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.

In recent years, a variety of efforts have been made in political science to enable, encourage, or require scholars to be more open and explicit about the bases of their empirical claims and, in turn, make those claims more readily evaluable by others. While qualitative scholars have long taken an interest in making their research open, reflexive, and systematic, the recent push for overarching transparency norms and requirements has provoked serious concern within qualitative research communities and raised fundamental questions about the meaning, value, costs, and intellectual relevance of transparency for qualitative inquiry. In this Perspectives Reflection, we crystallize the central findings of a three-year deliberative process—the Qualitative Transparency Deliberations (QTD)—involving hundreds of political scientists in a broad discussion of these issues. Following an overview of the process and the key insights that emerged, we present summaries of the QTD Working Groups’ final reports. Drawing on a series of public, online conversations that unfolded at www.qualtd.net, the reports unpack transparency’s promise, practicalities, risks, and limitations in relation to different qualitative methodologies, forms of evidence, and research contexts. Taken as a whole, these reports—the full versions of which can be found in the Supplementary Materials—offer practical guidance to scholars designing and implementing qualitative research, and to editors, reviewers, and funders seeking to develop criteria of evaluation that are appropriate—as understood by relevant research communities—to the forms of inquiry being assessed. We dedicate this Reflection to the memory of our coauthor and QTD working group leader Kendra Koivu.1

Through diversity of composition, sequence, and interfacial structure, hybrid materials greatly expand the palette of materials available to access novel functionality. The NSF Division of Materials Research recently supported a workshop (October 17–18, 2019) aiming to (1) identify fundamental questions and potential solutions common to multiple disciplines within the hybrid materials community; (2) initiate interfield collaborations between hybrid materials researchers; and (3) raise awareness in the wider community about experimental toolsets, simulation capabilities, and shared facilities that can accelerate this research. This article reports on the outcomes of the workshop as a basis for cross-community discussion. The interdisciplinary challenges and opportunities are presented, and followed with a discussion of current areas of progress in subdisciplines including hybrid synthesis, functional surfaces, and functional interfaces.

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 have detected 27 new supernova remnants (SNRs) using a new data release of the GLEAM survey from the Murchison Widefield Array telescope, including the lowest surface brightness SNR ever detected, G 0.1 – 9.7. Our method uses spectral fitting to the radio continuum to derive spectral indices for 26/27 candidates, and our low-frequency observations probe a steeper spectrum population than previously discovered. None of the candidates have coincident WISE mid-IR emission, further showing that the emission is non-thermal. Using pulsar associations we derive physical properties for six candidate SNRs, finding G 0.1 – 9.7 may be younger than 10 kyr. Sixty per cent of the candidates subtend areas larger than 0.2 deg2 on the sky, compared to < 25% of previously detected SNRs. We also make the first detection of two SNRs in the Galactic longitude range 220°–240°.

This work makes available a further $2\,860~\text{deg}^2$ of the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey, covering half of the accessible galactic plane, across 20 frequency bands sampling 72–231 MHz, with resolution $4\,\text{arcmin}-2\,\text{arcmin}$ . Unlike previous GLEAM data releases, we used multi-scale CLEAN to better deconvolve large-scale galactic structure. For the galactic longitude ranges $345^\circ < l < 67^\circ$ , $180^\circ < l < 240^\circ$ , we provide a compact source catalogue of 22 037 components selected from a 60-MHz bandwidth image centred at 200 MHz, with RMS noise $\approx10-20\,\text{mJy}\,\text{beam}^{-1}$ and position accuracy better than 2 arcsec. The catalogue has a completeness of 50% at ${\approx}120\,\text{mJy}$ , and a reliability of 99.86%. It covers galactic latitudes $1^\circ\leq|b|\leq10^\circ$ towards the galactic centre and $|b|\leq10^\circ$ for other regions, and is available from Vizier; images covering $|b|\leq10^\circ$ for all longitudes are made available on the GLEAM Virtual Observatory (VO).server and SkyView.

We examined the latest data release from the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey covering 345° < l < 60° and 180° < l < 240°, using these data and that of the Widefield Infrared Survey Explorer to follow up proposed candidate Supernova Remnant (SNR) from other sources. Of the 101 candidates proposed in the region, we are able to definitively confirm ten as SNRs, tentatively confirm two as SNRs, and reclassify five as H ii regions. A further two are detectable in our images but difficult to classify; the remaining 82 are undetectable in these data. We also investigated the 18 unclassified Multi-Array Galactic Plane Imaging Survey (MAGPIS) candidate SNRs, newly confirming three as SNRs, reclassifying two as H ii regions, and exploring the unusual spectra and morphology of two others.

Haplosporidian protist parasites are a major concern for aquatic animal health, as they have been responsible for some of the most significant marine epizootics on record. Despite their impact on food security, aquaculture and ecosystem health, characterizing haplosporidian diversity, distributions and host range remains challenging. In this study, water filtering bivalve species, cockles Cerastoderma edule, mussels Mytilus spp. and Pacific oysters Crassostrea gigas, were screened using molecular genetic assays using deoxyribonucleic acid (DNA) markers for the Haplosporidia small subunit ribosomal deoxyribonucleic acid region. Two Haplosporidia species, both belonging to the Minchinia clade, were detected in C. edule and in the blue mussel Mytilus edulis in a new geographic range for the first time. No haplosporidians were detected in the C. gigas, Mediterranean mussel Mytilus galloprovincialis or Mytilus hybrids. These findings indicate that host selection and partitioning are occurring amongst cohabiting bivalve species. The detection of these Haplosporidia spp. raises questions as to whether they were always present, were introduced unintentionally via aquaculture and or shipping or were naturally introduced via water currents. These findings support an increase in the known diversity of a significant parasite group and highlight that parasite species may be present in marine environments but remain undetected, even in well-studied host species.

The spread of the Zika virus (ZIKV) in the Americas led to large outbreaks across the region and most of the Southern hemisphere. Of greatest concern were complications following acute infection during pregnancy. At the beginning of the outbreak, the risk to unborn babies and their clinical presentation was unclear. This report describes the methods and results of the UK surveillance response to assess the risk of ZIKV to children born to returning travellers. Established surveillance systems operating within the UK – the paediatric and obstetric surveillance units for rare diseases, and national laboratory monitoring – enabled rapid assessment of this emerging public health threat. A combined total of 11 women experiencing adverse pregnancy outcomes after possible ZIKV exposure were reported by the three surveillance systems; five miscarriages, two intrauterine deaths and four children with clinical presentations potentially associated with ZIKV infection. Sixteen women were diagnosed with ZIKV during pregnancy in the UK. Amongst the offspring of these women, there was unequivocal laboratory evidence of infection in only one child. In the UK, the number and risk of congenital ZIKV infection for travellers returning from ZIKV-affected countries is very small.

We describe the parameters of a low-frequency all-sky survey of compact radio sources using Interplanetary Scintillation, undertaken with the Murchison Widefield Array. While this survey gives important complementary information to low-resolution survey, providing information on the sub-arsecond structure of every source, a survey of this kind has not been attempted in the era of low-frequency imaging arrays such as the Murchison Widefield Array and LOw Frequency Array. Here we set out the capabilities of such a survey, describing the limitations imposed by the heliocentric observing geometry and by the instrument itself. We demonstrate the potential for Interplanetary Scintillation measurements at any point on the celestial sphere and we show that at 160 MHz, reasonable results can be obtained within 30° of the ecliptic (2π str: half the sky). We also suggest some observational strategies and describe the first such survey, the Murchison Widefield Array Phase I Interplanetary Scintillation survey. Finally we analyse the potential of the recently upgraded Murchison Widefield Array and discuss the potential of the Square Kilometre Array-low to use Interplanetary Scintillation to probe sub-mJy flux density levels at sub-arcsecond angular resolution.

Antibodies at gastrointestinal mucosal membranes play a vital role in immunological protection against a range of pathogens, including helminths. Gastrointestinal health is central to efficient livestock production, and such infections cause significant losses. Fecal samples were taken from 114 cattle, across three beef farms, with matched blood samples taken from 22 of those animals. To achieve fecal antibody detection, a novel fecal supernatant was extracted. Fecal supernatant and serum samples were then analysed, using adapted enzyme-linked immunosorbent assay protocols, for levels of total immunoglobulin (Ig)A, IgG, IgM, and Teladorsagia circumcincta-specific IgA, IgG, IgM and IgE (in the absence of reagents for cattle-specific nematode species). Fecal nematode egg counts were conducted on all fecal samples. Assays performed successfully and showed that IgA was the predominant antibody in fecal samples, whereas IgG was predominant in serum. Total IgA in feces and serum correlated within individuals (0.581, P = 0.005), but other Ig types did not. Results support the hypothesis that the tested protocols are an effective method for the non-invasive assessment of cattle immunology. The method could be used as part of animal health assessments, although further work is required to interpret the relationship between results and levels of infection and immunity.

The Murchison Widefield Array (MWA), located in Western Australia, is one of the low-frequency precursors of the international Square Kilometre Array (SKA) project. In addition to pursuing its own ambitious science programme, it is also a testbed for wide range of future SKA activities ranging from hardware, software to data analysis. The key science programmes for the MWA and SKA require very high dynamic ranges, which challenges calibration and imaging systems. Correct calibration of the instrument and accurate measurements of source flux densities and polarisations require precise characterisation of the telescope’s primary beam. Recent results from the MWA GaLactic Extragalactic All-sky Murchison Widefield Array (GLEAM) survey show that the previously implemented Average Embedded Element (AEE) model still leaves residual polarisations errors of up to 10–20% in Stokes Q. We present a new simulation-based Full Embedded Element (FEE) model which is the most rigorous realisation yet of the MWA’s primary beam model. It enables efficient calculation of the MWA beam response in arbitrary directions without necessity of spatial interpolation. In the new model, every dipole in the MWA tile (4 × 4 bow-tie dipoles) is simulated separately, taking into account all mutual coupling, ground screen, and soil effects, and therefore accounts for the different properties of the individual dipoles within a tile. We have applied the FEE beam model to GLEAM observations at 200–231 MHz and used false Stokes parameter leakage as a metric to compare the models. We have determined that the FEE model reduced the magnitude and declination-dependent behaviour of false polarisation in Stokes Q and V while retaining low levels of false polarisation in Stokes U.

Escherichia coli O157 are zoonotic bacteria for which cattle are an important reservoir. Prevalence estimates for E. coli O157 in British cattle for human consumption are over 10 years old. A new baseline is needed to inform current human health risk. The British E. coli O157 in Cattle Study (BECS) ran between September 2014 and November 2015 on 270 farms across Scotland and England & Wales. This is the first study to be conducted contemporaneously across Great Britain, thus enabling comparison between Scotland and England & Wales. Herd-level prevalence estimates for E. coli O157 did not differ significantly for Scotland (0·236, 95% CI 0·166–0·325) and England & Wales (0·213, 95% CI 0·156–0·283) (P = 0·65). The majority of isolates were verocytotoxin positive. A higher proportion of samples from Scotland were in the super-shedder category, though there was no difference between the surveys in the likelihood of a positive farm having at least one super-shedder sample. E. coli O157 continues to be common in British beef cattle, reaffirming public health policy that contact with cattle and their environments is a potential infection source.

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.

We present low-frequency spectral energy distributions of 60 known radio pulsars observed with the Murchison Widefield Array telescope. We searched the GaLactic and Extragalactic All-sky Murchison Widefield Array survey images for 200-MHz continuum radio emission at the position of all pulsars in the Australia Telescope National Facility (ATNF) pulsar catalogue. For the 60 confirmed detections, we have measured flux densities in 20 × 8 MHz bands between 72 and 231 MHz. We compare our results to existing measurements and show that the Murchison Widefield Array flux densities are in good agreement.

The order of the authors in the published article is incorrect. The authors should appear as follows:

J. Schneider, B. Cornwell, A. Jonas, R. Behler, N. Lancki, B. Skaathun, L. E. Young, E. Morgan, S. Michaels, R. Duvoisin, A. S. Khanna, S. Friedman, P. Schumm, E. Laumann, for the uConnect Study Team

The authors regret the error.