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.

Discourse, knowledge, power and politics: towards critical epistemic discourse analysis

Although both are fundamental terms in the humanities and social sciences, discourse and knowledge have seldom been explicitly related, and even less so in critical discourse studies. After a brief summary of what we know about these relationships in linguistics, psychology, epistemology and the social sciences, with special emphasis on the role of knowledge in the formation of mental models as a basis for discourse, I examine in more detail how a critical study of discourse and knowledge may be articulated in critical discourse studies. Thus, several areas of critical epistemic discourse analysis are identified, and then applied in a study of Tony Blair’s Iraq speech on March 18, 2003, in which he sought to legitimatize his decision to go to war in Iraq with George Bush. The analysis shows the various modes of how knowledge is managed and manipulated of all levels of discourse of this speech.

Approximate knowledge of rationality and correlated equilibria

We extend Aumann's theorem [Aumann 1987], deriving correlated equilibria as a consequence of common priors and common knowledge of rationality, by explicitly allowing for non-rational behavior. Wereplace the assumption of common knowledge of rationality with a substantially weaker one, joint p-belief of rationality, where agents believe the other agents are rational with probability p or more. We show that behavior in this case constitutes a kind of correlated equilibrium satisfying certain p-belief constraints, and that it varies continuously in the parameters p and, for p sufficiently close to one,with high probability is supported on strategies that survive the iterated elimination of strictly dominated strategies. Finally, we extend the analysis to characterizing rational expectations of interimtypes, to games of incomplete information, as well as to the case of non-common priors.

Shared knowledge

Agents use their knowledge on the history of the economy in orderto choose what is the optimal action to take at any given moment of time,but each individual observes history with some noise. This paper showsthat the amount of information available on the past evolution of theeconomy is an endogenous variable, and that this leads to overconcentrationof the investment, which can be interpreted as underinvestment in research.It presents a model in which agents have to invest at each period in one of$K$ sectors, each of them paying an exogenous return that follows a welldefined stochastic path. At any moment of time each agent receives an unbiasednoisy signal on the payoff of each sector. The signals differ across agents,but all of them have the same variance, which depends on the aggregate investmentin that particular sector (so that if almost everybody invests in it theperceptions of everybody will be very accurate, but if almost nobody doesthe perceptions of everybody will be very noisy). The degree of hetereogeneityacross agents is then an endogenous variable, evolving across time determining,and being determined by, the amount of information disclosed.As long as both the level of social interaction and the underlying precisionof the observations are relatively large agents behave in a very preciseway. This behavior is unmodified for a huge range of informational parameters,and it is characterized by an excessive concentration of the investment ina few sectors. Additionally the model shows that generalized improvements in thequality of the information that each agent gets may lead to a worse outcomefor all the agents due to the overconcentration of the investment that thisproduces.

Strategic behavior and price discovery

The paper analyzes the effects of strategic behavior by an insider in a price discovery process, akin to an information tatonnement, in the presence of a competitive informed sector. Such processes are used in the preopening period of continuous trading systems in several exchanges. It is found that the insider manipulates the market using a contrarian strategy in order to neutralize the effect of the trades of competitive informed agents. Furthermore, consistently with the empirical evidence available, we find that information revelation accelerates close to the opening, that the market price does not converge to the fundamental value no matter how many rounds the tatonnement has, and that the expected trading volume displays a U-shaped pattern. We also find that a market with a larger competitive sector (smaller insider) has an improved informational efficiency and an increased trading volume. The insider provides a public good (a lower informativeness of the price) for the competitive informed sector.

On heuristic and linear models of judgment: Mapping the demand for knowledge

Research on judgment and decision making presents a confusing picture of human abilities. For example, much research has emphasized the dysfunctional aspects of judgmental heuristics, and yet, other findings suggest that these can be highly effective. A further line of research has modeled judgment as resulting from as if linear models. This paper illuminates the distinctions in these approaches by providing a common analytical framework based on the central theoretical premise that understanding human performance requires specifying how characteristics of the decision rules people use interact with the demands of the tasks they face. Our work synthesizes the analytical tools of lens model research with novel methodology developed to specify the effectiveness of heuristics in different environments and allows direct comparisons between the different approaches. We illustrate with both theoretical analyses and simulations. We further link our results to the empirical literature by a meta-analysis of lens model studies and estimate both human andheuristic performance in the same tasks. Our results highlight the trade-off betweenlinear models and heuristics. Whereas the former are cognitively demanding, the latterare simple to use. However, they require knowledge and thus maps of when andwhich heuristic to employ.

Disease discovery, sistema de predicció de malalties

L'objectiu d'aquest projecte consisteix en crear una eina per servir de referència a metges, per tal d'ajudar-los en els diagnòstics, sobretot de malalties més estranyes que són més difícils de diagnostica, ja que no són tant conegudes. Estem interessats en realitzar una aplicació la qual donats uns símptomes ens doni les malalties mé probables. El personal sanitari doncs podrà disposar d'una eina que l'ajudi a diagnosticar malalties segons els símptomes dels pacients. L'eina que es presenta en aquest treball, Disease Discovery, disposa d'una base de dades omplerta des de fonts molt fiables i amb una quantitat elevada d'informació sobre malalties i símptomes. Aquesta base de dades s'entrena segons diferents classificadors. Les prediccions de les malalties es faran emprant un model generat per mitjà d'un entrenament realitzat amb un classificador sobre la base de dades. A més a més, s'ha realitzat una interfície web per ajudar als usuaris i fer que l'eina sigui més usable alhora que més còmoda de distribuir el programari entre el personal sanitari interessat.

Bringing Funds of Family Knowledge to school. The Living Morocco Project (“برغملا شيعلا”)

The purpose of the study, grounded in sociocultural theory, is to describe the funds of knowledge of a Moroccan family living in Catalonia (Spain) in order to document how teachers can use these funds of knowledge to make direct links between students' lives and classroom teaching. The funds of knowledge approach is based on a simple premise: regardless of any socio-economical and sociocultural "deficit" that people may or may not have all families accumulate bodies of beliefs, ideas, skills and abilities based on their experiences (in areas such as their occupation or their religion). The challenge consists in connecting these bodies of educational resources with teaching practice in order to connect the curriculum with students' lives. In doing so, qualitative research can be carried out using several techniques such as self portraits, self-definition tasks, assessment of family artefacts, documenting routines through photographs, or the analysis of a person's significant circle. The results in terms of teaching practices illustrate the variety of ways teachers can make connections between home and school in ways that assist learners in their academic development. In this article, we propose using the term funds of identity to complement the concept of funds of knowledge

Lengua familiar y conocimiento de la lengua escolar en Cataluña al finalizar la Educación Infantil = Home Language and Knowledge of the School Language in Catalonia at the end of Nursery School

La infancia extranjera se escolariza en Cataluña en un programa de cambio de lengua del hogar a la escuela. Las investigaciones afirman que este alumnado tarda un mínimo de seis años en equiparar sus habilidades lingüístico-cognitivas con sus pares autóctonos, no así las habilidades conversacionales, las cuales se adquieren antes de los dos años de residencia. Sin embargo, no existen estudios sobre los efectos de la escolarización en el parvulario del alumnado alófono, así como de su lengua familiar, en relación con la adquisición de la lengua escolar. El artículo es un estudio comparativo de la adquisición del catalán de 567 autóctonos y 434 alófonos, al final del parvulario, en 50 escuelas de Cataluña que escolarizan a alumnado de origen extranjero. Las lenguas del alumnado autóctono son el catalán, el castellano y el bilingüismo catalán-castellano y las lenguas del alumnado alófono son el árabe, el soninké y el castellano. Los factores utilizados más relevantes han sido el nivel socioprofesional y educativo de las familias, el tiempo de residencia y el momento de escolarización del alumnado, el porcentaje de alumnado catalanohablante y de alumnado alófono en el aula y el contexto sociolingüístico del centro escolar. Los resultados muestran que el alumnado autóctono sabe más catalán que el alumnado alófono, pero las diferencias desaparecen respecto a algunos factores, de los cuales los más relevantes son los relacionados con las características del alumnado de las aulas. La lengua familiar del alumnado alófono no incide en sus resultados

Benchmarking for routines and organizational knowledge

We use best practice benchmarking rationales to propose a dynamic research design that accounts for the endogenous components of across-firms heterogeneous routines to study changes in performance and their link to organizational knowledge investments. We thus contribute to the operationalization of management theoretical frameworks based on resources and routines. The research design employs frontier measures that provide industry-level benchmarking in organizational settings, and proposes some new indicators for firm-level strategic benchmarking. A profit-oriented analysis of the U.S. technology industry during 2000-2011 illustrates the usefulness of our design. Findings reveal that industry revival following economic distress comes along with wider gaps between best and worst performers. Second stage analyses show that increasing intangibles stocks is positively associated with fixed target benchmarking, while enhancing R&D spending is linked to local frontier progress. The discussion develops managerial interpretations of the benchmarking measures that are suitable for control mechanisms and reward systems.

Differential regulation of RasGAPs in cancer

Ever since their discovery as cellular counterparts of viral oncogenes more than 25 years ago, much progress has been made in understanding the complex networks of signal transduction pathways activated by oncogenic Ras mutations in human cancers. The activity of Ras is regulated by nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), and much emphasis has been put into the biochemical and structural analysis of the Ras/GAP complex. The mechanisms by which GAPs catalyze Ras-GTP hydrolysis have been clarified and revealed that oncogenic Ras mutations confer resistance to GAPs and remain constitutively active. However, it is yet unclear how cells coordinate the large and divergent GAP protein family to promote Ras inactivation and ensure a certain biological response. Different domain arrangements in GAPs to create differential protein-protein and protein-lipid interactions are probably key factors determining the inactivation of the 3 Ras isoforms H-, K-, and N-Ras and their effector pathways. In recent years, in vitro as well as cell- and animal-based studies examining GAP activity, localization, interaction partners, and expression profiles have provided further insights into Ras inactivation and revealed characteristics of several GAPs to exert specific and distinct functions. This review aims to summarize knowledge on the cell biology of RasGAP proteins that potentially contributes to differential regulation of spatiotemporal Ras signaling.

Inter-firm labor mobility and knowledge diffusion: a theoretical approach

[cat] Analitzem una economia amb dues característiques principals: la mobilitat dels treballadors implica transferència de coneixement i la productivitat de l’empresa augmenta amb l’intercanvi de coneixement. Cada empresa desenvolupa un tipus de coneixement que serà trasmès a la resta de la indústria mitjançant la mobilitat de treballadors. Estudiem dues estructures de mercat laboral i utilitzant un anàlisi comparatiu derivem les implicacions del model. Els resultats revelen com la mobilitat de treballadors depèn en la varietat i nivell del coneixement, la presència de costos de mobilitat, les institucions, la capacitat d’absorvir coneixement per part de les empreses i la mida de la indústria. Els resultats no depenen de l’estructura del mercat laboral.

Inter-firm labor mobility and knowledge diffusion: a theoretical approach

[cat] Analitzem una economia amb dues característiques principals: la mobilitat dels treballadors implica transferència de coneixement i la productivitat de l’empresa augmenta amb l’intercanvi de coneixement. Cada empresa desenvolupa un tipus de coneixement que serà trasmès a la resta de la indústria mitjançant la mobilitat de treballadors. Estudiem dues estructures de mercat laboral i utilitzant un anàlisi comparatiu derivem les implicacions del model. Els resultats revelen com la mobilitat de treballadors depèn en la varietat i nivell del coneixement, la presència de costos de mobilitat, les institucions, la capacitat d’absorvir coneixement per part de les empreses i la mida de la indústria. Els resultats no depenen de l’estructura del mercat laboral.