On the use of principal components in contemporany population genetics: a case study

In human Population Genetics, routine applications of principal component techniques are oftenrequired. Population biologists make widespread use of certain discrete classifications of humansamples into haplotypes, the monophyletic units of phylogenetic trees constructed from severalsingle nucleotide bimorphisms hierarchically ordered. Compositional frequencies of the haplotypesare recorded within the different samples. Principal component techniques are then required as adimension-reducing strategy to bring the dimension of the problem to a manageable level, say two,to allow for graphical analysis.Population biologists at large are not aware of the special features of compositional data and normally make use of the crude covariance of compositional relative frequencies to construct principalcomponents. In this short note we present our experience with using traditional linear principalcomponents or compositional principal components based on logratios, with reference to a specificdataset

Validation of order rank scales based on compositional data analysis: a proposal

Usually, psychometricians apply classical factorial analysis to evaluate construct validity of order rankscales. Nevertheless, these scales have particular characteristics that must be taken into account: totalscores and rank are highly relevant

Reconstruction of a superscheme from its derived category

The aim of this paper is to construct a "super" version of a tensor triangulated category, and to show that super-schemes can be reconstructed from its category of perfect complexes in a way similar to Balmer [Bal05] provided we consider this extra structure.

Schwarz methods for a preconditioned WOPSIP method for elliptic problems

We construct and analyze non-overlapping Schwarz methods for a preconditioned weakly over-penalized symmetric interior penalty (WOPSIP) method for elliptic problems.

On spectral approximation, Folner sequences and crossed products

In this article we review first some of the possibilities in which the notions of Fo lner sequences and quasidiagonality have been applied to spectral approximation problems. We construct then a canonical Fo lner sequence for the crossed product of a concrete C* -algebra and a discrete amenable group. We apply our results to the rotation algebra (which contains interesting operators like almost Mathieu operators or periodic magnetic Schrödinger operators on graphs) and the C* -algebra generated by bounded Jacobi operators.

Al di là del fiume - attraverso il fiume: il basso corso del Ter in Catalogna

La ricerca prende in considerazione dal punto di vista dell’architettura e dell’urbanistica la relazione tra la città e il fiume che la attraversa o la lambisce; l’insediamento umano viene analizzato nel contesto del bacino idrografico al quale appartiene. La ricerca è stata sviluppata in seno alla tesi dottorale ora in fase di elaborazione presso il Departamento de Urbanismo y Ordenación del Territorio dell’Universidad Politecnica de Catalunya. La tesi ha come caso studio il tratto basso del fiume Ter in Catalogna. Nella discussione sul paesaggio urbano contemporaneo oggi la riflessione è centrata sulla città che si territorializza; la dimensione urbana interferisce con gran parte della superficie della terra facendo sfumare le tradizionali distinzioni tra urbano e non-urbano, tra spazio costruito e spazio aperto. In questo contesto, quale termine di conciliazione tra la dinamica naturale e la costruzione storica dei luoghi prodotta dall’intervento umano, il fiume si rivela uno strumento essenziale di analisi e progetto. L’obiettivo di questa ricerca è suggerire un’approssimazione al progetto della città che si sviluppa lungo il corso fluviale costruendo strumenti per la riflessione “attraverso il fiume”. Partendo dall’ipotesi che la città si insedia lungo un corso d’acqua secondo una sintassi territoriale stabilita dalla geografía e dalla geomorfologia del fiume stesso, il fine è fornire strumenti per il processo di recupero degli spazi fluviali in contesti urbanizzati. Il fiume diviene componente geografica chiave degli insediamenti dispersi e risorsa per costruirne l’abitabilità.

Searching patterns in painting images with computer vision techniques

This paper presents a pattern recognition method focused on paintings images. The purpose is construct a system able to recognize authors or art styles based on common elements of his work (here called patterns). The method is based on comparing images that contain the same or similar patterns. It uses different computer vision techniques, like SIFT and SURF, to describe the patterns in descriptors, K-Means to classify and simplify these descriptors, and RANSAC to determine and detect good results. The method are good to find patterns of known images but not so good if they are not.

Incidència de l’entorn educatiu, familiar i social en les actituds lingüístiques i identitàries dels joves d’origen xinès i llatinoamericà a Catalunya

From an interdisciplinary perspective, the present investigation undertaken by the GREILI-UPF research group has expanded a previous study aiming at explaining how young secondary school students of Latin American and Chinese origin in Catalonia construct their linguistic and cultural identity. Here we analyze the relationship between these youngsters and their social environment in order to determine how these relationships and the socialization process that derives from them influence language attitudes and practices. We focus on two spaces of socialization: (1) the school, where youngsters from diverse cultural and linguistic backgrounds coexist and interact, and (2) the neighborhood, a geographic and symbolic space where social identity is constructed and, consequently, where young newcomers construct their perceptions regarding the host society, including its linguistic reality. We have collected several sets of data in three public secondary schools and three neighborhoods from Barcelona’s metropolitan area with a high index of immigrant population: (1) interviews with secondary school students, (2) interviews with teachers, (3) social discourses in newspapers that consolidate the social image of the neighborhood, (4) narratives from immigrant families in relation to their neighborhood, (5) participant observation in schools, and (5) observation in the neighborhood. The results of the thematic and, when appropriate, discursive analysis of the data allow us to reach conclusions regarding: (a) the social image of the neighborhoods, (b) the socialization of young newcomers in the schools and the neighborhoods, (c) the identity games, and (d) the language and cultural practices and attitudes of young people, in relation to their countries and languages of origin as well as the school and the neighborhood investigated.

Art painting Data Collection

The classification of Art painting images is a computer vision applications that isgrowing considerably. The goal of this technology, is to classify an art paintingimage automatically, in terms of artistic style, technique used, or its author. For thispurpose, the image is analyzed extracting some visual features. Many articlesrelated with these problems have been issued, but in general the proposed solutionsare focused in a very specific field. In particular, algorithms are tested using imagesat different resolutions, acquired under different illumination conditions. Thatmakes complicate the performance comparison of the different methods. In thiscontext, it will be very interesting to construct a public art image database, in orderto compare all the existing algorithms under the same conditions. This paperpresents a large art image database, with their corresponding labels according to thefollowing characteristics: title, author, style and technique. Furthermore, a tool thatmanages this database have been developed, and it can be used to extract differentvisual features for any selected image. This data can be exported to a file in CSVformat, allowing researchers to analyze the data with other tools. During the datacollection, the tool stores the elapsed time in the calculation. Thus, this tool alsoallows to compare the efficiency, in computation time, of different mathematicalprocedures for extracting image data.

EU cohesion aid to Spain: a data set. Part II: 1994-99 planning period

In this paper we construct a data set on EU cohesion aid to Spain during the planning period 1994-99. The data are disaggregated by region, year and function and attempt to approximate the timing of actual executed expenditure on assisted projects.

Sistema d'AGV (vehicles-robot de guiatge automàtic) per a magatzems i plantes de manufactura

Una de les solucions per a minimitzar els costos de producció o d'emmagatzematge és automatitzarne la logística interna. Per dissenyar les aplicacions corresponents és convenient poder validar-les amb un prototipatge. Això ha motivat la realització d'aquest projecte, on s'ha obtingut un prototip d'AGV (automated guided vehicle) que rep les ordres per Bluetooth i, mitjançant uns infrarojos per poder seguir unes línies al terra, és capaç d'anar des del punt inicial fins on se li ha encarregat i tornar al punt inicial. Aquest vehicle pot servir de base per a la implementació d'AGV orientats a aplicacions reals i, per tant, per a la construcció de sistemes més grans i que poden ser utilitzats en plantes de producció, laboratoris, magatzems, ports i d'altres aplicacions diverses.

The COSMIN checklist for evaluating the methodological quality of studies on measurement properties: a clarification of its content

Background: The COSMIN checklist (COnsensus-based Standards for the selection of health status Measurement INstruments) was developed in an international Delphi study to evaluate the methodological quality of studies on measurement properties of health-related patient reported outcomes (HR-PROs). In this paper, we explain our choices for the design requirements and preferred statistical methods for which no evidence is available in the literature or on which the Delphi panel members had substantial discussion. Methods: The issues described in this paper are a reflection of the Delphi process in which 43 panel members participated. Results: The topics discussed are internal consistency (relevance for reflective and formative models, and distinction with unidimensionality), content validity (judging relevance and comprehensiveness), hypotheses testing as an aspect of construct validity (specificity of hypotheses), criterion validity (relevance for PROs), and responsiveness (concept and relation to validity, and (in) appropriate measures).Conclusions: We expect that this paper will contribute to a better understanding of the rationale behind the items, thereby enhancing the acceptance and use of the COSMIN checklist.

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.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci

For the ∼1% of the human genome in the ENCODE regions, only about half of the transcriptionally active regions (TARs) identified with tiling microarrays correspond to annotated exons. Here we categorize this large amount of “unannotated transcription.” We use a number of disparate features to classify the 6988 novel TARs—array expression profiles across cell lines and conditions, sequence composition, phylogenetic profiles (presence/absence of syntenic conservation across 17 species), and locations relative to genes. In the classification, we first filter out TARs with unusual sequence composition and those likely resulting from cross-hybridization. We then associate some of those remaining with proximal exons having correlated expression profiles. Finally, we cluster unclassified TARs into putative novel loci, based on similar expression and phylogenetic profiles. To encapsulate our classification, we construct a Database of Active Regions and Tools (DART.gersteinlab.org). DART has special facilities for rapidly handling and comparing many sets of TARs and their heterogeneous features, synchronizing across builds, and interfacing with other resources. Overall, we find that ∼14% of the novel TARs can be associated with known genes, while ∼21% can be clustered into ∼200 novel loci. We observe that TARs associated with genes are enriched in the potential to form structural RNAs and many novel TAR clusters are associated with nearby promoters. To benchmark our classification, we design a set of experiments for testing the connectivity of novel TARs. Overall, we find that 18 of the 46 connections tested validate by RT-PCR and four of five sequenced PCR products confirm connectivity unambiguously.

Generation of mouse-induced pluripotent stem cells by transient expression of a single nonviral polycistronic vector

Induced pluripotent stem (iPS) cells have generated keen interestdue to their potential use in regenerative medicine. They havebeen obtained from various cell types of both mice and humans byexogenous delivery of different combinations of Oct4, Sox2, Klf4,c-Myc, Nanog, and Lin28. The delivery of these transcription factorshas mostly entailed the use of integrating viral vectors (retrovirusesor lentiviruses), carrying the risk of both insertional mutagenesisand oncogenesis due to misexpression of these exogenousfactors. Therefore, obtaining iPS cells that do not carry integratedtransgene sequences is an important prerequisite for their eventualtherapeutic use. Here we report the generation of iPS cell linesfrom mouse embryonic fibroblasts with no evidence of integrationof the reprogramming vector in their genome, achieved by nucleofectionof a polycistronic construct coexpressing Oct4, Sox2, Klf4,and c-Myc