Do agonistic behaviours bias baited remote underwater video surveys of fish?

Marine environments require monitoring to determine the effects of impacts such as climate change, coastal development and pollution and also to assess the effectiveness of conservation measures. Marine protected areas (MPAs) are being established globally and require periodic monitoring to determine whether their objectives are being met. Baited underwater video systems are becoming a popular method for monitoring change within protected fish populations, because they are less damaging to habitats than bottom trawling and allow for more statistical powerful comparisons to determine spatial and temporal patterns in the relative abundances, lengths and biomass of demersal and pelagic fishes. However, much remains uncertain about how interactions between the fish and bait and between the fish themselves affect the results obtained. Agonistic behaviours are frequently observed around the bait of the camera and potentially bias fish density estimates by altering the number and size classes seen at cameras. Here we counted the number of agonistic behaviours between pink snappers (Pagrus auratus), the size of fish involved and whether the fish left the field of view following such behaviours. The study consisted of 20 baited underwater video deployments inside a New Zealand marine reserve and 20 in adjacent open areas. We observed a significant relationship between the peak number of fish observed at the camera and the total number of agonistic behaviours, as well as the number of both aggressor and subordinate fish leaving the camera field of view following interactions. The slope of the latter relationship and thus the absolute numbers of fish leaving were higher for subordinate fish. As subordinates were significantly smaller than aggressors, the apparent size frequency distribution is likely skewed away from smaller size classes. The staying time of the fish and thus the maximum number of fish present at the camera will be reduced by agonistic behaviours and the absolute magnitude of this effect appears to be greater at high fish densities. Our results suggest that an overall effect of these phenomena is to underestimate the differences in abundance between MPAs and open areas, but also to overestimate differences in average size

RGBD-Dog: Predicting Canine Pose from RGBD Sensors

The automatic extraction of animal 3D pose from images without markers is of interest in a range of scientific fields. Most work to date predicts animal pose from RGB images, based on 2D labelling of joint positions. However, due to the difficult nature of obtaining training data, no ground truth dataset of 3D animal motion is available to quantitatively evaluate these approaches. In addition, a lack of 3D animal pose data also makes it difficult to train 3D pose-prediction methods in a similar manner to the popular field of body-pose prediction. In our work, we focus on the problem of 3D canine pose estimation from RGBD images, recording a diverse range of dog breeds with several Microsoft Kinect v2s, simultaneously obtaining the 3D ground truth skeleton via a motion capture system. We generate a dataset of synthetic RGBD images from this data. A stacked hourglass network is trained to predict 3D joint locations, which is then constrained using prior models of shape and pose. We evaluate our model on both synthetic and real RGBD images and compare our results to previously published work fitting canine models to images. Finally, despite our training set consisting only of dog data, visual inspection implies that our network can produce good predictions for images of other quadrupeds – e.g. horses or cats – when their pose is similar to that contained in our training set

Benthic Structure and Pelagic Food Sources Determine Post-settlement Snapper (Chrysophrys auratus) Abundance

Nursery habitats provide increased survival and growth and are a crucial early life-stage component for many fish and invertebrate populations. The biogenic structures that provide this nursery function, however, are increasingly degraded. Therefore, any effort to conserve, restore or replace habitat with artificial structure should be guided by an understanding of the value provided by that nursery habitat. Here, we experimentally manipulated structure across a number of sites by inserting pinnind bivalve mimics into the seabed and deploying video cameras to observe the response of post-settlement stage snapper, Chrysophrys auratus (Forster in Bloch and Schneider 1801). We also collected a range of environmental variables across these sites to determine the relative importance to snapper of benthic vs. pelagic productivity. While the abundance of snapper was low, our results demonstrated a strong association to structure relative to control plots. The environmental variable with the highest correlation to snapper abundance was the abundance of zooplankton eaten by snapper. This result was well supported by the dominance of zooplankton over small benthic invertebrates in snapper gut contents, and the weak influence of benthic infauna in our regression models. These regressions also demonstrated that when combined with zooplankton abundance, turbidity had a negative relationship to snapper abundance. This highlights the importance of relatively clear water in estuaries, which allows post-settlement snapper to more efficiently consume the zooplankton that are present in the water column. The third component that post-settlement snapper require is of course the presence of benthic structure. While benthic habitat structure was the strongest factor affecting juvenile snapper abundance, we did not find any correlations to suggest that this importance was related to energetic sheltering and access to locations with high food flux

Correlated effects of ocean acidification and warming on behavioral and metabolic traits of a large pelagic fish

Ocean acidification and warming are co-occurring stressors, yet their effects on early life stages of large pelagic fishes are not well known. Here, we determined the effects of elevated CO2 and temperature at levels projected for the end of the century on activity levels, boldness, and metabolic traits (i.e., oxygen uptake rates) in larval kingfish (Seriola lalandi), a large pelagic fish with a circumglobal distribution. We also examined correlations between these behavioral and physiological traits measured under different treatments. Kingfish were reared from the egg stage to 25 days post-hatch in a full factorial design of ambient and elevated CO2 (~500 µatm and ~1000 µatm) and temperature (21 °C and 25 °C). Activity levels were higher in fish from the elevated temperature treatment compared with fish reared under ambient temperature. However, elevated CO2 did not affect activity, and boldness was not affected by either elevated CO2 or temperature. Both elevated CO2 and temperature resulted in increased resting oxygen uptake rates compared to fish reared under ambient conditions, but neither affected maximum oxygen uptake rates nor aerobic scope. Resting oxygen uptake rates and boldness were negatively correlated under ambient temperature, but positively correlated under elevated temperature. Maximum oxygen uptake rates and boldness were also negatively correlated under ambient temperature. These findings suggest that elevated temperature has a greater impact on behavioral and physiological traits of larval kingfish than elevated CO2. However, elevated CO2 exposure did increase resting oxygen uptake rates and interact with temperature in complex ways. Our results provide novel behavioral and physiological data on the responses of the larval stage of a large pelagic fish to ocean acidification and warming conditions, demonstrate correlations between these traits, and suggest that these correlations could influence the direction and pace of adaptation to global climate change

In-situ uniaxial drawing of poly-L-lactic acid (PLLA): Following the crystalline morphology development using time-resolved SAXS/WAXS

Simultaneous synchrotron small- and wide-angle X-ray scattering (SAXS/WAXS) was used to follow the crystalline morphology evolution of poly-L- lactic acid (PLLA) during uniaxial deformation at various draw temperatures (Td). The mechanical behaviour of PLLA, was found to be strongly dependent on Td. 2D SAXS/WAXS data taken during the draw showed that at low Tds cavitation and voiding occurred and the initial crystallites underwent ‘overdrawing’ where they slip and are partially destroyed. SEM confirmed that surface voiding and cavitation had occurred at Td = 60 and 65 °C but was absent at higher Tds. During the draw, no long-range macromolecular lamellar structure was seen in the SAXS, but small crystallites of the disordered α′ crystal form of PLLA were observed in the WAXS at all Tds. The PLLA samples were then step annealed in a second processing stage (post-draw) to develop the oriented crystalline lamellar structure and increase the amount of the stable α crystalline form. SAXS/WAXS data showed that a highly oriented lamellar stack macrostructure developed on annealing, with increased crystallite size and crystallinity at all Tds. Furthermore, step annealing drove the crystalline transition in all samples from the disordered α′ crystal form to the stable α crystal form. Therefore, varying pre- and post-processing parameters can significantly influence the mechanical properties, orientation, crystalline morphology and crystal phase transition of the final PLLA material

Holstein calves' preference for potential physical enrichment items on different presentation schedules

Impoverished housing environments are thought to prevent motivated behaviors and may result in frustration. We first aimed to investigate an effective physical enrichment protocol to improve dairy calves' welfare and initially determine their use of various items. Thereafter, we aimed to determine dairy calves' preference for and ways of interacting with various items, and whether this was influenced by social housing. In experiment 1, at 21 ± 3 d of age, 27 individually housed calves were assigned alternately into 1 of 3 treatments: control (CON, no additional items), rotating enrichment (RE, one item each week on a rotating presentation schedule), and fixed enrichment (FE, 4 types of item at the same time). The items were stationary brushes, ropes, springs, nets filled with strawberry-scented hay, and dry teats. Calves' behaviors were observed from 4 to 7 wk of age using focal observations after feeding, followed by instantaneous scan sampling. Their behavioral responses to a novel object were assessed at 43 ± 1 d of age. In the instantaneous scans, calves in FE tended to interact with items more often than calves in RE. Calves in RE and FE expressed less non-nutritive oral behavior than those in CON. Latency to touch novel objects did not differ significantly between treatments. Calves in RE and FE interacted with nets filled with strawberry-scented hay more often than with other items in instantaneous scans. In experiment 2, 24 calves were assigned alternately into 8 individual pens and 8 pair pens at 2 d of age. All pens were provided with a stationary brush, plastic chain, net filled with strawberry-scented hay, and dry teat. Calves' behaviors were collected from 2 to 5 wk of age using instantaneous scan sampling. Calves interacted with nets filled with strawberry-scented hay more often than with other items. Pair housing reduced calves' interactions with items compared with individual housing. Individually and pair-housed calves' frequencies of overall interaction with items varied with time of day, with frequencies increasing to peaks at 0700, 1500, and 1900 h. Calves showed scratching, sniffing, sucking, butting, and hay intake toward nets filled with strawberry-scented hay and showed the first 3 behaviors toward stationary brushes, plastic chains, and dry teats. In conclusion, dairy calves are likely to prefer a fixed multi-item enrichment presentation schedule over a rotating schedule with a single enrichment item presented at one time. For the fixed multi-item enrichment presentation schedule, items were used more in individual pens than in pair pens, and a diurnal pattern was observed for use of the items. Nets filled with scented hay might be the most multifunctional and attractive item of the items tested

Organ health and development in larval kingfish are unaffected by ocean acidification and warming

Anthropogenic CO₂ emissions are causing global ocean warming and ocean acidification. The early life stages of some marine fish are vulnerable to elevated ocean temperatures and CO₂ concentrations, with lowered survival and growth rates most frequently documented. Underlying these effects, damage to different organs has been found as a response to elevated CO₂ in larvae of several species of marine fish, yet the combined effects of acidification and warming on organ health are unknown. Yellowtail kingfish, Seriola lalandi, a circumglobal subtropical pelagic fish of high commercial and recreational value, were reared from fertilization under control (21 °C) and elevated (25 °C) temperature conditions fully crossed with control (500 µatm) and elevated (1,000 µatm) pCO₂ conditions. Larvae were sampled at 11 days and 21 days post hatch for histological analysis of the eye, gills, gut, liver, pancreas, kidney and liver. Previous work found elevated temperature, but not elevated CO₂, significantly reduced larval kingfish survival while increasing growth and developmental rate. The current histological analysis aimed to determine whether there were additional sublethal effects on organ condition and development and whether underlying organ damage could be responsible for the documented effects of temperature on survivorship. While damage to different organs was found in a number of larvae, these effects were not related to temperature and/or CO₂ treatment. We conclude that kingfish larvae are generally vulnerable during organogenesis of the digestive system in their early development, but that this will not be exacerbated by near-future ocean warming and acidification

Leveraging pediatric PROMIS item banks to assess physical functioning in children at risk for severe functional loss

Background: Pediatric neuromuscular illnesses often result in decreased health-related quality of life (HRQL), notably in physical functioning. Generic HRQL measures have been developed for use in general populations, but may not adequately assess patients with severe functional loss. To address this measurement gap, we created two custom parent-proxy physical functioning short forms for use among children at risk for low levels of functioning, using pediatric Patient Reported Outcomes Measurement Information System (PROMIS) item banks for Upper Extremity and Mobility. Methods: Two custom short forms from PROMIS Upper Extremity (13 items) and Mobility (13 items) parent-proxy item banks were created and administered to parents of children (ages 5 – 22 years) enrolled in an integrated care program for management of chronic respiratory insufficiency, largely due to neuromuscular illnesses. Standardized PROMIS T-scores have a mean of 50 (SD = 10); higher scores indicate better functioning. Physicians rated clinical severity. Single proxy-rated items on mental and physical health from the Child Health Rating Inventories (CHRIs) global health scale were completed by parents. Psychometric properties, including known groups comparisons, were explored. Results: Fifty-seven parents completed the parent-proxy custom PROMIS short forms. The mean Upper Extremity T-score was 21 (SD = 13); the mean Mobility T-score was 22 (SD = 11). Some participants scored at the measurement floor; two items on assistive devices did not perform well in this sample and were excluded from the Mobility T-score. Known groups comparisons showed that those with lower clinical severity had better median Upper Extremity (22 vs. 14, p < 0.001) and Mobility (28 vs. 16, p = 0.004) function than those with worse clinical severity. Both Upper Extremity and Mobility T-scores were higher in the subgroups defined by better physical and mental health, as measured by the CHRIs. Conclusions: Upper Extremity and Mobility T-scores were nearly three standard deviations below the PROMIS pediatric calibration population mean. Preliminary psychometrics demonstrated the potential to more accurately measure lower physical functioning using items from PROMIS item banks. However, some participants scored at the measurement floor despite targeting items at the lower end of the scale. Further short form refinement, enrichment of the item banks, and larger-scale field testing are needed

A baseline method for benchmarking mortality losses in Atlantic salmon (Salmo salar) production

On-farm databases provide a large diversity of information regarding fish health and stock performance. Mortality records held in on-farm database are indicators of fish health status and of great interest for studying fish health, such as patterns of diseases. Mortality records from a Scottish Atlantic salmon production database of one company were used to develop a method of benchmarking production losses due to mortality. The records used concerned mortality loss numbers of Atlantic salmon in the seawater phase. The median, 10th and 90th percentiles of mortality were calculated for each week of production from 88 production recorded cycles. These values were used to delimit the range of a standard mortality curve through the production cycle. The effects of the different mortality losses from each cycle on production in terms of costs and time consumed were also described. Likewise, substantial interannual variation in mortality time series is described as well as the mortality variation associated with three diseases (Pancreas Disease, Cardiomyopathy Syndrome and Infectious Pancreatic Necrosis)