This SHEA white paper identifies knowledge gaps and challenges in healthcare epidemiology research related to COVID-19 with a focus on core principles of healthcare epidemiology. These gaps, revealed during the worst phases of the COVID-19 pandemic, are described in 10 sections: epidemiology, outbreak investigation, surveillance, isolation precaution practices, personal protective equipment (PPE), environmental contamination and disinfection, drug and supply shortages, antimicrobial stewardship, healthcare personnel (HCP) occupational safety, and return to work policies. Each section highlights three critical healthcare epidemiology research questions with detailed description provided in supplemental materials. This research agenda calls for translational studies from laboratory-based basic science research to well-designed, large-scale studies and health outcomes research. Research gaps and challenges related to nursing homes and social disparities are included. Collaborations across various disciplines, expertise and across diverse geographic locations will be critical.

The Murchison Widefield Array (MWA) is an open access telescope dedicated to studying the low-frequency (80–300 MHz) southern sky. Since beginning operations in mid-2013, the MWA has opened a new observational window in the southern hemisphere enabling many science areas. The driving science objectives of the original design were to observe 21 cm radiation from the Epoch of Reionisation (EoR), explore the radio time domain, perform Galactic and extragalactic surveys, and monitor solar, heliospheric, and ionospheric phenomena. All together $60+$ programs recorded 20 000 h producing 146 papers to date. In 2016, the telescope underwent a major upgrade resulting in alternating compact and extended configurations. Other upgrades, including digital back-ends and a rapid-response triggering system, have been developed since the original array was commissioned. In this paper, we review the major results from the prior operation of the MWA and then discuss the new science paths enabled by the improved capabilities. We group these science opportunities by the four original science themes but also include ideas for directions outside these categories.

We present techniques developed to calibrate and correct Murchison Widefield Array low-frequency (72–300 MHz) radio observations for polarimetry. The extremely wide field-of-view, excellent instantaneous (u, v)-coverage and sensitivity to degree-scale structure that the Murchison Widefield Array provides enable instrumental calibration, removal of instrumental artefacts, and correction for ionospheric Faraday rotation through imaging techniques. With the demonstrated polarimetric capabilities of the Murchison Widefield Array, we discuss future directions for polarimetric science at low frequencies to answer outstanding questions relating to polarised source counts, source depolarisation, pulsar science, low-mass stars, exoplanets, the nature of the interstellar and intergalactic media, and the solar environment.

The current generation of experiments aiming to detect the neutral hydrogen signal from the Epoch of Reionisation (EoR) is likely to be limited by systematic effects associated with removing foreground sources from target fields. In this paper, we develop a model for the compact foreground sources in one of the target fields of the MWA’s EoR key science experiment: the ‘EoR1’ field. The model is based on both the MWA’s GLEAM survey and GMRT 150 MHz data from the TGSS survey, the latter providing higher angular resolution and better astrometric accuracy for compact sources than is available from the MWA alone. The model contains 5 049 sources, some of which have complicated morphology in MWA data, Fornax A being the most complex. The higher resolution data show that 13% of sources that appear point-like to the MWA have complicated morphology such as double and quad structure, with a typical separation of 33 arcsec. We derive an analytic expression for the error introduced into the EoR two-dimensional power spectrum due to peeling close double sources as single point sources and show that for the measured source properties, the error in the power spectrum is confined to high k ⊥ modes that do not affect the overall result for the large-scale cosmological signal of interest. The brightest 10 mis-modelled sources in the field contribute 90% of the power bias in the data, suggesting that it is most critical to improve the models of the brightest sources. With this hybrid model, we reprocess data from the EoR1 field and show a maximum of 8% improved calibration accuracy and a factor of two reduction in residual power in k-space from peeling these sources. Implications for future EoR experiments including the SKA are discussed in relation to the improvements obtained.

Around 70% of total seed phosphorus is represented by phytate which must be hydrolysed to be bioavailable in non-ruminant diets. The limited endogenous phytase activity in non-ruminant animals make it common practice to add an exogenous phytase source to most poultry and pig feeds. The mature grain phytase activity (MGPA) of cereal seeds provides a route for the seeds themselves to contribute to phytate digestion, but MGPA varies considerably between species and most varieties in current use make negligible contributions. Currently, all phytases used for feed supplementation and transgenic improvement of MGPA are derived from microbial enzymes belonging to the group of histidine acid phosphatases (HAP). Cereals contain HAP phytases, but the bulk of MGPA can be attributed to phytases belonging to a completely different group of phosphatases, the purple acid phosphatases (PAPhy). In recent years, increased MGPAs were achieved in cisgenic barley holding extra copies of barley PAPhy and in the wheat HIGHPHY mutant, where MGPA was increased to ~6200 FTU/kg. In the present study, the effect of replacing 33%, 66% and 100% of a standard wheat with HIGHPHY wheat was compared with a control diet with and without 500 FTU of supplemental phytase. Diets were compared by evaluating broiler performance, ileal Ca and P digestibility and tibia development, using nine replicate pens of four birds per diet over 3 weeks from hatch. There were no differences between treatments in any tibia or bird performance parameters, indicating the control diet did not contain sufficiently low levels of phosphorus to distinguish effect of phytase addition. However, in a comparison of the two wheats, the ileal Ca and P digestibility coefficients for the 100% HIGHPHY wheat diets are 22.9% and 35.6% higher, respectively, than for the control diet, indicating the wheat PAPhy is functional in the broiler digestive tract. Furthermore, 33% HIGHPHY replacement of conventional wheat, significantly improved Ca and P digestibility over the diet-supplemented exogenous phytase, probably due to the higher phytase activity in the HIGHPHY diet (1804 v. 1150 FTU). Full replacement by HIGHPHY gave 14.6% and 22.8% higher ileal digestibility coefficients for Ca and P, respectively, than for feed supplemented with exogenous HAP phytase at 500 FTU. This indicates that in planta wheat PAPhys has promising potential for improving P and mineral digestibility in animal feed.

We have compiled a catalogue of H ii regions detected with the Murchison Widefield Array between 72 and 231 MHz. The multiple frequency bands provided by the Murchison Widefield Array allow us identify the characteristic spectrum generated by the thermal Bremsstrahlung process in H ii regions. We detect 306 H ii regions between 260° < l < 340° and report on the positions, sizes, peak, integrated flux density, and spectral indices of these H ii regions. By identifying the point at which H ii regions transition from the optically thin to thick regime, we derive the physical properties including the electron density, ionised gas mass, and ionising photon flux, towards 61 H ii regions. This catalogue of H ii regions represents the most extensive and uniform low frequency survey of H ii regions in the Galaxy to date.

Grazing season length (GSL) on grassland farms with ruminant production systems can influence farm economics, livestock disease transmission, environmental impact, milk and meat quality, and consumer choice. Bioclimatic variables are biologically meaningful climate variables that may enable predictions of the impact of future climate change on GSL on European farms. The present study investigated the spatial relationship between current GSL (months) measured by EUROSTAT on dairy, beef and sheep farms in 706, 774 and 878 regions, respectively, and bioclimatic variables. A stepwise multiple regression model revealed a highly significant association between observed GSL and bioclimatic variables across Europe. Mean GSL was positively associated with the mean temperature of the coldest quarter and isothermality, and negatively associated with precipitation in the wettest month. Extrapolating these relationships to future climate change scenarios, most European countries were predicted to have a net increase in GSL with the increase being largest (up to 2·5 months) in the north-east of Europe. However, there were also predictions of increased variability between regions and decreases in GSL of up to 1·5 months in some areas such as the west of France, the south-west of Norway and the west coast of Britain. The study quantified and mapped the potential impact of climate change on GSL for dairy, beef and sheep farms across Europe.

The nematode Angiostrongylus vasorum is becoming more widely recorded globally, and is of increasing concern as a cause of disease in dogs. Apparent geographic spread is difficult to confirm due to a lack of standardized disease recording systems, increasing awareness among veterinary clinicians, and recent improvements in diagnostic technologies. This study examines the hypothesis that A. vasorum has spread in recent years by repeating the methods of a previous survey of the fox population. The hearts and lungs of 442 foxes from across Great Britain were collected and examined by dissection and flushing of the pulmonary circulation and microscopic inspection of tracheal scrapes. Sampling and parasite extraction methods were identical to an earlier survey in 2005 to ensure comparability. Prevalence of A. vasorum was 18·3% (exact binomial confidence bounds 14·9–22·3), compared with 7·3% previously (5·3–9·9, n = 546), and had increased significantly in most regions, e.g. 7·4% in the Northern UK (previously zero) and 50·8% in the south-east (previously 23·2%). Other nematodes identified were Crenosoma vulpis (prevalence 10·8%, CI 8·1–14·2) and Eucoleus aerophilus (31·6%, CI 27·3–36·2). These data support the proposal that A. vasorum has increased in prevalence and has spread geographically in Great Britain.

The Murchison Widefield Array is a new low-frequency interferometric radio telescope built in Western Australia at one of the locations of the future Square Kilometre Array. We describe the automated radio-frequency interference detection strategy implemented for the Murchison Widefield Array, which is based on the aoflagger platform, and present 72–231 MHz radio-frequency interference statistics from 10 observing nights. Radio-frequency interference detection removes 1.1% of the data. Radio-frequency interference from digital TV is observed 3% of the time due to occasional ionospheric or atmospheric propagation. After radio-frequency interference detection and excision, almost all data can be calibrated and imaged without further radio-frequency interference mitigation efforts, including observations within the FM and digital TV bands. The results are compared to a previously published Low-Frequency Array radio-frequency interference survey. The remote location of the Murchison Widefield Array results in a substantially cleaner radio-frequency interference environment compared to Low-Frequency Array’s radio environment, but adequate detection of radio-frequency interference is still required before data can be analysed. We include specific recommendations designed to make the Square Kilometre Array more robust to radio-frequency interference, including: the availability of sufficient computing power for radio-frequency interference detection; accounting for radio-frequency interference in the receiver design; a smooth band-pass response; and the capability of radio-frequency interference detection at high time and frequency resolution (second and kHz-scale respectively).

Human salmonellosis linked to contact with live poultry is an increasing public health concern. In 2012, eight unrelated outbreaks of human salmonellosis linked to live poultry contact resulted in 517 illnesses. In July 2012, PulseNet, a national molecular surveillance network, reported a multistate cluster of a rare strain of Salmonella Braenderup infections which we investigated. We defined a case as infection with the outbreak strain, determined by pulsed-field gel electrophoresis, with illness onset from 25 July 2012–27 February 2013. Ill persons and mail-order hatchery (MOH) owners were interviewed using standardized questionnaires. Traceback and environmental investigations were conducted. We identified 48 cases in 24 states. Twenty-six (81%) of 32 ill persons reported live poultry contact in the week before illness; case-patients named 12 different MOHs from eight states. The investigation identified hatchery D as the ultimate poultry source. Sampling at hatchery D yielded the outbreak strain. Hatchery D improved sanitation procedures and pest control; subsequent sampling failed to yield Salmonella. This outbreak highlights the interconnectedness of humans, animals, and the environment and the importance of industry knowledge and involvement in solving complex outbreaks. Preventing these infections requires a ‘One Health’ approach that leverages expertise in human, animal, and environmental health.

The influence of the substrate temperature on the morphology and ordering of InGaAs quantum dots (QD), grown on GaAs (001) wafers by Molecular Beam Epitaxy (MBE) under As2 flux has been studied using Transmission Electron Microscopy (TEM), Atomic Force Microscopy (AFM) and Photoluminescence (PL) measurements. The experimental results show that lateral and vertical orderings occur for temperatures greater than 520°C and that QDs self-organize in a 6-fold symmetry network on (001) surface for T=555°C. Vertical orderings of asymmetric QDs, along directions a few degrees off [001], are observed on a large scale and their formation is discussed.