Catalytic tuning of phosphinoethane ligand. An improved catalyst for hydrocarbon

Report for the scientific sojourn carried out at the Department of Chemistry University of North Texas (USA) from September until November 2006. It includes the performance of two computational chemistry studies: an experimental and computational study toward the intra- and intermolecular hydroarylation of isonitriles and the development of an improved catalyst for hydrocarbon functionalization.

Tree automorphisms and quasi-isometries of Thompson's group F

We prove that automorphisms of the infinite binary rooted tree T2 do not yield quasi-isometries of Thompson's group F, except for the map which reverses orientation on the unit interval, a natural outer automorphism of F. This map, together with the identity map, forms a subgroup of Aut(T2) consisting of 2-adic automorphisms, following standard terminology used in the study of branch groups. However, for more general p, we show that the analgous groups of p-adic tree automorphisms do not give rise to quasiisometries of F(p).

Communication for Public Goods

This paper studies information transmission between multiple agents with di¤erent preferences and a welfare maximizing decision maker who chooses the quality or quantity of a public good (e.g. provision of public health service; carbon emissions policy; pace of lectures in a classroom) that is consumed by all of them. Communication in such circumstances suffers from the agents' incentive to "exaggerate" their preferences relative to the average of the other agents, since the decision maker's reaction to each agent's message is weaker than in one-to-one communication. As the number of agents becomes larger the quality of information transmission diminishes. The use of binary messages (e.g. "yes" or "no") is shown to be a robust mode of communication when the main source of informational distortion is exaggeration.

Códigos binarios no lineales en MAGMA

La finalitat d'aquest projecte és aconseguir representar codis binaris no lineals de manera eficient en un ordinador. Per fer-ho, hem desenvolupat funcions per representar un codi binari a partir del super dual. Hem millorat la funció de càlcul del kernel d'un codi binari, implementada en projectes d'anys anteriors. També hem desenvolupat un paquet software per l'intèrpret MAGMA. Aquest paquet ens proveeix d'eines per al tractament de codis binaris no necessàriament lineals.

Disentangling the effects of key innovations on the diversification of Bromelioideae (bromeliaceae).

The evolution of key innovations, novel traits that promote diversification, is often seen as major driver for the unequal distribution of species richness within the tree of life. In this study, we aim to determine the factors underlying the extraordinary radiation of the subfamily Bromelioideae, one of the most diverse clades among the neotropical plant family Bromeliaceae. Based on an extended molecular phylogenetic data set, we examine the effect of two putative key innovations, that is, the Crassulacean acid metabolism (CAM) and the water-impounding tank, on speciation and extinction rates. To this aim, we develop a novel Bayesian implementation of the phylogenetic comparative method, binary state speciation and extinction, which enables hypotheses testing by Bayes factors and accommodates the uncertainty on model selection by Bayesian model averaging. Both CAM and tank habit were found to correlate with increased net diversification, thus fulfilling the criteria for key innovations. Our analyses further revealed that CAM photosynthesis is correlated with a twofold increase in speciation rate, whereas the evolution of the tank had primarily an effect on extinction rates that were found five times lower in tank-forming lineages compared to tank-less clades. These differences are discussed in the light of biogeography, ecology, and past climate change.

Reconocimiento de objetos multi-clase basado en descriptores de forma

Este trabajo presenta un sistema para detectar y clasificar objetos binarios según la forma de éstos. En el primer paso del procedimiento, se aplica un filtrado para extraer el contorno del objeto. Con la información de los puntos de forma se obtiene un descriptor BSM con características altamente descriptivas, universales e invariantes. En la segunda fase del sistema se aprende y se clasifica la información del descriptor mediante Adaboost y Códigos Correctores de Errores. Se han usado bases de datos públicas, tanto en escala de grises como en color, para validar la implementación del sistema diseñado. Además, el sistema emplea una interfaz interactiva en la que diferentes métodos de procesamiento de imágenes pueden ser aplicados.

Codis Z2Z4-additius en Magma

En aquest projecte es presenta el desenvolupament d'un paquet d'aplicacions en l'entorn de programació matemàtica Magma, per al tractament dels codis anomenats Z2Z4-additius. Els codis Z2Z4-additius permeten representar alguns codis binaris, com a codis lineals en l'espai dels codis Z2Z4-additius. Aquest fet permetrà l'estudi de tota una sèrie de codis binaris no lineals que fins ara eren intractables.

Gene duplication and neofunctionalization: POLR3G and POLR3GL.

RNA polymerase III (Pol III) occurs in two versions, one containing the POLR3G subunit and the other the closely related POLR3GL subunit. It is not clear whether these two Pol III forms have the same function, in particular whether they recognize the same target genes. We show that the POLR3G and POLR3GL genes arose from a DNA-based gene duplication, probably in a common ancestor of vertebrates. POLR3G- as well as POLR3GL-containing Pol III are present in cultured cell lines and in normal mouse liver, although the relative amounts of the two forms vary, with the POLR3G-containing Pol III relatively more abundant in dividing cells. Genome-wide chromatin immunoprecipitations followed by high-throughput sequencing (ChIP-seq) reveal that both forms of Pol III occupy the same target genes, in very constant proportions within one cell line, suggesting that the two forms of Pol III have a similar function with regard to specificity for target genes. In contrast, the POLR3G promoter-not the POLR3GL promoter-binds the transcription factor MYC, as do all other promoters of genes encoding Pol III subunits. Thus, the POLR3G/POLR3GL duplication did not lead to neo-functionalization of the gene product (at least with regard to target gene specificity) but rather to neo-functionalization of the transcription units, which acquired different mechanisms of regulation, thus likely affording greater regulation potential to the cell.

Sharp Bounds on Heterogeneous Individual Treatment Responses

This paper discusses how to identify individual-specific causal effects of an ordered discrete endogenous variable. The counterfactual heterogeneous causal information is recovered by identifying the partial differences of a structural relation. The proposed refutable nonparametric local restrictions exploit the fact that the pattern of endogeneity may vary across the level of the unobserved variable. The restrictions adopted in this paper impose a sense of order to an unordered binary endogeneous variable. This allows for a uni.ed structural approach to studying various treatment effects when self-selection on unobservables is present. The usefulness of the identi.cation results is illustrated using the data on the Vietnam-era veterans. The empirical findings reveal that when other observable characteristics are identical, military service had positive impacts for individuals with low (unobservable) earnings potential, while it had negative impacts for those with high earnings potential. This heterogeneity would not be detected by average effects which would underestimate the actual effects because different signs would be cancelled out. This partial identification result can be used to test homogeneity in response. When homogeneity is rejected, many parameters based on averages may deliver misleading information.

EEG-based functional brain networks: does the network size matter?

Functional connectivity in human brain can be represented as a network using electroencephalography (EEG) signals. These networks--whose nodes can vary from tens to hundreds--are characterized by neurobiologically meaningful graph theory metrics. This study investigates the degree to which various graph metrics depend upon the network size. To this end, EEGs from 32 normal subjects were recorded and functional networks of three different sizes were extracted. A state-space based method was used to calculate cross-correlation matrices between different brain regions. These correlation matrices were used to construct binary adjacency connectomes, which were assessed with regards to a number of graph metrics such as clustering coefficient, modularity, efficiency, economic efficiency, and assortativity. We showed that the estimates of these metrics significantly differ depending on the network size. Larger networks had higher efficiency, higher assortativity and lower modularity compared to those with smaller size and the same density. These findings indicate that the network size should be considered in any comparison of networks across studies.

Codis no lineals en MAGMA: construcció de codis perfectes

La finalitat d'aquest projecte és aconseguir construir codis binaris perfectes no lineals de manera eficient. Per a fer-ho, hem desenvolupat un paquet de software per a l'intèrpret MAGMA que conté funcions per a la construcció de codis perfectes, càlcul d'invariants de codis i altres funcions complementàries per a fer càlculs sobre les paraules d'un codi.

Quality of life: a potentially useful measure to indicate subclinical flares in Crohn disease.

Background:  While quality of life (QoL) is a well-recognised outcome measure of Crohn disease (CD) activity, its influence on other outcome measures, including exacerbation of CD is poorly understood. If QoL measures were to be associated with intestinal inflammatory activity, they might be useful for early detection of subclinical flares. Aims:  We hypothesised that low QoL might be associated with subsequent CD flares. Methods:  A cohort of 318 adult CD patients was observed for 1 year after assessment of baseline characteristics. Data were collected in Swiss university hospitals, regional hospitals and private practices. At inclusion, patients completed the Inflammatory Bowel Disease QoL Questionnaire (gastrointestinal QoL; range: 32 to 224 points) and the Short Form-36 Health Survey (general QoL; range: 35 to 145 points). During follow up, flares were recorded. Binary logistic regression was performed to estimate the relation between QoL and the odds of subsequent flares. Results:  A twofold decrease in the odds of flares (99% CI: 1.1; 4.0) per standard deviation of gastrointestinal QoL and a threefold decrease (99% CI: 1.5; 6.2) per standard deviation of general QoL were observed. Conclusions:  The close association between QoL and subsequent flares suggests that QoL measures might be useful in detecting upcoming flares before they become clinically apparent.

The analysis of approximate quickselect and related problems

Approximate Quickselect, a simple modification of the well known Quickselect algorithm for selection, can be used to efficiently find an element with rank k in a given range [i..j], out of n given elements. We study basic cost measures of Approximate Quickselect by computing exact and asymptotic results for the expected number of passes, comparisons and data moves during the execution of this algorithm. The key element appearing in the analysis of Approximate Quickselect is a trivariate recurrence that we solve in full generality. The general solution of the recurrence proves to be very useful, as it allows us to tackle several related problems, besides the analysis that originally motivated us. In particular, we have been able to carry out a precise analysis of the expected number of moves of the ith element when selecting the jth smallest element with standard Quickselect, where we are able to give both exact and asymptotic results. Moreover, we can apply our general results to obtain exact and asymptotic results for several parameters in binary search trees, namely the expected number of common ancestors of the nodes with rank i and j, the expected size of the subtree rooted at the least common ancestor of the nodes with rank i and j, and the expected distance between the nodes of ranks i and j.

Notch1 functions as a tumor suppressor in mouse skin.

Notch proteins are important in binary cell-fate decisions and inhibiting differentiation in many developmental systems, and aberrant Notch signaling is associated with tumorigenesis. The role of Notch signaling in mammalian skin is less well characterized and is mainly based on in vitro studies, which suggest that Notch signaling induces differentiation in mammalian skin. Conventional gene targeting is not applicable to establishing the role of Notch receptors or ligands in the skin because Notch1-/- embryos die during gestation. Therefore, we used a tissue-specific inducible gene-targeting approach to study the physiological role of the Notch1 receptor in the mouse epidermis and the corneal epithelium of adult mice. Unexpectedly, ablation of Notch1 results in epidermal and corneal hyperplasia followed by the development of skin tumors and facilitated chemical-induced skin carcinogenesis. Notch1 deficiency in skin and in primary keratinocytes results in increased and sustained expression of Gli2, causing the development of basal-cell carcinoma-like tumors. Furthermore, Notch1 inactivation in the epidermis results in derepressed beta-catenin signaling in cells that should normally undergo differentiation. Enhanced beta-catenin signaling can be reversed by re-introduction of a dominant active form of the Notch1 receptor. This leads to a reduction in the signaling-competent pool of beta-catenin, indicating that Notch1 can inhibit beta-catenin-mediated signaling. Our results indicate that Notch1 functions as a tumor-suppressor gene in mammalian skin.