Computational problems in perfect phylogeny haplotyping: Typing without calling the allele

A haplotype is an m-long binary vector. The XOR-genotype of two haplotypes is the m-vector of their coordinate-wise XOR. We study the following problem: Given a set of XOR-genotypes, reconstruct their haplotypes so that the set of resulting haplotypes can be mapped onto a perfect phylogeny (PP) tree. The question is motivated by studying population evolution in human genetics and is a variant of the PP haplotyping problem that has received intensive attention recently. Unlike the latter problem, in which the input is '' full '' genotypes, here, we assume less informative input and so may be more economical to obtain experimentally. Building on ideas of Gusfield, we show how to solve the problem in polynomial time by a reduction to the graph realization problem. The actual haplotypes are not uniquely determined by the tree they map onto and the tree itself may or may not be unique. We show that tree uniqueness implies uniquely determined haplotypes, up to inherent degrees of freedom, and give a sufficient condition for the uniqueness. To actually determine the haplotypes given the tree, additional information is necessary. We show that two or three full genotypes suffice to reconstruct all the haplotypes and present a linear algorithm for identifying those genotypes.

THE USEFUL SIDE OF AMBIVALENCE: Ambivalent attitudes can be adaptive and socially valued

En s'inspirant de la littérature récente qui a dépeint l'ambivalence comme étant adaptative et en lien avec des comportements stratégiques, cette thèse examine le versant utile des attitudes ambivalentes. Elle met tout d'abord en évidence que son expression peut-être sciemment contrôlée et mise en avant pour des raisons d'auto-présentation. De plus, elle démontre que les individus peuvent présenter une attitude ambivalente afin de gagner l'approbation sociale sur un objet d'attitude controversé alors que l'inverse a été observé sur des objets consensuels (Première ligne de recherche). Cette thèse a également révélé que l'expression d'attitudes ambivalentes pouvait amener à être valorisé socialement. En effet, contrairement à des attitudes plus tranchées (pro-normatives ou contre-normatives), les attitudes ambivalentes ont été évaluées de façon plus importante sur la dimension de l'utilité sociale (une dimension qui indique la compétence d'autrui ou encore la propension à évoluer dans la hiérarchie sociale). La valorisation de l'ambivalence n'est apparue que sur la dimension de l'utilité sociale et non sur la dimension de la désirabilité sociale (une dimension qui indique la sympathie d'autrui ainsi que la propension à être apprécié socialement). De plus, ce résultat a été observé sur des thèmes controversés et non sur des thèmes consensuels (Seconde ligne de recherche). Dans l'ensemble cette thèse soutient une approche de l'ambivalence comme donnant lieu à des bénéfices. Elle peut également ouvrir la voie à l'étude de l'ambivalence en lien avec la pensée critique. - Drawing on the recent literature that portrayed ambivalence as being adaptive and linked with strategic behaviors, this thesis examines the useful side of ambivalent attitudes. It first revealed that the expression of ambivalent attitudes could be controlled and purposely displayed for self-presentational concerns. Furthermore, it demonstrated that people could put ambivalence forward to gain social approval when expressing it on controversial social issues, whereas the opposite was true on consensual social issues (First line of research). The thesis also revealed that the expression of ambivalent attitudes could lead to be socially valued. Indeed, contrary to clear-cut attitudes (either pro-normative or counter-normative attitudes), ambivalent attitudes have been evaluated the highest on the social utility dimension (a dimension indicating people's competence as well as the extent to which they are likely to climb in social hierarchy). The valorization of ambivalent attitudes only appeared on social utility and not on social desirability (a dimension indicating people's niceness as well as the extent to which they are likely to be socially appreciated). This effect was true on controversial social issues but not on consensual ones (Second line of research). Overall, this thesis provides support for an approach that conceives attitudinal ambivalence as leading to benefits. It also may open avenues for the study of ambivalence in relation with critical thinking.

Aplicació del Value Stream Map (VSM) en un sistema de producció de feltres insonoritzants per a l'automòbil

Actualment en el sector industrial, les organitzacions tenen el repte d'optimitzar els seus sistemes productius per a millorar en quant a preu, qualitat i nivell de servei i poder adaptar-se a les exigències dels clients (excel·lència productiva). El present anàlisi, es basa en l'optimització d'una cadena de producció de feltres insonoritzants per a l'automòbil a través de l'eliminació de les pèrdues existents (operacions que no aporten valor afegit al producte final). Per dur-ho a terme, la metodologia emprada és el Value Stream Map (VSM). El VSM és una tècnica desenvolupada sota el model de gestió de la producció Lean Manufacturing, molt visual i entenedora, permet visualitzar i entendre l'estat actual d'un procés. Aquesta, abarca a tota la organització, i te per objectiu recolzar-la en el procés de redisseny dels seus entorns productius per assolir un estat futur millor que possibiliti obtenir resultats en un periode curt de temps. L'objectiu principal de l'estudi, és aplicar l'eina VSM com a mètode per a l'eliminació de les mudes o malbarataments que impedeix la consecució d'una cadena Lean amb el cas concret d'un sistema productiu de feltres insonoritzants. En la primera part del projecte s'introdueix al lector en la teoria del pensament Lean (quins principis té i quins són els objectius) com a marc teòric. Aquí es detalla el procediment, així com les característiques per a la correcta elaboració del VSM actual, per al seu corresponent anàlisi i per a la seva representació del estat futur. En una segona part del projecte, s'exposen les etapes que constitueixen la cadena de producció d'estudi i es duu a terme l'elaboració del Value Stream Map, on es posen de manifest les ineficiències del flux que conformen la línia de producció. Per últim s'analitzen els fluxes, s'identifiquen les pèrdues de la cadena, i a partir d'aquests, es dissenyen i es proposen projectes i accions que permitin establir línies d'actuació per a un millor estat futur. L'estudi ha permés demostrar la validesa del VSM com a eina per a facilitar la consecució i assoliment de millores en la productivitat, competitivitat i rendibilitat dels diferents processos de l'organització en la línia de fabricació de feltres insonoritzats.

Global periodicity conditions for maps and recurrences via Normal Forms

We face the problem of characterizing the periodic cases in parametric families of (real or complex) rational diffeomorphisms having a fixed point. Our approach relies on the Normal Form Theory, to obtain necessary conditions for the existence of a formal linearization of the map, and on the introduction of a suitable rational parametrization of the parameters of the family. Using these tools we can find a finite set of values p for which the map can be p-periodic, reducing the problem of finding the parameters for which the periodic cases appear to simple computations. We apply our results to several two and three dimensional classes of polynomial or rational maps. In particular we find the global periodic cases for several Lyness type recurrences

On the bicanonical map of irregular varieties

From the point of view of uniform bounds for the birationality of pluricanonical maps, irregular varieties of general type and maximal Albanese dimension behave similarly to curves. In fact Chen-Hacon showed that, at least when their holomorphic Euler characteristic is positive, the tricanonical map of such varieties is always birational. In this paper we study the bicanonical map. We consider the natural subclass of varieties of maximal Albanese dimension formed by primitive varieties of Albanese general type. We prove that the only such varieties with non-birational bicanonical map are the natural higher-dimensional generalization to this context of curves of genus $2$: varieties birationally equivalent to the theta-divisor of an indecomposable principally polarized abelian variety. The proof is based on the (generalized) Fourier-Mukai transform.

Let's K-map play : Juego de aprendizaje de Karnaugh Maps para móvil

En este informe se describe el trabajo de fin de máster, centrado en el estudio de la gamificación como herramienta de aprendizaje aplicada a dispositivos móviles. Se ha realizado una revisión de los artículos científicos que tratan sobre el tema de la gamificación como herramienta educativa, para terminar el trabajo desarrollando un prototipo de juego para el aprendizaje de mapas de Karnaugh. Se ha optado por un desarrollo multiplataforma y se han revisado los frameworks de desarrollo más populares para desarrollo móvil multiplataforma, así como los motores de juegos aplicables a este caso. Tras la implementación, se ha probado el prototipo en dos sistemas operativos móviles libres: Android y Firefox OS.

Iowa Transportation Map 2015-2016, March 2015

Transportation map of Iowa, updated march 1, 2014. map focuses on interstate highways, primary and secondary state roads, county roads, and scenic byways. Also includes railroad lines, airports, waterways, and locks and dams. All 99 counties are represented, as well as approximately 1,000 cities and towns. Points of interest are also marked. This record contains images of both the front and the back of the map.

Iowa 2015-2016 Bicycle Map, 2015

Iowa has more than 1,800 miles of beautiful trails available for a variety of uses, including bicycling, hiking/running, skating, equestrian use, cross-country skiing, snowmobiling, and photography/nature study. This map lists and highlights 60 trails of 5 miles length or great. It also indicates where shorter trails exist. This record contains PDFs of the full front and back of the map. Inset maps of 16 major cities and their trail systems are included in this record.

Typing less common ovarian tumors: A training tool based on a pattern-based algorithm applied to a set of 20 virtual slides.

Context: Ovarian tumors (OT) typing is a competency expected from pathologists, with significant clinical implications. OT however come in numerous different types, some rather rare, with the consequence of few opportunities for practice in some departments. Aim: Our aim was to design a tool for pathologists to train in less common OT typing. Method and Results: Representative slides of 20 less common OT were scanned (Nano Zoomer Digital Hamamatsu®) and the diagnostic algorithm proposed by Young and Scully applied to each case (Young RH and Scully RE, Seminars in Diagnostic Pathology 2001, 18: 161-235) to include: recognition of morphological pattern(s); shortlisting of differential diagnosis; proposition of relevant immunohistochemical markers. The next steps of this project will be: evaluation of the tool in several post-graduate training centers in Europe and Québec; improvement of its design based on evaluation results; diffusion to a larger public. Discussion: In clinical medicine, solving many cases is recognized as of utmost importance for a novice to become an expert. This project relies on the virtual slides technology to provide pathologists with a learning tool aimed at increasing their skills in OT typing. After due evaluation, this model might be extended to other uncommon tumors.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.

On the connectivity of the escaping set for complex exponential Misiurewicz parameters

Let $ E_{\lambda}(z)=\lambda {\rm exp}(z), \lambda\in \mathbb{C}$, be the complex exponential family. For all functions in the family there is a unique asymptotic value at 0 (and no critical values). For a fixed $ \lambda$, the set of points in $ \mathbb{C}$ with orbit tending to infinity is called the escaping set. We prove that the escaping set of $ E_{\lambda}$ with $ \lambda$ Misiurewicz (that is, a parameter for which the orbit of the singular value is strictly preperiodic) is a connected set.

Set reformulacions per a una dramatúrgia interactiva

La hibridació de les noves tecnologies amb la posada en escena, en obres i espais de representació, està obrint noves formes d'aproximació al fet dramatúrgic. Així s'ha esdevingut en la història del teatre sobre l'escriptura, l'escenografia o l'acció actoral. El que aquí volem tractar és com les tecnologies interactives poden representar un altre d'aquests moments d'inflexió. Aquest article parteix de l'experiència obtinguda en la direcció, juntament amb Montse Figueras, de la instal·lació Prometzeus presentada a la sala Muncunill de Terrassa el 2004. Una aproximació amateur en l’experimentació de noves dramatúrgies que feia ús de tecnologies audiovisuals interactives. Volem presentar una primera reflexió sobre la qüestió i exposar set d'aquestes possibles reformulacions. Set punts on les tecnologies interactives reformulen el llenguatge teatral.

On the preservation of combinatorial types for maps on trees

We study the preservation of the periodic orbits of an A-monotone tree map f:T→T in the class of all tree maps g:S→S having a cycle with the same pattern as A. We prove that there is a period-preserving injective map from the set of (almost all) periodic orbits of ƒ into the set of periodic orbits of each map in the class. Moreover, the relative positions of the corresponding orbits in the trees T and S (which need not be homeomorphic) are essentially preserved

Sierpinski curve Julia sets for quadratic rational maps

We investigate under which dynamical conditions the Julia set of a quadratic rational map is a Sierpiński curve.