Faster algorithms for 1-mappability of a sequence

In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y. We focus here on the version of the problem where k = 1. The fastest known algorithm for k = 1 requires time O(mn log n/ log log n) and space O(n). We present two algorithms that require worst-case time O(mn) and O(n log^2 n), respectively, and space O(n), thus greatly improving the state of the art. Moreover, we present an algorithm that requires average-case time and space O(n) for integer alphabets if m = {\Omega}(log n/ log {\sigma}), where {\sigma} is the alphabet size

Possible surface plasmon polariton excitation under femtosecond laser irradiation of silicon

The mechanisms of ripple formation on silicon surface by femtosecond laser pulses are investigated. We demonstrate the transient evolution of the density of the excited free-carriers. As a result, the experimental conditions required for the excitation of surface plasmon polaritons are revealed. The periods of the resulting structures are then investigated as a function of laser parameters, such as the angle of incidence, laser fluence, and polarization. The obtained dependencies provide a way of better control over the properties of the periodic structures induced by femtosecond laser on the surface of a semiconductor material.Comment: 11 pages, 8 figures, accepted for publication in Journal of Applied Physic

A robust SNP barcode for typing Mycobacterium tuberculosis complex strains

Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type

The origins, evolution, and functional potential of alternative splicing in vertebrates.

Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution

TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors.

The genomic regulatory programmes that underlie human organogenesis are poorly understood. Pancreas development, in particular, has pivotal implications for pancreatic regeneration, cancer and diabetes. We have now characterized the regulatory landscape of embryonic multipotent progenitor cells that give rise to all pancreatic epithelial lineages. Using human embryonic pancreas and embryonic-stem-cell-derived progenitors we identify stage-specific transcripts and associated enhancers, many of which are co-occupied by transcription factors that are essential for pancreas development. We further show that TEAD1, a Hippo signalling effector, is an integral component of the transcription factor combinatorial code of pancreatic progenitor enhancers. TEAD and its coactivator YAP activate key pancreatic signalling mediators and transcription factors, and regulate the expansion of pancreatic progenitors. This work therefore uncovers a central role for TEAD and YAP as signal-responsive regulators of multipotent pancreatic progenitors, and provides a resource for the study of embryonic development of the human pancreas

Nonlinear bias correction for satellite data assimilation using Taylor series polynomials

Output from a high-resolution ensemble data assimilation system is used to assess the ability of an innovative nonlinear bias correction (BC) method that uses a Taylor series polynomial expansion of the observation-minus background departures to remove linear and nonlinear conditional biases from all-sky satellite infrared brightness temperatures. Univariate and multivariate experiments were performed in which the satellite zenith angle and variables sensitive to clouds and water vapor were used as the BC predictors. The results showed that even though the bias of the entire observation departure distribution is equal to zero regardless of the order of the Taylor series expansion, there are often large conditional biases that vary as a nonlinear function of the BC predictor. The linear 1st order term had the largest impact on the entire distribution as measured by reductions in variance; however, large conditional biases often remained in the distribution when plotted as a function of the predictor. These conditional biases were typically reduced to near zero when the nonlinear 2nd and 3rd order terms were used. The univariate results showed that variables sensitive to the cloud top height are effective BC predictors especially when higher order Taylor series terms are used. Comparison of the statistics for clear-sky and cloudy-sky observations revealed that nonlinear departures are more important for cloudy-sky observations as signified by the much larger impact of the 2nd and 3rd order terms on the conditional biases. Together, these results indicate that the nonlinear BC method is able to effectively remove the bias from all-sky infrared observation departures

Fertile Prototaxites taiti: a basal ascomycete with inoperculate, polysporous asci lacking croziers

The affinities of Prototaxites have been debated ever since its fossils, some attaining tree-trunk proportions, were discovered in Canadian Lower Devonian rocks in 1859. Putative assignations include conifers, red and brown algae, liverworts and fungi (some lichenised). Detailed anatomical investigation led to the reconstruction of the type species, P. logani, as a giant sporophore (basidioma) of an agaricomycete (= holobasidiomycete), but evidence for its reproduction remained elusive. Tissues associated with P. taiti in the Rhynie chert plus charcoalified fragments from southern Britain are investigated here to describe the reproductive characters and hence affinities of Prototaxites. Thin sections and peels (Pragian Rhynie chert, Aberdeenshire) were examined using light and confocal microscopy; Přídolí and Lochkovian charcoalified samples (Welsh Borderland) were liberated from the rock and examined with scanning electron microscopy. Prototaxites taiti possessed a superficial hymenium comprising an epihymenial layer, delicate septate paraphyses, inoperculate polysporic asci lacking croziers and a subhymenial layer composed predominantly of thin-walled hyphae and occasional larger hyphae. Prototaxites taiti combines features of extant Taphrinomycotina (Neolectomycetes lacking croziers) and Pezizomycotina (epihymenial layer secreted by paraphyses) but is not an ancestor of the latter. Brief consideration is given to its nutrition and potential position in the phylogeny of the Ascomycota

Une méthode générale d'estimation des paramètres génétiques dans un échantillon sélectionné, avec une application à une sélection sur un indice à trois caractères

L’estimation des paramètres génétiques d’une population, héritabilités et corrélations génétiques, à partir d’un échantillon repose sur de nombreuses hypothèses, qui concernent tant la population elle-même que l’échantillon qu’on en tire. La principale condition à laquelle doit satisfaire l’échantillon est d’être aléatoire, ce qui n’est pas le cas lorsque les individus mesurés, ou leurs parents, sont sélectionnés, situation fréquente chez les animaux d’élevage. Dans ce cas, les estimations obtenues par les techniques classiques de régression et d’analyse de variance peuvent être faussées et des corrections sont nécessaires pour tenir compte de la sélection. Lorsque la sélection se fait sur plusieurs caractères simultanément, combinés par exemple dans un indice de sélection, la correction repose sur la connaissance des variances-covariances des parents sélectionnés relativement à celles de la population non sélectionnée, selon une méthode générale décrite, en particulier, par AI TKEN (1934). Cette méthode inclut, comme cas particulier, les résultats de plusieurs travaux récents concernant les effets de la sélection sur un seul caractère. Cependant, la variance d’échantillonnage des estimations corrigées ainsi obtenues a une expression complexe. Un exemple numérique, concernant une sélection sur un indice à 3 caractères chez le Porc, est traité. Il montre un bon accord entre les estimées corrigées pour les effets de la sélection et les estimées tirées de l’échantillon non sélectionné.The estimation of genetic parameters rests on several hypotheses, concerning either the population considered itself or the sample drawn from it. In particular, random sampling has to be assumed, which is not the case when the individuals measured, or their parents, are selected, a frequent situation in farm animals. In this case, the usual estimates from regression and analysis of variance may be biassed. When selection is based on several traits, which for instance are combined into an index, the bias may be derived from the knowledge of the phenotypic variance-covariance matrix of the selected parents, according to a general method described, in particular, by AiruErt (1934). This method includes, as particular cases, several more recent results concerning the bias due to selection on one character. However, the sampling variances of the estimates so obtained have complex expressions. A numerical illustration is given, which concerns a three-trait index selection in the pig. The results show a good agreement between the estimates corrected for the bias due to selection and the estimates drawn from the unselected sample

Sources of variation in simulated ecosystem carbon storage capacity from the 5th Climate Model Intercomparison Project (CMIP5)

Ecosystem carbon (C) storage strongly regulates climate-C cycle feedback and is largely determined by both C residence time and C input from net primary productivity (NPP). However, spatial patterns of ecosystem C storage and its variation have not been well quantified in earth system models (ESMs), which is essential to predict future climate change and guide model development. We intended to evaluate spatial patterns of ecosystem C storage capacity simulated by ESMs as part of the 5th Climate Model Intercomparison Project (CMIP5) and explore the sources of multi-model variation from mean residence time (MRT) and/or C inputs. Five ESMs were evaluated, including C inputs (NPP and [gross primary productivity] GPP), outputs (autotrophic/heterotrophic respiration) and pools (vegetation, litter and soil C). ESMs reasonably simulated the NPP and NPP/GPP ratio compared with Moderate Resolution Imaging Spectroradiometer (MODIS) estimates except NorESM. However, all of the models significantly underestimated ecosystem MRT, resulting in underestimation of ecosystem C storage capacity. CCSM predicted the lowest ecosystem C storage capacity (~10 kg C m−2) with the lowest MRT values (14 yr), while MIROC-ESM estimated the highest ecosystem C storage capacity (~36 kg C m−2) with the longest MRT (44 yr). Ecosystem C storage capacity varied considerably among models, with larger variation at high latitudes and in Australia, mainly resulting from the differences in the MRTs across models. Our results indicate that additional research is needed to improve post-photosynthesis C-cycle modelling, especially at high latitudes, so that ecosystem C residence time and storage capacity can be appropriately simulated