Consistency of objective Bayes factors as the model dimension grows

In the class of normal regression models with a finite number of regressors, and for a wide class of prior distributions, a Bayesian model selection procedure based on the Bayes factor is consistent [Casella and Moreno J. Amer. Statist. Assoc. 104 (2009) 1261--1271]. However, in models where the number of parameters increases as the sample size increases, properties of the Bayes factor are not totally understood. Here we study consistency of the Bayes factors for nested normal linear models when the number of regressors increases with the sample size. We pay attention to two successful tools for model selection [Schwarz Ann. Statist. 6 (1978) 461--464] approximation to the Bayes factor, and the Bayes factor for intrinsic priors [Berger and Pericchi J. Amer. Statist. Assoc. 91 (1996) 109--122, Moreno, Bertolino and Racugno J. Amer. Statist. Assoc. 93 (1998) 1451--1460]. We find that the the Schwarz approximation and the Bayes factor for intrinsic priors are consistent when the rate of growth of the dimension of the bigger model is $O(n^b)$ for $b<1$. When $b=1$ the Schwarz approximation is always inconsistent under the alternative while the Bayes factor for intrinsic priors is consistent except for a small set of alternative models which is characterized.Comment: Published in at http://dx.doi.org/10.1214/09-AOS754 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Consistency of Bayesian procedures for variable selection

It has long been known that for the comparison of pairwise nested models, a decision based on the Bayes factor produces a consistent model selector (in the frequentist sense). Here we go beyond the usual consistency for nested pairwise models, and show that for a wide class of prior distributions, including intrinsic priors, the corresponding Bayesian procedure for variable selection in normal regression is consistent in the entire class of normal linear models. We find that the asymptotics of the Bayes factors for intrinsic priors are equivalent to those of the Schwarz (BIC) criterion. Also, recall that the Jeffreys--Lindley paradox refers to the well-known fact that a point null hypothesis on the normal mean parameter is always accepted when the variance of the conjugate prior goes to infinity. This implies that some limiting forms of proper prior distributions are not necessarily suitable for testing problems. Intrinsic priors are limits of proper prior distributions, and for finite sample sizes they have been proved to behave extremely well for variable selection in regression; a consequence of our results is that for intrinsic priors Lindley's paradox does not arise.Comment: Published in at http://dx.doi.org/10.1214/08-AOS606 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org

Genomic analysis of eight native plasmids of the phytopathogen Pseudomonas syringae

Comunicación a conferenciaThe pPT23A family of plasmids (PFPs) appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. PFPs are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces. Further understanding of the evolution of the pPT23A plasmid family and the role of these plasmids in P. syringae biology and pathogenesis, requires the determination and analysis of additional complete, closed plasmid genome sequences. Therefore, our main objective was to obtain complete genome sequences from PFPs from three different P. syringae pathovars and perform a comparative genomic analysis. In this work plasmid DNA isolation, purification by CsCl-EtBr gradients, and sequencing using 454 platform, were used to obtain the complete sequence of P. syringae plasmids. Different bioinformatic tools were used to analyze the plasmid synteny, to identify virulence genes (i.e. type 3 effectors) and to unravel the evolutionary history of PFPs. Our sequence analysis revealed that PFPs from P. syringae encode suites of accessory genes that are selected at different levels (universal, interpathovar and intrapathovar). The conservation of type IVSS encoding conjugation functions also contributes to the distribution of these plasmids within P. syringae populations. Thus, this study contributes to unravel the genetic basis of the role of PFPs in different P. syringae lifestyles.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

On Broadwater Farm: Dub Housing and other planes of consistency (part one) Edward George in conversation with Louis Moreno

Edward George’s Visual Cultures research fellowship begins with a conversation about 'Dub Housing' - a new project based around the Broadwater Farm estate during Covid that explores how the music of dub sonifies a different consciousness of people and place, time and geography, history and architecture, race and metropolis. Edward George is a writer and broadcaster. Founder of Black Audio Film Collective, George wrote and presented the ground-breaking science fiction documentary Last Angel of History (1996). George’s series The Strangeness of Dub (Morley Radio) dives into reggae, dub, versions and versioning, drawing on critical theory, social history, and a deep and wide cross-genre musical selection. George is a Research Fellow in the Department of Visual Cultures, Goldsmiths

Intermolecular N-H...O=C hydrogen bonding in the crystal structure of 6-amino-1,3-dimethyluracil

The 6-amino- 1,3-dimethyluracil molecule [6-amino- 1,3- dimethyl-2,4(1H,3H)-pyrimidinedione], C6H9N302 (I), lies on a crystallographic mirror plane and participates in an extensive two-dimensional hydrogen-bonding network in the solid state. Each molecule is involved in N-- H...O=C hydrogen bonding involving the amino and carbonyl gr. oups, with O...N separations of 2.894 (3) and 2.904 (3) A

Comparative genomic analysis of native pseudomonas syringae plasmids belonging to the ppt23 a family reveals their role in p. Syringae epiphytic and pathogenic lifestyles

Backgrounds The pPT23A family of plasmids (PFPs) appears to be indigenous to the plant pathogen Pseudomonas syringae and these plasmids are widely distributed and widely transferred among pathovars of P. syringae and related species. PFPs are sources of accessory genes for their hosts that can include genes important for virulence and epiphytic colonization of plant leaf surfaces. Objectives Further understanding of the evolution of the pPT23A plasmid family and the role of these plasmids in P. syringae biology and pathogenesis, requires the determination and analysis of additional complete, closed plasmid genome sequences. Therefore, our main objective was to obtain complete genome sequences of PFPs from three different P. syringae pathovars and perform a comprehensive comparative genomic analysis. Methods In this work plasmid DNA isolation, purification by CsCl-EtBr gradients, and sequencing using 454 platform, were carried out to obtain the complete sequence of P. syringae plasmids. Different bioinformatic tools were used to analyze the plasmid synteny, to identify virulence genes (i.e. type 3 effectors) and to unravel the evolutionary history of PFPs. Conclusions Our sequence analysis revealed that PFPs from P. syringae encode suites of accessory genes that are selected at different levels (universal, interpathovar and intrapathovar). The conservation of type IVSS encoding conjugation functions also contributes to the distribution of these plasmids within P. syringae populations. Thus, this study contributes to unravel the genetic bases of the role of PFPs in different P. syringae lifestyles. This work was supported by grants Proyecto de Excelencia, Junta de Andalucía (P07-AGR-02471; P12-AGR-1473) and by Michigan State University AgBioResearch.This work was supported by grants Proyecto de Excelencia, Junta de Andalucía (P07-AGR-02471; P12-AGR-1473) and by Michigan State University AgBioResearch; Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Latent Birds:A Bird's-Eye View Exploration of the Latent Space

The use of a generative approach for sound synthesis breaks through the limitations of traditional approaches, proposing novel ways to explore creative ideas. This paper demonstrates a method to generate original bird vocalizations using a Variational Convolutional Autoencoder trained on mel-spectrograms of bird song and call recordings. The vocalizations are reconstructed by sampling the latent space and decompressing the resulting mel-spectrogram. The results are quite promising, in that our system is able to generate a variety of bird vocalizations depicting plausible songs and calls, by interpolating between existing vocalizations or sampling the latent space. A Twitter bot that publishes a unique daily bird vocalization is also implemented

Detailed molecular characterisation of acute myeloid leukaemia with a normal karyotype using targeted DNA capture

This work is licensed under a Creative Commons Attribution 3.0 Unported License.-- et al.Advances in sequencing technologies are giving unprecedented insights into the spectrum of somatic mutations underlying acute myeloid leukaemia with a normal karyotype (AML-NK). It is clear that the prognosis of individual patients is strongly influenced by the combination of mutations in their leukaemia and that many leukaemias are composed of multiple subclones, with differential susceptibilities to treatment. Here, we describe a method, employing targeted capture coupled with next-generation sequencing and tailored bioinformatic analysis, for the simultaneous study of 24 genes recurrently mutated in AML-NK. Mutational analysis was performed using open source software and an in-house script (Mutation Identification and Analysis Software), which identified dominant clone mutations with 100% specificity. In each of seven cases of AML-NK studied, we identified and verified mutations in 2-4 genes in the main leukaemic clone. Additionally, high sequencing depth enabled us to identify putative subclonal mutations and detect leukaemia-specific mutations in DNA from remission marrow. Finally, we used normalised read depths to detect copy number changes and identified and subsequently verified a tandem duplication of exons 2-9 of MLL and at least one deletion involving PTEN. This methodology reliably detects sequence and copy number mutations, and can thus greatly facilitate the classification, clinical research, diagnosis and management of AML-NK.We acknowledge the use of the National Institute of Health Research (NIHR) Biomedical Research Centre, University of Cambridge. We thank Drs J Craig and C Crawley of Cambridge University NHS Hospitals trust for allowing us to approach their patients for samples. GV is funded by a Wellcome Trust Senior Fellowship in Clinical Science. Work in GV’s laboratory is also funded by Leukaemia Lymphoma Research and the Kay Kendal Leukaemia Fund.Peer Reviewe