Hardy-Weinberg Equilibrium and the Ternary Plot

The Hardy-Weinberg law, formulated about 100 years ago, states that under certainassumptions, the three genotypes AA, AB and BB at a bi-allelic locus are expected to occur inthe proportions p2, 2pq, and q2 respectively, where p is the allele frequency of A, and q = 1-p.There are many statistical tests being used to check whether empirical marker data obeys theHardy-Weinberg principle. Among these are the classical xi-square test (with or withoutcontinuity correction), the likelihood ratio test, Fisher's Exact test, and exact tests in combinationwith Monte Carlo and Markov Chain algorithms. Tests for Hardy-Weinberg equilibrium (HWE)are numerical in nature, requiring the computation of a test statistic and a p-value.There is however, ample space for the use of graphics in HWE tests, in particular for the ternaryplot. Nowadays, many genetical studies are using genetical markers known as SingleNucleotide Polymorphisms (SNPs). SNP data comes in the form of counts, but from the countsone typically computes genotype frequencies and allele frequencies. These frequencies satisfythe unit-sum constraint, and their analysis therefore falls within the realm of compositional dataanalysis (Aitchison, 1986). SNPs are usually bi-allelic, which implies that the genotypefrequencies can be adequately represented in a ternary plot. Compositions that are in exactHWE describe a parabola in the ternary plot. Compositions for which HWE cannot be rejected ina statistical test are typically “close" to the parabola, whereas compositions that differsignificantly from HWE are “far". By rewriting the statistics used to test for HWE in terms ofheterozygote frequencies, acceptance regions for HWE can be obtained that can be depicted inthe ternary plot. This way, compositions can be tested for HWE purely on the basis of theirposition in the ternary plot (Graffelman & Morales, 2008). This leads to nice graphicalrepresentations where large numbers of SNPs can be tested for HWE in a single graph. Severalexamples of graphical tests for HWE (implemented in R software), will be shown, using SNPdata from different human populations

Steven Spielberg descubre Tintín con El secreto del unicornio

El secreto del Unicornio es la décima novela gráfica de la serie Las aventuras de Tintín,3 del autor belga Georges Prosper Remi, más conocido por su seudónimo Hergé. El relato que ahora presentamos5 es la primera parte del que le sigue, El tesoro de Rackham el Rojo, y cinematográficamente corresponderá a una futura segunda parte del filme. Tintín, joven reportero belga, se mete a menudo en problemas por defender causas justas.

Greek by Steven Berkoff (1980): The Risky Transformation of Sophocles’ Oedipus Rex into a Love Story

[eng] Can Sophocles’ Oedipus Rex really be transformed into a love story, as in Steven Berkoff’s drama entitled Greek? This article will show that, although Greek may be viewed by some critics as simply a provocative drama by no means intended to justify incest, directors, actors and critics in the end become enthralled by the powerful love story that ensues between Eddy and his wife and mother. This perspective reveals that Berkoff’s adaptation, intended to portray the social degradation of 1980s Great Britain, is in reality a quite risky proposition since it represents a flat denial of the tragic awareness of contemporary men and women. However, if this is the case, the audience, apart from enjoying the performance of Berkoff’s drama, might question, even from a non-fundamentalist perspective within the classical tradition, to what degree it makes sense to take inspiration from a text by Sophocles that precisely illustrates the great tragic awareness of the ancient Greeks.

Greek de Steven Berkoff (1980): L’arriscada conversió de l’Èdip rei de Sòfocles en una love story

[cat] ¿Podem convertir l’Èdip rei de Sòfocles en una història d’amor com ho fa Berkoff a Greek?. Tot i que alguns crítics llegeixen Greek només com un drama provocador que de cap manera intenta justificar l’incest, directors, actors i crítics resten finalment captivats per la impactant història d’amor entre Eddy i la seva esposa-mare. Això demostraria que l’adaptació de Berkoff, pensada per a il·lustrar la degradació social de la Gran Bretanya dels 80s, esdevé una proposta arriscada, car significa negar de fet la consciència tràgica dels homes i dones contemporanis. Tanmateix, si aquest és el cas, lectors i espectadors, a banda de l’indubtable plaer d’assistir a la representació de Greek, poden preguntar-se, fins i tot des d’una perspectiva no fonamentalista de la tradició clàssica, si té sentit inspirar-se en el text de Sòfocles, el qual mostra precisament la gran consciència tràgica dels grecs.

Conversation is the Key : A Short History of Smarthistory.org

Smarthistory.org is a proven, sustainable model for open educational resources in the Humanities. We discuss lessons learned during its agile development. Smarthistory.org is a free, creative-commons licensed, multi-media web-book designed as a dynamic enhancement or substitute for the traditional art history textbook. It uses conversation instead of the impersonal voice of the typical textbook in-order to reveal disagreement, emotion, and the experience of looking. The listener remains engaged with both the content and the interaction of the speakers. These conversations model close looking and a willingness to encounter and engage the unfamiliar. Smarthistory takes the inherent dialogic and multimedia nature of the web and uses it as a pedagogical method. This extendable Humanities framework uses an open-source content management system making Smarthistory inexpensive to create, and easy to manage and update. Its chronological timeline/chapter-based format integrates new contributions into a single historical framework, a structure applicable across the Humanities.

Quantifying rock fabrics: a test of autocorrelation of the spatial distribution of cristals

A novel test of spatial independence of the distribution of crystals or phases in rocksbased on compositional statistics is introduced. It improves and generalizes the commonjoins-count statistics known from map analysis in geographic information systems.Assigning phases independently to objects in RD is modelled by a single-trial multinomialrandom function Z(x), where the probabilities of phases add to one and areexplicitly modelled as compositions in the K-part simplex SK. Thus, apparent inconsistenciesof the tests based on the conventional joins{count statistics and their possiblycontradictory interpretations are avoided. In practical applications we assume that theprobabilities of phases do not depend on the location but are identical everywhere inthe domain of de nition. Thus, the model involves the sum of r independent identicalmultinomial distributed 1-trial random variables which is an r-trial multinomialdistributed random variable. The probabilities of the distribution of the r counts canbe considered as a composition in the Q-part simplex SQ. They span the so calledHardy-Weinberg manifold H that is proved to be a K-1-affine subspace of SQ. This isa generalisation of the well-known Hardy-Weinberg law of genetics. If the assignmentof phases accounts for some kind of spatial dependence, then the r-trial probabilitiesdo not remain on H. This suggests the use of the Aitchison distance between observedprobabilities to H to test dependence. Moreover, when there is a spatial uctuation ofthe multinomial probabilities, the observed r-trial probabilities move on H. This shiftcan be used as to check for these uctuations. A practical procedure and an algorithmto perform the test have been developed. Some cases applied to simulated and realdata are presented.Key words: Spatial distribution of crystals in rocks, spatial distribution of phases,joins-count statistics, multinomial distribution, Hardy-Weinberg law, Hardy-Weinbergmanifold, Aitchison geometry

Improving gene annotation using peptide mass spectrometry

Annotation of protein-coding genes is a key goal of genome sequencing projects. In spite of tremendous recent advances in computational gene finding, comprehensive annotation remains a challenge. Peptide mass spectrometry is a powerful tool for researching the dynamic proteome and suggests an attractive approach to discover and validate protein-coding genes. We present algorithms to construct and efficiently search spectra against a genomic database, with no prior knowledge of encoded proteins. By searching a corpus of 18.5 million tandem mass spectra (MS/MS) from human proteomic samples, we validate 39,000 exons and 11,000 introns at the level of translation. We present translation-level evidence for novel or extended exons in 16 genes, confirm translation of 224 hypothetical proteins, and discover or confirm over 40 alternative splicing events. Polymorphisms are efficiently encoded in our database, allowing us to observe variant alleles for 308 coding SNPs. Finally, we demonstrate the use of mass spectrometry to improve automated gene prediction, adding 800 correct exons to our predictions using a simple rescoring strategy. Our results demonstrate that proteomic profiling should play a role in any genome sequencing project.

@neurIST infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services

The increasing volume of data describing humandisease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the@neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets the investigation and treatment of cerebral aneurysms, the system’s architecture is generic enough that it could be adapted to the treatment of other diseases.Innovations in @neurIST include confining the patient data pertaining to aneurysms inside a single environment that offers cliniciansthe tools to analyze and interpret patient data and make use of knowledge-based guidance in planning their treatment. Medicalresearchers gain access to a critical mass of aneurysm related data due to the system’s ability to federate distributed informationsources. A semantically mediated grid infrastructure ensures that both clinicians and researchers are able to seamlessly access andwork on data that is distributed across multiple sites in a secure way in addition to providing computing resources on demand forperforming computationally intensive simulations for treatment planning and research.

Creación de una empresa: Bambú Lògic

Este trabajo analiza el desarrollo y viabilidad de un proyecto empresarial que pretende introducir un producto muy poco explotado en España. Se trata de un sustitutivo casi perfecto de los suelos de madera, de menor coste para el consumidor y totalmente ecológico, el parquet de bambú. Sin embargo, entrar en el mercado español actualmente puede ser muy arriesgado puesto que se trata de un producto de la construcción.A lo largo de este documento se analizan los posibles factores que podrían provocar dicho fracaso como el estado del sector de la construcción o el clima económico general para las empresas en España. También se estudia el comportamiento del consumidor frente a nuevos productos de la construcción y su compromiso con los problemas medioambientales y el interés de empresas de distintos sectores por ofrecer a sus clientes una imagen más cercana fundamentada en los pilares de la sostenibilidad. Posteriormente, este trabajo también realiza un plan financiero, económico y de marketing con resultados sorprendentemente positivos para tener una imagen un poco más real de esta futura empresa en el caso que los socios decidieran establecerse en España.

Macroprudential policy, countercyclical bank capital buffers and credit supply: Evidence from the Spanish dynamic provisioning experiments

We analyze the impact of countercyclical capital buffers held by banks on the supplyof credit to firms and their subsequent performance. Spain introduced dynamicprovisioning unrelated to specific bank loan losses in 2000 and modified its formulaparameters in 2005 and 2008. In each case, individual banks were impacteddifferently. The resultant bank-specific shocks to capital buffers, coupled withcomprehensive bank-, firm-, loan-, and loan application-level data, allow us toidentify its impact on the supply of credit and on real activity. Our estimates showthat countercyclical dynamic provisioning smooths cycles in the supply of credit andin bad times upholds firm financing and performance.

The evolution of personally disadvantageous punishment among cofoundresses of the ant Acromyrmex versicolor

Cofoundresses of the desert fungus garden ant Acromyrmex versicolorexhibit a forager specialist who subsumes all foraging risk priorto first worker eclosion (Rissing et al. 1989). In an experimentdesigned to mimic a "cheater" who refuses foraging assignment whenher lot, cofoundresses delayed/failed to replace their forager,often leading to demise of their garden (Rissing et al. 1996). Thecheater on task assignment is harmed, but so too is the punisher,as all will die without a healthy garden. In this paper we studythrough simulation the cofoundress interaction with haploid, asexualgenotypes which either replace a cheater or not (punishment), underboth foundress viscosity (likely for A. versicolor) and randomassortment. We find replacement superior to punishment only whenthere is no foraging risk and cheating is not costly to groupsurvival. Generally, punishment is evolutionarily superior,especially as forager risk increases, under both forms of dispersal.

Development and Validation of Single Nucleotide Polymorphisms (SNPs) Markers from Two Transcriptome 454-Runs of Turbot (Scophthalmus maximus) Using High-Throughput Genotyping

The turbot (Scophthalmus maximus) is a commercially valuable flatfish and one of the most promising aquaculture species in Europe. Two transcriptome 454-pyrosequencing runs were used in order to detect Single Nucleotide Polymorphisms (SNPs) in genesrelated to immune response and gonad differentiation. A total of 866 true SNPs were detected in 140 different contigs representing 262,093 bp as a whole. Only one true SNP was analyzed in each contig. One hundred and thirteen SNPs out of the 140 analyzed were feasible (genotyped), while Ш were polymorphic in a wild population. Transition/transversion ratio (1.354) was similar to that observed in other fish studies. Unbiased gene diversity (He) estimates ranged from 0.060 to 0.510 (mean = 0.351), minimum allele frequency (MAF) from 0.030 to 0.500 (mean = 0.259) and all loci were in Hardy-Weinberg equilibrium after Bonferroni correction. A large number of SNPs (49) were located in the coding region, 33 representing synonymous and 16 non-synonymous changes. Most SNP-containing genes were related to immune response and gonad differentiation processes, and could be candidates for functional changes leading to phenotypic changes. These markers will be useful for population screening to look for adaptive variation in wild and domestic turbot

Buy-and-Hold Strategies and Comonotonic Approximations

[cat] En aquest article estudiem estratègies “comprar i mantenir” per a problemes d’optimitzar la riquesa final en un context multi-període. Com que la riquesa final és una suma de variables aleatòries dependents, on cadascuna d’aquestes correspon a una quantitat de capital que s’ha invertit en un actiu particular en una data determinada, en primer lloc considerem aproximacions que redueixen l’aleatorietat multivariant al cas univariant. A continuació, aquestes aproximacions es fan servir per determinar les estratègies “comprar i mantenir” que optimitzen, per a un nivell de probabilitat donat, el VaR i el CLTE de la funció de distribució de la riquesa final. Aquest article complementa el treball de Dhaene et al. (2005), on es van considerar estratègies de reequilibri constant.

Buy-and-Hold Strategies and Comonotonic Approximations

[cat] En aquest article estudiem estratègies “comprar i mantenir” per a problemes d’optimitzar la riquesa final en un context multi-període. Com que la riquesa final és una suma de variables aleatòries dependents, on cadascuna d’aquestes correspon a una quantitat de capital que s’ha invertit en un actiu particular en una data determinada, en primer lloc considerem aproximacions que redueixen l’aleatorietat multivariant al cas univariant. A continuació, aquestes aproximacions es fan servir per determinar les estratègies “comprar i mantenir” que optimitzen, per a un nivell de probabilitat donat, el VaR i el CLTE de la funció de distribució de la riquesa final. Aquest article complementa el treball de Dhaene et al. (2005), on es van considerar estratègies de reequilibri constant.