In this work, we present a methodology and a corresponding code-base for constructing mock integral field spectrograph (IFS) observations of simulated galaxies in a consistent and reproducible way. Such methods are necessary to improve the collaboration and comparison of observation and theory results, and accelerate our understanding of how the kinematics of galaxies evolve over time. This code, SimSpin, is an open-source package written in R, but also with an API interface such that the code can be interacted with in any coding language. Documentation and individual examples can be found at the open-source website connected to the online repository. SimSpin is already being utilised by international IFS collaborations, including SAMI and MAGPI, for generating comparable data sets from a diverse suite of cosmological hydrodynamical simulations.

As the scale of cosmological surveys increases, so does the complexity in the analyses. This complexity can often make it difficult to derive the underlying principles, necessitating statistically rigorous testing to ensure the results of an analysis are consistent and reasonable. This is particularly important in multi-probe cosmological analyses like those used in the Dark Energy Survey (DES) and the upcoming Legacy Survey of Space and Time, where accurate uncertainties are vital. In this paper, we present a statistically rigorous method to test the consistency of contours produced in these analyses and apply this method to the Pippin cosmological pipeline used for type Ia supernova cosmology with the DES. We make use of the Neyman construction, a frequentist methodology that leverages extensive simulations to calculate confidence intervals, to perform this consistency check. A true Neyman construction is too computationally expensive for supernova cosmology, so we develop a method for approximating a Neyman construction with far fewer simulations. We find that for a simulated dataset, the 68% contour reported by the Pippin pipeline and the 68% confidence region produced by our approximate Neyman construction differ by less than a percent near the input cosmology; however, they show more significant differences far from the input cosmology, with a maximal difference of 0.05 in $\Omega_{M}$ and 0.07 in w. This divergence is most impactful for analyses of cosmological tensions, but its impact is mitigated when combining supernovae with other cross-cutting cosmological probes, such as the cosmic microwave background.

Background: The Canadian Registry for Amyloidosis Research (CRAR) is a nationwide disease registry of transthyretin (ATTR) and light-chain (AL) amyloidosis. Recent advances in disease-modifying therapy have improved prognosis, however there is a critical need for real-world evidence to address knowledge gaps, particularly longer-term therapeutic outcomes and surveillance strategies. Methods: A multi-stakeholder process was undertaken to develop a consensus dataset for ATTR- and AL-amyloidosis. This process included surveys to rank the importance of potential data items, and a consensus meeting of the CRAR steering committee, (comprised of multidisciplinary clinical experts, and patient organization representatives). Patients and patient organizations supported the development and implementation of a patient-reported dataset. Results: Consensus data items include disease onset, progression, severity, treatments, and outcomes, as well as patient-reported outcomes. Both prospective and retrospective (including deceased) patient cohorts are included. Further baseline data will be presented on an initial cohort of patients. Conclusions: CRAR has been established to collect a longitudinal, multidisciplinary dataset that will evaluate amyloidosis care and outcomes. CRAR has launched at multiple specialty amyloidosis centers nationally and is continually expanding. The growth of this program will promote opportunities to assess real-world safety and efficacy and inform the cost-effectiveness of therapies while supporting patient recruitment for research.

We present Hubble Space Telescope Wide Field Camera 3 photometric and grism observations of the candidate ultra-high-redshift ($z>7$) radio galaxy, GLEAM J0917–0012. This radio source was selected due to the curvature in its 70–230 MHz, low-frequency Murchison Widefield Array radio spectrum and its faintness in K-band. Follow-up spectroscopic observations of this source with the Jansky Very Large Array and Atacama Large Millimetre Array were inconclusive as to its redshift. Our F105W and F0986M imaging observations detect the host of GLEAM J0917–0012 and a companion galaxy, $\sim$ one arcsec away. The G102 grism observations reveal a single weak line in each of the spectra of the host and the companion. To help identify these lines we utilised several photometric redshift techniques including template fitting to the grism spectra, fitting the ultraviolet (UV)-to-radio photometry with galaxy templates plus a synchrotron model, fitting of the UV-to-near-infrared photometry with EAZY, and fitting the radio data alone with RAiSERed. For the host of GLEAM J0917–0012 we find a line at $1.12\,\mu$m and the UV-to-radio spectral energy distribution (SED) fitting favours solutions at $z\sim 2$ or $z\sim 8$. While this fitting shows a weak preference for the lower redshift solution, the models from the higher redshift solution are more consistent with the strength of the spectral line. The redshift constraint by RAiSERed of $>6.5$ also supports the interpretation that this line could be Lyman$-\alpha$ at $z=8.21$; however EAZY favours the $z\sim 2$ solution. We discuss the implications of both solutions. For the companion galaxy we find a line at $0.98\,\mu$m and the SED fitting favours solutions at $z<3$ implying that the line could be the [OII]$\lambda3727$ doublet at $z=1.63$ (although the EAZY solution is $z\sim 2.6\pm 0.5$). Further observations are still required to unambiguously determine the redshift of this intriguing candidate ultra-high-redshift radio galaxy.

Consumption of pork and pork products can be associated with outbreaks of human salmonellosis. Salmonella infection is usually subclinical in pigs, and farm-based control measures are challenging to implement. To obtain data on Salmonella prevalence, samples can be collected from pigs during the slaughter process. Here we report the results of a Great Britain (GB) based abattoir survey conducted by sampling caecal contents from pigs in nine British pig abattoirs during 2019. Samples were collected according to a randomised stratified scheme, and pigs originating from 286 GB farms were included in this survey. Salmonella was isolated from 112 pig caecal samples; a prevalence of 32.2% [95% confidence interval (CI) 27.4–37.4]. Twelve different Salmonella serovars were isolated, with the most common serovars being S. 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium (36.6% of Salmonella-positive samples), followed by S. Derby (25.9% of Salmonella-positive samples). There was no significant difference compared to the estimate of overall prevalence (30.5% (95% CI 26.5–34.6)) obtained in the last abattoir survey conducted in the UK (2013). Abattoir-based control measures are often effective in the reduction of Salmonella contamination of carcasses entering the food chain. In this study, the effect of abattoir hygiene practices on the prevalence of Salmonella on carcasses was not assessed. Continuing Salmonella surveillance at slaughter is recommended to assess effect of farm-based and abattoir-based interventions and to monitor potential public health risk associated with consumption of Salmonella-contaminated pork products.

We present an overview of the Middle Ages Galaxy Properties with Integral Field Spectroscopy (MAGPI) survey, a Large Program on the European Southern Observatory Very Large Telescope. MAGPI is designed to study the physical drivers of galaxy transformation at a lookback time of 3–4 Gyr, during which the dynamical, morphological, and chemical properties of galaxies are predicted to evolve significantly. The survey uses new medium-deep adaptive optics aided Multi-Unit Spectroscopic Explorer (MUSE) observations of fields selected from the Galaxy and Mass Assembly (GAMA) survey, providing a wealth of publicly available ancillary multi-wavelength data. With these data, MAGPI will map the kinematic and chemical properties of stars and ionised gas for a sample of 60 massive (${>}7 \times 10^{10} {\mathrm{M}}_\odot$) central galaxies at $0.25 < z <0.35$ in a representative range of environments (isolated, groups and clusters). The spatial resolution delivered by MUSE with Ground Layer Adaptive Optics ($0.6-0.8$ arcsec FWHM) will facilitate a direct comparison with Integral Field Spectroscopy surveys of the nearby Universe, such as SAMI and MaNGA, and at higher redshifts using adaptive optics, for example, SINS. In addition to the primary (central) galaxy sample, MAGPI will deliver resolved and unresolved spectra for as many as 150 satellite galaxies at $0.25 < z <0.35$, as well as hundreds of emission-line sources at $z < 6$. This paper outlines the science goals, survey design, and observing strategy of MAGPI. We also present a first look at the MAGPI data, and the theoretical framework to which MAGPI data will be compared using the current generation of cosmological hydrodynamical simulations including EAGLE, Magneticum, HORIZON-AGN, and Illustris-TNG. Our results show that cosmological hydrodynamical simulations make discrepant predictions in the spatially resolved properties of galaxies at $z\approx 0.3$. MAGPI observations will place new constraints and allow for tangible improvements in galaxy formation theory.

Maternal nutrition is critical in mammalian development, influencing the epigenetic reprogramming of gametes, embryos, and fetal programming. We evaluated the effects of different levels of sulfur (S) and cobalt (Co) in the maternal diet throughout the pre- and periconceptional periods on the biochemical and reproductive parameters of the donors and the DNA methylome of the progeny in Bos indicus cattle. The low-S/Co group differed from the control with respect to homocysteine, folic acid, B12, insulin growth factor 1, and glucose. The oocyte yield was lower in heifers from the low S/Co group than that in the control heifers. Embryos from the low-S/Co group exhibited 2320 differentially methylated regions (DMRs) across the genome compared with the control embryos. We also characterized candidate DMRs linked to the DNMT1 and DNMT3B genes in the blood and sperm cells of the adult progeny. A DMR located in DNMT1 that was identified in embryos remained differentially methylated in the sperm of the progeny from the low-S/Co group. Therefore, we associated changes in specific compounds in the maternal diet with DNA methylation modifications in the progeny. Our results help to elucidate the impact of maternal nutrition on epigenetic reprogramming in livestock, opening new avenues of research to study the effect of disturbed epigenetic patterns in early life on health and fertility in adulthood. Considering that cattle are physiologically similar to humans with respect to gestational length, our study may serve as a model for studies related to the developmental origin of health and disease in humans.

We present a detailed analysis of the radio galaxy PKS $2250{-}351$, a giant of 1.2 Mpc projected size, its host galaxy, and its environment. We use radio data from the Murchison Widefield Array, the upgraded Giant Metre-wavelength Radio Telescope, the Australian Square Kilometre Array Pathfinder, and the Australia Telescope Compact Array to model the jet power and age. Optical and IR data come from the Galaxy And Mass Assembly (GAMA) survey and provide information on the host galaxy and environment. GAMA spectroscopy confirms that PKS $2250{-}351$ lies at $z=0.2115$ in the irregular, and likely unrelaxed, cluster Abell 3936. We find its host is a massive, ‘red and dead’ elliptical galaxy with negligible star formation but with a highly obscured active galactic nucleus dominating the mid-IR emission. Assuming it lies on the local M–$\sigma$ relation, it has an Eddington accretion rate of $\lambda_{\rm EDD}\sim 0.014$. We find that the lobe-derived jet power (a time-averaged measure) is an order of magnitude greater than the hotspot-derived jet power (an instantaneous measure). We propose that over the lifetime of the observed radio emission (${\sim} 300\,$Myr), the accretion has switched from an inefficient advection-dominated mode to a thin disc efficient mode, consistent with the decrease in jet power. We also suggest that the asymmetric radio morphology is due to its environment, with the host of PKS $2250{-}351$ lying to the west of the densest concentration of galaxies in Abell 3936.

Campylobacteriosis is the most common notifiable disease in New Zealand. While the risk of campylobacteriosis has been found to be strongly associated with the consumption of undercooked poultry, other risk factors include rainwater-sourced drinking water, contact with animals and consumption of raw dairy products. Despite this, there has been little investigation of raw milk as a risk factor for campylobacteriosis. Recent increases in demand for untreated or ‘raw’ milk have also raised concerns that this exposure may become a more important source of disease in the future. This study describes the cases of notified campylobacteriosis from a sentinel surveillance site. Previously collected data from notified cases of raw milk-associated campylobacteriosis were examined and compared with campylobacteriosis cases who did not report raw milk consumption. Raw milk campylobacteriosis cases differed from non-raw milk cases on comparison of age and occupation demographics, with raw milk cases more likely to be younger and categorised as children or students for occupation. Raw milk cases were more likely to be associated with outbreaks than non-raw milk cases. Study-suggested motivations for raw milk consumption (health reasons, natural product, produced on farm, inexpensive or to support locals) were not strongly supported by cases. More information about the raw milk consumption habits of New Zealanders would be helpful to better understand the risks of this disease, especially with respect to increased disease risk observed in younger people. Further discussion with raw milk consumers around their motivations may also be useful to find common ground between public health concerns and consumer preferences as efforts continue to manage this ongoing public health issue.

The majority of paediatric Clostridioides difficile infections (CDI) are community-associated (CA), but few data exist regarding associated risk factors. We conducted a case–control study to evaluate CA-CDI risk factors in young children. Participants were enrolled from eight US sites during October 2014–February 2016. Case-patients were defined as children aged 1–5 years with a positive C. difficile specimen collected as an outpatient or ⩽3 days of hospital admission, who had no healthcare facility admission in the prior 12 weeks and no history of CDI. Each case-patient was matched to one control. Caregivers were interviewed regarding relevant exposures. Multivariable conditional logistic regression was performed. Of 68 pairs, 44.1% were female. More case-patients than controls had a comorbidity (33.3% vs. 12.1%; P = 0.01); recent higher-risk outpatient exposures (34.9% vs. 17.7%; P = 0.03); recent antibiotic use (54.4% vs. 19.4%; P < 0.0001); or recent exposure to a household member with diarrhoea (41.3% vs. 21.5%; P = 0.04). In multivariable analysis, antibiotic exposure in the preceding 12 weeks was significantly associated with CA-CDI (adjusted matched odds ratio, 6.25; 95% CI 2.18–17.96). Improved antibiotic prescribing might reduce CA-CDI in this population. Further evaluation of the potential role of outpatient healthcare and household exposures in C. difficile transmission is needed.

The type specimen of liskeardite, (Al, Fe)3AsO4(OH)6·5H2O, from the Marke Valley Mine, Liskeard District, Cornwall, has been reinvestigated. The revised composition from electron microprobe analyses and structure refinement is [Al29.2Fe2.8(AsO4)18(OH)42(H2O)22]·52H2O.The crystal structure was determined using synchrotron data collected on a 2 μm diameter fibre at 100 K. Liskeardite has monoclinic symmetry, space group I2, with the unit-cell parameters a = 24.576(5), b = 7.754(2) Å, c = 24.641(5) Å, and β= 90.19(1)º. The structure was refined to R = 0.059 for 9769 reflections with I > 3σ(I). It is of an open framework type in which intersecting polyhedral slabs parallel to (101) and (10) form 17.4 Å × 17.4 Å channels along [010], with watermolecules occupying the channels. Small amounts (<1 wt.%) of Na, K and Cu are probably adsorbed at the channel walls The framework comprises columns of pharmacoalumite-type, intergrown with chiral chains of six cis edge-shared octahedra. It can be described in terms of cubic closepacking, with vacancies at both the anion and cation sites. The compositional and structural relationships between liskeardite and pharmacoalumite are discussed and a possible mechanism for liskeardite formation is presented.

The mineral in bones and teeth is an impure form of hydroxylapatite (HAP), the principal impurity being 2—5 wt.% carbonate. This mineral dissolves during remodelling of bone and also in dental caries as a result of the action of acids produced by osteoclasts and by bacteria, respectively. In enamel, demineralization proceeds with preferential loss of carbonate relative to phosphate. Surprisingly, in the early stages, the demineralization is subsurface. In order to facilitate the understanding of physical chemical aspects of these processes, we have undertaken studies of demineralization in model systems. We give three examples here. The first two used scanning microradiography in which the specimen is stepped across a 10—30 μm diameter X-ray beam. Intensity measurements allow calculation of the mineral mass per unit area in the X-ray path through the specimen. In the first experiment, porous HAP sections were separated from a reservoir of acidic buffer by a column initially filled with water (the diffusion length) and scanned with the X-ray beam perpendicular to the axis of the diffusion length. The rate of total loss of mineral along each profile was calculated from the scans. The rate of demineralization fell as the diffusion length increased. We believe the explanation is that the rate-controlling step is the diffusion of dissolved HAP away from the solid to the buffer reservoir. In the second experiment, demineralizing solution and water were pumped alternately, for equal lengths of time, past blocks of porous HAP or enamel. The X-ray beam was perpendicular to the exposed surface. As the rate of switching between solutions decreased, the mean rate of demineralization also fell. We propose that this effect is due to retention of acid in the pores of the HAP during the time when water flows, allowing further demineralization to take place during this time. The third study used X-ray microtomography, a form of 3D microscopy, to study the loss of mineral in compacted carbonate apatite powders. The powders were packed in six 10 mm internal diameter acrylic cylinders to a depth of 4 mm (after pressing). One end was covered with a porous polyethylene disc and each tube placed in acidic buffer for 70 days. Periodic examination by microtomography showed the development of subsurface demineralization. Infrared spectroscopy of the dissected-out surface layers showed preferential loss of carbonate over phosphate by comparison with deeper layers. Rietveld analysis of X-ray powder diffraction data showed changes in the crystallographic structures of the apatites between the initial and dissected-out apatite.

The Taipan galaxy survey (hereafter simply ‘Taipan’) is a multi-object spectroscopic survey starting in 2017 that will cover 2π steradians over the southern sky (δ ≲ 10°, |b| ≳ 10°), and obtain optical spectra for about two million galaxies out to z < 0.4. Taipan will use the newly refurbished 1.2-m UK Schmidt Telescope at Siding Spring Observatory with the new TAIPAN instrument, which includes an innovative ‘Starbugs’ positioning system capable of rapidly and simultaneously deploying up to 150 spectroscopic fibres (and up to 300 with a proposed upgrade) over the 6° diameter focal plane, and a purpose-built spectrograph operating in the range from 370 to 870 nm with resolving power R ≳ 2000. The main scientific goals of Taipan are (i) to measure the distance scale of the Universe (primarily governed by the local expansion rate, H 0) to 1% precision, and the growth rate of structure to 5%; (ii) to make the most extensive map yet constructed of the total mass distribution and motions in the local Universe, using peculiar velocities based on improved Fundamental Plane distances, which will enable sensitive tests of gravitational physics; and (iii) to deliver a legacy sample of low-redshift galaxies as a unique laboratory for studying galaxy evolution as a function of dark matter halo and stellar mass and environment. The final survey, which will be completed within 5 yrs, will consist of a complete magnitude-limited sample (i ⩽ 17) of about 1.2 × 106 galaxies supplemented by an extension to higher redshifts and fainter magnitudes (i ⩽ 18.1) of a luminous red galaxy sample of about 0.8 × 106 galaxies. Observations and data processing will be carried out remotely and in a fully automated way, using a purpose-built automated ‘virtual observer’ software and an automated data reduction pipeline. The Taipan survey is deliberately designed to maximise its legacy value by complementing and enhancing current and planned surveys of the southern sky at wavelengths from the optical to the radio; it will become the primary redshift and optical spectroscopic reference catalogue for the local extragalactic Universe in the southern sky for the coming decade.

Ortles mountain (3905 m a.s.l.), South Tyrol, Italy, is the highest mountain of the Eastern European Alps, and its upper glacier, Alto dell’Ortles, presents a unique opportunity to obtain the first paleoenvironmental record from an ice core in this area. To study the suitability of this glacier as a drilling site, in 2009 we performed the first preliminary study of its glaciological characteristics at ˜3830 m a.s.l. The maximum thickness is ˜75 m, and lamination of the exposed ice layers is excellent down to bedrock. Firn and ice lenses were observed in a 10 m shallow core, and the firn/ice transition was below ˜24m. The seasonal chemical signal is clearly preserved only within the uppermost 2008 and 2009 snow/firn. A simple mass-balance model, the incipient ‘smoothing’ of the chemical record, and the observed ice lenses provide evidence that melting, infiltration and refreezing cycles occurred within the firn layers formed before 2008. Nevertheless, the mass balance of the upper part of Alto dell’Ortles was positive (˜800mma_1) during the last few years. We suggest that an environmental history is likely to be well preserved only within the ice layers formed before ˜1980, when summer air temperature was ˜2°C colder than today in this area. Clearly the continued warming trend predicted to occur over the next few decades, and the consequent increase in frequency and/or intensity of infiltration processes, will endanger the preservation of the glacial archive conserved in the deep ice layers of Ortles mountain.

The northern New England region includes the states of Vermont, New Hampshire, and Maine and encompasses a large degree of climate and edaphic variation across a relatively small spatial area, making it ideal for studying climate change impacts on agricultural weed communities. We sampled weed seedbanks and measured soil physical and chemical characteristics on 77 organic farms across the region and analyzed the relationships between weed community parameters and select geographic, climatic, and edaphic variables using multivariate procedures. Temperature-related variables (latitude, longitude, mean maximum and minimum temperature) were the strongest and most consistent correlates with weed seedbank composition. Edaphic variables were, for the most part, relatively weaker and inconsistent correlates with weed seedbanks. Our analyses also indicate that a number of agriculturally important weed species are associated with specific U.S. Department of Agriculture plant hardiness zones, implying that future changes in climate factors that result in geographic shifts in these zones will likely be accompanied by changes in the composition of weed communities and therefore new management challenges for farmers.