The gut microbiome in dogs with congestive heart failure: a pilot study

Compromised gut health and dysbiosis in people with heart failure has received a great deal of attention over the last decade. Whether dogs with heart failure have a similar dysbiosis pattern to what is described in people is currently unknown. We hypothesised that dogs with congestive heart failure have quantifiable dysbiosis compared to healthy dogs that are similar in sex and age. A total of 50 dogs (15 healthy dogs and 35 dogs with congestive heart failure) were prospectively recruited, and their faecal gut microbiome was assessed using 16S rRNA sequencing (Illumina MiSeq platform). There was no significant change in the microbial diversity and richness in dogs with congestive heart failure. However, there was an increase in abundance of Proteobacteria in the congestive heart failure group (p = 0.014), particularly due to an increase in the family Enterobacteriaceae (p = 0.002) and Escherichia coli (p = 0.033). We conclude that dogs with congestive heart failure have dysbiosis, and we show additional trends in our data suggesting that dogs may have a similar pattern to that described in people. The results of this study provide useful preliminary information and raise the possibility that dogs represent a clinically relevant animal model of dysbiosis in people with heart failure

Organizational Heterogeneity of Vertebrate Genomes

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as “texts” using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter - GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences

A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation

Sequence database searches require accurate estimation of the statistical significance of scores. Optimal local sequence alignment scores follow Gumbel distributions, but determining an important parameter of the distribution (λ) requires time-consuming computational simulation. Moreover, optimal alignment scores are less powerful than probabilistic scores that integrate over alignment uncertainty (“Forward” scores), but the expected distribution of Forward scores remains unknown. Here, I conjecture that both expected score distributions have simple, predictable forms when full probabilistic modeling methods are used. For a probabilistic model of local sequence alignment, optimal alignment bit scores (“Viterbi” scores) are Gumbel-distributed with constant λ = log 2, and the high scoring tail of Forward scores is exponential with the same constant λ. Simulation studies support these conjectures over a wide range of profile/sequence comparisons, using 9,318 profile-hidden Markov models from the Pfam database. This enables efficient and accurate determination of expectation values (E-values) for both Viterbi and Forward scores for probabilistic local alignments

Genetic Evidence for a Mitochondriate Ancestry in the ‘Amitochondriate’ Flagellate Trimastix pyriformis

Most modern eukaryotes diverged from a common ancestor that contained the α-proteobacterial endosymbiont that gave rise to mitochondria. The ‘amitochondriate’ anaerobic protist parasites that have been studied to date, such as Giardia and Trichomonas harbor mitochondrion-related organelles, such as mitosomes or hydrogenosomes. Yet there is one remaining group of mitochondrion-lacking flagellates known as the Preaxostyla that could represent a primitive ‘pre-mitochondrial’ lineage of eukaryotes. To test this hypothesis, we conducted an expressed sequence tag (EST) survey on the preaxostylid flagellate Trimastix pyriformis, a poorly-studied free-living anaerobe. Among the ESTs we detected 19 proteins that, in other eukaryotes, typically function in mitochondria, hydrogenosomes or mitosomes, 12 of which are found exclusively within these organelles. Interestingly, one of the proteins, aconitase, functions in the tricarboxylic acid cycle typical of aerobic mitochondria, whereas others, such as pyruvate:ferredoxin oxidoreductase and [FeFe] hydrogenase, are characteristic of anaerobic hydrogenosomes. Since Trimastix retains genetic evidence of a mitochondriate ancestry, we can now say definitively that all known living eukaryote lineages descend from a common ancestor that had mitochondria

Integrality Gaps of Linear and Semi-definite Programming Relaxations for Knapsack

Recent years have seen an explosion of interest in lift and project methods, such as those proposed by Lovász and Schrijver [40], Sherali and Adams [49], Balas, Ceria and Cornuejols [6], Lasserre [36, 37] and others. These methods are systematic procedures for constructing a sequence of increasingly tight mathematical programming relaxations for 0-1 optimization problems. One major line of research in this area has focused on understanding the strengths and limitations of these procedures. Of particular interest to our community is the question of how the integrality gaps for interesting combinatorial optimization problems evolve through a series of rounds of one of these procedures. On the one hand, if the integrality gap of successive relaxations drops sufficiently fast, there is the potential for an improved approximation algorithm. On the other hand, if the integrality gap for a problem persists, this can be viewed as a lower bound in a certain restricted model of computation. In this paper, we study the integrality gap in these hierarchies for the knapsack problem. We have two main results. First, we show that an integrality gap of 2 − ɛ persists up to a linear number of rounds of Sherali-Adams. This is interesting, since it is well known that knapsack has a fully polynomial time approximation scheme [30, 39]. Second, we show that Lasserre’s hierarchy closes the gap quickly. Specifically, after t 2 rounds of Lasserre, the integrality gap decreases to t/(t − 1). Thus, we provide a second example of an integrality gap separation between Lasserre and Sherali Adams. The only other such gap we are aware of is in the recent work of Fernandez de la Vega and Mathieu [19] (respectively of Charikar, Makarychev and Makarychev [12]) showing that the integrality gap for MAXCUT remains 2 − ɛ even after ω(1) (respectively n γ) rounds of Sherali-Adams. On the other hand, it is known that 2 rounds of Lasserre yields a relaxation as least as strong as the Goemans-Williamson SDP, which has an integrality gap of 0.878

Etude par diffusion RAMAN de la stabilite thermo-chimique et de la deformation in-situ des fibres SiC Hi"TM - Nicalon

Communication to : 10emes Journees nationales sur les composites 'JNC10', ENSAM - Paris (France), 29-31 octobre 1996SIGLEAvailable at INIST (FR), Document Supply Service, under shelf-number : 22419, issue : a.1996 n.190 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Fracture of oxide ceramic matrix/oxide fibre woven fabric composites

Communication to : ECCM-7 Proceedings - Symposium MMC58CMC London (UK), May 14-16, 1996SIGLEAvailable at INIST (FR), Document Supply Service, under shelf-number : 22419, issue : a.1996 n.83 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc