Magnetic Domain Patterns Depending on the Sweeping Rate of Magnetic Fields

The domain patterns in a thin ferromagnetic film are investigated in both experiments and numerical simulations. Magnetic domain patterns under a zero field are usually observed after an external magnetic field is removed. It is demonstrated that the characteristics of the domain patterns depend on the decreasing rate of the external field, although it can also depend on other factors. Our numerical simulations and experiments show the following properties of domain patterns: a sea-island structure appears when the field decreases rapidly from the saturating field to the zero field, while a labyrinth structure is observed for a slowly decreasing field. The mechanism of the dependence on the field sweeping rate is discussed in terms of the concepts of crystallization.Comment: 4 pages, 3 figure

Analysis of IgE turnover in non-sensitized and sensitized rats.

BACKGROUND: Although the levels of immunoglobulin E (IgE) in the circulating blood are often elevated in patients with allergic diseases, such levels cannot always be considered as pathognomonic signs of allergy. The induction of allergic reactions in the tissue was inferred to be related to the amount of IgE passing through the vascular wall. AIMS: We attempted to clarify which compartment, the intravascular or extravascular, plays an important role in the regulation of the turnover of rat IgE. METHODS: The level of DNP-specific rat IgE in the serum was estimated by IgE-capture enzyme-linked immunosorbent assay, and the turnover of IgE was analyzed from its pharmacokinetic parameters. RESULTS: The transfer rate constants from the central to tissue compartment (Kct) were larger than those from the tissue to central compartment (Ktc) irrespective of the sensitized state. The value of the distribution volume of the tissue compartment (Vt) was larger than that of the distribution volume of the central compartment (Vc) irrespective of the sensitized state. CONCLUSIONS: These Findings suggest that the short half-life of rat IgE in the circulation could be attributable to the distribution of IgE from the intravascular to the extravascular compartment

Threatened Corals Provide Underexplored Microbial Habitats

Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs

Proximity to Fermi-surface topological change in superconducting LaO0.54F0.46BiS2

The electronic structure of nearly optimally-doped novel superconductor LaO$_{1-x}$F$_x$BiS$_2$ (${\it x}$ = 0.46) was investigated using angle-resolved photoemission spectroscopy (ARPES). We clearly observed band dispersions from 2 to 6 eV binding energy and near the Fermi level (${\it E}_{\rm F}$), which are well reproduced by first principles calculations when the spin-orbit coupling is taken into account. The ARPES intensity map near ${\it E}_{\rm F}$ shows a square-like distribution around the $\Gamma$(Z) point in addition to electronlike Fermi surface (FS) sheets around the X(R) point, indicating that FS of LaO$_{0.54}$F$_{0.46}$BiS$_2$ is in close proximity to the theoretically-predicted topological change.Comment: 6 pages, 3 figures, + supplemental materia

CONGAS: a collaborative ontology development framework based on Named GrAphS

The process of ontology development involves a range of skills and know-how often requiring team work of different people, each of them with his own way of contributing to the definition and formalization of the domain representation. For this reason, collaborative development is an important feature for ontology editing tools, and should take into account the different characteristics of team participants, provide them with a dedicated working environment allowing to express their ideas and creativity, still protecting integrity of the shared work. In this paper we present CONGAS, a collaborative version of the Knowledge Management and Acquisition platform Semantic Turkey which, exploiting the potentialities brought by recent introduction of context management into RDF triple graphs, offers a collaborative environment where proposals for ontology evolution can emerge and coexist, be evaluated by team users, trusted across different perspectives and eventually converged into the main development stream

MOCAT2: a metagenomic assembly, annotation and profiling framework

MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes. Availability and Implementation: MOCAT2 is implemented in Perl 5 and Python 2.7, designed for 64-bit UNIX systems and offers support for high-performance computer usage via LSF, PBS or SGE queuing systems; source code is freely available under the GPL3 license at http://mocat.embl.de. Contact: [email protected]

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont

<p>Abstract</p> <p>Background</p> <p>The most diverse marine ecosystems, coral reefs, depend upon a functional symbiosis between cnidarian hosts and unicellular dinoflagellate algae. The molecular mechanisms underlying the establishment, maintenance, and breakdown of the symbiotic partnership are, however, not well understood. Efforts to dissect these questions have been slow, as corals are notoriously difficult to work with. In order to expedite this field of research, we generated and analyzed a collection of expressed sequence tags (ESTs) from the sea anemone <it>Aiptasia pallida </it>and its dinoflagellate symbiont (<it>Symbiodinium </it>sp.), a system that is gaining popularity as a model to study cellular, molecular, and genomic questions related to cnidarian-dinoflagellate symbioses.</p> <p>Results</p> <p>A set of 4,925 unique sequences (UniSeqs) comprising 1,427 clusters of 2 or more ESTs (contigs) and 3,498 unclustered ESTs (singletons) was generated by analyzing 10,285 high-quality ESTs from a mixed host/symbiont cDNA library. Using a BLAST-based approach to predict which unique sequences derived from the host versus symbiont genomes, we found that the contribution of the symbiont genome to the transcriptome was surprisingly small (1.6–6.4%). This may reflect low levels of gene expression in the symbionts, low coverage of alveolate genes in the sequence databases, a small number of symbiont cells relative to the total cellular content of the anemones, or failure to adequately lyse symbiont cells. Furthermore, we were able to identify groups of genes that are known or likely to play a role in cnidarian-dinoflagellate symbioses, including oxidative stress pathways that emerged as a prominent biological feature of this transcriptome. All ESTs and UniSeqs along with annotation results and other tools have been made accessible through the implementation of a publicly accessible database named AiptasiaBase.</p> <p>Conclusion</p> <p>We have established the first large-scale transcriptomic resource for <it>Aiptasia pallida </it>and its dinoflagellate symbiont. These data provide researchers with tools to study questions related to cnidarian-dinoflagellate symbioses on a molecular, cellular, and genomic level. This groundwork represents a crucial step towards the establishment of a tractable model system that can be utilized to better understand cnidarian-dinoflagellate symbioses. With the advent of next-generation sequencing methods, the transcriptomic inventory of <it>A. pallida </it>and its symbiont, and thus the extent of AiptasiaBase, should expand dramatically in the near future.</p