We present a detailed overview of the cosmological surveys that we aim to carry out with Phase 1 of the Square Kilometre Array (SKA1) and the science that they will enable. We highlight three main surveys: a medium-deep continuum weak lensing and low-redshift spectroscopic HI galaxy survey over 5 000 deg2; a wide and deep continuum galaxy and HI intensity mapping (IM) survey over 20 000 deg2 from $z = 0.35$ to 3; and a deep, high-redshift HI IM survey over 100 deg2 from $z = 3$ to 6. Taken together, these surveys will achieve an array of important scientific goals: measuring the equation of state of dark energy out to $z \sim 3$ with percent-level precision measurements of the cosmic expansion rate; constraining possible deviations from General Relativity on cosmological scales by measuring the growth rate of structure through multiple independent methods; mapping the structure of the Universe on the largest accessible scales, thus constraining fundamental properties such as isotropy, homogeneity, and non-Gaussianity; and measuring the HI density and bias out to $z = 6$ . These surveys will also provide highly complementary clustering and weak lensing measurements that have independent systematic uncertainties to those of optical and near-infrared (NIR) surveys like Euclid, LSST, and WFIRST leading to a multitude of synergies that can improve constraints significantly beyond what optical or radio surveys can achieve on their own. This document, the 2018 Red Book, provides reference technical specifications, cosmological parameter forecasts, and an overview of relevant systematic effects for the three key surveys and will be regularly updated by the Cosmology Science Working Group in the run up to start of operations and the Key Science Programme of SKA1.

The Square Kilometre Array (SKA) is a planned large radio interferometer designed to operate over a wide range of frequencies, and with an order of magnitude greater sensitivity and survey speed than any current radio telescope. The SKA will address many important topics in astronomy, ranging from planet formation to distant galaxies. However, in this work, we consider the perspective of the SKA as a facility for studying physics. We review four areas in which the SKA is expected to make major contributions to our understanding of fundamental physics: cosmic dawn and reionisation; gravity and gravitational radiation; cosmology and dark energy; and dark matter and astroparticle physics. These discussions demonstrate that the SKA will be a spectacular physics machine, which will provide many new breakthroughs and novel insights on matter, energy, and spacetime.

Whole-grain cereal breakfast consumption has been associated with beneficial effects on glucose and insulin metabolism as well as satiety. Pearl millet is a popular ancient grain variety that can be grown in hot, dry regions. However, little is known about its health effects. The present study investigated the effect of a pearl millet porridge (PMP) compared with a well-known Scottish oats porridge (SOP) on glycaemic, gastrointestinal, hormonal and appetitive responses. In a randomised, two-way crossover trial, twenty-six healthy participants consumed two isoenergetic/isovolumetric PMP or SOP breakfast meals, served with a drink of water. Blood samples for glucose, insulin, glucagon-like peptide 1, glucose-dependent insulinotropic polypeptide (GIP), peptide YY, gastric volumes and appetite ratings were collected 2 h postprandially, followed by an ad libitum meal and food intake records for the remainder of the day. The incremental AUC (iAUC2h) for blood glucose was not significantly different between the porridges (P > 0·05). The iAUC2h for gastric volume was larger for PMP compared with SOP (P = 0·045). The iAUC2h for GIP concentration was significantly lower for PMP compared with SOP (P = 0·001). Other hormones and appetite responses were similar between meals. In conclusion, the present study reports, for the first time, data on glycaemic and physiological responses to a pearl millet breakfast, showing that this ancient grain could represent a sustainable alternative with health-promoting characteristics comparable with oats. GIP is an incretin hormone linked to TAG absorption in adipose tissue; therefore, the lower GIP response for PMP may be an added health benefit.

Low atmospheric pressure stunning (LAPS) is a novel approach to pre-slaughter stunning of chickens using progressive hypobaric hypoxia by the application of gradual decompression (280s cycle) according to a set of prescribed pressure curves. Low atmospheric pressure stunning produces a non-recovery state. Concerns have been raised relating to the possible pathological and welfare consequences of expansion of air in the body during LAPS. In a randomised trial, we compared the gross pathology of broilers exposed to LAPS with a control group euthanised by intravenous injection of pentobarbital sodium (60 mixed sex broilers per treatment). The birds were exposed to each treatment in triplets and all birds were subject to necropsy examination to detect and score (1 to 5, minimal to severe) haemorrhagic lesions or congestion for all major organs and cavities (e.g. air sacs, joints, ears and heart) as well as external assessment for product quality (e.g. wing tips). Behavioural data (latency to loss of posture and motionless) and chamber cycle data (temperature, humidity, pressure and oxygen availability) confirmed that LAPS had been applied in a manner representative of the commercial process. All of the organs observed were structurally intact for both treatment groups. No lesions were observed in the external ears, oral cavity, tracheal lumen, crop and air sacs of birds from either treatment group. There was no difference between treatments in the wingtips, nasal turbinates, thymus, biceps femoralis and colon. Haemorrhagic lesions were observed in the calvaria, brains, hearts and lungs of both treatment groups, but lesions in these areas were more severe in the LAPS treatment group. It was not possible to distinguish between pathological changes induced by decompression or recompression. In the barbiturate group, more severe haemorrhagic lesions were observed in the superficial pectoral muscles as well as greater congestion of the infraorbital sinuses, liver, spleens, duodenum, kidneys and gonads. These findings provide evidence that LAPS did not result in distension of the intestines and air sacs sufficient to cause changes, which were grossly visible on postmortem examination. There was also no evidence of barotrauma in the ears and sinuses. The pathological changes observed in the barbiturate treatment were as expected based on barbiturate toxicity. Low atmospheric pressure stunning appears to produce pathological changes by a variety of well-established mechanisms, and while these pathological data have limited value as welfare indicators, the results confirm that organ integrity was not compromised by the process.

The discovery of the first electromagnetic counterpart to a gravitational wave signal has generated follow-up observations by over 50 facilities world-wide, ushering in the new era of multi-messenger astronomy. In this paper, we present follow-up observations of the gravitational wave event GW170817 and its electromagnetic counterpart SSS17a/DLT17ck (IAU label AT2017gfo) by 14 Australian telescopes and partner observatories as part of Australian-based and Australian-led research programs. We report early- to late-time multi-wavelength observations, including optical imaging and spectroscopy, mid-infrared imaging, radio imaging, and searches for fast radio bursts. Our optical spectra reveal that the transient source emission cooled from approximately 6 400 K to 2 100 K over a 7-d period and produced no significant optical emission lines. The spectral profiles, cooling rate, and photometric light curves are consistent with the expected outburst and subsequent processes of a binary neutron star merger. Star formation in the host galaxy probably ceased at least a Gyr ago, although there is evidence for a galaxy merger. Binary pulsars with short (100 Myr) decay times are therefore unlikely progenitors, but pulsars like PSR B1534+12 with its 2.7 Gyr coalescence time could produce such a merger. The displacement (~2.2 kpc) of the binary star system from the centre of the main galaxy is not unusual for stars in the host galaxy or stars originating in the merging galaxy, and therefore any constraints on the kick velocity imparted to the progenitor are poor.

Next generation radio experiments such as LOFAR, HERA and SKA are expected to probe the Epoch of Reionization and claim a first direct detection of the cosmic 21cm signal within the next decade. One of the major challenges for these experiments will be dealing with enormous incoming data volumes. Machine learning is key to increasing our data analysis efficiency. We consider the use of an artificial neural network to emulate 21cmFAST simulations and use it in a Bayesian parameter inference study. We then compare the network predictions to a direct evaluation of the EoR simulations and analyse the dependence of the results on the training set size. We find that the use of a training set of size 100 samples can recover the error contours of a full scale MCMC analysis which evaluates the model at each step.

The ability to quickly detect transient sources in optical images and trigger multi-wavelength follow up is key for the discovery of fast transients. These include events rare and difficult to detect such as kilonovae, supernova shock breakout, and ‘orphan’ Gamma-ray Burst afterglows. We present the Mary pipeline, a (mostly) automated tool to discover transients during high-cadenced observations with the Dark Energy Camera at Cerro Tololo Inter-American Observatory (CTIO). The observations are part of the ‘Deeper Wider Faster’ programme, a multi-facility, multi-wavelength programme designed to discover fast transients, including counterparts to Fast Radio Bursts and gravitational waves. Our tests of the Mary pipeline on Dark Energy Camera images return a false positive rate of ~2.2% and a missed fraction of ~3.4% obtained in less than 2 min, which proves the pipeline to be suitable for rapid and high-quality transient searches. The pipeline can be adapted to search for transients in data obtained with imagers other than Dark Energy Camera.

By applying a display ecology to the Deeper, Wider, Faster proactive, simultaneous telescope observing campaign, we have shown a dramatic reduction in the time taken to inspect DECam CCD images for potential transient candidates and to produce time-critical triggers to standby telescopes. We also show how facilitating rapid corroboration of potential candidates and the exclusion of non-candidates improves the accuracy of detection; and establish that a practical and enjoyable workspace can improve the experience of an otherwise taxing task for astronomers. We provide a critical road test of two advanced displays in a research context—a rare opportunity to demonstrate how they can be used rather than simply discuss how they might be used to accelerate discovery.

Between 2005 and 2007, E. coli obtained from clinical diagnostic submissions from cattle, goats, pigs and sheep to government laboratories in England and Wales were tested for sensitivity to 16 antimicrobials. Resistance was most commonly observed against ampicillin, streptomycin, sulphonamides and tetracyclines. Resistance levels varied significantly between species, with isolates from cattle frequently showing the highest levels. Verocytotoxigenic E. coli (VTEC) expressed less resistance than non-VTEC. Only 19·3% of non-VTEC and 43·5% of VTEC were susceptible to all antimicrobials, while 47·1% and 30·4%, respectively, were resistant to ⩾5 antimicrobials. The resistance phenotype SSuT was commonly observed, and isolates resistant to third-generation cephalosporins were also identified. We recommend judicious antimicrobial usage in the livestock industry in order to preserve efficacy.

We discuss a selection of semi-numerical simulations of reionization whose analysis investigates the effect of small absorbing systems, neutral hydrogen within galaxies and the efficiency with which galaxies produce X-rays. We focus on the consequences for both observing the 21–cm 1-point statistics and their interpretation.

We provide a high-resolution map of elevation change rates at the Juneau Icefield (JIF), southeastern Alaska, in order to quantify its contribution to sea-level rise between 2000 and 2009/2013. We also produce the first high-resolution map of ice speeds at the JIF, which we use to constrain flux and look for acceleration. We calculate using stacked digital elevation models (DEMs) from the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instrument and the Shuttle Radar Topography Mission (SRTM), taking into account SRTM C-band penetration via comparison with SRTM X-band elevations. Overall, the JIF is losing mass less rapidly (0.13 ± 0.12 m w.e. a–1) than other Alaskan icefields (0.79 m w.e. a–1). We determine glacier speeds using pixel-tracking on optical image pairs acquired from 2001 to 2010 by ASTER, from radar image pairs acquired between 2007 and 2011 and from radar interferometry in 1995. We detect seasonal speed variations but no interannual acceleration, ruling out dynamics as the cause of the observed thinning. Thinning must therefore be due to the documented warming in the region. Flux measurements confirm this for Mendenhall Glacier, showing that calving constitutes only 2.5–5% of mass loss there.

Local people's involvement in the management of conservation initiatives is central to ongoing debates on the relative merits of distinct biodiversity conservation models. Since different governance models provide distinct opportunities for local people to participate in the management of protected areas, their knowledge of these governance models and motivation to collaborate will vary. This paper analyses cognisance and participation in (1) government-imposed biosphere reserves and (2) community conservation areas, in which ecotourism projects take place. Qualitative and quantitative data (n = 205) were gathered in two indigenous communities in Yucatan Peninsula, Mexico. Whereas local cognisance of community-driven conservation initiatives is not always greater than cognisance of government-imposed Biosphere Reserves, local participation is always greater. Cognisance of and participation in conservation initiatives depend on the management approach, extent of external resource support, and a community's social organization. Gender and land holding status influence access to information about conservation initiatives, since men with land rights had more access than other people. More participatory mechanisms for decision-making and direct communication strategies between managers and local people are required to improve communities’ involvement in conservation.

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

Ice streams provide major drainage pathways for the Antarctic ice sheet. The stress distribution and style of flow in such ice streams produce elastic and rheological anisotropy, which informs ice-flow modelling as to how ice masses respond to external changes such as global warming. Here we analyse elastic anisotropy in Rutford Ice Stream, West Antarctica, using observations of shear-wave splitting from three-component icequake seismograms to characterize ice deformation via crystal-preferred orientation. Over 110 high-quality measurements are made on 41 events recorded at five stations deployed temporarily near the ice-stream grounding line. To the best of our knowledge, this is the first well-documented observation of shear-wave splitting from Antarctic icequakes. The magnitude of the splitting ranges from 2 to 80 ms and suggests a maximum of 6% shear-wave splitting. The fast shear-wave polarization direction is roughly perpendicular to ice-flow direction. We consider three mechanisms for ice anisotropy: a cluster model (vertical transversely isotropic (VTI) model); a girdle model (horizontal transversely isotropic (HTI) model); and crack-induced anisotropy (HTI model). Based on the data, we can rule out a VTI mechanism as the sole cause of anisotropy – an HTI component is needed, which may be due to ice crystal a-axis alignment in the direction of flow or the alignment of cracks or ice films in the plane perpendicular to the flow direction. The results suggest a combination of mechanisms may be at play, which represent vertical variations in the symmetry of ice crystal anisotropy in an ice stream, as predicted by ice fabric models.

In situ conservation is central to contemporary global biodiversity protection and is the predominant emphasis of international regulation and funding strategies. Ex situ approaches, in contrast, have been relegated to a subsidiary role and their direct contributions to conservation have been limited. We draw on a variety of sources to make the case for an enhanced role for ex situ conservation. We note the advances occurring within institutions specializing in ex situ conservation and stress that, although much remains to be done, many constraints are being addressed. We argue that the evidence of increasing extinction rates, exacerbated by climate change, challenges the wisdom of a heavy dependence on in situ strategies and necessitates increased development of ex situ approaches. A number of different techniques that enable species and their habitats to survive should now be explored. These could build on the experience of management systems that have already demonstrated the effective integration of in situ and ex situ techniques and hybrid approaches. For organizations specializing in ex situ conservation to become more effective, however, they will require tangible support from the institutions of global biodiversity governance. Resistance is anticipated because in situ conservation is entrenched through powerful groups and organizations that exert influence on global conservation policy and facilitate the flow of funding. The chasm that has traditionally divided in situ and ex situ approaches may diminish as approaches are combined. Moreover, the relentless loss of the ‘wild’ may soon render the in situ / ex situ distinction misleading, or even obsolete.

Renal cell carcinoma is an important clinical disease with poorly understood etiology. ELF5 is an epithelial-specific member of the Ets family of transcription factors, characterized by the 80 amino acid Ets domain that binds the purine-rich GGAA/T Ets motif found in the promoter regions of a variety of genes. Since ELF5 is highly expressed in kidney and has been postulated to function as a tumor suppressor, at least in the context of the breast, we investigated its role in kidney cancer. In renal cell carcinoma ELF5 expression was consistently decreased in tumor samples versus normal. ELF5 mRNA was decreased in 94% of lesions tested and ELF5 protein was undetectable in 40/40 kidney-derived carcinomas. Re-expression of the ELF5 gene in 786-O renal carcinoma cells suppressed their tumorigenic capacity in vitro and in vivo. This work is the first to suggest that ELF5 has tumor suppressor activity in the kidney.