posible aproximarse a él ajeno a los marcos que lo vehiculan. El marco es una estrategia activa de contención que no sólo contiene lo que es sino también su justificación y su interpretación, y en un contexto de guerra el marco dictamina, además de la justificación, la distinción entre las vidas que merecen ser preservadas y lloradas, y las que no.

Frames: a maximum entropy statistical estimate of the inverse problem

A maximum entropy statistical treatment of an inverse problem concerning frame theory is presented. The problem arises from the fact that a frame is an overcomplete set of vectors that defines a mapping with no unique inverse. Although any vector in the concomitant space can be expressed as a linear combination of frame elements, the coefficients of the expansion are not unique. Frame theory guarantees the existence of a set of coefficients which is “optimal” in a minimum norm sense. We show here that these coefficients are also “optimal” from a maximum entropy viewpoint.

The impact of adopting a CLIL approach on EFL learners reading skills in Catalonia school

En els últims anys, un gran nombre de docents i escoles han estat introduint programes AICLE a les escoles catalanes. A la majoria d’escoles, però, només s'ensenya anglès com a llengua estrangera, la qual cosa, limita les oportunitats d'estar en contacte amb la llengua estrangera en un context diferent. L’objectiu d'aquest estudi és analitzar si els infants milloren en les seves habilitats lectores i comprovar si existeix un avantatge significatiu respecte els alumnes que només estudien anglès com a llengua estrangera. L’estudi empíric que us presento a continuació, compara els resultats obtinguts en dues proves de comprensió lectora. A les proves hi van participar dos grups d’alumnes de cinquè de d’Educació Primària. Un dels grups seguia un programa AICLE (1 hora a la setmana i , a més aprenia anglès coma llengua estrangera); l’altre grup només estudiava anglès com a llengua estrangera. L'objectiu principal d'aquest projecte d'investigació és esbrinar si els programes AICLE tenen un impacte en les habilitats lectores en llengua anglesa dels alumnes. Així doncs, humilment intentaré contribuir a la literatura existent sobre els beneficis de l’AICLE.

Patriarchal hauntings : re-reading villainy and gender in Daphne du Maurier’s 'Rebecca'

Daphne du Maurier’s popular classic Rebecca (1938) was traditionally marketed as a Gothic romance in which two lovers conquered the evil women that separated them. In more recent years, some feminist critics have provided a very different view of the story as a Gothic narrative about the dangers women suffer under patriarchal control. In this thesis, I propose, through a Gothic Studies and a Gender Studies reading, that the victim/abuser statuses in du Maurier’s novel cannot be equated to femininity and masculinity, respectively. Instead, I argue that villainy in Rebecca comes from being in a powerful position within patriarchy—a position that is occupied by both male and female characters