Distinguishing Quasiparticle-Phonon Interactions by Ultrahigh-Resolution Lifetime Measurements.

We present a determination of quasiparticle-phonon interaction strengths at surfaces through measurements of phonon spectra with ultrahigh energy resolution. The lifetimes of low energy surface phonons on a pristine Ru(0001) surface were determined over a wide range of temperatures and an analysis of the temperature dependence enables us to attribute separate contributions from electron-phonon interactions, phonon-phonon interactions, and defect-phonon interactions. Strong electron-phonon interactions are evident at all temperatures and we show they dominate over phonon-phonon interactions below 400 K.

Long COVID in a highly vaccinated but largely unexposed Australian population following the 2022 SARS-CoV-2 Omicron wave: a cross-sectional survey.

OBJECTIVE: To estimate the prevalence of long COVID among Western Australian adults, a highly vaccinated population whose first major exposure to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was during the 2022 Omicron wave, and to assess its impact on health service use and return to work or study. STUDY DESIGN: Follow-up survey (completed online or by telephone). SETTING, PARTICIPANTS: Adult Western Australians surveyed 90 days after positive SARS-CoV-2 test results (polymerase chain reaction or rapid antigen testing) during 16 July - 3 August 2022 who had consented to follow-up contact for research purposes. MAIN OUTCOME MEASURES: Proportion of respondents with long COVID (ie, reporting new or ongoing symptoms or health problems, 90 days after positive SARS-CoV-2 test result); proportion with long COVID who sought health care for long COVID-related symptoms two to three months after infection; proportion who reported not fully returning to previous work or study because of long COVID-related symptoms. RESULTS: Of the 70 876 adults with reported SARS-CoV-2 infections, 24 024 consented to contact (33.9%); after exclusions, 22 744 people were invited to complete the survey, of whom 11 697 (51.4%) provided complete responses. Our case definition for long COVID was satisfied by 2130 respondents (18.2%). The risk of long COVID was greater for women (v men: adjusted risk ratio [aRR], 1.5; 95% confidence interval [CI], 1.4-1.6) and for people aged 50-69 years (v 18-29 years: aRR, 1.6; 95% CI, 1.4-1.9) or with pre-existing health conditions (aRR, 1.5; 95% CI, 1.4-1.7), as well as for people who had received two or fewer COVID-19 vaccine doses (v four or more: aRR, 1.4; 95% CI, 1.2-1.8) or three doses (aRR, 1.3; 95% CI, 1.1-1.5). The symptoms most frequently reported by people with long COVID were fatigue (1504, 70.6%) and concentration difficulties (1267, 59.5%). In the month preceding the survey, 814 people had consulted general practitioners (38.2%) and 34 reported being hospitalised (1.6%) with long COVID. Of 1779 respondents with long COVID who had worked or studied before the infection, 318 reported reducing or discontinuing this activity (17.8%). CONCLUSION: Ninety days after infection with the Omicron SARS-CoV-2 variant, 18.2% of survey respondents reported symptoms consistent with long COVID, of whom 38.7% (7.1% of all survey respondents) sought health care for related health concerns two to three months after the acute infection.

Testing the intrinsic mechanisms driving the dynamics of Ross River Virus across Australia.

The mechanisms driving dynamics of many epidemiologically important mosquito-borne pathogens are complex, involving combinations of vector and host factors (e.g., species composition and life-history traits), and factors associated with transmission and reporting. Understanding which intrinsic mechanisms contribute most to observed disease dynamics is important, yet often poorly understood. Ross River virus (RRV) is Australia's most important mosquito-borne disease, with variable transmission dynamics across geographic regions. We used deterministic ordinary differential equation models to test mechanisms driving RRV dynamics across major epidemic centers in Brisbane, Darwin, Mandurah, Mildura, Gippsland, Renmark, Murray Bridge, and Coorong. We considered models with up to two vector species (Aedes vigilax, Culex annulirostris, Aedes camptorhynchus, Culex globocoxitus), two reservoir hosts (macropods, possums), seasonal transmission effects, and transmission parameters. We fit models against long-term RRV surveillance data (1991-2017) and used Akaike Information Criterion to select important mechanisms. The combination of two vector species, two reservoir hosts, and seasonal transmission effects explained RRV dynamics best across sites. Estimated vector-human transmission rate (average ß = 8.04x10-4per vector per day) was similar despite different dynamics. Models estimate 43% underreporting of RRV infections. Findings enhance understanding of RRV transmission mechanisms, provide disease parameter estimates which can be used to guide future research into public health improvements and offer a basis to evaluate mitigation practices.

Experimental Characterization of Defect-Induced Phonon Lifetime Shortening.

We present the first direct experimental measurement of defect-induced lifetime shortening of acoustic surface phonons. Defects are found to contribute a temperature-independent component to the linewidths of Rayleigh wave phonons on a Ni(111) surface. We also characterized the increase in phonon scattering with both surface defect density and phonon wave vector. A quantitative estimate of the scattering rate between phonon modes and surface line defects is extracted from the experimental data for the first time.

Single-molecular diffusivity and long jumps of large organic molecules: CoPc on Ag(100).

Energy dissipation and the transfer rate of adsorbed molecules do not only determine the rates of chemical reactions but are also a key factor that often dictates the growth of organic thin films. Here, we present a study of the surface dynamical motion of cobalt phthalocyanine (CoPc) on Ag(100) in reciprocal space based on the helium spin-echo technique in comparison with previous scanning tunnelling microscopy studies. It is found that the activation energy for lateral diffusion changes from 150 meV at 45-50 K to ≈100 meV at 250-350 K, and that the process goes from exclusively single jumps at low temperatures to predominantly long jumps at high temperatures. We thus illustrate that while the general diffusion mechanism remains similar, upon comparing the diffusion process over widely divergent time scales, indeed different jump distributions and a decrease of the effective diffusion barrier are found. Hence a precise molecular-level understanding of dynamical processes and thin film formation requires following the dynamics over the entire temperature scale relevant to the process. Furthermore, we determine the diffusion coefficient and the atomic-scale friction of CoPc and establish that the molecular motion on Ag(100) corresponds to a low friction scenario as a consequence of the additional molecular degrees of freedom.

2D Helium Atom Diffraction from a Microscopic Spot.

A method for measuring helium atom diffraction with micron-scale spatial resolution is demonstrated in a scanning helium microscope (SHeM) and applied to study a micron-scale spot on the (100) plane of a lithium fluoride (LiF) crystal. The positions of the observed diffraction peaks provide an accurate measurement of the local lattice spacing, while a combination of close-coupled scattering calculations and Monte Carlo ray-tracing simulations reproduce the main variations in diffracted intensity. Subsequently, the diffraction results are used to enhance image contrast by measuring at different points in reciprocal space. The results open up the possibility for using helium microdiffraction to characterize the morphology of delicate or electron-sensitive materials on small scales. These include many fundamentally and technologically important samples which cannot be studied in conventional atom scattering instruments, such as small grain size exfoliated 2D materials, polycrystalline samples, and other surfaces that do not exhibit long-range order.

3He spin-echo scattering indicates hindered diffusion of isolated water molecules on graphene-covered Ir(111).

The dynamics of water diffusion on carbon surfaces are of interest in fields as diverse as furthering the use of graphene as an industrial-coating technology and understanding the catalytic role of carbon-based dust grains in the interstellar medium. The early stages of water-ice growth and the mobility of water adsorbates are inherently dependent on the microscopic mechanisms that facilitate water diffusion. Here, we use 3He spin-echo quasi-inelastic scattering to probe the microscopic mechanisms responsible for the diffusion of isolated water molecules on graphene-covered and bare Ir(111). The scattering of He atoms provides a non-invasive and highly surface-sensitive means to measure the rate at which absorbates move around on a substrate at very low coverage. Our results provide an approximate upper limit on the diffusion coefficient for water molecules on GrIr(111) of <10-12 m2/s, an order of magnitude lower than the coefficient that describes the diffusion of water molecules on the bare Ir(111) surface. We attribute the hindered diffusion of water molecules on the GrIr(111) surface to water trapping at specific areas of the corrugated moiré superstructure. Lower mobility of water molecules on a surface is expected to lead to a lower ice nucleation rate and may enhance the macroscopic anti-icing properties of a surface.

Evolution of ordered nanoporous phases during h-BN growth: controlling the route from gas-phase precursor to 2D material by in situ monitoring.

Large-area single-crystal monolayers of two-dimensional (2D) materials such as graphene and hexagonal boron nitride (h-BN) can be grown by chemical vapour deposition (CVD). However, the high temperatures and fast timescales at which the conversion from a gas-phase precursor to the 2D material appears, make it extremely challenging to simultaneously follow the atomic arrangements. We utilise helium atom scattering to discover and control the growth of novel 2D h-BN nanoporous phases during the CVD process. We find that prior to the formation of h-BN from the gas-phase precursor, a metastable (3 × 3) structure is formed, and that excess deposition on the resulting 2D h-BN leads to the emergence of a (3 × 4) structure. We illustrate that these nanoporous structures are produced by partial dehydrogenation and polymerisation of the borazine precursor upon adsorption. These steps are largely unexplored during the synthesis of 2D materials and we unveil the rich phases during CVD growth. Our results provide significant foundations for 2D materials engineering in CVD, by adjusting or carefully controlling the growth conditions and thus exploiting these intermediate structures for the synthesis of covalent self-assembled 2D networks.

Whole genome sequencing of SARS-CoV-2 from wastewater links to individual cases in catchments.

After a limited first wave of community transmission in March 2020 and until 2022, Western Australia was largely free of COVID-19, with cases restricted to hotel quarantine, commercial vessels, and small, infrequent community clusters. Despite the low case load setting, sequencing of wastewater samples from large municipal treatment plants produced SARS-CoV-2 genomes with coverage up to 99.7 % and depth to 4000×, which was sufficient to link wastewater sequences to those of active cases in the catchment at the time. This study demonstrates that ≤5 positive individuals can be enough to produce high genomic coverage (>90 %) assemblies even in catchments of up to a quarter of a million people. Genomic analysis of wastewater contemporaneous with clinical cases can also be used to rule out transmission between cases in different catchments, when their SARS-CoV-2 genomes have distinguishing nucleotide polymorphisms. These findings reveal a greater potential of wastewater WGS to inform outbreak management and disease surveillance than previously recognized.

Clinical associations of SARS-CoV-2 viral load using the first WHO International Standard for SARS-CoV-2 RNA.

SARS-CoV-2 viral load declines from the time of symptom onset; in some studies viral load is higher or persists longer in more severe COVID-19 infection, and viral load correlates with culture positivity. This was a retrospective cohort study of inpatients and outpatients during the first wave of COVID-19 infection in Western Australia, March to May 2020, of the relationship of SARS-CoV-2 viral load (using the First WHO International Standard for SARS-CoV-2 RNA) from symptom onset, by clinical subgroups determined from the public health database and hospital records, using regression analysis. We studied 320 samples from 201 COVID-19 cases: 181 mild, seven severe, 11 critical, and four cases who died (two were also critical cases). At symptom onset the mean viral load was 4.34 log10 IU/mL (3.92-4.77 log10 IU/mL 95% CI, cobas SARS-CoV-2 assay ORF1a Ct 28.9 cycles). The mean viral load change was -0.09 log10 IU/mL/day (-0.12 to -0.06 95% CI). R2 was 0.08 and residual standard deviation 2.68 log10 IU/mL. Viral load at symptom onset was higher for those reporting fever compared to those not reporting fever. Viral load kinetics were not different for gender, age, shortness of breath, or those requiring oxygen. Mean viral load at usual release from isolation at 14 days was 2.5 log10 IU/mL or day 20 was 1.8 log10 IU/mL. Variability in respiratory sample SARS-CoV-2 viral load kinetics suggests viral loads will only have a role supporting clinical decision making, and an uncertain role for prognostication.

Motion of water monomers reveals a kinetic barrier to ice nucleation on graphene.

The interfacial behaviour of water remains a central question to fields as diverse as protein folding, friction and ice formation. While the properties of water at interfaces differ from those in the bulk, major gaps in our knowledge limit our understanding at the molecular level. Information concerning the microscopic motion of water comes mostly from computation and, on an atomic scale, is largely unexplored by experiment. Here, we provide a detailed insight into the behaviour of water monomers on a graphene surface. The motion displays remarkably strong signatures of cooperative behaviour due to repulsive forces between the monomers, enhancing the monomer lifetime ( ≈ 3 s at 125 K) in a free-gas phase that precedes the nucleation of ice islands and, in turn, provides the opportunity for our experiments to be performed. Our results give a molecular perspective on a kinetic barrier to ice nucleation, providing routes to understand and control the processes involved in ice formation.

Ultrafast Diffusion at the Onset of Growth: O/Ru(0001).

Nanoscopic clustering in a 2D disordered phase is observed for oxygen on Ru(0001) at low coverages and high temperatures. We study the coexistence of quasistatic clusters (with a characteristic length of ∼9 Å) and highly mobile atomic oxygen which diffuses between the energy-inequivalent, threefold hollow sites of the substrate. We determine a surprisingly low activation energy for diffusion of 385±20 meV. The minimum of the O-O interadsorbate potential appears to be at lower separations than previously reported.

Optimising predictive modelling of Ross River virus using meteorological variables.

BACKGROUND: Statistical models are regularly used in the forecasting and surveillance of infectious diseases to guide public health. Variable selection assists in determining factors associated with disease transmission, however, often overlooked in this process is the evaluation and suitability of the statistical model used in forecasting disease transmission and outbreaks. Here we aim to evaluate several modelling methods to optimise predictive modelling of Ross River virus (RRV) disease notifications and outbreaks in epidemiological important regions of Victoria and Western Australia. METHODOLOGY/PRINCIPAL FINDINGS: We developed several statistical methods using meteorological and RRV surveillance data from July 2000 until June 2018 in Victoria and from July 1991 until June 2018 in Western Australia. Models were developed for 11 Local Government Areas (LGAs) in Victoria and seven LGAs in Western Australia. We found generalised additive models and generalised boosted regression models, and generalised additive models and negative binomial models to be the best fit models when predicting RRV outbreaks and notifications, respectively. No association was found with a model's ability to predict RRV notifications in LGAs with greater RRV activity, or for outbreak predictions to have a higher accuracy in LGAs with greater RRV notifications. Moreover, we assessed the use of factor analysis to generate independent variables used in predictive modelling. In the majority of LGAs, this method did not result in better model predictive performance. CONCLUSIONS/SIGNIFICANCE: We demonstrate that models which are developed and used for predicting disease notifications may not be suitable for predicting disease outbreaks, or vice versa. Furthermore, poor predictive performance in modelling disease transmissions may be the result of inappropriate model selection methods. Our findings provide approaches and methods to facilitate the selection of the best fit statistical model for predicting mosquito-borne disease notifications and outbreaks used for disease surveillance.

Material properties particularly suited to be measured with helium scattering: selected examples from 2D materials, van der Waals heterostructures, glassy materials, catalytic substrates, topological insulators and superconducting radio frequency materials.

Helium Atom Scattering (HAS) and Helium Spin-Echo scattering (HeSE), together helium scattering, are well established, but non-commercial surface science techniques. They are characterised by the beam inertness and very low beam energy (<0.1 eV) which allows essentially all materials and adsorbates, including fragile and/or insulating materials and light adsorbates such as hydrogen to be investigated on the atomic scale. At present there only exist an estimated less than 15 helium and helium spin-echo scattering instruments in total, spread across the world. This means that up till now the techniques have not been readily available for a broad scientific community. Efforts are ongoing to change this by establishing a central helium scattering facility, possibly in connection with a neutron or synchrotron facility. In this context it is important to clarify what information can be obtained from helium scattering that cannot be obtained with other surface science techniques. Here we present a non-exclusive overview of a range of material properties particularly suited to be measured with helium scattering: (i) high precision, direct measurements of bending rigidity and substrate coupling strength of a range of 2D materials and van der Waals heterostructures as a function of temperature, (ii) direct measurements of the electron-phonon coupling constant λ exclusively in the low energy range (<0.1 eV, tuneable) for 2D materials and van der Waals heterostructures (iii) direct measurements of the surface boson peak in glassy materials, (iv) aspects of polymer chain surface dynamics under nano-confinement (v) certain aspects of nanoscale surface topography, (vi) central properties of surface dynamics and surface diffusion of adsorbates (HeSE) and (vii) two specific science case examples - topological insulators and superconducting radio frequency materials, illustrating how combined HAS and HeSE are necessary to understand the properties of quantum materials. The paper finishes with (viii) examples of molecular surface scattering experiments and other atom surface scattering experiments which can be performed using HAS and HeSE instruments.

Inter-adsorbate forces and coherent scattering in helium spin-echo experiments.

In studies of dynamical systems, helium atoms scatter coherently from an ensemble of adsorbates as they diffuse on the surface. The results give information on the co-operative behaviour of interacting adsorbates and thus include the effects of both adsorbate-substrate and adsorbate-adsorbate interactions. Here, we discuss a method to disentangle the effects of interactions between adsorbates from those with the substrate. The result gives an approximation to observations that would be obtained if the scattering was incoherent. Information from the experiment can therefore be used to distinguish more clearly between long-range inter-adsorbate forces and the short range effects arising from the local lattice potential and associated thermal excitations. The method is discussed in the context of a system with strong inter-adsorbate interactions, sodium atoms diffusing on a copper (111) surface.

Alkali metal adsorption on metal surfaces: new insights from new tools.

The adsorption of sodium on Ru(0001) is studied using 3He spin-echo spectroscopy (HeSE), molecular dynamics simulations (MD) and density functional theory (DFT). In the multi-layer regime, an analysis of helium reflectivity, gives an electron-phonon coupling constant of λ = 0.64 ± 0.06. At sub-monolayer coverage, DFT calculations show that the preferred adsorption site changes from hollow site to top site as the supercell increases and the effective coverage, θ, is reduced from 0.25 to 0.0625 adsorbates per substrate atom. Energy barriers and adsorption geometries taken from DFT are used in molecular dynamics calculations to generate simulated data sets for comparison with measurements. We introduce a new Bayesian method of analysis that compares measurement and model directly, without assuming analytic lineshapes. The value of adsorbate-substrate energy exchange rate (friction) in the MD simulation is the sole variable parameter. Experimental data at a coverage θ = 0.028 compares well with the low-coverage DFT result, giving an effective activation barrier Eeff = 46 ± 4 meV with a friction γ = 0.3 ps-1. Better fits to the data can be achieved by including additional variable parameters, but in all cases, the mechanism of diffusion is predominantly on a Bravais lattice, suggesting a single adsorption site in the unit cell, despite the close packed geometry.

Phylogenetic and Timescale Analysis of Barmah Forest Virus as Inferred from Genome Sequence Analysis.

Barmah Forest virus (BFV) is a medically important mosquito-borne alphavirus endemic to Australia. Symptomatic disease can be a major cause of morbidity, associated with fever, rash, and debilitating arthralgia. BFV disease is similar to that caused by Ross River virus (RRV), the other major Australian alphavirus. Currently, just four BFV whole-genome sequences are available with no genome-scale phylogeny in existence to robustly characterise genetic diversity. Thirty novel genome sequences were derived for this study, for a final 34-taxon dataset sampled over a 44 year period. Three distinct BFV genotypes were characterised (G1-3) that have circulated in Australia and Papua New Guinea (PNG). Evidence of spatio-temporal co-circulation of G2 and G3 within regions of Australia was noted, including in the South West region of Western Australia (WA) during the first reported disease outbreaks in the state's history. Compared with RRV, the BFV population appeared more stable with less frequent emergence of novel lineages. Preliminary in vitro assessment of RRV and BFV replication kinetics found that RRV replicates at a significantly faster rate and to a higher, more persistent titre compared with BFV, perhaps indicating mosquitoes may be infectious with RRV for longer than with BFV. This investigation resolved a greater diversity of BFV, and a greater understanding of the evolutionary dynamics and history was attained.

Genome-Scale Phylogeny and Evolutionary Analysis of Ross River Virus Reveals Periodic Sweeps of Lineage Dominance in Western Australia, 1977-2014.

Ross River virus (RRV), an alphavirus of the Togaviridae family, is the most medically significant mosquito-borne virus of Australia. Past RRV phylogenetic and evolutionary analyses have been based on partial genome analyses only. Three geographically distinct RRV lineages, the Eastern, the Western, and the supposedly extinct North-Eastern lineage, were classified previously. We sought to expand on past phylogenies through robust genome-scale phylogeny to better understand RRV genetic diversity and evolutionary dynamics. We analyzed 106 RRV complete coding sequences, which included 13 genomes available on NCBI and 94 novel sequences derived for this study, sampled throughout Western Australia (1977-2014) and during the substantial Pacific Islands RRV epidemic (1979-1980). Our final data set comprised isolates sampled over 59 years (1959-2018) from a range of locations. Four distinct genotypes were defined, with the newly described genotype 4 (G4) found to be the contemporary lineage circulating in Western Australia. The prior geographical classification of RRV lineages was not supported by our findings, with evidence of geographical and temporal cocirculation of distinct genetic groups. Bayesian Markov chain Monte Carlo (MCMC) analysis revealed that RRV lineages diverged from a common ancestor approximately 94 years ago, with distinct lineages emerging roughly every 10 years over the past 50 years in periodic bursts of genetic diversity. Our study has enabled a more robust analysis of RRV evolutionary history and resolved greater genetic diversity that had been previously defined by partial E2 gene analysis.IMPORTANCE Ross River virus (RRV) causes the most common mosquito-borne infection in Australia and causes a significant burden of suffering to infected individuals as well as being a large burden to the Australian economy. The genetic diversity of RRV and its evolutionary history have so far only been studied using partial E2 gene analysis with a limited number of isolates. Robust whole-genome analysis has not yet been conducted. This study generated 94 novel near-whole-genome sequences to investigate the evolutionary history of RRV to better understand its genetic diversity through comprehensive whole-genome phylogeny. A better understanding of RRV genetic diversity will enable better diagnostics, surveillance, and potential future vaccine design.

Evaluation of a Health Communication Campaign to Improve Mosquito Awareness and Prevention Practices in Western Australia.

Fight the Bite represents the Department of Health's first attempt to actively raise awareness and improve prevention practices related to mosquitoes in Western Australia (WA). The multi-faceted campaign model involved a range of stakeholders and delivery methods over a 2 year period, achieving a recall rate of 8.2% among 2,500 survey participants. Significant regional differences were noted in campaign exposure, reflecting the variation in mosquito management issues throughout the State, and subsequent engagement by local government. Of those individuals with campaign recall, 43.8% reported an increase in awareness and 27.4% reported a change in behavior, which equated to a 1.7 and 1.2% change across the total survey population, respectively. The results of this study demonstrate that Fight the Bite has significantly improved awareness and prevention practices among those individuals who were exposed to the campaign. This was particularly promising, given the modest budget, resources, and time period over which the campaign was run prior to evaluation. This outcome means that Fight the Bite can be confidently adopted as a proven and standardized but regionally adaptable campaign approach to raising awareness about mosquito avoidance and mosquito-borne diseases by the Department of Health and its stakeholders. Future campaign aims include increasing reach through heightened and sustained promotion of Fight the Bite by both the Department and local government, as well as expanded collaboration with a range of stakeholders within the community.