Principal components for multivariate functional data

This is the author's version of a work that was accepted for publication in Computational Statistics and Data Analysis. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in COMPUTATIONAL STATISTICS AND DATA ANALYSIS, Vol 55, Issue 9, (2011) http://dx.doi.org/10.1016/j.csda.2011.03.01

Maritime antarctic lakes as sentinels of climate change

Remote lakes, such as lakes from the Maritime Antarctica, can be used as sentinels of climate change, because they are mostly free of direct anthropogenic pressures, and they experience climate change as a main stressor capable of modifying the ecosystem structure and function. In this paper, the content of a lecture that has been presented at the First Conference of Lake Sustainability, which has been centred in our studies on lakes from Byers Peninsula (Maritime Antarctica), are summarized. These included physical, chemical and biological studies of these lakes and other freshwater ecosystems, which highlighted the relevance of biotic interactions for these ecosystems and its sensibility to temperature variations and to biological invasions, which is of rel- evance given the acute regional warming occurring during the last decades in the area, concomitant with the enhancement of dispersion of alien species linked to the increased presence of humans

A Comparison of Marginal Likelihood Computation Methods

In a Bayesian analysis, different models can be compared on the basis of theexpected or marginal likelihood they attain. Many methods have been devised to compute themarginal likelihood, but simplicity is not the strongest point of most methods. At the sametime, the precision of methods is often questionable.In this paper several methods are presented in a common framework. The explanation of thedifferences is followed by an application, in which the precision of the methods is testedon a simple regression model where a comparison with analytical results is possible

Modelagem em grafos a partir de bancos de dados relacionais

A importância de trazer dados do modelo relacional para outros modelos e tecnologias tem sido amplamente debatidos, como por exemplo a publicação de dados como grafos. Este modelo permite executar análises topológicas, tal como ocorre nas análises de redes sociais, predição de ligações e sistemas de recomendação. Existem iniciativas para mapear de um banco de dados relacional para a representação em grafo. No entanto, eles não consideram as diferentes maneiras de gerar esses grafos, especialmente quando o objetivo é realizar análises topológicas. Este trabalho propõe heurísticas para facilitar a sistematização do mapeamento de dados do modelo relacional para a representação em grafos. A principal contribuição é que a escolha do modelo do grafo deve considerar o tipo de análise topológica que será realizada pelo usuário. Experimentos são apresentados e mostram resultados interessantes, incluindo heurísticas para apoiar o usuário na escolha da modelagem do grafo.Sociedad Argentina de Informática e Investigación Operativa (SADIO

Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.

IMP dehydrogenase(IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the guanine nucleotide pathway. In eukaryotic cells, GTP binding to the regulatory domain allosterically controls the activity of IMPDH by a mechanism that is fine-tuned by post-translational modifications and enzyme polymerization. Nonetheless, the mechanisms of regulation of IMPDH in bacterial cells remain unclear. Using biochemical, structural, and evolutionary analyses, we demonstrate that, in most bacterial phyla, (p)ppGpp compete with ATP to allosterically modulate IMPDH activity by binding to a, previously unrecognized, conserved high affinity pocket within the regulatory domain. This pocket was lost during the evolution of Proteobacteria, making their IMPDHs insensitive to these alarmones. Instead, most proteobacterial IMPDHs evolved to be directly modulated by the balance between ATP and GTP that compete for the same allosteric binding site. Altogether, we demonstrate that the activity of bacterial IMPDHs is allosterically modulated by a universally conserved nucleotide-controlled conformational switch that has divergently evolved to adapt to the specific particularities of each organism. These results reconcile the reported data on the crosstalk between (p)ppGpp signaling and the guanine nucleotide biosynthetic pathway and reinforce the essential role of IMPDH allosteric regulation on bacterial GTP homeostasis.post-print540 K

Mejora de la memoria gracias al entrenamiento musical en niños en edad preescolar

El objetivo de este trabajo es examinar el efecto del entrenamiento musical activo y receptivo por un periodo de 4 o 10 semanas sobre la memoria emocional de niños de 4 y 5 años de edad. Se espera que los chicos recuerden más imágenes emocionales que neutras (efecto de arousal). Además, que recuerden más las imágenes negativas que las positivas (efecto de valencia). Por otro lado, se predice que, debido a los patrones esperables de desarrollo, los nenes de mayor edad rindan mejor que los niños más pequeños. Finalmente, se espera que el patrón de recuerdo se vea afectado por el entrenamiento musical, siendo más pronunciadas las diferencias con el entrenamiento activo y que cuanto más tiempo de entrenamiento tenga el niño, mayores sean las diferencias (4 vs 10 semanas).Facultad de ArtesLaboratorio para el Estudio de la Experiencia Musica

Dos biomarcadores de la plasticidad de la expresión génica en corales Pocillopora del arrecife Carrizales, Pacífico Tropical Mexicano

Background. Gene expression (GE) plasticity is an acclimation response that allows organisms to adjust rapidly to environmental changes, providing an adaptive advantage. GE biomarkers are emerging as a valua-ble tool for linking the organism’s physiological plasticitywith the synergetic effects of large-scale climatic conditions and local impacts such as temperature and nutrients. Objectives. In this study, we investigate the GE plasticity of the 70-kDa heat shock protein (hsp70) and the carbonic anhydrase enzyme (CA) to confirm the ability of those two genes as biomarkers of the Cellular Stress Response and Cellular Homeostasis Res-ponse, respectively. Methods. Using qPCR, we evaluate the GE plasticity of coral colonies from Pocillopora capitata, Pocillopora damicornis,and Pocillopora verrucosa at the Carrizales reef (Colima coast of Mexico) naturally exposed to environmental changes in the Sea Surface Temperature (SST), productivity and nutrients using the cellular density of Symbiodiniaceae and chlorophyll content as health indices. Results. Our results clearly show GE plasticity in the hsp70 for Pocillopora verrucosa and Pocillopora damicornis related to a daily environmental change in temperature and nutrients. On the other hand, the CA gene expression shows no change in response to daily variations. However, there was a significantly high expression of CA and a lower expression of hsp70 in Pocillopora capitata. Furthermore, we found no significant differences in the health in-dices, suggesting some degree of physiological plasticity in Pocillopora corals like its extensive morphological plasticity that could reflect different adaptation capacities to low temperatures and high nutrients during the spring season in the central Mexican Pacific. Conclusions. Evaluating the phenotypic plasticity (morphology and molecular physiology) could help identify coral colonies with a more significant potential to survive en-vironmental stressors. The latter is an essential consideration for managing, conserving, and restoring coral reefs in the Mexican Pacific.Antecedentes. La plasticidad de la expresión génica (GE) es una respuesta inmediata de aclimatación al cambio ambiental que puede proporcionar una ventaja adaptativa. Los biomarcadores de GE están emer-giendo como una herramienta valiosa para vincular la plasticidad fisiológica del organismo con los efectos sinérgicos del cambio climático y el impacto local como la temperatura y nutrientes. Objetivos. Investigamos la plasticidad de la expresión de genes que codifican para la proteína de choque térmico de 70-kDa (hsp70) y la enzima anhidrasa carbónica (CA) para confirmar su utilidad como biomarcadores de la respuesta de estrés y de homeostasis celular, respectivamente. Métodos. Evaluamos la GE mediante qPCR en colonias de corales Pocilloporacapitata, Pocillopora damicornis y Pocillopora verrucosa del arrecife Carrizales (Colima, México) expuestas a un cambio natural en la temperatura de la superficie del mar (SST), productividad pri-maria y nutrientes utilizando la densidad de Symbiodiniaceae y el contenido de clorofila como indicadores de salud. Resultados. La plasticidad de la GE de hsp70 en Pocillopora damicornis y Pocillopora verrucosa se asocia con la variación diaria de temperatura y nutrientes, mientras que el gen de la CA no muestra cambios de expresión relacionada con esta variabilidad. Sin embargo, en Pocillopora capitata se encontró una expresión significativamente mayor de CA y una menor expresión de hsp70. Estos resultados reflejan un grado de plasticidad fisiológica en corales Pocillopora similar a la extensa plasticidad morfológica dentro de este género, lo que podría sugerir diferentes capacidades de adaptación a la temporada primave-ral de bajas temperaturas y alto contenido de nutrientes en la región. Conclusiones. Evaluar la plasticidad fenotípica (morfología y fisiolo-gía molecular) podría ser útil para identificar colonias de corales con un mayor potencial de sobrevivencia al estrés ambiental. Lo anterior resulta relevante para la conservación, manejo y restauración de los arrecifes de coral del Pacífico mexicano.   &nbsp

Can compact optimisation algorithms be structurally biased?

In the field of stochastic optimisation, the so-called structural bias constitutes an undesired behaviour of an algorithm that is unable to explore the search space to a uniform extent. In this paper, we investigate whether algorithms from a subclass of estimation of distribution algorithms, the compact algorithms, exhibit structural bias. Our approach, justified in our earlier publications, is based on conducting experiments on a test function whose values are uniformly distributed in its domain. For the experiment, 81 combinations of compact algorithms and strategies of dealing with infeasible solutions have been selected as test cases. We have applied two approaches for determining the presence and severity of structural bias, namely an (existing) visual and an (updated) statistical (Anderson-Darling) test. Our results suggest that compact algorithms are more immune to structural bias than their counterparts maintaining explicit populations. Both tests indicate that strong structural bias is found only in the cBFO algorithm, regardless of the choice of strategy of dealing with infeasible solutions, and cPSO with mirror strategy. For other test cases, statistical and visual tests disagree on some cases classified as having mild or strong structural bias: the former one tends to make harsher decisions, thus needing further investigation

Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner

Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we identify a function of histone H1 in chromatin structure and transcription using a range of genomic approaches. In the absence of histone H1, there is an increase in the transcription of non-coding RNAs, together with reduced levels of m6A modification leading to their accumulation on chromatin and causing replication-transcription conflicts. This strongly suggests that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism, and DNA replication to maintain genome performance.Work at the M.G. lab was supported by the Spanish Ministry of Sciences and Innovation (BFU2016-78849-P and PID2019-105949GB-I00, co-financed by the European Union FEDER funds), a CSIC grant (2019AEP004), and a Salvador de Madariaga mobility grant (PRX19/00293). J.M.F.-J., C.S.-M., and J.I.-A. were supported by the Spanish Ministry of Sciences and Innovation fellowships (BES-2014-070050, BES-2017-079897, and PRE2020-095071, respectively); S.M.-V. was supported by a predoctoral fellowship from the Spanish Ministry of Education and Universities (FPU18/04794); and M.S.-P. was supported by an AGAUR-FI predoctoral fellowship co-financed by Generalitat de Catalunya and the European Social Fund. A.J. was supported by the Spanish Ministry of Sciences and Innovation (BFU2017-82805-C2-1-P and PID2020-112783GB-C21) and J.F.C. by core funding to the MRC Human Genetics Unit from the Medical Research Council (UK)