Optical doping and damage formation in AIN by Eu implantation

AlN films grown on sapphire were implanted with 300 keV Eu ions to fluences from 3×1014 to 1.4×1017 atoms/cm2 in two different geometries: “channeled” along the c-axis and “random” with a 10° angle between the ion beam and the surface normal. A detailed study of implantation damage accumulation is presented. Strong ion channeling effects are observed leading to significantly decreased damage levels for the channeled implantation within the entire fluence range. For random implantation, a buried amorphous layer is formed at the highest fluences. Red Eu-related photoluminescence at room temperature is observed in all samples with highest intensities for low damage samples (low fluence and channeled implantation) after annealing. Implantation damage, once formed, is shown to be stable up to very high temperatures.FCT - POCI/FIS/57550/2004FCT - PTDC/FIS/66262/2006FCT - PTDC/CTM/100756/200

Association of Fecal Microbial Diversity and Taxonomy with Selected Enzymatic Functions

Few microbial functions have been compared to a comprehensive survey of the human fecal microbiome. We evaluated determinants of fecal microbial β-glucuronidase and β-glucosidase activities, focusing especially on associations with microbial alpha and beta diversity and taxonomy. We enrolled 51 healthy volunteers (26 female, mean age 39) who provided questionnaire data and multiple aliquots of a stool, from which proteins were extracted to quantify β-glucuronidase and β-glucosidase activities, and DNA was extracted to amplify and pyrosequence 16S rRNA gene sequences to classify and quantify microbiome diversity and taxonomy. Fecal β-glucuronidase was elevated with weight loss of at least 5 lb. (P = 0.03), whereas β-glucosidase was marginally reduced in the four vegetarians (P = 0.06). Both enzymes were correlated directly with microbiome richness and alpha diversity measures, directly with the abundance of four Firmicutes Clostridia genera, and inversely with the abundance of two other genera (Firmicutes Lactobacillales Streptococcus and Bacteroidetes Rikenellaceae Alistipes) (all P = 0.05–0.0001). Beta diversity reflected the taxonomic associations. These observations suggest that these enzymatic functions are performed by particular taxa and that diversity indices may serve as surrogates of bacterial functions. Independent validation and deeper understanding of these associations are needed, particularly to characterize functions and pathways that may be amenable to manipulation

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/human​n. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.National Institutes of Health (U.S.) (U54HG004968

A comparative structural investigation of GaN implanted with rare earth ions at room temperature and 500 °C

The crystallographic damage induced in GaN by 300 keV rare earth ions implantation has been investigated as a function of the implantation temperature. The defect structure of GaN thin films implanted at 500 °C with Eu or Er ions with fluences ranging between 1 × 1015 and 2 × 1016 at./cm2 has been compared with the case of implantation performed at room temperature (RT). Transmission electron microscopy (TEM) investigation shows that less damage is formed during implantation at the higher temperature: basal stacking faults with a majority of I1 type and prismatic stacking faults have been observed as in GaN implanted at RT, but with a lower density. The nanocrystalline layer observed when GaN was implanted at RT with rare earth ion fluences higher than 3 × 1015 at./cm2, did not form for fluences up to 2 × 1016 at./cm2. Implantation of GaN at 500 °C through an ultrathin AlN cap points out the protective role of this cap against the GaN surface erosion that occurs from 8 × 1015 at./cm2. This method appears as a promising way to reduce the induced damage during the GaN implantation process

A comparative investigation of the damage build-up in GaN and Si during rare earth ion implantation

The medium range implantation of rare earth ions at room temperature in GaN layers leads to the formation of point defect clusters, basal and prismatic stacking faults from the lowest fluence. When a threshold fluence of about 3 × 1015 at/cm2 is reached, a highly disordered ‘nanocrystalline layer' (NL) is observed to form at the surface. This layer is made of a mixture of misoriented nanocrystallites and voids. Beyond this NL, I1, I2 and E basal stacking faults (BSFs) have been identified, as well as in GaN implanted at lower fluences than the threshold. Prismatic stacking faults (PSFs) with Drum atomic configuration connect the I1 BSFs. A similar investigation of the damage in Eu implanted Si shows a completely different behaviour; in this case, from the relatively low fluence 1 × 1014 at/cm2, amorphization starts in patches at the projected range and extends very rapidly towards the surface and the bulk, to form a uniform amorphous layer already at 2 × 1014 at/cm2

Rare Earth Ion Implantation in GaN: Damage Formation and Recovery

Rare earth ions implanted GaN has been investigated by transmission electron microscopy versus the fluence, using Er, Eu or Tm ions at 150 keV or 300 keV and at room temperature. Point defect clusters and stacking faults are generated from low fluences (7×10$\text{}^{13}$ at/cm$\text{}^{2}$), their density increases with the fluence up to the formation of a highly disordered layer at the surface. This highly disordered layer is observed from a threshold fluence of 3×10$\text{}^{14}$ at/cm$\text{}^{2}$ at 150 keV and 3×10$\text{}^{15}$ at/cm$\text{}^{2}$ at 300 keV, and appears to be composed of voids and misoriented nanocrystallites. Its thickness rapidly increases with the fluence, and then saturates. Both basal and prismatic stacking faults were observed. Basal stacking faults are I$\text{}_{1}$ in majority, but E or I$\text{}_{2}$ have also been identified. I$\text{}_{1}$ basal stacking faults propagate easily through GaN by folding from basal to prismatic planes. Channelling implantation, increasing the implantation temperature from room temperature to 500ºC, or implanting through a 10 nm thick AlN cap reduce the crystallographic damage, particularly by retarding the formation of the highly disordered layer. Implanting through the AlN cap allows the highly disordered layer formation threshold fluence to be increased by one order of magnitude, as well as the annealing at high temperature (1300ºC) which brings about a strong optical activation of the rare earths

Osmoprotection of Escherichia coli by ectoine: uptake and accumulation characteristics.

Ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) is a cyclic amino acid, identified as a compatible solute in moderately halophilic bacteria. Exogenously provided ectoine was found to stimulate growth of Escherichia coli in media of inhibitory osmotic strength. The stimulation was independent of any specific solute, electrolyte or nonelectrolyte. It is accumulated in E. coli cells proportionally to the osmotic strength of the medium, and it is not metabolized. Its osmoprotective ability was as potent as that of glycine betaine. The ProP and ProU systems are both involved in ectoine uptake and accumulation in E. coli. ProP being the main system for ectoine transport. The intracellular ectoine pool is regulated by both influx and efflux systems

A European perspective on acceptability of innovative agri-environment-climate contract solutions

The agri-environment-climate measures of the European Union Common Agricultural Policy are incentives aiming to reduce negative environmental impacts and increase positive effects generated from agriculture. Several criticisms have been addressed to their efficiency and effectiveness and thus, the design of innovative contract solutions is currently suggested. Among the novel contractual solutions, there are result-based payments, collective implementation of measures, the engagement of private and business actors in value chains, and new forms of land tenure systems coupled with environmental clauses. Little is known about the factors at interplay influencing farmers’ decision to uptake such contracts. The present paper investigates the acceptability determinants of the above-mentioned novel contractual solutions concerning a sample of nearly 1900 farmers from 10 European Union countries. The analysis is based on a questionnaire built through a common research framework. We apply ordered logistic regressions: both proportional and partial proportional odds models are used. Farmers’ preferences are interpreted by splitting the innovative contractual solutions into 13 individual contractual features which are then modeled in combination with the structural characteristics of the farms and the sociodemographic and behavioral characteristics of the farmers. We estimate farmers’ willingness to enroll in result-based, collective, value-chain, and land tenure contracts and highlight the positive and negative factors potentially influencing farmers’ acceptability of each type of contract

Structure and role of ultrathin AlN layers for improving optical activation of rare earth implanted GaN

International audienceIn this work we carry out characterization of GaN implanted with Tm and Eu ions by scanning and transmission electron microscopy. Structural investigation is supported by optical measurements. We have investigated samples implanted at room temperature with different energies (150–300 keV) and fluences (1–7 × 1015 at/cm2). High temperature annealing was performed at 1200 °C and 1300 °C with the GaN surface protected by a 10nm thick AlN cap grown by MOCVD prior to the implantation. Direct implantation in GaN, results in the formation of a high density of stacking faults in the damaged surface layer and a nanocrystalline surface layer when a critical dose is exceeded. Implanting through the AlN capping layer prevents the formation of the nanocrystalline layer even for high fluences but the stacking faults are still generated. The AlN cap also protects the surface during high temperature annealing