The Accuracy of Al and Cu Film Thickness Determinations and the Implications for Electron Probe Microanalysis

AbstractThe accuracy to which Cu and Al coatings can be determined, and the effect this has on the quantification of the substrate, is investigated. Cu and Al coatings of nominally 5, 10, 15, and 20 nm were sputter coated onto polished Bi using two configurations of coater: One with the film thickness monitor (FTM) sensor colocated with the samples, and one where the sensor is located to one side. The FTM thicknesses are compared against those calculated from measured Cu Lαand Al Kα k-ratios using PENEPMA, GMRFilm, and DTSA-II. Selected samples were also cross-sectioned using focused ion beam. Both systems produced repeatable coatings, the thickest coating being approximately four times the thinnest coating. The side-located FTM sensor indicated thicknesses less than half those of the software modeled results, propagating on to 70% errors in substrate quantification at 5 kV. The colocated FTM sensor produced errors in film thickness and substrate quantification of 10–20%. Over the range of film thicknesses and accelerating voltages modeled both the substrate and coatingk-ratios can be approximated by linear trends as functions of film thickness. The Al films were found to have a reduced density of ~2 g/cm2.</jats:p

Estimates of crop responses to climate change with quantified ranges of uncertainty

In estimating responses of crops to future climate realisations, it is necessary to understand and differentiate between the sources of uncertainty in climate models and how these lead to errors in estimating the past climate and biases in future projections, and how these affect crop model estimates. This paper investigates the complexities in using climate model projections representing different spatial scales within climate change impacts and adaptation studies. This is illustrated by simulating spring barley with three crop models run using site-specific observed, original (50•50 km) and bias corrected downscaled (site-specific) hindcast (1960-1990) weather data from the HadRM3 Regional Climate Model (RCM). Original and bias corrected downscaled weather data were evaluated against the observed data. The comparisons made between the crop models were in the light of lessons learned from this data evaluation. Though the bias correction downscaling method improved the match between observed and hindcast data, this did not always translate into better matching of crop models estimates. At four sites the original HadRM3 data produced near identical mean simulated yield values as from the observed weather data, despite differences in the weather data, giving a situation of ‘right results for the wrong reasons’. This was likely due to compensating errors in the input weather data and non-linearity in crop models processes, making interpretation of results problematic. Overall, bias correction downscaling improved the quality of simulated outputs. Understanding how biases in climate data manifest themselves in crop models gives greater confidence in the utility of the estimates produced using downscaled future climate projections. The results indicate implications on how future projections of climate change impacts are interpreted. Fundamentally, considerable care is required in determining the impact weather data sources have in climate change impact and adaptation studies, whether from individual models or ensembles

Using agent-based modelling to simulate social-ecological systems across scales

Agent-based modelling (ABM) simulates Social-Ecological-Systems (SESs) based on the decision-making and actions of individual actors or actor groups, their interactions with each other, and with ecosystems. Many ABM studies have focused at the scale of villages, rural landscapes, towns or cities. When considering a geographical, spatially-explicit domain, current ABM architecture is generally not easily translatable to a regional or global context, nor does it acknowledge SESs interactions across scales sufficiently; the model extent is usually determined by pragmatic considerations, which may well cut across dynamical boundaries. With a few exceptions, the internal structure of governments is not included when representing them as agents. This is partly due to the lack of theory about how to represent such as actors, and because they are not static over the time-scales typical for social changes to have significant effects. Moreover, the relevant scale of analysis is often not known a priori, being dynamically determined, and may itself vary with time and circumstances. There is a need for ABM to cross the gap between micro-scale actors and larger-scale environmental, infrastructural and political systems in a way that allows realistic spatial and temporal phenomena to emerge; this is vital for models to be useful for policy analysis in an era when global crises can be triggered by small numbers of micro-level actors. We aim with this thought-piece to suggest conceptual avenues for implementing ABM to simulate SESs across scales, and for using big data from social surveys, remote sensing or other sources for this purpose

Early rheumatoid arthritis is characterized by a distinct and transient synovial fluid cytokine profile of T cell and stromal cell origin

Pathological processes involved in the initiation of rheumatoid synovitis remain unclear. We undertook the present study to identify immune and stromal processes that are present soon after the clinical onset of rheumatoid arthritis ( RA) by assessing a panel of T cell, macrophage, and stromal cell related cytokines and chemokines in the synovial fluid of patients with early synovitis. Synovial fluid was aspirated from inflamed joints of patients with inflammatory arthritis of duration 3 months or less, whose outcomes were subsequently determined by follow up. For comparison, synovial fluid was aspirated from patients with acute crystal arthritis, established RA and osteoarthritis. Rheumatoid factor activity was blocked in the synovial fluid samples, and a panel of 23 cytokines and chemokines measured using a multiplex based system. Patients with early inflammatory arthritis who subsequently developed RA had a distinct but transient synovial fluid cytokine profile. The levels of a range of T cell, macrophage and stromal cell related cytokines ( e. g. IL-2, IL-4, IL-13, IL-17, IL-15, basic fibroblast growth factor and epidermal growth factor) were significantly elevated in these patients within 3 months after symptom onset, as compared with early arthritis patients who did not develop RA. In addition, this profile was no longer present in established RA. In contrast, patients with non-rheumatoid persistent synovitis exhibited elevated levels of interferon-gamma at initiation. Early synovitis destined to develop into RA is thus characterized by a distinct and transient synovial fluid cytokine profile. The cytokines present in the early rheumatoid lesion suggest that this response is likely to influence the microenvironment required for persistent RA

A mouse informatics platform for phenotypic and translational discovery

The International Mouse Phenotyping Consortium (IMPC) is providing the world’s first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function

A chemical survey of exoplanets with ARIEL

Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planet’s birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25–7.8 μm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10–100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed – using conservative estimates of mission performance and a full model of all significant noise sources in the measurement – using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL – in line with the stated mission objectives – will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio

Effect of personalized nutrition on health-related behaviour change: evidence from the Food4me European randomized controlled trial

Background: Optimal nutritional choices are linked with better health, but many current interventions to improve diet have limited effect. We tested the hypothesis that providing personalized nutrition (PN) advice based on information on individual diet and lifestyle, phenotype and/or genotype would promote larger, more appropriate, and sustained changes in dietary behaviour. Methods: Adults from seven European countries were recruited to an internet-delivered intervention (Food4Me) and randomized to: (i) conventional dietary advice (control) or to PN advice based on: (ii) individual baseline diet; (iii) individual baseline diet plus phenotype (anthropometry and blood biomarkers); or (iv) individual baseline diet plus phenotype plus genotype (five diet-responsive genetic variants). Outcomes were dietary intake, anthropometry and blood biomarkers measured at baseline and after 3 and 6 months’ intervention. Results: At baseline, mean age of participants was 39.8 years (range 18–79), 59% of participants were female and mean body mass index (BMI) was 25.5 kg/m2. From the enrolled participants, 1269 completed the study. Following a 6-month intervention, participants randomized to PN consumed less red meat [-5.48 g, (95% confidence interval:- 10.8,-0.09), P=0.046], salt [-0.65 g, (-1.1,-0.25), P=0.002] and saturated fat [-1.14 % of energy, (-1.6,-0.67), P<0.0001], increased folate [29.6 mg, (0.21,59.0), P=0.048] intake and had higher Healthy Eating Index scores [1.27, (0.30, 2.25), P=0.010) than those randomized to the control arm. There was no evidence that including phenotypic and phenotypic plus genotypic information enhanced the effectiveness of the PN advice. Conclusions: Among European adults, PN advice via internet-delivered intervention produced larger and more appropriate changes in dietary behaviour than a conventional approach