Epidemic management and control through risk-dependent individual contact interventions.

Testing, contact tracing, and isolation (TTI) is an epidemic management and control approach that is difficult to implement at scale because it relies on manual tracing of contacts. Exposure notification apps have been developed to digitally scale up TTI by harnessing contact data obtained from mobile devices; however, exposure notification apps provide users only with limited binary information when they have been directly exposed to a known infection source. Here we demonstrate a scalable improvement to TTI and exposure notification apps that uses data assimilation (DA) on a contact network. Network DA exploits diverse sources of health data together with the proximity data from mobile devices that exposure notification apps rely upon. It provides users with continuously assessed individual risks of exposure and infection, which can form the basis for targeting individual contact interventions. Simulations of the early COVID-19 epidemic in New York City are used to establish proof-of-concept. In the simulations, network DA identifies up to a factor 2 more infections than contact tracing when both harness the same contact data and diagnostic test data. This remains true even when only a relatively small fraction of the population uses network DA. When a sufficiently large fraction of the population (≳ 75%) uses network DA and complies with individual contact interventions, targeting contact interventions with network DA reduces deaths by up to a factor 4 relative to TTI. Network DA can be implemented by expanding the computational backend of existing exposure notification apps, thus greatly enhancing their capabilities. Implemented at scale, it has the potential to precisely and effectively control future epidemics while minimizing economic disruption.

Characterization of buried interfaces using Ga Kα hard X-ray photoelectron spectroscopy (HAXPES).

The extension of X-ray photoelectron spectroscopy (XPS) to measure layers and interfaces below the uppermost surface requires higher X-ray energies and electron energy analysers capable of measuring higher electron kinetic energies. This has been enabled at synchrotron radiation facilities and by using lab-based instruments which are now available with sufficient sensitivity for measurements to be performed on reasonable timescales. Here, we detail measurements on buried interfaces using a Ga Kα (9.25 keV) metal jet X-ray source and an EW4000 energy analyser (ScientaOmicron GmbH) in the Henry Royce Institute at the University of Manchester. Development of the technique has required the calculation of relative sensitivity factors (RSFs) to enable quantification analogous to Al Kα XPS, and here we provide further substantiation of the Ga Kα RSF library. Examples of buried interfaces include layers of memory and energy materials below top electrode layers, semiconductor heterostructures, ions implanted in graphite, oxide layers at metallic surfaces, and core-shell nanoparticles. The use of an angle-resolved mode enables depth profiling from the surface into the bulk, and is complemented with surface-sensitive XPS. Inelastic background modelling allows the extraction of information about buried layers at depths up to 20 times the photoelectron inelastic mean free path.

A role for SPEECHLESS in the integration of leaf stomatal patterning with the growth vs disease trade-off in poplar.

Occurrence of stomata on both leaf surfaces (amphistomaty) promotes higher stomatal conductance and photosynthesis while simultaneously increasing exposure to potential disease agents in black cottonwood (Populus trichocarpa). A genome-wide association study (GWAS) with 2.2M single nucleotide polymorphisms generated through whole-genome sequencing found 280 loci associated with variation in adaxial stomatal traits, implicating genes regulating stomatal development and behavior. Strikingly, numerous loci regulating plant growth and response to biotic and abiotic stresses were also identified. The most significant locus was a poplar homologue of SPEECHLESS (PtSPCH1). Individuals possessing PtSPCH1 alleles associated with greater adaxial stomatal density originated primarily from environments with shorter growing seasons (e.g. northern latitudes, high elevations) or with less precipitation. PtSPCH1 was expressed in developing leaves but not developing stem xylem. In developing leaves, RNA sequencing showed patterns of coordinated expression between PtSPCH1 and other GWAS-identified genes. The breadth of our GWAS results suggests that the evolution of amphistomaty is part of a larger, complex response in plants. Suites of genes underpin this response, retrieved through genetic association to adaxial stomata, and show coordinated expression during development. We propose that the occurrence of amphistomaty in P. trichocarpa involves PtSPCH1 and reflects selection for supporting rapid growth over investment in immunity.

InGaN µLEDs integrated onto colloidal quantum dot functionalized ultra-thin glass.

Red-, orange-, and green-emitting integrated optoelectronic sources are demonstrated by transfer printing blue InGaN µLEDs onto ultra-thin glass platforms functionally enhanced with II-VI colloidal quantum dots (CQDs). The forward optical power conversion efficiency of these heterogeneously integrated devices is, respectively, 9%, 15%, and 14% for a blue light absorption over 95%. The sources are demonstrated in an orthogonal frequency division multiplexed (OFDM) visible light communication link reaching respective data transmission rates of 46 Mbps, 44 Mbps and 61 Mbps.

Periostin as a marker of mucosal remodelling in chronic rhinosinusitis.

BACKGROUND: Although extracellular matrix (ECM) proteins are associated with irreversible lower airway changes, the relationship with upper airway remodelling which occurs during chronic rhinosinusitis (CRS) is poorly understood. This study assessed the expression of ECM proteins periostin, fibulin-1, fibronectin and collagenIV in nasal mucosa of patients with and without histologic features of remodelling. METHODS: A cross-sectional study of sinonasal mucosal biopsies taken from patients, undergoing surgery for CRS was performed, where patients were grouped according to remodelling, defined by basement membrane thickening (BMT over 7.5 micrometer) and subepithelial fibrosis. An overall view and three random fields of immunostained tissue sections that included epithelium, basement membrane and submucosa, were imaged using Zeiss Zen software. The area and intensity of positive staining were scored by two blinded observers, using a 12-point ordinal scale of weak to strong. RESULTS: 65 patients (47.6 +/- 13.4years, 44.6% female) were assessed. Patients were grouped as controls 26.2%, BMT/no fibrosis 38.5% or BMT and fibrosis 33.8%. Stronger grade of periostin expression was associated with remodelling changes and tissue eosinophilia over 10/HPF. Fibulin-1, fibronectin and collagenIV did not differ. CONCLUSION: Periostin expression was associated with the presence of BMT, fibrosis and tissue eosinophilia and may identify patients undergoing remodelling changes.

Stable Speckle Patterns for Nano-scale Strain Mapping up to 700 °C.

The digital image correlation (DIC) of speckle patterns obtained by vapour-assisted gold remodelling at 200 - 350 °C has already been used to map plastic strains with submicron resolution. However, it has not so far proved possible to use such patterns for testing at high temperatures. Here we demonstrate how a gold speckle pattern can be made that is stable at 700 °C, to study deformation in a commercial TiAl alloy (Ti-45Al-2Nb-2Mn(at%)-0.8 vol% TiB2). The pattern is made up of a uniformly sized random array of Au islands as small as 15 nm in diameter, depending on reconstruction parameters, with a sufficiently small spacing to be suitable for nano-scale, nDIC, strain mapping at a subset size of 60 × 60 nm2. It can be used at temperatures up to 700 °C for many hours, for high cycle fatigue testing for instance. There is good particle attachment to the substrate. It can withstand ultra-sound cleaning, is thermally stable and has a high atomic number contrast for topography-free backscatter electron imaging.

Efficiency droop in zincblende InGaN/GaN quantum wells.

The decrease in emission efficiency with increasing drive current density, known as 'droop', of c-plane wurtzite InGaN/GaN quantum wells presently limits the use of light-emitting diodes based on them for high brightness lighting applications. InGaN/GaN quantum wells grown in the alternative zincblende phase are free of the strong polarisation fields that exacerbate droop and so were investigated by excitation-dependent photoluminescence and photoreflectance studies. Polarisation-resolved measurements revealed that for all excitation densities studied the emission from such samples largely originates from similar microstructures or combinations of microstructures that form within the quantum well layers. Emission efficiency varies significantly with excitation at 10 K showing that non-radiative recombination processes are important even at low temperature. The onset of efficiency droop, as determined by photomodulated reflection measurements, occurred at a carrier density of around 1.2 × 1020 cm-3 - an order of magnitude greater than the value reported for a reference wurtzite quantum well sample using the same method. The high carrier density droop onset combined with the much shorter carrier lifetime within zincblende InGaN/GaN quantum wells indicate they have the potential to effectively delay efficiency droop when used in GaN based light-emitting diodes. However, the material quality of the quantum well layers need to be improved by preventing the formation of microstructures within these layers, and the importance of the role played by non-radiative centres in the QW layer needs to be elucidated, to fully realise the material's potential.

Arogenate dehydratase isoenzymes profoundly and differentially modulate carbon flux into lignins.

How carbon flux differentially occurs in vascular plants following photosynthesis for protein formation, phenylpropanoid metabolism (i.e. lignins), and other metabolic processes is not well understood. Our previous discovery/deduction that a six-membered arogenate dehydratase (ADT1-6) gene family encodes the final step in Phe biosynthesis in Arabidopsis thaliana raised the fascinating question whether individual ADT isoenzymes (or combinations thereof) differentially modulated carbon flux to lignins, proteins, etc. If so, unlike all other lignin pathway manipulations that target cell wall/cytosolic processes, this would be the first example of a plastid (chloroplast)-associated metabolic process influencing cell wall formation. Homozygous T-DNA insertion lines were thus obtained for five of the six ADTs and used to generate double, triple, and quadruple knockouts (KOs) in different combinations. The various mutants so obtained gave phenotypes with profound but distinct reductions in lignin amounts, encompassing a range spanning from near wild type levels to reductions of up to ∼68%. In the various KOs, there were also marked changes in guaiacyl:syringyl ratios ranging from ∼3:1 to 1:1, respectively; these changes were attributed to differential carbon flux into vascular bundles versus that into fiber cells. Laser microscope dissection/pyrolysis GC/MS, histochemical staining/lignin analyses, and pADT::GUS localization indicated that ADT5 preferentially affects carbon flux into the vascular bundles, whereas the adt3456 knock-out additionally greatly reduced carbon flux into fiber cells. This plastid-localized metabolic step can thus profoundly differentially affect carbon flux into lignins in distinct anatomical regions and provides incisive new insight into different factors affecting guaiacyl:syringyl ratios and lignin primary structure.

Poor histological healing of a femoral fracture following 12 months of oestrogen deficiency in rats.

SUMMARY: Fractures in post-menopausal osteoporosis cause significant morbidity; however, animal models for post-menopausal fracture healing lack the effect of ageing. Therefore, we developed a model using aged animals with chronic oestrogen deficiency, which demonstrates inferior fracture repair (decreased healing histologically, bone mineral density and content and strength). This novel model may help develop molecular strategies for osteoporotic fracture repair. INTRODUCTION: The femur is susceptible to damage by both systemic conditions such as osteoporosis and locally by traumatic injury. The capacity for fracture repair decreases with age, while the risk of fracture increases. As studies of osteoporotic fracture healing in rats traditionally use a period of 3 months or less of oestrogen deficiency prior to fracturing, we aimed to establish a osteoporosis model in rats with chronic oestrogen deficiency by 12 months to better mimic human female osteoporosis. METHODS: Seventy female Sprague-Dawley rats (10 weeks old) were ovariectomised or sham operated and housed for 12 months. The right femur was fractured by way of an open osteotomy and fixed with an intramedullary Kirschner wire. Animals were sacrificed at 1, 3 and 6 weeks for radiography, dual-energy X-ray absorptiometry, tensile testing and histology. RESULTS: Bone mineral density and bone mineral content were lower by 60 and 63 %, respectively, (p < 0.05) in the bilaterally ovariectomized (OVX) groups than those in the sham groups at 6 weeks in the right fractured femurs. Maximum breaking force of the OVX group was lower than that of the sham group, with the greatest difference seen at 6 weeks following osteotomy. Histologically, the OVX groups demonstrated a delay in cellular differentiation within the fracture callus and the presence of bone resorption. The sham animals had a superior histological healing pattern with an Allen score of 4 at 6 weeks compared to a score of 1 for the OVX groups (p < 0.01). CONCLUSIONS: Long-term ovariectomy has a deleterious effect on fracture healing in a rodent model.

Quantitative analysis of carbon impurity concentrations in GaN epilayers by cathodoluminescence.

In this work, a technique for quantifying carbon doping concentrations in GaN:C/AlGaN buffer structures using cathodoluminescence (CL) is presented. The method stems from the knowledge that the blue and yellow luminescence intensity in CL spectra of GaN varies with the carbon doping concentration. By calculating the blue and yellow luminescence peak intensities normalised to the peak GaN near-band-edge intensity for GaN layers of known carbon concentrations, calibration curves that show the change in normalised blue and yellow luminescence intensity with carbon concentration in the 1016 - 1019 cm-3 range were derived at both room temperature and 10 K. The utility of such calibration curves was then examined by testing against an unknown sample containing multiple carbon-doped GaN layers. The results obtained from CL using the normalised blue luminescence calibration curves are in close agreement with those from secondary-ion mass spectroscopy (SIMS). However,the method fails when applying calibration curves obtained from the normalised yellow luminescence likely due to the influence of native VGa defects acting in this luminescence region. Although this work shows that indeed CL can be used as a quantitative tool to measure carbon doping concentrations in GaN:C, it is noted that the intrinsic broadening effects innate to CL can make it difficult to differentiate between the intensity variations in thin ( < 500 nm) multilayered GaN:C structures such as the ones studied in this work.

Disentangling the Impact of Point Defect Density and Carrier Localization-Enhanced Auger Recombination on Efficiency Droop in (In,Ga)N/GaN Quantum Wells.

The internal quantum efficiency of (In,Ga)N/GaN quantum wells can surpass 90% for blue-emitting structures at moderate drive current densities but decreases significantly for longer emission wavelengths and at higher excitation rates. This latter effect is known as efficiency "droop" and limits the brightness of light-emitting diodes (LEDs) based on such quantum wells. Several mechanisms have been proposed to explain efficiency droop including Auger recombination, both intrinsic and defect-assisted, carrier escape, and the saturation of localized states. However, it remains unclear which of these mechanisms is most important because it has proven difficult to reconcile theoretical calculations of droop with measurements. Here, we first present experimental photoluminescence measurements extending over three orders of magnitude of excitation for three samples grown at different temperatures that indicate that droop behavior is not dependent on the point defect density in the quantum wells studied. Second, we use an atomistic tight-binding electronic structure model to calculate localization-enhanced radiative and Auger rates and show that both the corresponding carrier density-dependent internal quantum efficiency and the carrier density decay dynamics are in excellent agreement with our experimental measurements. Moreover, we show that point defect density, Auger recombination, and the effect of the polarization field on recombination rates only limit the peak internal quantum efficiency to about 70% in the resonantly excited green-emitting quantum wells studied. This suggests that factors external to the quantum wells, such as carrier injection efficiency and homogeneity, contribute appreciably to the significantly lower peak external quantum efficiency of green LEDs.

3D Perovskite Passivation with a Benzotriazole-Based 2D Interlayer for High-Efficiency Solar Cells.

2H-Benzotriazol-2-ylethylammonium bromide and iodide and its difluorinated derivatives are synthesized and employed as interlayers for passivation of formamidinium lead triiodide (FAPbI3) solar cells. In combination with PbI2 and PbBr2, these benzotriazole derivatives form two-dimensional (2D) Ruddlesden-Popper perovskites (RPPs) as evidenced by their crystal structures and thin film characteristics. When used to passivate n-i-p FAPbI3 solar cells, the power conversion efficiency improves from 20% to close to 22% by enhancing the open-circuit voltage. Quasi-Fermi level splitting experiments and scanning electron microscopy cathodoluminescence hyperspectral imaging reveal that passivation provides a reduced nonradiative recombination at the interface between the perovskite and hole transport layer. Photoluminescence spectroscopy, angle-resolved grazing-incidence wide-angle X-ray scattering, and depth profiling X-ray photoelectron spectroscopy studies of the 2D/three-dimensional (3D) interface between the benzotriazole RPP and FAPbI3 show that a nonuniform layer of 2D perovskites is enough to passivate defects, enhance charge extraction, and decrease nonradiative recombination.

Dislocations at coalescence boundaries in heteroepitaxial GaN/sapphire studied after the epitaxial layer has completely coalesced.

We have performed cross-sectional scanning capacitance microscopy (SCM), cathodoluminescence (CL) microscopy in the scanning electron microscope (SEM) and transmission electron microscopy (TEM) all on the same few-micron region of a GaN/sapphire sample. To achieve this, it was necessary to develop a process flow which allowed the same features viewed in a cleaved cross-section to be traced from one microscope to the next and to adapt the focused ion beam preparation of the TEM lamella to allow preparation of a site-specific sample on a pre-cleaved cross-section. Growth of our GaN/sapphire samples involved coalescence of three-dimensional islands to form a continuous film. Highly doped marker layers were included in the sample so that coalescence boundaries formed late in the film growth process could be identified in SCM and CL. Using TEM, we then identified one or more dislocations associated with each of several such late-coalescing boundaries. In contrast, previous studies have addressed coalescence boundaries formed earlier in the growth process and have shown that early-stage island coalescence does not lead to dislocation formation.

Directly correlated microscopy of trench defects in InGaN quantum wells.

Directly correlated measurements of the surface morphology, light emission and subsurface structure and composition were carried out on the exact same nanoscale trench defects in InGaN quantum well (QW) structures. Multiple scanning probe, scanning electron and transmission electron microscopy techniques were used to explain the origin of their unusual emission behaviour and the relationship between surface morphology and cathodoluminescence (CL) redshift. Trench defects comprise of an open trench partially or fully enclosing material in InGaN QWs with different CL emission properties to their surroundings. The CL redshift was shown to typically vary with the width of the trench and the prominence of the material enclosed by the trench above its surroundings. Three defects, encompassing typical and atypical features, were prepared into lamellae for transmission electron microscopy (TEM). A cross marker technique was used in the focused ion beam-scanning electron microscope (FIB-SEM) to centre the previously characterised defects in each lamella for further analysis. The defects with wider trenches and strong redshifts in CL emission had their initiating basal-plane stacking fault (BSF) towards the bottom of the QW stack, while the BSF formed near the top of the QW stack for a defect with a narrow trench and minimal redshift. The raised-centre, prominent defect showed a slight increase in QW thickness moving up the QW stack while QW widths in the level-centred defect remained broadly constant. The indium content of the enclosed QWs increased above the BSF positions up to a maximum, with an increase of approximately 4% relative to the surroundings seen for one defect examined. Gross fluctuations in QW width (GWWFs) were present in the surrounding material in this sample but were not seen in QWs enclosed by the defect volumes. These GWWFs have been linked with indium loss from surface step edges two or more monolayers high, and many surface step edges appear pinned by the open trenches, suggesting another reason for the higher indium content seen in QWs enclosed by trench defects.

Cross-shaped markers for the preparation of site-specific transmission electron microscopy lamellae using focused ion beam techniques.

We describe the use of a cross-shaped platinum marker deposited using electron-beam-induced deposition (EBID) in a focused ion beam - scanning electron microscope (FIB-SEM) system to facilitate site-specific preparation of a TEM foil containing a trench defect in an InGaN/GaN multiple quantum well structure. The defect feature is less than 100 nm wide at the surface. The marker is deposited prior to the deposition of a protective platinum strap (also by EBID) with the centre of the cross indicating the location of the feature of interest, while the arms of the square cross make an acute angle of 45° with the strap's long axis. During the ion-beam thinning process, the marker may be viewed in cross-section from both sides of the sample alternately, and the coming together of the features relating to the arms of the cross indicates increasing proximity to the feature of interest. Although this approach does allow increased precision in locating the region of interest during thinning, it also increases the time required to complete the sample preparation. Hence, this method is particularly well suited to directly correlated multi-microscopy investigations in previously characterised material where high yield and the precise location are more important than preparation time. In addition to TEM lamella preparation, this method could equally be useful for preparing site-specific atom probe tomography (APT) samples.

Publisher Correction: Impact of alloy fluctuations and Coulomb effects on the electronic and optical properties of c-plane GaN/AlGaN quantum wells.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Impact of alloy fluctuations and Coulomb effects on the electronic and optical properties of c-plane GaN/AlGaN quantum wells.

We report on a combined theoretical and experimental study of the impact of alloy fluctuations and Coulomb effects on the electronic and optical properties of [Formula: see text]-plane GaN/AlGaN multi-quantum well systems. The presence of carrier localization effects in this system was demonstrated by experimental observations, such as the "S-shape" temperature dependence of the photoluminescence (PL) peak energy, and non-exponential PL decay curves that varied across the PL spectra at 10 K. A three-dimensional modified continuum model, coupled with a self-consistent Hartree scheme, was employed to gain insight into the electronic and optical properties of the experimentally studied [Formula: see text]-plane GaN/AlGaN quantum wells. This model confirmed the existence of strong hole localization arising from the combined effects of the built-in polarization field along the growth direction and the alloy fluctuations at the quantum well/barrier interface. However, for electrons these localization effects are less pronounced in comparison to the holes. Furthermore, our calculations show that the attractive Coulomb interaction between electron and hole results in exciton localization. This behavior is in contrast to the picture of independently localized electrons and holes, often used to explain the radiative recombination process in [Formula: see text]-plane InGaN/GaN quantum well systems.

Epithelial-derived TGF-ß1 acts as a pro-viral factor in the lung during influenza A infection.

Mucosal surfaces are under constant bombardment from potentially antigenic particles and so must maintain a balance between homeostasis and inappropriate immune activation and consequent pathology. Epithelial cells have a vital role orchestrating pulmonary homeostasis and defense against pathogens. TGF-ß regulates an array of immune responses-both inflammatory and regulatory-however, its function is highly location- and context-dependent. We demonstrate that epithelial-derived TGF-ß acts as a pro-viral factor suppressing early immune responses during influenza A infection. Mice specifically lacking bronchial epithelial TGF-ß1 (epTGFßKO) displayed marked protection from influenza-induced weight loss, airway inflammation, and pathology. However, protection from influenza-induced pathology was not associated with a heightened lymphocytic immune response. In contrast, the kinetics of interferon beta (IFNß) release into the airways was significantly enhanced in epTGFßKO mice compared with control mice, with elevated IFNß on day 1 in epTGFßKO compared with control mice. This induced a heighted antiviral state resulting in impaired viral replication in epTGFßKO mice. Thus, epithelial-derived TGF-ß acts to suppress early IFNß responses leading to increased viral burden and pathology. This study demonstrates the importance of the local epithelial microenvironmental niche in shaping initial immune responses to viral infection and controlling host disease.

Resonant photoluminescence studies of carrier localisation in c-plane InGaN/GaN quantum well structures.

In this paper we report on changes in the form of the low temperature (12 K) photoluminescence spectra of an InGaN/GaN quantum well structure as a function of excitation photon energy. As the photon energy is progressively reduced we observe at a critical energy a change in the form of the spectra from one which is determined by the occupation of the complete distribution of hole localisation centres to one which is determined by the resonant excitation of specific localisation sites. This change is governed by an effective mobility edge whereby the photo-excited holes remain localised at their initial energy and are prevented from scattering to other localisation sites. This assignment is confirmed by the results of atomistic tight binding calculations which show that the wave function overlap of the lowest lying localised holes with other hole states is low compared with the overlap of higher lying hole states with other higher lying hole states.

Inception of early-life allergen-induced airway hyperresponsiveness is reliant on IL-13+CD4+ T cells.

Airway hyperresponsiveness (AHR) is a critical feature of wheezing and asthma in children, but the initiating immune mechanisms remain unconfirmed. We demonstrate that both recombinant interleukin-33 (rIL-33) and allergen [house dust mite (HDM) or Alternaria alternata] exposure from day 3 of life resulted in significantly increased pulmonary IL-13+CD4+ T cells, which were indispensable for the development of AHR. In contrast, adult mice had a predominance of pulmonary LinnegCD45+CD90+IL-13+ type 2 innate lymphoid cells (ILC2s) after administration of rIL-33. HDM exposure of neonatal IL-33 knockout (KO) mice still resulted in AHR. However, neonatal CD4creIL-13 KO mice (lacking IL-13+CD4+ T cells) exposed to allergen from day 3 of life were protected from AHR despite persistent pulmonary eosinophilia, elevated IL-33 levels, and IL-13+ ILCs. Moreover, neonatal mice were protected from AHR when inhaled Acinetobacter lwoffii (an environmental bacterial isolate found in cattle farms, which is known to protect from childhood asthma) was administered concurrent with HDM. A. lwoffii blocked the expansion of pulmonary IL-13+CD4+ T cells, whereas IL-13+ ILCs and IL-33 remained elevated. Administration of A. lwoffii mirrored the findings from the CD4creIL-13 KO mice, providing a translational approach for disease protection in early life. These data demonstrate that IL-13+CD4+ T cells, rather than IL-13+ ILCs or IL-33, are critical for inception of allergic AHR in early life.