On prediction of individual sequences

Sequential randomized prediction of an arbitrary binary sequence isinvestigated. No assumption is made on the mechanism of generating the bit sequence. The goal of the predictor is to minimize its relative loss, i.e., to make (almost) as few mistakes as the best ``expert'' in a fixed, possibly infinite, set of experts. We point out a surprising connection between this prediction problem and empirical process theory. First, in the special case of static (memoryless) experts, we completely characterize the minimax relative loss in terms of the maximum of an associated Rademacher process. Then we show general upper and lower bounds on the minimaxrelative loss in terms of the geometry of the class of experts. As main examples, we determine the exact order of magnitude of the minimax relative loss for the class of autoregressive linear predictors and for the class of Markov experts.

A zero-delay sequential scheme for lossy coding of individual sequences

We consider adaptive sequential lossy coding of bounded individual sequences when the performance is measured by the sequentially accumulated mean squared distortion. Theencoder and the decoder are connected via a noiseless channel of capacity $R$ and both are assumed to have zero delay. No probabilistic assumptions are made on how the sequence to be encoded is generated. For any bounded sequence of length $n$, the distortion redundancy is defined as the normalized cumulative distortion of the sequential scheme minus the normalized cumulative distortion of the best scalarquantizer of rate $R$ which is matched to this particular sequence. We demonstrate the existence of a zero-delay sequential scheme which uses common randomization in the encoder and the decoder such that the normalized maximum distortion redundancy converges to zero at a rate $n^{-1/5}\log n$ as the length of the encoded sequence $n$ increases without bound.

André spectral sequences for Baues-Wirsching cohomology of categories

We construct spectral sequences in the framework of Baues-Wirsching cohomology and homology for functors between small categories and analyze particular cases including Grothendieck fibrations. We also give applications to more classical cohomology and homology theories including Hochschild-Mitchell cohomology and those studied before by Watts, Roos, Quillen and others

Phenotypic plasticity in the Caribbean sponge Callyspongia vaginalis (Porifera: Haplosclerida)

Sponge morphological plasticity has been a long-standing source of taxonomic difficulty. In the Caribbean, several morphotypes of the sponge Callyspongia vaginalis have been observed. To determine the taxonomic status of three of these morphotypes and their relationship with the congeneric species C. plicifera and C. fallax, we compared the spicule composition, spongin fiber skeleton and sequenced fragments of the mitochondrial genes 16S and COI and nuclear genes 28S and 18S ribosomal RNA. Phylogenetic analyses with ribosomal markers 18S and 28S rRNA confirmed the position of our sequences within the Callyspongiidae. None of the genetic markers provided evidence for consistent differentiation among the three morphotypes of C. vaginalis and C. fallax, and only C. plicifera stood as a distinct species. The 16S mtDNA gene was the most variable molecular marker for this group, presenting a nucleotide variability (π = 0.024) higher than that reported for COI. Unlike recent studies for other sponge genera, our results indicate that species in the genus Callyspongia maintain a high degree of phenotypic plasticity, and that morphological characteristics may not reflect reproductive boundaries in C. vaginalis.

Low environmental impact bleaching sequences for attaining high brightness level with eucalyptus SPP pulp

The alternatives used for minimizing the usage of chlorine dioxide in bleaching sequences included a hot acid hydrolysis (Ahot) stage, the use of hot chlorine dioxide (Dhot) and ozone stages at medium consistency and high consistency (Zmc and Zhc), in addition to stages with atmospheric hydrogen peroxide (P) and pressurized hydrogen peroxide (PO). The results were interpreted based on the cost of the chemical products, bleaching process yields and on minimizing the environmental impact of the bleaching process. In spite of some process restrictions, high ISO brightness levels were kept around 90 % brightness. Additionally, the inclusion of stages like acid hydrolysis, pressurized peroxide and ozone in the bleaching sequences provided an increase in operating flexibility, aimed at reducing environmental impact (ECF Light). The Dhot(EOP)D(PO) sequence presented lower operating cost for ISO brightness above 92 %. However, this kind of sequence was not allowed for closing the wastewater circuit, even partially. For ISO brightness level around 91%, the AhotZhcDP sequence presented a lower operating cost than the others

Interpolating and sampling sequences in finite Riemann surfaces

We provide a description of the interpolating and sampling sequences on a space of holomorphic functions on a finite Riemann surface, where a uniform growth restriction is imposed on the holomorphic functions.

Rational periodic sequences for the Lyness recurrence

Consider the celebrated Lyness recurrence $x_{n+2}=(a+x_{n+1})/x_{n}$ with $a\in\Q$. First we prove that there exist initial conditions and values of $a$ for which it generates periodic sequences of rational numbers with prime periods $1,2,3,5,6,7,8,9,10$ or $12$ and that these are the only periods that rational sequences $\{x_n\}_n$ can have. It is known that if we restrict our attention to positive rational values of $a$ and positive rational initial conditions the only possible periods are $1,5$ and $9$. Moreover 1-periodic and 5-periodic sequences are easily obtained. We prove that for infinitely many positive values of $a,$ positive 9-period rational sequences occur. This last result is our main contribution and answers an open question left in previous works of Bastien \& Rogalski and Zeeman. We also prove that the level sets of the invariant associated to the Lyness map is a two-parameter family of elliptic curves that is a universal family of the elliptic curves with a point of order $n, n\ge5,$ including $n$ infinity. This fact implies that the Lyness map is a universal normal form for most birrational maps on elliptic curves.

Cardiac motion estimation by joint alignment of tagged MRI sequences

Image registration has been proposed as an automatic method for recovering cardiac displacement fields from Tagged Magnetic Resonance Imaging (tMRI) sequences. Initially performed as a set of pairwise registrations, these techniques have evolved to the use of 3D+t deformation models, requiring metrics of joint image alignment (JA). However, only linear combinations of cost functions defined with respect to the first frame have been used. In this paper, we have applied k-Nearest Neighbors Graphs (kNNG) estimators of the -entropy (H ) to measure the joint similarity between frames, and to combine the information provided by different cardiac views in an unified metric. Experiments performed on six subjects showed a significantly higher accuracy (p < 0.05) with respect to a standard pairwise alignment (PA) approach in terms of mean positional error and variance with respect to manually placed landmarks. The developed method was used to study strains in patients with myocardial infarction, showing a consistency between strain, infarction location, and coronary occlusion. This paper also presentsan interesting clinical application of graph-based metric estimators, showing their value for solving practical problems found in medical imaging.

Comparison of the gut microbiota from soldier and worker castes of the termite Reticulitermes grassei

The bacterial microbiota from the whole gut of soldier and worker castes of the termite Reticulitermes grassei was isolated and studied. In addition, the 16S rDNA bacterial genes from gut DNA were PCR-amplified using Bacteria-selective primers, and the 16S rDNA amplicons subsequently cloned into Escherichia coli. Sequences of the cloned inserts were then used to determine closest relatives by comparison with published sequences and with sequences from our previous work. The clones were found to be affiliated with the phyla Spirochaetes, Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Synergistetes, Verrucomicrobia, and candidate phyla Termite Group 1 (TG1) and Termite Group 2 (TG2). No significant differences were observed with respect to the relative bacterial abundances between soldier and worker phylotypes. The phylotypes obtained in this study were compared with reported sequences from other termites, especially those of phylotypes related to Spirochaetes, Wolbachia (an Alphaproteobacteria), Actinobacteria, and TG1. Many of the clone phylotypes detected in soldiers grouped with those of workers. Moreover, clones CRgS91 (soldiers) and CRgW68 (workers), both affiliated with"Endomicrobia", were the same phylotype. Soldiers and workers also seemed to have similar relative protist abundances. Heterotrophic, poly-β-hydroxyalkanoate-accumulating bacteria were isolated from the gut of soldiers and shown to be affiliated with Actinobacteria and Gammaproteobacteria. We noted that Wolbachia was detected in soldiers but not in workers. Overall, the maintenance by soldiers and workers of comparable axial and radial redox gradients in the gut is consistent with the similarities in the prokaryotes and protists comprising their microbiota.

Molecular phylogenetics and temporal diversification in the genus Aeromonas based on the sequences of five housekeeping genes

Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.

A note on the degree sequences of graphs with restrictions

Degree sequences of some types of graphs will be studied and characterizedin this paper.

The odd couple: contrasting phylogeographic patterns in two sympatric sibling species of woodlouse-­‐hunter spiders in the Canary Islands

Comparative phylogeography seeks for commonalities in the spatial demographic history of sympatric organisms to characterize the mechanisms that shaped such patterns. The unveiling of incongruent phylogeographic patterns in co-occurring species, on the other hand, may hint to overlooked differences in their life histories or microhabitat preferences. The woodlouse-hunter spiders of the genus Dysdera have undergone a major diversi cation on the Canary Islands. The species pair Dysdera alegranzaensis and Dysdera nesiotes are endemic to the island of Lanzarote and nearby islets, where they co-occur at most of their known localities. The two species stand in sharp contrast to other sympatric endemic Dysdera in showing no evidence of somatic (non-genitalic) differentiation. Phylogenetic and population genetic analyses of mitochondrial cox1 sequences from an exhaustive sample of D. alegranzaensis and D. nesiotes specimens, and additional mitochondrial (16S, L1, nad1) and nuclear genes (28S, H3) were analysed to reveal their phylogeographic patterns and clarify their phylogenetic relationships. Relaxed molecular clock models using ve calibration points were further used to estimate divergence times between species and populations. Striking differences in phylogeography and population structure between the two species were observed. Dysdera nesiotes displayed a metapopulation-like structure, while D. alegranzaensis was characterized by a weaker geographical structure but greater genetic divergences among its main haplotype lineages, suggesting more complex population dynamics. Our study con rms that co-distributed sibling species may exhibit contrasting phylogeographic patterns in the absence of somatic differentiation. Further ecological studies, however, will be necessary to clarify whether the contrasting phylogeographies may hint at an overlooked niche partitioning between the two species. In addition, further comparisons with available phylogeographic data of other eastern Canarian Dysdera endemics con rm the key role of lava ows in structuring local populations in oceanic islands and identify localities that acted as refugia during volcanic eruptions

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

Coal deposition in carbonate rich shallow Lacustrine systems: The Calaf and Mequinenza sequences (Oligocene, eastern Ebro Basin, NE Spain)

Two main coal-bearing sequences developed during the Oligocene in the Tertiary Ebro Basin, the Calaf (early Oligocene) and Mequinenza (late Oligocene) coal basins. Coal deposition took place in shallow marsh-swamp-lake complexes which sometimes became closed and evolved under warm climatic conditions with fluctuating humidity. These shallow lacustrine systems are closely interrelated with the terminal parts of the distributive fluvial systems which spread from the tectonically active Ebro basin margins. Laterally extensive lignite-bearing sequences, including rather thin, lenticular autochthonous and/or hypautochthonous coal seams with high ash and sulphur contents, characterized coal deposition in the shallow lacustrine systems. Coal seam geometry, which makes them nearly subeconomic, resulted from the tectonic instability during basin margin evolution and the sometimes closed, arid conditions under which the lacustrine systems evolved. High ash and sulphur contents resulted from the inadequate isolation of peat forming environments from clastic influx and from the very low acidity and sometimes high sulphate contents of the lacustrine waters. Coal exploration in shallow lacustrine sequences similar to those described here must take into account that the spread of coal-forming environments and maxima of coal deposition are usually coincident with lake expansions and retraction or shifting of the terminal fluvial zones interrelated with the lacustrine areas.