bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of welfare from physiological and behavioural responses of New Zealand dairy cows exposed to cold and wet conditions
Authors: Webster JR , Stewart M , Rogers AR , Verkerk GA 
Published: January 2023

AbstractThere is a need to assess the welfare of dairy cows that live outdoors under cold and wet conditions. This study combined a number of techniques to measure stress and make an assessment of welfare in this situation. Two groups of ten non-pregnant, non-lactating Holstein Friesian cows were exposed to a week of wind and rain (WR) or housed indoors (I) with pre- and post-treatment weeks indoors in a cross-over design. Wind and rain consisted of continual air movement (7.1 kph) using fans, water sprinkling for 15 min (3.0 mm) per hour, a mean temperature of 3.4°C and wind chill of –0.3°C. Internal body temperature was recorded every ten min and behaviour for 16 h per day. Blood, faeces and infrared temperatures were sampled at 0800h each morning during treatment weeks, and three times per week during pre- and post-treatment weeks. All cows were challenged with 2 ml Leptoshield Vaccine (CSL Animal Health, Australia) subcutaneously after 3 days of cold exposure to test immune responses. During WR, cows spent a greater proportion of time standing and less time lying down and eating than during I. Infrared temperatures were lower during WR than I in both dorsal and orbital (eye) regions. There was a distinct diurnal pattern of internal body temperature which had a greater amplitude during WR than I resulting from both a lower minimum and a higher maximum. The time of the minimum was 40 min later for WR than I. The overall mean body temperature was 0.07°C higher in WR than I. There were greater increases in plasma and faecal cortisol during WR than I, respectively. Total T4 was higher during WR than I. Non-esterified fatty acid concentration was higher in the week following WR than I. Total white blood cell numbers were lower during WR than I. No treatment differences were found for creatine kinase or for tumour necrosis factor, heat shock protein 90, interleukin 6 or interferon gamma expression in response to vaccination. In conclusion, this study applied a suite of stress measures to dairy cows exposed to extreme cold and wet conditions. Together, these measures indicated activation of the stress axis, physiological and behavioural adaptations to cold and a reduction in welfare. A number of these measures could be used to assess welfare under cold conditions on farms.
Body condition score as an indicator of ewe survival under extensive conditions
Authors: Morgan-Davies C , Waterhouse A , Pollock ML , Milner JM 
Published: January 2023

AbstractSurvival and mortality of extensive hill ewes are important commercial factors and valuable indicators of welfare, but difficult to study. Body condition scoring is a tried-and-tested management and monitoring tool which has been defined as a good predictor of fitness in ewes and is easily measured under hill farm conditions. This paper presents the results of a study on ewe survival rates in hill conditions in Scotland. Ewe performance and survival rates were measured in two contrasting hill flocks over a five-year period. Statistical analysis showed that mid-pregnancy body condition score was the most reliable indicator of subsequent ewe survival, followed closely by age of the ewe and environmental and management conditions. This study confirms that there are considerable welfare issues related to hill flocks and that improved winter nutritional management is a key component to good welfare and productivity. It also reinforces the view that body condition score is a good quantitative predictor of animal welfare and that poor mid-winter score indicates high risk of mortality, both at the flock and individual ewe level.
Gas killing of rats: the effect of supplemental oxygen on aversion to carbon dioxide
Authors: Kirkden RD , Niel L , Stewart SA , Weary DM 
Published: January 2023

AbstractHigh concentrations of carbon dioxide (CO2), used for killing laboratory rodents, are known to be more strongly aversive to rats than sweet food items are attractive. This study investigated whether the maintenance of a high oxygen (O2) concentration, using a gas mixture of 70% CO2and 30% O2, would reduce aversion to CO2during a gradual-fill procedure. Eight male Wistar rats, aged 10 months, were housed individually in an apparatus consisting of two cages, one higher than the other and joined by a tube. In a series of trials, subjects entered the lower cage for a reward of 20 sweet food items. The gas was turned on at the moment the rat started eating the reward items and flowed into the lower cage at a fixed rate. There were four treatments: 1) 100% CO2at 14.5% cage volume min–1; 2) gas mixture at 14.5% min–1; 3) gas mixture at 21.0% min–1, which delivered CO2at approximately 14.5% min–1and 4) air, with each subject tested with each treatment four times. Measures of willingness to stay and eat in the lower cage (latency to stop eating, latency to leave and the number of reward items eaten) were much lower in all three gas treatments than in air, indicating that the CO2and the CO2+ O2mixture were both more strongly aversive than sweet food items were attractive. Comparing the gas mixture with 100% CO2, the latency to leave and the number of reward items eaten were slightly higher in the CO2+ O2mixture at 21% min–1than in CO2at 14.5% min–1, indicating that the addition of O2slightly reduced the aversiveness of CO2in the gradual-fill procedure. This reduction is not enough to warrant recommending the use of CO2+ O2mixtures for killing rats.
The effect of substrate availability on behavioural and physiological indicators of welfare in the African cichlid (Oreochromis mossambicus)
Authors: Galhardo L , Correia J , Oliveira RF 
Published: January 2023

AbstractMale African cichlids (Oreochromis mossambicus) establish territories on the substrate upon which spawning pits are dug, thus attracting females. The substrate, therefore, plays a very significant role in its lifecycle. The effects of substrate access on behaviour and physiology in captivity were assessed. Mixed-sex, all-male and all-female groups were observed for five days, with and without substrate. Social patterns, behaviour directed towards the substrate, locomotor activity and spatial behaviour were recorded, and haematocrit, plasma cortisol and glucose levels were measured. Substrate inclusion saw a significant increase in behavioural diversity, sexual behaviour of dominant males in mixed groups, pit digging and territoriality whereas a lack of substrate was characterised by increased chafing and inactivity. Vacuum-pit digging was also observed. Frequency of aggression did not differ significantly and female behaviour was not affected by the presence of substrate. For both sexes, no differences in cortisol and glucose levels were found between the two treatments, but haematocrit increased with substrate. The key role played by substrate in territorial males is consistent with the behavioural and physiological data reported. In the absence of substrate, decreased territorial behaviour is contrasted with similar levels of aggression, cortisol and glucose; all of which are suggestive of a stress-related context. Moreover, the exhibition of vacuum activities is a signal that behavioural needs are not being met and may be some form of coping mechanism. These findings, taken in conjunction with the variations in behavioural diversity and inactivity, suggest that the welfare of male cichlids may be adversely affected by the absence of substrate.
The reduction of stereotypic pacing in tigers (Panthera tigris) by obstructing the view of neighbouring individuals
Authors: Miller LJ , Bettinger T , Mellen J 
Published: January 2023

AbstractUntil recently, little attention has been focused on the influence of social interactions and the presence of conspecifics on stereotypic pacing in captive carnivores. This study examined the effect of adding a visual barrier between two tiger (Panthera tigris) exhibits on stereotypic pacing behaviour. Continuous sampling was used to record the duration of time tigers spent pacing and the total number of pacing bouts. The results show a significant decrease in stereotypic pacing for the group of six female tigers after obstruction of the view of neighbouring tigers. These results suggest that the opportunity for tigers to view conspecifics in other exhibits may influence time spent pacing therefore it is felt that the design or renovation of tiger exhibits should take the visibility of neighbouring individuals into account.
A review of welfare in cattle, sheep and pig lairages, with emphasis on stocking rates, ventilation and noise
Authors: Weeks CA 
Published: January 2023

AbstractAppropriate space allowances for animals are yet to be specifically determined for lairage. Space allowances that may be suitable for animals in lairage are suggested, based on reviewed studies of animals in transport, lairage and on farm. The longer animals are in lairage the more space they require, in order to be able to get up and lie down and lie undisturbed by congeners. Little work has been done on air quality and air flow characteristics in lairages. The range of ventilation must be sufficient to control levels of toxic or irritant gases such as carbon dioxide and ammonia and to remove excess heat and humidity; the latter being particularly relevant for pig lairages in hot weather. Intensities of sound measured in lairages often exceed 85 dB and there is evidence to suggest that such levels can be stressful especially for pigs; and human shouting appears particularly aversive to animals. Cattle vocalise in response to painful stimuli and to convey information to conspecifics that may be related to fear and distress. There is limited evidence that sheep adapt to continuous sound, provided it is not too loud, but respond to intermittent sounds such as gates banging and human shouting. Vocal communication between sheep may be less important than that between cattle and pigs. Levels of vocalisation are potential indices of animal welfare. Animals' prior experiences and factors such as sex, group size and constitution, pen design, and climatic or environmental conditions affect their welfare and responses to conditions in lairage.
Exploring heifers' perception of ‘positive’ treatment through their motivation to pursue a retreated human
Authors: Bertenshaw CE , Rowlinson P 
Published: January 2023

AbstractThis pilot study investigates dairy heifers' perception of ‘positive treatment’ by a human (stroking and brushing) through a test of appetitive motivation. The hypothesis was that positive treatment by a human results in heifers pursuing a human to seek further positive treatment. Thirty-seven dairy heifers were assigned to either minimal human contact or positive treatment during rearing for five minutes per week, for a total of four hours, between ages six to 24 months. Six months after treatment ceased, the heifers were tested in a suite of four sequential tests, conducted while free ranging in their home pen with a group of familiar conspecifics. The tests explored whether dairy heifers that received positive treatment had: 1) a lower flight distance than controls; 2) accepted initial positive treatment during the test; and (for those who voluntarily re-approached and interacted with the human after the human had retreated) whether this was due to 3) curiosity; or 4) motivation for further positive treatment. Positive treatment heifers had a lower flight distance in component 1 of the test and more of this group voluntarily approached the human compared to the control heifers. The positive treatment allowed more initial positive treatment (component 2) and sought further positive treatment in components 3 and 4. It is concluded that ‘positive’ treatment is rewarding for many heifers. It is suggested that positive treatment constitutes environmental enrichment of dairy cattle and can enhance cattle's quality of life and the human-animal relationship.
Exploiting SMILEs and the CMIP5 Archive to Understand Arctic Climate Change Seasonality and Uncertainty
Authors: Wu You‐Ting , Liang Yu‐Chiao , Kuo Yan‐Ning , Lehner Flavio , Previdi Michael , Polvani Lorenzo M. , Lo Min‐Hui , Lan Chia‐Wei 
Published: January 2023

AbstractArctic Amplification (AA) exhibits a distinct seasonal dependence; it is weakest in boreal summer and strongest in winter. Here, we analyze simulations from single‐model initial‐condition large ensembles and Coupled Model Intercomparison Project Phase 5 to decipher the seasonal evolution of Arctic climate change. Models agree that the annual maximum AA shifts from autumn into winter over the 21st century, accompanied by similar shifts in sea‐ice loss and surface turbulent heat fluxes, whereas the maximum precipitation shifts only into late autumn. However, the exact seasonal timing and magnitude of these shifts are highly uncertain. Decomposing the uncertainty into model structural differences, emission scenarios, and internal variability reveals that model differences dominate the total uncertainty, which also undergo autumn‐to‐winter shifts. We also find that the scenario uncertainty is unimportant for projections of AA. These results highlight that understanding model differences is critical to reducing uncertainty in projected Arctic climate change.
Assessing Controls on the Incomplete Draining of Martian Open‐Basin Lakes
Authors: Goudge Timothy A. , Fassett Caleb I. , Coholich Marianne , Bamber Emily R. 
Published: January 2023

AbstractOver 250 hydrologically open paleolakes, which filled with water before catastrophically breaching, have been identified on Mars. These open‐basin lakes are recognized by the topographic geometry of a closed contour below the elevation of the outlet, indicating that the lake was incompletely drained by the breach flood. Here, we explore factors that controlled how completely a given open‐basin lake on Mars drained using (a) observations of 24 open‐basin lakes on Mars and (b) numerical modeling experiments of lake breach flooding. Observational results suggest that the key parameters for promoting more complete draining in open‐basin lakes on Mars were steeper regional slopes and taller crater rims. From a suite of 303 numerical experiments, we find that more complete draining is accomplished with larger basins, steeper regional slopes, basins with steeper walls, taller crater rims, and a more erodible substrate (parameterized by grain size in our model). Outliers in the observational results suggest that complete draining was inhibited by the presence of another lake immediately downstream of the breach as well as a less erodible substrate relative to other basins. We observe no correlation between open‐basin lake area and drained fraction on Mars, contrary to the strong trend in our numerical experiments. We hypothesize that this is the result of increasing resistance to erosion with depth in the Martian crust, which is not incorporated into our model. Our results provide new insights into controls on the fluvial integration of the early Mars landscape as well as the spatially variable erodibility of the shallow Martian crust.
A Generalized Multistep Dynamic (GMD) TOPMODEL
Authors: Goudarzi Salim , Milledge David , Holden Joseph 
Published: January 2023

AbstractThere is a lack of Ordinary Differential Equation (ODE) formulations in numerical hydrology, contributing to the lack of application of canned adaptive timestep solvers; hence the continued dominance of fixed (e.g., Euler) timestep techniques despite their fundamental problems. In this paper, we reformulate Dynamic‐TOPMODEL into a constraint‐handling ODE form and use MATLAB's advanced adaptive ODE‐solvers to solve the resulting system of equations. For wider applicability, but based on existing research and/or first principles, we developed Generalized Multistep Dynamic TOPMODEL which includes: iso‐basin spatial discretization, diffusion wave routing, depth‐dependent overland flow velocity, relaxing the assumption of water‐table parallelism to the ground surface, a power‐law hydraulic conductivity profile, new unsaturated zone flux, and a reference frame adjustment. To demonstrate the model we calibrate it to a peat catchment case study, for which we also test sensitivity to spatial discretization. Our results suggest that (a) a five‐fold improvement in model runtime can result from adaptive timestepping; (b) the additional iso‐basin discretization layer, as a way to further constrain spatial information where needed, also improves performance; and (c) the common‐practice arbitrary Topographic Index (TI) discretization substantially alters calibrated parameters. More objective and physically constrained (e.g., top‐down) approaches to TI classification may be needed.
Nitrate Hysteresis as a Tool for Revealing Storm‐Event Dynamics and Improving Water Quality Model Performance
Authors: Husic Admin , Fox James F. , Clare Evan , Mahoney Tyler , Zarnaghsh Amirreza 
Published: January 2023

AbstractUnderstanding the physics of nitrate contamination in surface and subsurface water is vital for mitigating downstream water quality impairment. Though high frequency sensor data have become readily available and computational models more accessible, the integration of these two methods for improved prediction is underdeveloped. The objective of this study was to utilize high‐frequency data to advance our understanding and model representation of nitrate transport for an agricultural karst spring in Kentucky, USA. We collected 2‐years of 15‐min nitrate and specific conductance data and analyzed source‐timing dynamics across dozens of events to develop a conceptual model for nitrate hysteresis in karst. Thereafter, we used the sensing data, specifically discharge‐concentration indices, to constrain modeled nitrate prediction bounds as well as the uncertainty of hydrologic and nitrogen processes, such as soil percolation and biogeochemical transformation. Observed nitrate hysteresis behavior at the spring was complex and included clockwise (n = 11), counterclockwise (n = 13), and figure‐eight (n = 10) shapes, which contrasts with surface systems that are often dominated by a single hysteresis shape. Sensing results highlight the importance of antecedent connectivity to nitrate‐rich storages in determining the timing of nitrate delivery to the spring. After integrating hysteresis analysis into our numerical model evaluation, simulated nitrate prediction bounds were reduced by 43 ± 12% and parameter uncertainty by 36 ± 20%. Taken together, this study suggests that discharge‐concentration indices derived from high‐frequency sensor data can be successfully integrated into numerical models to improve process representation and reduce modeled uncertainty.
Discovery and replication of blood-based proteomic signature of PTSD in 9/11 responders
Authors: Waszczuk Monika A. , Kuan Pei-Fen , Yang Xiaohua , Miao Jiaju , Kotov Roman , Luft Benjamin J. 
Published: January 2023

AbstractProteomics provides an opportunity to develop biomarkers for the early detection and monitoring of post-traumatic stress disorder (PTSD). However, research to date has been limited by small sample sizes and a lack of replication. This study performed Olink Proseek Multiplex Platform profiling of 81 proteins involved in neurological processes in 936 responders to the 9/11 disaster (mean age at blood draw = 55.41 years (SD = 7.93), 94.1% white, all men). Bivariate correlations and elastic net regressions were used in a discovery subsample to identify concurrent associations between PTSD symptom severity and the profiled proteins, and to create a multiprotein composite score. In hold-out subsamples, nine bivariate associations between PTSD symptoms and differentially expressed proteins were replicated: SKR3, NCAN, BCAN, MSR1, PVR, TNFRSF21, DRAXIN, CLM6, and SCARB2 (|r| = 0.08–0.17, p < 0.05). There were three replicated bivariate associations between lifetime PTSD diagnosis and differentially expressed proteins: SKR3, SIGLEC, and CPM (OR = 1.38–1.50, p < 0.05). The multiprotein composite score retained 38 proteins, including 10/11 proteins that replicated in bivariate tests. The composite score was significantly associated with PTSD symptom severity (β = 0.27, p < 0.001) and PTSD diagnosis (OR = 1.60, 95% CI: 1.17–2.19, p = 0.003) in the hold-out subsample. Overall, these findings suggest that PTSD is characterized by altered expression of several proteins implicated in neurological processes. Replicated associations with TNFRSF21, CLM6, and PVR support the neuroinflammatory signature of PTSD. The multiprotein composite score substantially increased associations with PTSD symptom severity over individual proteins. If generalizable to other populations, the current findings may inform the development of PTSD biomarkers.
Community Genetics screening in a pandemic: solutions for pre-test education, informed consent, and specimen collection
Authors: Terrill Bronwyn , McKnight Lauren , Pearce Angela , Gordon Heather , Lo William , Lee I-Chieh Jennifer , Runiewicz Monica , Palmer Alex , Andrews Lesley , Kirk Edwin , Goldberg Daniel , Tucker John , Murray David , Kaplan Warren , Kummerfeld Sarah , Burnett Leslie 
Published: January 2023

AbstractA Community Genetics carrier screening program for the Jewish community has operated on-site in high schools in Sydney (Australia) for 25 years. During 2020, in response to the COVID-19 pandemic, government-mandated social-distancing, ‘lock-down’ public health orders, and laboratory supply-chain shortages prevented the usual operation and delivery of the annual testing program. We describe development of three responses to overcome these challenges: (1) pivoting to online education sufficient to ensure informed consent for both genetic and genomic testing; (2) development of contactless telehealth with remote training and supervision for collecting genetic samples using buccal swabs; and (3) a novel patient and specimen identification ‘GeneTrustee’ protocol enabling fully identified clinical-grade specimens to be collected and DNA extracted by a research laboratory while maintaining full participant confidentiality and privacy. These telehealth strategies for education, consent, specimen collection and sample processing enabled uninterrupted delivery and operation of complex genetic testing and screening programs even amid pandemic restrictions. These tools remain available for future operation and can be adapted to other programs.
Migration direction in a songbird explained by two loci
Authors: Sokolovskis Kristaps , Lundberg Max , Åkesson Susanne , Willemoes Mikkel , Zhao Tianhao , Caballero-Lopez Violeta , Bensch Staffan 
Published: January 2023

AbstractMigratory routes and remote wintering quarters in birds are often species and even population specific. It has been known for decades that songbirds mainly migrate solitarily, and that the migration direction is genetically controlled. Yet, the underlying genetic mechanisms remain unknown. To investigate the genetic basis of migration direction, we track genotyped willow warblers Phylloscopus trochilus from a migratory divide in Sweden, where South-West migrating, and South-East migrating subspecies form a hybrid swarm. We find evidence that migration direction follows a dominant inheritance pattern with epistatic interaction between two loci explaining 74% of variation. Consequently, most hybrids migrate similarly to one of the parental subspecies, and therefore do not suffer from the cost of following an inferior, intermediate route. This has significant implications for understanding the selection processes that maintain narrow migratory divides.