Topological Floquet edge states in periodically curved waveguides

We study the Floquet edge states in arrays of periodically curved optical waveguides described by the modulated Su-Schrieffer-Heeger model. Beyond the bulk-edge correspondence, our study explores the interplay between band topology and periodic modulations. By analysing the quasi-energy spectra and Zak phase, we reveal that, although topological and non-topological edge states can exist for the same parameters, \emph{they can not appear in the same spectral gap}. In the high-frequency limit, we find analytically all boundaries between the different phases and study the coexistence of topological and non-topological edge states. In contrast to unmodulated systems, the edge states appear due to either band topology or modulation-induced defects. This means that periodic modulations may not only tune the parametric regions with nontrivial topology, but may also support novel edge states.Comment: 11 pages, 5 figure

Metatranscriptomic analysis reveals active bacterial communities in diabetic foot infections

Despite the extended view of the composition of diabetic foot infections (DFIs), little is known about which transcriptionally active bacterial communities are pertinent to infection, and if any differences are associated with increased infection severity. We applied a RNA sequencing approach to analyze the composition, function, and pathogenicity of the active bacterial communities in DFIs. Taxonomic profiling of bacterial transcripts revealed the presence of 14 bacterial phyla in DFIs. The abundance of the Spiroplasma, Vibrio, and Mycoplasma were significantly different in different infection severities (P < 0.05). Mild and severe stages of infections were dominated by Staphylococcus aureus and Porphyromonas asaccharolytica, respectively. A total of 132 metabolic pathways were identified of which ribosome and thiamin being among the most highly transcribed pathways. Moreover, a total of 131 antibiotic resistance genes, primarily involved in the multidrug efflux pumps/exporters, were identified. Furthermore, iron acquisition systems (synthesize and regulation of siderophores) and pathways involved in the synthesis and regulation of cell-surface components associated with adhesion, colonization, and movement of bacterial cells were the most common virulence factors. These virulence factors may help bacteria compete for scares resources and survive the host wound proteases. Characterization of transcriptionally active bacterial communities can help to provide an understanding of the role of key pathogens in the development of DFIs. Such information can be clinically useful allowing replacement of DFIs empirical therapy with targeted treatment

Oxidation of Silicon Implanted with High-Dose Aluminum

Si(100) wafers were implanted with Al at 500 C to high doses at multi-energies and were oxidized in 1 atm flowing oxygen at 1000-1200 C. Morphology, structure, and oxidation behavior of the implanted and oxidized Si were studied using optical microscopy, atomic force microscopy, and cross-sectional transmission electron microscopy in conjunction with selected area electron diffraction and energy dispersive x-ray analysis. Large Al precipitates were formed and embedded near the surface region of the implanted Si. Oxidation rate of the Al-implanted Si wafers was lower than that of virgin Si. The unique morphology of the implanted Si results from rpaid Al diffusion and segregation promoted by hot implantation. Reduction of the oxidation rate of Si by Al implantation is attributed to preferential oxidation of Al and formation of a continuous diffusion barrier of Al{sub 2}O{sub 3}

Association of Soil Aggregation with the Distribution and Quality of Organic Carbon in Soil along an Elevation Gradient on Wuyi Mountain in China

Forest soils play a critical role in the sequestration of atmospheric CO2 and subsequent attenuation of global warming. The nature and properties of organic matter in soils have an influence on the sequestration of carbon. In this study, soils were collected from representative forestlands, including a subtropical evergreen broad-leaved forest (EBF), a coniferous forest (CF), a subalpine dwarf forest (DF), and alpine meadow (AM) along an elevation gradient on Wuyi Mountain, which is located in a subtropical area of southeastern China. These soil samples were analyzed in the laboratory to examine the distribution and speciation of organic carbon (OC) within different size fractions of water-stable soil aggregates, and subsequently to determine effects on carbon sequestration. Soil aggregation rate increased with increasing elevation. Soil aggregation rate, rather than soil temperature, moisture or clay content, showed the strongest correlation with OC in bulk soil, indicating soil structure was the critical factor in carbon sequestration of Wuyi Mountain. The content of coarse particulate organic matter fraction, rather than the silt and clay particles, represented OC stock in bulk soil and different soil aggregate fractions. With increasing soil aggregation rate, more carbon was accumulated within the macroaggregates, particularly within the coarse particulate organic matter fraction (250-2000 μm), rather than within the microaggregates (53-250μm) or silt and clay particles (< 53μm). In consideration of the high instability of macroaggregates and the liability of SOC within them, further research is needed to verify whether highly-aggregated soils at higher altitudes are more likely to lose SOC under warmer conditions

Response and inbreeding from a genomic selection experiment in layer chickens

International audienceGenomic selection (GS) using estimated breeding values (GS-EBV) based on dense marker data is a promising approach for genetic improvement. A simulation study was undertaken to illustrate the opportunities offered by GS for designing breeding programs. It consisted of a selection program for a sex-limited trait in layer chickens, which was developed by deterministic predictions under different scenarios. Later, one of the possible schemes was implemented in a real population of layer chicken.MethodsIn the simulation, the aim was to double the response to selection per year by reducing the generation interval by 50 %, while maintaining the same rate of inbreeding per year. We found that GS with retraining could achieve the set objectives while requiring 75 % fewer reared birds and 82 % fewer phenotyped birds per year. A multi-trait GS scenario was subsequently implemented in a real population of brown egg laying hens. The population was split into two sub-lines, one was submitted to conventional phenotypic selection, and one was selected based on genomic prediction. At the end of the 3-year experiment, the two sub-lines were compared for multiple performance traits that are relevant for commercial egg production.ResultsBirds that were selected based on genomic prediction outperformed those that were submitted to conventional selection for most of the 16 traits that were included in the index used for selection. However, although the two programs were designed to achieve the same rate of inbreeding per year, the realized inbreeding per year assessed from pedigree was higher in the genomic selected line than in the conventionally selected line.ConclusionsThe results demonstrate that GS is a promising alternative to conventional breeding for genetic improvement of layer chickens

Segmental duplication as one of the driving forces underlying the diversity of the human immunoglobulin heavy chain variable gene region

Background: Segmental duplication and deletion were implicated for a region containing the human immunoglobulin heavy chain variable (IGHV) gene segments, 1.9III/hv3005 (possible allelic variants of IGHV3-30) and hv3019b9 (a possible allelic variant of IGHV3-33). However, very little is known about the ranges of the duplication and the polymorphic region. This is mainly because of the difficulty associated with distinguishing between allelic and paralogous sequences in the IGHV region containing extensive repetitive sequences. Inability to separate the two parental haploid genomes in the subjects is another serious barrier. To address these issues, unique DNA sequence tags evenly distributed within and flanking the duplicated region implicated by the previous studies were selected. The selected tags in single sperm from six unrelated healthy donors were amplified by multiplex PCR followed by microarray detection. In this way, individual haplotypes of different parental origins in the sperm donors could be analyzed separately and precisely. The identified polymorphic region was further analyzed at the nucleotide sequence level using sequences from the three human genomic sequence assemblies in the database. Results: A large polymorphic region was identified using the selected sequence tags. Four of the 12 haplotypes were shown to contain consecutively undetectable tags spanning in a variable range. Detailed analysis of sequences from the genomic sequence assemblies revealed two large duplicate sequence blocks of 24,696 bp and 24,387 bp, respectively, and an incomplete copy of 961 bp in this region. It contains up to 13 IGHV gene segments depending on haplotypes. A polymorphic region was found to be located within the duplicated blocks. The variants of this polymorphism unusually diverged at the nucleotide sequence level and in IGHV gene segment number, composition and organization, indicating a limited selection pressure in general. However, the divergence level within the gene segments is significantly different from that in the intergenic regions indicating that these regions may have been subject to different selection pressures and that the IGHV gene segments in this region are functionally important. Conclusions: Non-reciprocal genetic rearrangements associated with large duplicate sequence blocks could substantially contribute to the IGHV region diversity. Since the resulting polymorphisms may affect the number, composition and organization of the gene segments in this region, it may have significant impact on the function of the IGHV gene segment repertoire, antibody diversity, and therefore, the immune system. Because one of the gene segments, 3-30 (1.9III), is associated with autoimmune diseases, it could be of diagnostic significance to learn about the variants in the haplotypes by using the multiplex haplotype analysis system used in the present study with DNA sequence tags specific for the variants of all gene segments in this regio

Oxidation of silicon implanted with high-dose aluminum

Si(100) wafers were implanted with Al at 500 C to high doses at multi-energies and were oxidized in 1 atm flowing oxygen at 1000-1200 C. Morphology, structure, and oxidation behavior of the implanted and oxidized Si were studied using optical microscopy, atomic force microscopy, and cross-sectional transmission electron microscopy in conjunction with selected area electron diffraction and energy dispersive x-ray analysis. Large Al precipitates were formed and embedded near the surface region of the implanted Si. Oxidation rate of the Al-implanted Si wafers was lower than that of virgin Si. The unique morphology of the implanted Si results from rpaid Al diffusion and segregation promoted by hot implantation. Reduction of the oxidation rate of Si by Al implantation is attributed to preferential oxidation of Al and formation of a continuous diffusion barrier of Al{sub 2}O{sub 3}