GeSn alloys with Sn contents of 8.4 % and 10.7 % are grown pseudomorphically on Ge buffers on Si (001) substrates. The alloys as-grown are compressively strained, and therefore indirect bandgap. ...Undercut GeSn on Ge microdisk structures are fabricated and strained by silicon nitride stressor layers, which leads to tensile strain in the alloys, and direct bandgap photoluminescence in the 3-5 µm gas sensing window of the electromagnetic spectrum. The use of pseudomorphic layers and external stress mitigates the need for plastic deformation to obtain direct bandgap alloys. It is demonstrated, that the optically pumped light emission overlaps with the methane absorption lines, suggesting that GeSn alloys are well suited for mid-infrared integrated gas sensors on Si chips.
Viral and bacterial pathogens are a significant economic concern to the US broiler industry and the ecological epicenter for poultry pathogens is the mixture of bedding material, chicken excrement ...and feathers that comprises the litter of a poultry house. This study used high-throughput sequencing to assess the richness and diversity of poultry litter bacterial communities, and to look for connections between these communities and the environmental characteristics of a poultry house including its history of gangrenous dermatitis (GD). Cluster analysis of 16S rRNA gene sequences revealed differences in the distribution of bacterial phylotypes between Wet and Dry litter samples and between houses. Wet litter contained greater diversity with 90% of total bacterial abundance occurring within the top 214 OTU clusters. In contrast, only 50 clusters accounted for 90% of Dry litter bacterial abundance. The sixth largest OTU cluster across all samples classified as an Arcobacter sp., an emerging human pathogen, occurring in only the Wet litter samples of a house with a modern evaporative cooling system. Ironically, the primary pathogenic clostridial and staphylococcal species associated with GD were not found in any house; however, there were thirteen 16S rRNA gene phylotypes of mostly gram-positive phyla that were unique to GD-affected houses and primarily occurred in Wet litter samples. Overall, the poultry house environment appeared to substantially impact the composition of litter bacterial communities and may play a key role in the emergence of food-borne pathogens.
This paper presents a numerical method to simulate a Gaussian random field over a 3D surface whereas the existing methods in the literature are limited to simple 2D surfaces. This new approach is ...summarized in the following. First, a covariance function is proposed based on the shortest path between two points on the 3D surface. Second, the Karhunen–Loève expansion is discretized using a coupling between two methods: the Galerkin method with the fast marching method (for computing the covariance function with the shortest path). The proposed numerical method is illustrated with an application to a composite structure representing a chair. The fiber volume fraction, the ratio between fibers and resin volumes, is considered to be uncertain. This uncertain parameter is directly linked to the mechanical parameters of the material. The structural integrity of this structure is represented by the maximal deflection and the maximal Tsai–Wu criterion. Monte Carlo simulations are used to carry out the uncertainty quantification of these responses with respect to the uncertain parameter.
Low-voltage swing (≤1.0 V) high-contrast ratio (6 dB) electro-absorption modulation covering 1460 to 1560 nm wavelength has been demonstrated using Ge/SiGe quantum confined Stark effect (QCSE) diodes ...grown on a silicon substrate. The heterolayers for the devices were designed using an 8-band k.p Poisson-Schrödinger solver which demonstrated excellent agreement with the experimental results. Modelling and experimental results demonstrate that by changing the quantum well width of the device, low power Ge/SiGe QCSE modulators can be designed to cover the S- and C-telecommunications bands.
Targeted resequencing with high-throughput sequencing (HTS) platforms can be used to efficiently interrogate the genomes of large numbers of individuals. A critical issue for research and ...applications using HTS data, especially from long-read platforms, is error in base calling arising from technological limits and bioinformatic algorithms. We found that the community standard long amplicon analysis (LAA) module from Pacific Biosciences is prone to substantial bioinformatic errors that raise concerns about findings based on this pipeline, prompting the need for a new method.
A single molecule real-time (SMRT) sequencing-error correction and assembly pipeline, C3S-LAA, was developed for libraries of pooled amplicons. By uniquely leveraging the structure of SMRT sequence data (comprised of multiple low quality subreads from which higher quality circular consensus sequences are formed) to cluster raw reads, C3S-LAA produced accurate consensus sequences and assemblies of overlapping amplicons from single sample and multiplexed libraries. In contrast, despite read depths in excess of 100X per amplicon, the standard long amplicon analysis module from Pacific Biosciences generated unexpected numbers of amplicon sequences with substantial inaccuracies in the consensus sequences. A bootstrap analysis showed that the C3S-LAA pipeline per se was effective at removing bioinformatic sources of error, but in rare cases a read depth of nearly 400X was not sufficient to overcome minor but systematic errors inherent to amplification or sequencing.
C3S-LAA uses a divide and conquer processing algorithm for SMRT amplicon-sequence data that generates accurate consensus sequences and local sequence assemblies. Solving the confounding bioinformatic source of error in LAA allowed for the identification of limited instances of errors due to DNA amplification or sequencing of homopolymeric nucleotide tracts. For research and development in genomics, C3S-LAA allows meaningful conclusions and biological inferences to be made from accurately polished sequence output.
The problem of computing the ply lay-outs of a composite structure from the definition of the stacking sequences of the zones is studied in this paper. These stacking sequences result from the design ...of the composite structure and they are considered to be admissible with respect to standard composite design and manufacturing rules. This paper shows that the definition of blended stacking sequences does not necessarily lead to a possible solution for the ply layouts. Therefore, the design process of a composite structure must include a further step after computing the stacking sequences which is to compute the ply layouts. The paper presents an algorithm to compute a ply layout solution for a given set of stacking sequences. Using a backtracking approach, it efficiently checks all the possible ply layout combinations to find a solution. Some numerical experiments are presented to study the mapping between stacking sequences and ply layouts and the existence of a ply layout solution.
This paper deals with the preliminary design of a composite structure where the design variables are the thicknesses and the percentages of fiber orientations in the zones of the structure. In this ...paper, we propose to include the design and manufacturing rules in the preliminary design. A stacking sequence generator is used to compute admissible stacking sequences with respect to these rules and which correspond to the design variables. Given that an admissible stacking sequence does not exist for every set of values of the design variables, a repair operator is proposed to cope with this problem. It aims at changing the values of the percentages of the fiber orientations in order to guarantee the existence of admissible stacking sequences with respect to the manufacturing rules. The repair operator is integrated into an optimization loop which uses a genetic algorithm to perform the preliminary design of a composite structure. Its efficiency is shown with a test case which involves a large number of fiber orientations and stacking sequences.
Buccal cells are a valid source of vertebrate DNA for genetic analysis, typically collected with mouth swabs on captured individuals. Yet, advances in DNA storage and processing now permit recovering ...genomic material from traces of saliva in food remains. For example, the feeding habits of canopy-dwelling frugivorous birds, e.g. large macaws (Psittaciformes), could present an ideal opportunity to obtain environmental DNA (eDNA) from partially consumed fruits. We tested this by collecting tropical almond (
Terminalia catappa
) fruits, eaten and discarded by scarlet macaws (
Ara macao
), and processed them using three different collection/storage methods. We successfully isolated DNA molecules from macaw residual saliva in fruits. This genetic material allowed the amplification of 7 microsatellite markers and of the CHD region of the avian sex chromosomes using two different primer pairs. Macaw eDNA concentration (mean 12 ng/µl) was similar to the reported in other avian studies using buccal swabs but overall microsatellite (60% success) and CHD-gen (20% success) amplification was low. The best results were obtained for samples preserved in ethanol. We conclude that saliva eDNA in partially consumed food items is an underused source of non-invasive bird DNA for genetic analyses. Based on our results, we recommend that a combination of specialized collection swabs or ethanol stored swabs along with commercial DNA extraction kits be used. Protocols should be modified accordingly to reach a consistent level of individual identification and gender determination that closely matches traditional sampling.
The recombination suppression models of chromosomal speciation posit that chromosomal rearrangements act as partial barriers to gene flow allowing these regions to accumulate genetic ...incompatibilities, thus contributing to the divergence of populations. Empirical and theoretical studies exploring the requirements of these models have mostly focused on the role of inversions. Here, the recombination landscape of heterozygosity for Robertsonian (Rb) fusions is investigated in the house mouse. Laboratory-bred F1 males and females between highly differentiated races from Tunisia (Rb: 2n=22, Standard, St: 2n=40) were produced in which all Rb fusions are present as trivalents in meiosis. Recombination patterns were determined by the analysis of chiasmata and compared with previous data on the Tunisian parental mice. A comparative analysis was performed on wild-caught male mice spanning the hybrid zone between two Italian races (2n=40, 2n=22). The results showed that the chiasma characteristics of both male and female Tunisian F1 and Italian hybrids clearly differed from those of Rb and St mice. Not only was the mean chiasma number (CN) intermediate between those of the parental mice in both geographic samples, but the distribution of chiasmata along the chromosomal arms of the F1 showed a distinct mosaic pattern. In short, the proximal region in the F1 exhibited a reduced CN similar to that observed in homozygous Rb, whereas distal regions more closely matched those in St mice. These results suggest that Rb rearrangements (homozygous or heterozygous) reduce recombination in the proximal regions of the chromosomes supporting their potential role in recombination-mediated speciation models.
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