Recent research has shown the potential of speleothem δ13C to record a range of environmental processes. Here, we report on 230Th-dated stalagmite δ13C records for southwest Sulawesi, Indonesia, over the last 40,000 yr to investigate the relationship between tropical vegetation productivity and atmospheric methane concentrations. We demonstrate that the Sulawesi stalagmite δ13C record is driven by changes in vegetation productivity and soil respiration and explore the link between soil respiration and tropical methane emissions using HadCM3 and the Sheffield Dynamic Global Vegetation Model. The model indicates that changes in soil respiration are primarily driven by changes in temperature and CO2, in line with our interpretation of stalagmite δ13C. In turn, modelled methane emissions are driven by soil respiration, providing a mechanism that links methane to stalagmite δ13C. This relationship is particularly strong during the last glaciation, indicating a key role for the tropics in controlling atmospheric methane when emissions from high-latitude boreal wetlands were suppressed. With further investigation, the link between δ13C in stalagmites and tropical methane could provide a low-latitude proxy complementary to polar ice core records to improve our understanding of the glacial–interglacial methane budget.

The stratified inclined duct (SID) sustains an exchange flow in a long, gently sloping duct as a model for continuously forced density-stratified flows such as those found in estuaries. Experiments have shown that the emergence of interfacial waves and their transition to turbulence as the tilt angle is increased appears to be linked to a threshold in the exchange flow rate given by inviscid two-layer hydraulics. We uncover these hydraulic mechanisms by (i) using recent direct numerical simulations (DNS) providing full flow data in the key flow regimes (Zhu et al., J. Fluid Mech., vol. 969, 2023, A20), (ii) averaging these DNS into two layers, and (iii) using an inviscid two-layer shallow-water and instability theory to diagnose interfacial wave behaviour and provide physical insight. The laminar flow is subcritical and stable throughout the duct and hydraulically controlled at the ends of the duct. As the tilt is increased, the flow becomes supercritical everywhere and unstable to long waves. An internal jump featuring stationary waves first appears near the centre of the duct, then leads to larger-amplitude travelling waves, and to stronger jumps, wave breaking and intermittent turbulence at the largest tilt angle. Long waves described by the (nonlinear) shallow-water equation are interpreted locally as linear waves on a two-layer parallel base flow described by the Taylor–Goldstein equation. This link helps us to interpret long-wave instability and contrast it with short-wave (e.g. Kelvin–Helmholtz) instability. Our results suggest a transition to turbulence in SID through long-wave instability relying on vertical confinement by the top and bottom walls.

Vaccination against hepatitis B virus (HBV) is effective at preventing vertical transmission. Sierra Leone, Liberia, and Guinea are hyperendemic West African countries; yet, childhood vaccination coverage is suboptimal, and the determinants of incomplete vaccination are poorly understood. We analyzed national survey data (2018–2020) of children aged 4–35 months to assess complete HBV vaccination (receiving 3 doses of the pentavalent vaccine) and incomplete vaccination (receiving <3 doses). Statistical analysis was conducted using the complex sample command in SPSS (version 28). Multivariate logistic regression was used to identify determinants of incomplete immunization. Overall, 11,181 mothers were analyzed (4,846 from Sierra Leone, 2,788 from Liberia, and 3,547 from Guinea). Sierra Leone had the highest HBV childhood vaccination coverage (70.3%), followed by Liberia (64.6%) and Guinea (39.3%). Within countries, HBV vaccination coverage varied by socioeconomic characteristics and healthcare access. In multivariate regression analysis, factors that were significantly associated with incomplete vaccination in at least one country included sex of the child, Muslim mothers, lower household wealth index, <4 antenatal visits, home delivery, and distance to health facility vaccination (all p < 0.05). Understanding and addressing modifiable determinants of incomplete vaccination will be essential to help achieve the 2030 viral hepatitis elimination goals.

Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph–based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly “Question-of-the-Month (QotM) Challenge” series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and ATP1A3-related phenotypes; the scientific insights that have been gleaned during the challenges; and the technical issues that were identified over the course of the challenges and that can now be addressed to foster further development of the prototype Translator system. We close with a discussion on Large Language Models such as ChatGPT and highlight differences between those models and the Translator system.

The Australian SKA Pathfinder (ASKAP) radio telescope has carried out a survey of the entire Southern Sky at 887.5 MHz. The wide area, high angular resolution, and broad bandwidth provided by the low-band Rapid ASKAP Continuum Survey (RACS-low) allow the production of a next-generation rotation measure (RM) grid across the entire Southern Sky. Here we introduce this project as Spectral and Polarisation in Cutouts of Extragalactic sources from RACS (SPICE-RACS). In our first data release, we image 30 RACS-low fields in Stokes I, Q, U at 25$^{\prime\prime}$ angular resolution, across 744–1032 MHz with 1 MHz spectral resolution. Using a bespoke, highly parallelised, software pipeline we are able to rapidly process wide-area spectro-polarimetric ASKAP observations. Notably, we use ‘postage stamp’ cutouts to assess the polarisation properties of 105912 radio components detected in total intensity. We find that our Stokes Q and U images have an rms noise of $\sim$80 $\unicode{x03BC}$Jy PSF$^{-1}$, and our correction for instrumental polarisation leakage allows us to characterise components with $\gtrsim$1% polarisation fraction over most of the field of view. We produce a broadband polarised radio component catalogue that contains 5818 RM measurements over an area of $\sim$1300 deg$^{2}$ with an average error in RM of $1.6^{+1.1}_{-1.0}$ rad m$^{-2}$, and an average linear polarisation fraction $3.4^{+3.0}_{-1.6}$ %. We determine this subset of components using the conditions that the polarised signal-to-noise ratio is $>$8, the polarisation fraction is above our estimated polarised leakage, and the Stokes I spectrum has a reliable model. Our catalogue provides an areal density of $4\pm2$ RMs deg$^{-2}$; an increase of $\sim$4 times over the previous state-of-the-art (Taylor, Stil, Sunstrum 2009, ApJ, 702, 1230). Meaning that, having used just 3% of the RACS-low sky area, we have produced the 3rd largest RM catalogue to date. This catalogue has broad applications for studying astrophysical magnetic fields; notably revealing remarkable structure in the Galactic RM sky. We will explore this Galactic structure in a follow-up paper. We will also apply the techniques described here to produce an all-Southern-sky RM catalogue from RACS observations. Finally, we make our catalogue, spectra, images, and processing pipeline publicly available.

The stratified inclined duct (SID) experiment consists of a zero-net-volume exchange flow in a long tilted rectangular duct, which allows the study of realistic stratified shear flows with sustained internal forcing. We present the first three-dimensional direct numerical simulations (DNS) of SID to explore the transitions between increasingly turbulent flow regimes first described by Meyer & Linden (J. Fluid Mech., vol. 753, 2014, pp. 242–253). We develop a numerical set-up that faithfully reproduces the experiments and sustains the flow for arbitrarily long times at minimal computational cost. We recover the four qualitative flow regimes found experimentally in the same regions of parameter space: laminar flow, waves, intermittent turbulence and fully developed turbulence. We find good qualitative and quantitative agreement between DNS and experiments and highlight the added value of DNS to complement experimental diagnostics and increase our understanding of the transition to turbulence, both temporally (laminar/turbulent cycles) and parametrically (as the tilt angle of the duct and the Reynolds number are increased). These results demonstrate that numerical studies of SID – and deeper integration between simulations and experiments – have the potential to lead to a better understanding of stratified turbulence.

Background: Saccade and pupil responses are potential neurodegenerative disease biomarkers due to overlap between oculomotor circuitry and disease-affected areas. Instruction-based tasks have previously been examined as biomarker sources, but are arduous for patients with limited cognitive abilities; additionally, few studies have evaluated multiple neurodegenerative pathologies concurrently. Methods: The Ontario Neurodegenerative Disease Research Initiative recruited individuals with Alzheimer’s disease (AD), mild cognitive impairment (MCI), amyotrophic lateral sclerosis (ALS), frontotemporal dementia, progressive supranuclear palsy, or Parkinson’s disease (PD). Patients (n=274, age 40-86) and healthy controls (n=101, age 55-86) viewed 10 minutes of frequently changing video clips without instruction while their eyes were tracked. We evaluated differences in saccade and pupil parameters (e.g. saccade frequency and amplitude, pupil size, responses to clip changes) between groups. Results: Preliminary data indicates low-level behavioural alterations in multiple disease cohorts: increased centre bias, lower overall saccade rate and reduced saccade amplitude. After clip changes, patient groups generally demonstrated lower saccade rate but higher microsaccade rate following clip change to varying degrees. Additionally, pupil responses were blunted (AD, MCI, ALS) or exaggerated (PD). Conclusions: This task may generate behavioural biomarkers even in cognitively impaired populations. Future work should explore the possible effects of factors such as medication and disease stage.

Documenting the intentional structuring of space by hunter-gatherers can be challenging, especially in complex cave contexts. One approach is the spatial analysis of discard patterns. Here, the authors consider the spatial distribution of faunal remains from the Lower Magdalenian Level 115 in El Mirón Cave, Cantabria, to assess a possible structuring function for an unusual alignment of rocks. Although it is impossible to determine whether the alignment was intentionally constructed, differences in the distributions of taxa and in specimen sizes on different sides of this feature suggest that it played a role in structuring the living space of the cave's inhabitants.

The modern dairy industry involves close contact between the stockperson and their animals and thus complex relationships develop between stockperson and cow. This study examines the assessment of stockmanship quality on commercial dairy farms and aims to develop useable protocols for on-farm assessment of stockmanship for inclusion in a quality-assurance scheme. In this study the behaviour of cows was used to assess the quality of stockmanship on fifteen commercial dairy farms, which varied in level of production and intensification. The behavioural reactions of cows to a novel human and the behaviour of the stockperson before, during and after milking were scored, and stockpersons completed a fifty-question psychometric attitude questionnaire, which was made up of seven subgroups of questions. Preliminary results indicated that stockpersons differ in the behaviour they use when handling cows. Stockpersons on zero-grazing farms appeared to use fewer positive tactile behaviours and more severe negative behaviour. The behavioural responses of cows in a novel human approach test differed between farm types. Cows on straw-court farms appeared to be more flighty and less confident in the presence of a novel human. Differences were observed in mean attitude scores for the seven subgroups of questions. Job type appears to have an effect on the extent of the stockperson's positive attitude toward cows, animals in general, job satisfaction and farm economics. The results indicate that there are differences in quality of stockmanship between farms and that the three methods chosen do identify these. They show that the human-animal relationship is a potential source of fear for cows in dairy production and therefore can be used to identify poor stockmanship.

Previous research has shown that pre-parturient primiparous pigs (gilts) housed in behaviourally restrictive farrowing crates without straw redirect their nest-building behaviour to non-manipulable substrates such as the bars of the crate. These gilts also show elevated plasma adrenocorticotropic hormone (ACTH) and Cortisol levels, particularly around the peak of nest-building activity, when compared to gilts in larger pens that have been provided with a manipulable substrate (straw). It remains unclear whether these behavioural and physiological responses to crating result from the lack of a suitable nesting substrate or from the restricted space. This study investigated the effects of space (crate [C] versus pen [P] and straw (straw [S] versus no straw [NS]) using a 2 × 2 factorial design. Thirty-four gilts were implanted with an indwelling jugular catheter at around 12 days before parturition. They were moved to one of the four environments five days before parturition, and blood sampling and recording of behaviour were carried out during the pre-parturient period. Penned gilts (P), irrespective of straw availability, spent more time standing and walking and performed more total substrate-directed behaviour than crated (C) gilts. When straw was not available to penned gilts, a large proportion of their substrate-directed behaviour was redirected to the floor. Space also had an effect on ACTH and Cortisol levels across the entire pre-parturient phase, with C gilts having higher levels than P gilts irrespective of straw availability, but particularly so at the peak of nest-building activity. There was no effect of straw on ACTH or Cortisol levels. Overall, it appears that increased space, perhaps through allowing locomotion, increases substrate-directed behaviour of pre-parturient gilts. When space is available but straw is absent, pre-parturient gilts redirect their nest-building behaviour to the floor. The ability to express substrate-directed behaviour as a result of increased space is reflected in lower levels of indicators of physiological stress.

There is a trend toward increasing intensification in dairy farming in the United Kingdom. In particular, there is concern over systems in which cows are housed throughout the year, as the behavioural restriction implicit in these systems is associated with poor welfare in other species. The aim of this on-going project is to determine how this affects the behaviour and welfare of dairy cattle. A range of behavioural, physical and health measures are being used to assess cow welfare on about 40 commercial British dairy farms. Initially, five farm types were identified from analysis of returns from a farmer questionnaire. Milk production level and housing type were the principal factors explaining variation in farm type. The sample groups are: high-, mid- and low-production cubicle-housing units, mid-production straw-court units, and cubicle-housing high-production zero-grazing units. Observations will take place over three winter housing periods (2000/01 to 2002/03), with recording on each unit taking five days. Our main hypothesis is that the behavioural and physical responses of ‘at-risk’ younger cows provide a sensitive indication of farm-level ‘stress’. Cows are marked according to age, and the feed-face videotaped continuously to record feeding time and social interactions. Temporal organisation of behaviour will be analysed using fractal mathematics and qualitative assessment approaches used in a human interaction test. Cow cleanliness, condition score, response to a novel object and the incidences of lameness and leg injury are recorded, and building quality is assessed. Ultimately, multivariate methods will be used to test our underlying hypothesis and to assess effects of housing and production type on behaviour and welfare. This analysis may identify key objective measures of welfare for use in farm assurance schemes.

As part of a larger on-farm dairy cow welfare and behaviour project, data were collected from 22 commercial dairy farms over two winters (2000-2001 and 2001-2002). A further winter of farm sampling will complete the project (2002-2003), with five types of housing and production systems being assessed: high-, medium- and low-milk-production herds with cubicle housing, high-production herds with zero grazing and cubicle housing, and medium-production herds with straw courts. All cows in one early or mid-lactation group from each farm were observed. For the current analysis, locomotion, cleanliness and body condition were scored for the group, and an audit of building quality was carried out. Analysis of the available data shows that some aspects of building design affect the welfare of dairy cows. A positive correlation was found between mean body condition score of the cows and mean locomotion score (P = 0.047). Body condition score correlated negatively with the number of cows in the group (P = 0.049). Negative correlations were found between locomotion score and the ratio of cubicles to cows (P = 0.033) and between the size of cubicles and leg cleanliness (P = 0.012). Trends were also seen in the relationships between farm type and locomotion score (P = 0.048), production level and locomotion score (P = 0.074) and cow cleanliness and cubicle size (P = 0.061). These results indicate that the quality of the housing and the management system can affect cow welfare. These measures may be useful to include in on-farm welfare assessment schemes.

Increasing litter size has long been a goal of pig breeders and producers, and may have implications for pig (Sus scrofa domesticus) welfare. This paper reviews the scientific evidence on biological factors affecting sow and piglet welfare in relation to large litter size. It is concluded that, in a number of ways, large litter size is a risk factor for decreased animal welfare in pig production. Increased litter size is associated with increased piglet mortality, which is likely to be associated with significant negative animal welfare impacts. In surviving piglets, many of the causes of mortality can also occur in non-lethal forms that cause suffering. Intense teat competition may increase the likelihood that some piglets do not gain adequate access to milk, causing starvation in the short term and possibly long-term detriments to health. Also, increased litter size leads to more piglets with low birth weight which is associated with a variety of negative long-term effects. Finally, increased production pressure placed on sows bearing large litters may produce health and welfare concerns for the sow. However, possible biological approaches to mitigating health and welfare issues associated with large litters are being implemented. An important mitigation strategy is genetic selection encompassing traits that promote piglet survival, vitality and growth. Sow nutrition and the minimisation of stress during gestation could also contribute to improving outcomes in terms of piglet welfare. Awareness of the possible negative welfare consequences of large litter size in pigs should lead to further active measures being taken to mitigate the mentioned effects.

In many countries, including the UK, the majority of domestic sows are housed in farrowing crates during the farrowing and lactation periods. Such systems raise welfare problems due to the close confinement of the sow. Despite the fact that many alternative housing systems have been developed, no commercially viable/feasible option has emerged for large scale units. Current scientific and practical knowledge of farrowing systems were reviewed in this study to identify alternative systems, their welfare and production potential. The aim was to establish acceptable trade-offs between profit and welfare within alternative farrowing systems. Linear programming (LP) was used to examine possible trade-offs and to support the design of welfare-friendly yet commercially viable alternatives. The objective of the LP was to optimise the economic performance of conventional crates, simple pens and designed pens subject to both managerial and animal welfare constraints. Quantitative values for constraints were derived from the literature. The potential effects of each welfare component on productivity were assessed by a group of animal welfare scientists and used in the model. The modelled welfare components (inputs) were extra space, substrate and temperature. Results showed that, when using piglet survival rate in the LP based on data drawn from the literature and incorporating costs of extra inputs in the model, the crates obtained the highest annual net margin and the designed pens and the pens were in second and third place, respectively. The designed pens and the pens were able to improve their annual net margin once alternative reference points, following expert-derived production functions, were used to adjust piglet survival rates in response to extra space, extra substrate and modified pen heating. The non-crate systems then provided higher welfare and higher net margin for sows and piglets than crates, implying the possibility of a win-win situation.