Implementation of U.K. Earth system models for CMIP6

We describe the scientific and technical implementation of two models for a core set of experiments contributing to the sixth phase of the Coupled Model Intercomparison Project (CMIP6). The models used are the physical atmosphere-land-ocean-sea ice model HadGEM3-GC3.1 and the Earth system model UKESM1 which adds a carbon-nitrogen cycle and atmospheric chemistry to HadGEM3-GC3.1. The model results are constrained by the external boundary conditions (forcing data) and initial conditions.We outline the scientific rationale and assumptions made in specifying these. Notable details of the implementation include an ozone redistribution scheme for prescribed ozone simulations (HadGEM3-GC3.1) to avoid inconsistencies with the model's thermal tropopause, and land use change in dynamic vegetation simulations (UKESM1) whose influence will be subject to potential biases in the simulation of background natural vegetation.We discuss the implications of these decisions for interpretation of the simulation results. These simulations are expensive in terms of human and CPU resources and will underpin many further experiments; we describe some of the technical steps taken to ensure their scientific robustness and reproducibility

Intravascular Ultrasound for Assessment of Residual Coarctation of the Aorta after Balloon Angioplasty in Infants

Intravascular ultrasound (IVUS) has been introduced as an accurate and minimally invasive diagnostic technique for the assessment of vascular anatomy and its abnormalities. We believe that IVUS can be used for clarifying the reasons for failure of balloon angiography in infantile coarctation of the aorta (CoA), because post-balloon angioplasty tearing, intimal flap, thrombosis and pseudoaneurysm of the aorta can be evaluated by IVUS with greater sensitivity and specificity. We aimed to assess the outcome of balloon angioplasty of CoA using angiography as the gold standard and IVUS as a new method in infants, comparing the two techniques for the evaluation of the diameter and area of CoA segment pre- and post-procedure. This cross-sectional study was performed on 18 infants hospitalized with a final diagnosis of CoA. All the infants underwent angiography and were also assessed by IVUS to measure the preoperative and postoperative diameter of the narrow segment in the two anterior�posterior and lateral views. In assessment by IVUS, the mean diameter of the coarctation site increased from 2.10 ± 0.30 mm to 4.50 ± 0.94 mm (P < 0.001). Similarly, the average minimum area of the coarctation level increased from 5.26 ± 1.50 mm2 to 13.77 ± 3.48 mm2 after angioplasty (P < 0.001). Comparing these findings, angiography and IVUS showed a high level of agreement. In the assessment of a dissection flap, there was a high level of agreement between angioplasty and IVUS before the procedure, but IVUS had higher accuracy after the procedure. Our study showed that IVUS was more reliable than angiography in the assessment of residual coarctation. IVUS yielded high sensitivity (58.3) and specificity (100) for discriminating the presence and absence of residual coarctation as well as the need for repeating the procedure. The assessment of coarctation before and after angioplasty procedures in children is possible using the IVUS method, with high accuracy. IVUS can offer greater accuracy than angiography in the evaluation of the coarctation area, detecting tears, dissection and flaps, and assessment of residual coarctation. © 2021, Springer Science+Business Media, LLC, part of Springer Nature

Intravascular Ultrasound for Assessment of Residual Coarctation of the Aorta after Balloon Angioplasty in Infants

Intravascular ultrasound (IVUS) has been introduced as an accurate and minimally invasive diagnostic technique for the assessment of vascular anatomy and its abnormalities. We believe that IVUS can be used for clarifying the reasons for failure of balloon angiography in infantile coarctation of the aorta (CoA), because post-balloon angioplasty tearing, intimal flap, thrombosis and pseudoaneurysm of the aorta can be evaluated by IVUS with greater sensitivity and specificity. We aimed to assess the outcome of balloon angioplasty of CoA using angiography as the gold standard and IVUS as a new method in infants, comparing the two techniques for the evaluation of the diameter and area of CoA segment pre- and post-procedure. This cross-sectional study was performed on 18 infants hospitalized with a final diagnosis of CoA. All the infants underwent angiography and were also assessed by IVUS to measure the preoperative and postoperative diameter of the narrow segment in the two anterior�posterior and lateral views. In assessment by IVUS, the mean diameter of the coarctation site increased from 2.10 ± 0.30 mm to 4.50 ± 0.94 mm (P < 0.001). Similarly, the average minimum area of the coarctation level increased from 5.26 ± 1.50 mm2 to 13.77 ± 3.48 mm2 after angioplasty (P < 0.001). Comparing these findings, angiography and IVUS showed a high level of agreement. In the assessment of a dissection flap, there was a high level of agreement between angioplasty and IVUS before the procedure, but IVUS had higher accuracy after the procedure. Our study showed that IVUS was more reliable than angiography in the assessment of residual coarctation. IVUS yielded high sensitivity (58.3) and specificity (100) for discriminating the presence and absence of residual coarctation as well as the need for repeating the procedure. The assessment of coarctation before and after angioplasty procedures in children is possible using the IVUS method, with high accuracy. IVUS can offer greater accuracy than angiography in the evaluation of the coarctation area, detecting tears, dissection and flaps, and assessment of residual coarctation. © 2021, Springer Science+Business Media, LLC, part of Springer Nature

Boundary friction characterisation of a used cylinder liner subject to fired engine conditions and surface deposition

In cylinder friction contributes as a primary source of parasitic dissipations in IC engines. For future engines to become more efficient, with enhanced fuel economy and increased power output, accurate prediction of new designs is required over the full lifetime of an engine. The work carried out presents use of a local pressure coefficient of boundary shear strength of asperities value, taking into account the localised effects of surface texture, coating and surface deposition. XPS spectra analysis was also carried out to identify the surface depositions as a result of combustion, not previously taken into account during piston ring pack simulation. Friction was shown by simulation to drop by up to 30% between the compression and combustion stroke as a result of using a carriable coefficient of boundary shear strength of asperities. It was found that piston varnish on the liner corresponded to higher values of the pressure coefficient of boundary shear strength of asperities, therefore showing the importance of using real system components run under representative operating conditions or numerical analyses

Health-seeking behaviours of older black women living with non-communicable diseases in an urban township in South Africa

BACKGROUND: Various studies have shown that non-communicable diseases (NCDs) especially diabetes and hypertension are prevalent among older women living in South African urban areas, placing a heavy burden on the healthcare system. This study aimed to understand the health-seeking behaviour, healthcare practices and prevalence of traditional herbal medicine (THM) use among older women self-reporting NCDs from the Prospective Urban Rural Epidemiology study (PURE). METHOD: A homogenous purposive sampling of PURE participants was used to recruit women who were 50 years or older (n = 250). Descriptive statistics were used to examine the number of NCDs reported by the study sample, health seeking behaviour and practices as well as THM use. Logistic regression was also employed to investigate possible associations between reported conditions and THM use or medical pluralism. RESULTS: Within the study sample, 72 % self-reported an NCD. Of those with self-reported NCDs, 46 % had one, and 54 % had two or more NCDs. Those with NCDs usually visited public clinics (80 %), relied on doctors (90 %) and nurses (85 %) for health information, and mostly used conventional medicine (CM) to manage high blood pressure (81 %). About 30 % of those with NCDs indicated using THM, of whom 29 (53 %) reported practicing medical pluralism. Participants with dental problems (OR: 3.24, 95 % CI: 1.30–8.20), headaches (OR: 2.42, 95 % CI: 1.24–4.94), heart burn (OR: 2.30, 95 % CI: 1.18–4.48) and severe tiredness (OR: 2.05, 95 % CI: 1.08–3.99) were more likely to use THM. Anxiety and allergies increased the likelihood to practise medical pluralism by five and 20 times, respectively. CONCLUSION: Self-reported NCD with co-morbidities was prevalent among the participants in the study. Most of the study participants utilized state-owned clinics and hospitals for the management of their chronic conditions. THM use was not very common. However, among those who used THM, medical pluralism was prevalent. Family history was the most common reason for THM use, with many THM patrons utilizing these for treatment of a health condition. Older black women with anxiety and allergies were more likely to practise medical pluralism

IlsA, A Unique Surface Protein of Bacillus cereus Required for Iron Acquisition from Heme, Hemoglobin and Ferritin

The human opportunistic pathogen Bacillus cereus belongs to the B. cereus group that includes bacteria with a broad host spectrum. The ability of these bacteria to colonize diverse hosts is reliant on the presence of adaptation factors. Previously, an IVET strategy led to the identification of a novel B. cereus protein (IlsA, Iron-regulated leucine rich surface protein), which is specifically expressed in the insect host or under iron restrictive conditions in vitro. Here, we show that IlsA is localized on the surface of B. cereus and hence has the potential to interact with host proteins. We report that B. cereus uses hemoglobin, heme and ferritin, but not transferrin and lactoferrin. In addition, affinity tests revealed that IlsA interacts with both hemoglobin and ferritin. Furthermore, IlsA directly binds heme probably through the NEAT domain. Inactivation of ilsA drastically decreases the ability of B. cereus to grow in the presence of hemoglobin, heme and ferritin, indicating that IlsA is essential for iron acquisition from these iron sources. In addition, the ilsA mutant displays a reduction in growth and virulence in an insect model. Hence, our results indicate that IlsA is a key factor within a new iron acquisition system, playing an important role in the general virulence strategy adapted by B. cereus to colonize susceptible hosts

Set Pseudophasors to Stun for Flow Cytometry

Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP's fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼ 1.5 ns vs ∼ 3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a "pseudophasor" that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation

Comparative Transcriptional Profiling of Bacillus cereus Sensu Lato Strains during Growth in CO2-Bicarbonate and Aerobic Atmospheres

Bacillus species are spore-forming bacteria that are ubiquitous in the environment and display a range of virulent and avirulent phenotypes. This range is particularly evident in the Bacillus cereus sensu lato group; where closely related strains cause anthrax, food-borne illnesses, and pneumonia, but can also be non-pathogenic. Although much of this phenotypic range can be attributed to the presence or absence of a few key virulence factors, there are other virulence-associated loci that are conserved throughout the B. cereus group, and we hypothesized that these genes may be regulated differently in pathogenic and non-pathogenic strains.Here we report transcriptional profiles of three closely related but phenotypically unique members of the Bacillus cereus group--a pneumonia-causing B. cereus strain (G9241), an attenuated strain of B. anthracis (Sterne 34F(2)), and an avirulent B. cereus strain (10987)--during exponential growth in two distinct atmospheric environments: 14% CO(2)/bicarbonate and ambient air. We show that the disease-causing Bacillus strains undergo more distinctive transcriptional changes between the two environments, and that the expression of plasmid-encoded virulence genes was increased exclusively in the CO(2) environment. We observed a core of conserved metabolic genes that were differentially expressed in all three strains in both conditions. Additionally, the expression profiles of putative virulence genes in G9241 suggest that this strain, unlike Bacillus anthracis, may regulate gene expression with both PlcR and AtxA transcriptional regulators, each acting in a different environment.We have shown that homologous and even identical genes within the genomes of three closely related members of the B. cereus sensu lato group are in some instances regulated very differently, and that these differences can have important implications for virulence. This study provides insights into the evolution of the B. cereus group, and highlights the importance of looking beyond differences in gene content in comparative genomics studies

Global patterns in endemicity and vulnerability of soil fungi

Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high-resolution, long-read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West-Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land-cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early-diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms