Abstract
Motivation
The 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as proxies for species. The ...canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data.
Results
Using a large set of high-quality 16S rRNA sequences from finished genomes, I assessed the correspondence of OTUs to species for five representative clustering algorithms using four accuracy metrics. All algorithms had comparable accuracy when tuned to a given metric. Optimal identity thresholds were ∼99% for full-length sequences and ∼100% for the V4 hypervariable region.
Availability and implementation
Reference sequences and source code are provided in the Supplementary Material.
Supplementary information
Supplementary data are available at Bioinformatics online.
Multiple sequence alignments are widely used to infer evolutionary relationships, enabling inferences of structure, function, and phylogeny. Standard practice is to construct one alignment by some ...preferred method and use it in further analysis; however, undetected alignment bias can be problematic. I describe Muscle5, a novel algorithm which constructs an ensemble of high-accuracy alignment with diverse biases by perturbing a hidden Markov model and permuting its guide tree. Confidence in an inference is assessed as the fraction of the ensemble which supports it. Applied to phylogenetic tree estimation, I show that ensembles can confidently resolve topologies with low bootstrap according to standard methods, and conversely that some topologies with high bootstraps are incorrect. Applied to the phylogeny of RNA viruses, ensemble analysis shows that recently adopted taxonomic phyla are probably polyphyletic. Ensemble analysis can improve confidence assessment in any inference from an alignment.
Amplified marker-gene sequences can be used to understand microbial community structure, but they suffer from a high level of sequencing and amplification artifacts. The UPARSE pipeline reports ...operational taxonomic unit (OTU) sequences with ≤1% incorrect bases in artificial microbial community tests, compared with >3% incorrect bases commonly reported by other methods. The improved accuracy results in far fewer OTUs, consistently closer to the expected number of species in a community.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
9.
En même temps Colin, Robert C
Le Coq-Héron,
3/2023, Volume:
252, Issue:
1
Journal Article
« L’accueil de l’ infans dans l’adulte », notion plus ferenczienne que freudienne, ne fait pas l’unanimité chez les psychanalystes. Plutôt que d’entrer dans un débat intellectuel qui chercherait à ...affirmer de quel côté politique il est souhaitable de se trouver – Freud ou Ferenczi ? – j’ai choisi de me former ma propre opinion à travers quelques courtes séquences cliniques de psychanalyse d’adultes glanées pour l’occasion. Cette étude m’amène à mesurer l’importance du modèle du « en même temps ».
Since their discovery in the 1950s there has been an increasing degree of interest in the hexagonal ferrites, also know as hexaferrites, which is still growing exponentially today. These have become ...massively important materials commercially and technologically, accounting for the bulk of the total magnetic materials manufactured globally, and they have a multitude of uses and applications. As well as their use as permanent magnets, common applications are as magnetic recording and data storage materials, and as components in electrical devices, particularly those operating at microwave/GHz frequencies. The important members of the hexaferrite family are shown below, where Me=a small 2+ ion such as cobalt, nickel or zinc, and Ba can be substituted by Sr: times M-type ferrites, such as BaFe12O19 (BaM or barium ferrite), SrFe12O19 (SrM or strontium ferrite), and cobalt-titanium substituted M ferrite, Sr- or BaFe12-2xCoxTixO19 (CoTiM). times Z-type ferrites (Ba3Me2Fe24O41) such as Ba3Co2Fe24O41, or Co2Z. times Y-type ferrites (Ba2Me2Fe12O22), such as Ba2Co2Fe12O22, or Co2Y. times W-type ferrites (BaMe2Fe16O27), such as BaCo2Fe16O27, or Co2W. times X-type ferrites (Ba2Me2Fe28O46), such as Ba2Co2Fe28O46, or Co2X. times U-type ferrites (Ba4Me2Fe36O60), such as Ba4Co2Fe36O60, or Co2U . The best known hexagonal ferrites are those containing barium and cobalt as divalent cations, but many variations of these and hexaferrites containing other cations (substituted or doped) will also be discussed, especially M, W, Z and Y ferrites containing strontium, zinc, nickel and magnesium. The hexagonal ferrites are all ferrimagnetic materials, and their magnetic properties are intrinsically linked to their crystalline structures. They all have a magnetocrystalline anisotropy (MCA), that is the induced magnetisation has a preferred orientation within the crystal structure. They can be divided into two main groups: those with an easy axis of magnetisation, the uniaxial hexaferrites, and those with an easy plane (or cone) of magnetisation, known as the ferroxplana or hexaplana ferrites. The structure, synthesis, solid state chemistry and magnetic properties of the ferrites shall be discussed here. This review will focus on the synthesis and properties of bulk ceramic ferrites. This is because the depth of research into thin film hexaferrites is enough for a review of its own. There has been an explosion of interest in hexaferrites in the last decade for more exotic applications. This is particularly true as electronic components for mobile and wireless communications at microwave/GHz frequencies, electromagnetic wave absorbers for EMC, RAM and stealth technologies (especially the X and U ferrites), and as composite materials. There is also a clear recent interest in nanotechnology, the development of nanofibres and fibre orientation and alignment effects in hexaferrite fibres, and composites with carbon nanotubes (CNT). One of the most exciting developments has been the discovery of single phase magnetoelectric/multiferroic hexaferrites, firstly Ba2Mg2Fe12O22 Y ferrite at cryogenic temperatures, and now Sr3Co2Fe24O41 Z ferrite at room temperature. Several M, Y, Z and U ferrites have now been characterised as room temperature multiferroics, and are discussed here. Current developments in all these key areas will be discussed in detail in Sections of this review, and for this reason now is the appropriate time for a fresh and critical appraisal of the synthesis, properties and applications of hexagonal ferrites.
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