triact package for R: analyzing the lying behavior of cows from accelerometer data.

Accelerometers are sensors proven to be useful to analyze the lying behavior of cows. For reasons of algorithm transparency and control, researchers often prefer to use their own data analysis scripts rather than proprietary software. We developed the triact R package that assists animal scientists in analyzing the lying behavior of cows from raw data recorded with a triaxial accelerometer (manufacturer agnostic) attached to a hind leg. In a user-friendly workflow, triact allows the determination of common measures for lying behavior including total lying duration, the number of lying bouts, and the mean duration of lying bouts. Further capabilities are the description of lying laterality and the calculation of proxies for the level of physical activity of the cow. In this publication we describe the functionality of triact and the rationales behind the implemented algorithms. The triact R package is developed as an open-source project and freely available via the CRAN repository.

Risk factors differ for viable and low viable crushed piglets in free farrowing pens.

Newborn piglets have a high risk of being crushed by the sow, and this risk implies welfare and economic consequences. The aim of this study was to investigate the importance of differentiating between low viable (secondary crushing losses) and viable crushed (primary crushing losses) piglets for the evaluation of risk factors for crushing related to characteristics of the sow, the litter, and the environment. Eleven Swiss farmers recorded sows' production data (parity class, gestation length, numbers of live-born and stillborn piglets), data (age, sex, weight, cause of death, and signs of weakness) for every live-born piglet that died in the first week after birth (piglet loss), and ambient temperature. Piglet losses were assigned to five categorical events: piglet loss, subdivided into not crushed and crushed, the latter being further subdivided into low viable crushed and viable crushed. Piglets recorded by the farmer as crushed were assigned to the events low viable crushed and viable crushed based on the piglet's body weight and signs of weakness (diseases, malformations). Data of 9,543 live-born piglets from 740 litters were eventually used to statistically model the hazard of dying at any given time in the first week after birth due to one of these events (mixed-effects Cox model). Five potential risk factors were analyzed as co-variates: parity class, gestation length, number of live-born piglets, number of stillborn piglets, and daily number of hours with ambient temperature >30°C. We identified two risk factors for dying from the event viable crushed that were not identified as risk factors for low viable crushed, namely shorter gestation length and higher daily number of hours with ambient temperature > 30°C. Vice-versa, we identified additional live-born piglets in the litter as risk factor for low viable crushed, but not for viable crushed. Our results show the importance of differentiating between low viable and viable crushed piglets for the interpretation of risk factors for crushing losses. Therefore, we suggest that for breeding purposes and in research, this differentiation should be made.

Dairy sheep and goats prefer the single components over the mixed ration.

Mixed rations provide ruminants with a balanced diet by aiming to prevent selective feeding. However, this is a natural behavior of sheep and goats based on their dietary needs and the nutritional properties of feedstuffs. Therefore, the present study investigates non-lactating dairy sheep's and goats' acceptance of a mixed ration when it is offered as choice next to its single components. Because all offered feeds were of comparable nutritional value, the animals were expected to not show a particular preference. Twelve pairs of sheep and goats each, were offered three different feeds simultaneously for 5 replicate days. Two feeds consisted of a single component, hay (H) or grass-silage (G) of similar nutritional value. The third feed was a mixed ration (M) including both single-feed components in a 50:50 dry matter (DM) ratio. Feeds were offered ad libitum twice daily. The animals' intake of each feed was recorded at six time points per day by weighing the leftovers. Feed preference was expressed as the natural logarithm of the ratio of the intake of the single component to the intake of M and analyzed using linear mixed-effects models. Additionally, the animals' first choices after gaining access to the feeds were recorded at each weighing event and analyzed using an item response tree generalized mixed-effects model. The sheep's average daily DM intake was 59 (±11)% G, 26 (±10)% H, and 15 (±10)% M (mean ± standard deviation). Goats consumed an average of 56 (±13)% G, 37 (±12)% H, and 7 (±6)% M daily. Both species preferred the single components to M in all observation periods. The proportions of the three feeds consumed differed throughout the day and between species. For both species, the estimated probability that an animal chooses a single component over M first was over 94% at all time points. These results show that, contrary to our expectations, non-lactating dairy sheep and goats prefer single components over a mixed ration of the same components and similar nutritional value. This might be caused by the animals seeking to diversify their feed throughout the day independent of apparent nutritional values and/or because sensory properties of the single components, indicating palatability, are relevantly reduced by mixing.

Responsiveness of domesticated goats towards various stressors following long-term cognitive test exposure.

Current evidence suggests that frequent exposure to situations in which captive animals can solve cognitive tasks may have positive effects on stress responsiveness and thus on welfare. However, confounding factors often hamper the interpretation of study results. In this study, we used human-presented object-choice tests (in form of visual discrimination and reversal learning tests and a cognitive test battery), to assess the effect of long-term cognitive stimulation (44 sessions over 4-5 months) on behavioural and cardiac responses of female domestic goats in subsequent stress tests. To disentangle whether cognitive stimulation per se or the reward associated with the human-animal interaction required for testing was affecting the stress responsiveness, we conditioned three treatment groups: goats that were isolated for participation in human-presented cognitive tests and rewarded with food ('Cognitive', COG treatment), goats that were isolated as for the test exposure and rewarded with food by the experimenter without being administered the object-choice tests ('Positive', POS treatment), and goats that were isolated in the same test room but neither received a reward nor were administered the tests ('Isolation', ISO treatment). All treatment groups were subsequently tested in four stress tests: a novel arena test, a novel object test, a novel human test, and a weighing test in which goats had to enter and exit a scale cage. All treatment groups weretested at the same two research sites, each using two selection lines, namely dwarf goats, not selected for production traits, and dairy goats, selected for high productivity. Analysing the data with principal component analysis and linear mixed-effects models, we did not find evidence that cognitive testing per se (COG-POS contrast) reduces stress responsiveness of goats in subsequent stress tests. However, for dwarf goats but not for dairy goats, we found support for an effect of reward-associated human-animal interactions (POS-ISO contrast) at least for some stress test measures. Our results highlight the need to consider ontogenetic and genetic variation when assessing stress responsiveness and when interacting with goats.

Reductive solubilization of arsenic in a mining-impacted river floodplain: Influence of soil properties and temperature.

Mining activities have contaminated many riverine floodplains with arsenic (As). When floodplain soils become anoxic under water-saturated conditions, As can be released from the solid phase. Several microbially-driven As solubilization processes and numerous influential factors were recognized in the past. However, the interplay and relative importance of soil properties and the influence of environmental factors such as temperature remain poorly understood, especially considering the (co)variation of soil properties in a floodplain. We conducted anoxic microcosm experiments at 10, 17.5, and 25 °C using 65 representative soils from the mining-impacted Ogosta River floodplain in Bulgaria. To investigate the processes of As solubilization and its quantitative variation we followed the As and Fe redox dynamics in the solid and the dissolved phase and monitored a range of other solution parameters including pH, Eh, dissolved organic C, and dissolved Mn. We related soil properties to dissolved As observed after 20 days of microcosm incubation to identify key soil properties for As solubilization. Our results evidenced reductive dissolution of As-bearing Fe(III)-oxyhydroxides as the main cause for high solubilization. The availability of nutrients, most likely organic C as the source of energy for microorganisms, was found to limit this process. Following the vertical nutrient gradient common in vegetated soil, we observed several hundred µM dissolved As after 1-2 weeks for some topsoils (0-20 cm), while for subsoils (20-40 cm) with comparable total As levels only minor solubilization was observed. While high Mn contents were found to inhibit As solubilization, the opposite applied for higher temperature (Q10 2.3-6.1 for range 10-25 °C). Our results suggest that flooding of nutrient-rich surface layers might be more problematic than water-saturation of nutrient-poor subsoil layers, especially in summer floodings when soil temperature is higher than in winter or spring.

Soil-to-plant transfer of arsenic and phosphorus along a contamination gradient in the mining-impacted Ogosta River floodplain.

Riverine floodplains downstream of active or former metal sulfide mines are in many cases contaminated with trace metals and metalloids, including arsenic (As). Since decontamination of such floodplains on a large scale is unfeasible, management of contaminated land must focus on providing land use guidelines or even restrictions. This should be based on knowledge about how contaminants enter the food chain. For As, uptake by plants may be an important pathway, but the As soil-to-plant transfer under field conditions is poorly understood. Here, we investigated the soil-to-shoot transfer of As and phosphorus (P) in wild populations of herbaceous species growing along an As contamination gradient across an extensive pasture in the mining-impacted Ogosta River floodplain. The As concentrations in the shoots of Trifolium repens and Holcus lanatus reflected the soil contamination gradient. However, the soil-to-shoot transfer factors (TF) were fairly low, with values mostly below 0.07 (TF=Asshoot/Assoil). We found no evidence for interference of As with P uptake by plants, despite extremely high molar As:P ratios (up to 2.6) in Olsen soil extracts of the most contaminated topsoils (0-20cm). Considering the restricted soil-to-shoot transfer, we estimated that for grazing livestock As intake via soil ingestion is likely more important than intake via pasture herbage.

Cadmium concentrations in new zealand pastures: relationships to soil and climate variables.

Cadmium (Cd) is a nonessential element that occurs at above-background concentrations in many New Zealand (NZ) soils. Most of this Cd is due to the historical application of single superphosphate that was made from Nauru phosphate rock containing between 400 and 600 mg Cd kg P. Pasture Cd uptake exacerbates the entry of Cd into animal products. We sought to determine the critical environmental factors affecting Cd uptake in NZ pastures and to calculate the likely Cd intake of sheep and cattle. We tested 69 pastures throughout NZ for a range of variables, including Cd. Soil Cd and pasture Cd were positively correlated with soil P and soil concentrations of other elements found in phosphate fertilizers. We found that no single environmental variable adequately predicted pasture Cd uptake. Nevertheless, pseudo-total soil Cd and Cd extracted using a 0.05 mol L Ca(NO) solution were positively correlated with pasture Cd. Although soil pH, soil Fe, and soil Cd provided an excellent predictor of the Ca(NO)-extractable soil Cd fraction, regression models explained just 38% of the variation of the Cd concentration in pasture grasses. Incorporating the effect of pasture species composition is a crucial next step in improving these models. A calculation of the likely exposure to Cd of sheep and cattle revealed that no pastures tested resulted in sheep and cattle ingesting Cd at a rate that would result in breaching muscle-tissue food standards. For offal products, which the NZ meat industry does not sell for human consumption, food safety standards exceedence was calculated in a few cases.

Lignite reduces the solubility and plant uptake of cadmium in pasturelands.

Repeated application of Cd-rich phosphate fertilizers can lead to the accumulation of this nonessential element in soil. This can result in increased plant uptake, with possible breaches of food or feed safety standards. We aimed to determine whether lignite (brown coal) can reduce Cd solubility and plant uptake in New Zealand pasture soils. In batch sorption experiments, we tested the capacity of lignite and lignite-soil mixtures to sorb Cd at various soil pH and Cd loadings. Over a pH range of 4-7, Cd sorption by lignite was 1-2 orders of magnitude greater than by a typic immature pallic soil containing 2% carbon. The addition of 5 wt % lignite to a range of soils revealed that lignite addition was most effective in reducing soluble Cd in soils with low pH. In a greenhouse experiment, we tested the effect of lignite on the accumulation of Cd and other elements by perennial ryegrass, Lolium perenne (L.). The addition of just 1 wt % lignite to the aforementioned soil reduced plant Cd uptake by 30%, without adversely affecting biomass or the uptake of essential nutrient elements including copper and zinc. This may be due to preferential binding of Cd to organic sulfur in lignite.