RECERCAT - Articles publicats en revistes (Estadística)

North African populations carry the signature of admixture with Neandertals

North African populations carry the signature of admixture with Neandertals Sánchez Quinto, F.; Rodríguez Botigué, L..; Civit Vives, Sergi; Arenas Solà, Concepción; Ávila-Arcos, M.C.; Bustamante, C.D.; Comas, D.; Lalueza Fox, Carles, 1965- One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics

Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics García Garcerà, M.; Gigli, E.; Sanchez Quinto, F.; Ramirez, O.; Calafell, F.; Civit Vives, Sergi; Lalueza Fox, C. Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks.

Search for Specific Biomarkers of IFNb Bioactivity in Patients with Multiple Sclerosis

Search for Specific Biomarkers of IFNb Bioactivity in Patients with Multiple Sclerosis Malhotra, S.; Bustamante, Marta F.; Perez Miralles, F.; Riol, J.; Ruiz de Villa, M.C.; Vegas, E.; Nonell, L.; Deisenhammer, F.; Fissolo, N.; Nurtdinov, Ramil N.; Montalban, X.; Comabella, M. Myxovirus A (MxA), a protein encoded by the MX1 gene with antiviral activity, has proven to be a sensitive measure of IFNβ bioactivity in multiple sclerosis (MS). However, the use of MxA as a biomarker of IFNβ bioactivity has been criticized for the lack of evidence of its role on disease pathogenesis and the clinical response to IFNβ. Here, we aimed to identify specific biomarkers of IFNβ bioactivity in order to compare their gene expression induction by type I IFNs with the MxA, and to investigate their potential role in MS pathogenesis. Gene expression microarrays were performed in PBMC from MS patients who developed neutralizing antibodies (NAB) to IFNβ at 12 and/or 24 months of treatment and patients who remained NAB negative. Nine genes followed patterns in gene expression over time similar to the MX1, which was considered the gold standard gene, and were selected for further experiments: IFI6, IFI27, IFI44L, IFIT1, HERC5, LY6E, RSAD2, SIGLEC1, and USP18. In vitro experiments in PBMC from healthy controls revealed specific induction of selected biomarkers by IFNβ but not IFNγ, and several markers, in particular USP18 and HERC5, were shown to be significantly induced at lower IFNβ concentrations and more selective than the MX1 as biomarkers of IFNβ bioactivity. In addition, USP18 expression was deficient in MS patients compared with healthy controls (p = 0.0004). We propose specific biomarkers that may be considered in addition to the MxA to evaluate IFNβ bioactivity, and to further explore their implication in MS pathogenesis.

Ultra-Deep Pyrosequencing Detects Conserved Genomic Sites and Quantifies Linkage of Drug-Resistant Amino Acid Changes in the Hepatitis B Virus Genome

Ultra-Deep Pyrosequencing Detects Conserved Genomic Sites and Quantifies Linkage of Drug-Resistant Amino Acid Changes in the Hepatitis B Virus Genome Rodriguez Frías, F.; Tabernero, D.; Quer, J.; Esteban, J.I.; Ortega, I.; Domingo, E.; Cubero, M.; Camos, S.; Ferrer Costa, C.; Sànchez, Àlex (Sànchez Pla); Jardí, R.; Schaper, M.; Homs, M.; García Cehic, M.; Guardia, J.; Esteban, R.; Buti, M. Selection of amino acid substitutions associated with resistance to nucleos(t)ide-analog (NA) therapy in the hepatitis B virus (HBV) reverse transcriptase (RT) and their combination in a single viral genome complicates treatment of chronic HBV infection and may affect the overlapping surface coding region. In this study, the variability of an overlapping polymerase-surface region, critical for NA resistance, is investigated before treatment and under antiviral therapy, with assessment of NA-resistant amino acid changes simultaneously occurring in the same genome (linkage analysis) and their influence on the surface coding region.

Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli.

Similar and Divergent Effects of ppGpp and DksA Deficiencies on Transcription in Escherichia coli. Aberg, A.; Fernández Vázquez, Jorge; Cabrer-Panes, J.D.; Sànchez, Àlex (Sànchez Pla); Balsalobre Parra, Carlos The concerted action of ppGpp and DksA in transcription has been widely documented. In disparity with this model, phenotypic studies showed that ppGpp and DksA might also have independent and opposing roles in gene expression in Escherichia coli. In this study we used a transcriptomic approach to compare the global transcriptional patterns of gene expression in strains deﬁcient in ppGpp (ppGpp0) and/or DksA ( dksA). Approximately 6 and 7% of all genes were signiﬁcantly affected by more than twofold in ppGpp- and DksAdeﬁcient strains, respectively, increasing to 13% of all genes in the ppGpp0 dksA strain. Although the data indicate that most of the affected genes were copositively or conegatively regulated by ppGpp and DksA, some genes that were independently and/or differentially regulated by the two factors were found. The large functional group of chemotaxis and ﬂagellum synthesis genes were notably differentially affected, with all genes being upregulated in the DksA-deﬁcient strain but 60% of them being downregulated in the ppGpp-deﬁcient strain. Revealingly, mutations in the antipausing Gre factors suppress the upregulation observed in the DksA-deﬁcient strain, emphasizing the importance of the secondary channel of the RNA polymerase for regulation and ﬁne-tuning of gene expression in E. coli.

White eye phenotypes and their genetic analysis

White eye phenotypes and their genetic analysis Mestres i Naval, Francesc; Arenas Solà, Concepción An interesting case for undergraduate students of general Genetics is to consider that different genes can produce the same or similar phenotypes. We present here an experiment to discover that the same phenotype could be produced by different genes, and then, to carry out the genetic analysis of these genes. For this laboratory study we have used the following Drosophila melanogaster strains: white (white eyes) and scarlet
brown (white eyes).

El análisis canónico y su aplicación en Geologia

El análisis canónico y su aplicación en Geologia Cuadras, C. M. (Carlos María); Campá Viñeta, Juan A.; Montoriol-Pous, Joaquín, 1924-2011 Se exponen los fundamentos del análisis canóiiico, combinación del análisis de la varianza y del factorial, así como sus posibles aplicaciones a los problemas geológicos.

Adaptación española del cuestionario E.P.I. de Eysenck

Adaptación española del cuestionario E.P.I. de Eysenck Sánchez Turet, Miguel, 1942-2008; Cuadras, C. M. (Carlos María) A partir de la evolución de la estructura del gasto alimentario en los hogares españoles a lo largo de los últimos cuarenta, el artículo analiza la relación entre los cambios sociales, económicos, tecnológicos, demogrdficos, ideológicos, sanitarios, de estética corporal, etc. y los cambios habidos en 10s comportamientos alimentarios. Estos cambios permiten caracterizar una ccmodemidad alimentarias cuyos contenidos referirían a una articulación dinámica y compleja entre una revalorizacibn de las tradiciones culinarias y una udlización cada vez más frecuente de los productos elaborados por las industrias alimentarias.

El tratamiento numérico de la realidad. Reflexiones sobre la importancia actual de la estadística en la Sociedad de la Información.

El tratamiento numérico de la realidad. Reflexiones sobre la importancia actual de la estadística en la Sociedad de la Información. Monleón Getino, Toni La estadística se ha convertido en un método práctico para describir los valores de datos económicos, políticos, sociales, psicológicos, médicos, biológicos y físicos, como herramienta para relacionar y analizar dichos datos. El trabajo del estadístico no consiste sólo en obtener, reunir o tabular los datos, sino sobre todo el proceso de interpretación de esa información solo o en colaboración con los expertos en cada ámbito. A pesar de que es imposible entender la Sociedad de la Información sin la estadística, es preocupante la situación actual de las ciencias matemáticas y más concretamente de la estadística, ya que a pesar de su imprescindibilidad existe una falta de vocación entre los jóvenes por su estudio y uso, ya sea por su dificultad matemática, desconocimiento u otros motivos. Este artículo pretende reflexionar sobre la importancia de la misma en la sociedad actual que permite tratar numéricamente la realidad.

Applications of the bootstrap to survival analysis

Applications of the bootstrap to survival analysis Utzet i Civit, Frederic; Sànchez, Àlex (Sànchez Pla) En este trabajo se revisan algunas de las aplicaciones clásicas del bootstrap al análisis de la supervivencia. Se consideran en primer lugar el estimador bootstrap de la varianza y el estimador de la mediana corregido para el sesgo del estimador de Kaplan-Meier de la función de supervivencia. A continuación se consideran algunos aspectos mas recientes, tales como métodos para construir bandas de confianza para el estimador de la funcidn de supervivencia y contrastes aproximados para la comparación de funciones de supervivencia. En ambas situaciones el bootstrap resulta de gran utilidad para la aproximación de 10s valores críticos necesarios.

Recent statistical methods based on distances

Recent statistical methods based on distances Arenas Solà, Concepción; Cuadras, C. M. (Carlos María) El concepte de distància s'ha utilizat en diferents camps i és bàsic en alguns mètodes estadístics recents, vàlids per a variables no numèriques així com per a una barreja de diferents tipus de variables. A aquest article expliquem i il·lustrem mètodes recents basats en distàncies: regressió basada en distàncies; discriminant basat en distàncies, related metric scaling i continuous scaling. Aquests mètodes formen part de la recerca actual del grup d'anàlisi multivariant, dirigit per C. M. Cuadras, del Departament d' Estadística de la Universitat de Barcelona. Aquest grup, que treballa a les Facultats de Biologia i Matemàtiques, està format per set investigadors: C. Arenas, C. M. Cuadras, D. Cuadras, A. Esteve, J. Fortiana, A. Grané i F. Oliva.

Evaluación taxonómica de la variabilidad intraespecífica de Galium brockmannii briq. (Rubiaceae).

Evaluación taxonómica de la variabilidad intraespecífica de Galium brockmannii briq. (Rubiaceae). Sáez, Llorenç; Galbany Casals, Mercè; Cáceres Ainsa, Miquel de 5 poblaciones diferentes, utilizados como referencia externa en este análisis, se muestran claramente agrupados y separados de las poblaciones de G. brockmannii. En resumen, todos los dados disponibles sugieren que G. brockmannii subsp. aterratzense debe ser considerado un sinónimo de G. brockmannii.

Quantification of human adenoviruses in European recreational waters

Quantification of human adenoviruses in European recreational waters Bofill Mas, Sílvia; Calgua, Byron; Clemente Casares, Pilar; La Rosa, Giuseppina; Iaconelli, Marcello; Muscillo, Michele; Rutjes, Saskia; Roda Husman, Ana Maria de; Grünert, Andreas; Graver, Ingeburg; Verani, Marco; Carducci, Annalaura; Calvo, Miquel; Wyn-Jones, A. Peter; Gironès Llop, Rosina The presence of human adenoviruses in recreational water might cause disease in the population upon exposure. Human adenoviruses detected by PCR could also serve as indicators of the virological water quality. In order to assess the applicability of human adenoviruses to the evaluation of the faecal contamination in European bathing waters, a real-time quantitative PCR assay was developed for the quantification of human adenoviruses in 132 samples collected from 24 different recreational marine and freshwater sites in nine European countries.Selected samples presenting positive nested-PCR results for human adenoviruses were analyzed using quantitative PCR and 80 samples from a total of 132 produced quantitative results with mean values of 3.2x102 10 per 100 ml of water, human adenovirus 41 being the most prevalent serotype. Human adenoviruses were quantified in samples from all 15 surveillance laboratories. Statistical analysis showed no homogeneous linear relation between humanadenoviruses and E. coli, intestinal enterococci or somatic coliphages concentrations in the tested samples when considering all the data together. Significant correlations between human adenoviruses and at least one of the other indicators were observed only when data from individual Laboratories were considered. The quantification of human adenoviruses may provide complementary information in relation to the use of bacterial standards in the control of water quality in bathing water.

Differential equations driven by fractional Brownian motion

Differential equations driven by fractional Brownian motion Nualart, David, 1951-; Rascanu, Aurel A global existence and uniqueness result of the solution for multidimensional, time dependent, stochastic differential equations driven by a fractional Brownian motion with Hurst parameter H& is proved. It is shown, also, that the solution has finite moments. The result is based on a deterministic existence and uniqueness theorem whose proof uses a contraction principle and a priori estimates.