Defect filtering for thermal expansion induced dislocations in III-V lasers on silicon

Epitaxially integrated III-V semiconductor lasers for silicon photonics have the potential to dramatically transform information networks, but currently, dislocations limit performance and reliability even in defect tolerant InAs quantum dot (QD) based lasers. Despite being below critical thickness, QD layers in these devices contain previously unexplained misfit dislocations, which facilitate non-radiative recombination. We demonstrate here that these misfit dislocations form during post-growth cooldown due to the combined effects of (1) thermal-expansion mismatch between the III-V layers and silicon and (2) precipitate and alloy hardening in the active region. By incorporating an additional sub-critical thickness, indium-alloyed misfit dislocation trapping layer, we leverage these mechanical hardening effects to our advantage, successfully displacing 95% of misfit dislocations from the QD layer in model structures. Unlike conventional dislocation mitigation strategies, the trapping layer reduces neither the number of threading dislocations nor the number of misfit dislocations. It simply shifts the position of misfit dislocations away from the QD layer, reducing the defects' impact on luminescence. In full lasers, adding a misfit dislocation trapping layer both above and below the QD active region displaces misfit dislocations and substantially improves performance: we measure a twofold reduction in lasing threshold currents and a greater than threefold increase in output power. Our results suggest that devices employing both traditional threading dislocation reduction techniques and optimized misfit dislocation trapping layers may finally lead to fully integrated, commercially viable silicon-based photonic integrated circuits.Comment: 9 pages, 6 figure

Interfacial adhesion of compositional gradient ternary FCC alloy films

Combinatorial materials design of thin films allows for the investigation of fundamental mechanic relationships and optimization of thin films for engineering applications. By depositing a wide range of compositions on a single sample, a systematic study of the full alloy composition of particular material system can be investigated for a number of different properties in a relatively short amount of time. Using an integrated shutter controller, specifically designed and manufactured to allow for precise control over coating design, ternary alloys with the full compositional range can be deposited on a single wafer. By specifically programming the shutters it was possible to create multilayered thickness gradients of three elements, which were then annealed to create thin films with a large compositional gradient across the wafer. The adhesion strength of an Al2O3­ ALD coating on two such compositional gradient FCC alloy adhesion layers, AlCuAu and AuAgPd, was investigated as a function of the changing composition. The AlCuAu alloy sample consists of multiple phases and intermetallics across the wafer which are dependent on composition; whereas the AuAgPd alloy is a solid-solution across the compositional gradient. For this investigation, instrumented indentation with a conical diamond tip was used to locally measure the adhesion of the ALD coating with different adhesion layer compositions. By performing small arrays of indents over the surface of the coating, it was possible to test the adhesion-promoting properties of a broad spectrum of interface compositions in a single sample. Please click Additional Files below to see the full abstract

Molecular basis for PrimPol recruitment to replication forks by RPA

DNA damage and secondary structures can stall the replication machinery. Cells possess numerous tolerance mechanisms to complete genome duplication in the presence of such impediments. In addition to translesion synthesis (TLS) polymerases, most eukaryotic cells contain a multi-functional replicative enzyme called Primase-Polymerase (PrimPol) that is capable of directly bypassing DNA damage by TLS, as well as repriming replication downstream of impediments. Here, we report that PrimPol is recruited to reprime through its interaction with RPA. Using biophysical and crystallographic approaches, we identify that PrimPol possesses two RPA-binding motifs and ascertained the key residues required for these interactions. We demonstrate that one of these motifs is critical for PrimPolʼs recruitment to stalled replication forks in vivo. In addition, biochemical analysis reveals that RPA serves to stimulate the primase activity of PrimPol. Together, these findings provide significant molecular insights into PrimPolʼs mode of recruitment to stalled forks to facilitate repriming and restart

Combinatorial Materials Design Approach to Investigate Adhesion Layer Chemistry for Optimal Interfacial Adhesion Strength

A combinatorial material adhesion study was used to optimize the composition of an adhesion promoting layer for a nanocrystalline diamond (NCD) coating on silicon. Three different adhesion promoting metals, namely W, Cr, and Ta, were selected to fabricate arrays of co-sputtered binary alloy films, with patches of seven different, distinct alloy compositions for each combination, and single element reference films on a single Si wafer (three wafers in total; W–Cr, Cr–Ta, Ta–W). Scratch testing was used to determine the critical failure load and practical work of adhesion for the NCD coatings as a function of adhesion layer chemistry. All tested samples eventually exhibit delamination of the NCD coating, with buckles radiating perpendicularly away from the scratch track. Application of any of the presented adhesion layers yields an increase of the critical failure load for delamination as compared to NCD on Si. While the influence of adhesion layers on the maximum buckle length is less pronounced, shorter buckles are obtained with pure W and Cr–Ta alloy layers. As a general rule, the addition of an adhesion layer showed a 75% improvement in the measured adhesion energies of the NCD films compared to the NCD coating without an adhesion layer, with specific alloys and compositions showing up to 125% increase in calculated practical work of adhesion.H2020 Marie Skłodowska-Curie Action

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni.

Modern agriculture has dramatically changed the distribution of animal species on Earth. Changes to host ecology have a major impact on the microbiota, potentially increasing the risk of zoonotic pathogens being transmitted to humans, but the impact of intensive livestock production on host-associated bacteria has rarely been studied. Here, we use large isolate collections and comparative genomics techniques, linked to phenotype studies, to understand the timescale and genomic adaptations associated with the proliferation of the most common food-born bacterial pathogen (Campylobacter jejuni) in the most prolific agricultural mammal (cattle). Our findings reveal the emergence of cattle specialist C. jejuni lineages from a background of host generalist strains that coincided with the dramatic rise in cattle numbers in the 20th century. Cattle adaptation was associated with horizontal gene transfer and significant gene gain and loss. This may be related to differences in host diet, anatomy, and physiology, leading to the proliferation of globally disseminated cattle specialists of major public health importance. This work highlights how genomic plasticity can allow important zoonotic pathogens to exploit altered niches in the face of anthropogenic change and provides information for mitigating some of the risks posed by modern agricultural systems

Uncharacterized bacterial structures revealed by electron cryotomography

Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells

Data quality influences the predicted distribution and habitat of four southern-hemisphere albatross species

Few studies have assessed the influence of data quality on the predicted probability of occurrence and preferred habitat of marine predators. We compared results from four species distribution models (SDMs) for four southern-hemisphere albatross species, Buller’s (Thalassarche bulleri), Campbell (T. impavida), grey-headed (T. chrysostoma), and white-capped (T. steadi), based on datasets of differing quality, ranging from no location data to twice-daily locations of individual birds collected by geolocation devices. Two relative environmental suitability (RES) models were fit using minimum and maximum preferred and absolute values for each environmental variable based on (1) monthly 50% kernel density contours and background environmental data, and (2) primary literature or expert opinion. Additionally, two boosted regression tree (BRT) models were fit using (1) opportunistic sightings data, and (2) geolocation data from bird-borne electronic tags. Using model-specific threshold values, habitat was quantified for each species and model. Model variables included distance from land, bathymetry, sea surface temperature, and chlorophyll-a concentration. Results from both RES models and the BRT model fit with opportunistic sightings were compared to those from the BRT model fit using geolocation data to assess the influence of data quality on predicted occupancy and habitat. For all species, BRT models outperformed RES models. BRT models offer a predictive advantage over RES models by being able to identify relevant variables, incorporate environmental interactions, and provide spatially explicit estimates of model uncertainty. RES models resulted in larger, less refined areas of predicted habitat for all species. Our study highlights the importance of data quality in predicting the distribution and habitat of albatrosses and emphasises the need to consider the pros and cons associated with different levels of data quality when using SDMs to inform management decisions. Furthermore, we examine the overlap in preferred habitat predicted by each SDM with fishing effort. We discuss the influence of data quality on predicting the wide-scale distributions of pelagic seabirds and how these impacts could result in different protection measures

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

HLA Class I Binding of HBZ Determines Outcome in HTLV-1 Infection

CD8(+) T cells can exert both protective and harmful effects on the virus-infected host. However, there is no systematic method to identify the attributes of a protective CD8(+) T cell response. Here, we combine theory and experiment to identify and quantify the contribution of all HLA class I alleles to host protection against infection with a given pathogen. In 432 HTLV-1-infected individuals we show that individuals with HLA class I alleles that strongly bind the HTLV-1 protein HBZ had a lower proviral load and were more likely to be asymptomatic. We also show that in general, across all HTLV-1 proteins, CD8(+) T cell effectiveness is strongly determined by protein specificity and produce a ranked list of the proteins targeted by the most effective CD8(+) T cell response through to the least effective CD8(+) T cell response. We conclude that CD8(+) T cells play an important role in the control of HTLV-1 and that CD8(+) cells specific to HBZ, not the immunodominant protein Tax, are the most effective. We suggest that HBZ plays a central role in HTLV-1 persistence. This approach is applicable to all pathogens, even where data are sparse, to identify simultaneously the HLA Class I alleles and the epitopes responsible for a protective CD8(+) T cell response