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03 Apr 2025
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A pipeline with pre-processing options to detect behaviour from accelerometer data using Machine Learning tested on dairy goats.

Introducing a feature extraction method and implementing a gradient boosting algorithm to predict behavioral traits in animals

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

In the livestock industry, the concerns of society and livestock farmers have changed in recent decades, moving from a focus solely on production traits to sustainable production while respecting animal welfare (Ducrot et al., 2024). Animal behavior parameters can serve as a reliable proxy for animal welfare, but collecting large data sets of behavioral data on farm is very time-consuming when not automatized.  Accelerometers are promising devices to detect animal behavior. A key element of the efficiency of the prediction of animal behavior from accelerometer data is the adequacy of pre-processing methods (Riaboff et al., 2019,Riaboff et al., 2022, Vidal et al., 2023).  

The article of Mauny et al., (2025) aims to find a solution for using huge automatized data. So, livestock farmers can effectively use new technologies to monitor animal behavior and then correct poor husbandry routines. Authors used the pipeline ACT4Behav - (Accelerometer-based Classification Tool for identifying Behaviours) - (Mauny et al., 2024) for the pre-processing of accelerometer data with the aim of selecting the most important features of dairy goats related to rumination, head in the feeder, lying and standing (using  data based on video recordings for the validation of behavior activity). Mauny et al., (2025) established a clear methodology that systematically obtain the best features and processing techniques to predict each targeted variable from raw accelerometer data. The work provides valuable information for both animal husbandry specialists and data mining scientists. The main limitation of the work is the small number of animals for both training and model testing. 

References 

Ducrot C, Barrio MB, Boissy A, Charrier F, Even S, Mormède P, Petit S, Pinard-van der laan M-H, Schelcher F, Casabianca F, Ducos A, Foucras G, Guatteo R, Peyraud J-L, Vayssier-Taussat M, Veysset P, Friggens NC and Fernandez X. 2024. Animal board invited review: Improving animal health and welfare in the transition of livestock farming systems: Towards social acceptability and sustainability. animal 18, 101100. https://doi.org/10.1016/j.animal.2024.101100

Mauny, S, Kwon J, Friggens NC, Duvaux-Ponter C, Taghipoor M. 2024. ACT4Behav (Accelerometer-based Classification Tool for identifying Behaviours): a Machine Learning pipeline with extensive pre-processing and feature creation options. Zenodo. https://doi.org/10.5281/zenodo.12624796

Mauny S, Kwon J, Friggens NC, Duvaux-Ponter C, Taghipoor M. 2025. A pipeline with pre-processing options to detect behaviour from accelerometer data using Machine Learning tested on dairy goats.. Zenodo, ver. 6 peer-reviewed and recommended by PCI Animal Science. https://doi.org/10.5281/zenodo.12627197

Riaboff L, Aubin S, Bédère N, Couvreur S, Madouasse A, Goumand E, Chauvin A, Plantier G. 2019. Evaluation of pre-processing methods for the prediction of cattle behaviour from accelerometer data. Computers and Electronics in Agriculture 165, 104961. https://doi.org/10.1016/j.compag.2019.104961

Riaboff L, Shalloo L, Smeaton AF, Couvreur S, Madouasse A, Keane MT. 2022. Predicting livestock behaviour using accelerometers: A systematic review of processing techniques for ruminant behaviour prediction from raw accelerometer data. Computers and Electronics in Agriculture 192, 106610. https://doi.org/10.1016/j.compag.2021.106610

Vidal G, Sharpnack J, Pinedo P, Tsai IC, Lee AR, Martínez-López B. 2023. Impact of sensor data pre-processing strategies and selection of machine learning algorithm on the prediction of metritis events in dairy cattle. Preventive Veterinary Medicine 215, 105903. https://doi.org/10.1016/j.prevetmed.2023.105903

 

A pipeline with pre-processing options to detect behaviour from accelerometer data using Machine Learning tested on dairy goats.Sarah Mauny, Joon Kwon, Nicolas C. Friggens, Christine Duvaux-Ponter, Masoomeh Taghipoor<p style="text-align: justify;">Animal behaviour is a significant component in the evaluation of animal welfare. Conducting continuous observations of animal behaviour is a time-consuming task and may not be feasible over extended periods for all ...Animal behaviour , Animal welfare, Precision livestock farming, Small ruminantsSeyed Abbas Rafat2024-07-04 12:45:42 View
04 Apr 2025
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Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic lines

Advancing sustainable aquaculture: behavioral insights for climate-change resilient fishes

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The study by Lagarde et al. (2025) is part of efforts aiming to meet the challenges of adapting livestock farming, and more specifically of aquaculture, to the effects of climate change. In fact, during heat waves, water temperatures rise and oxygen becomes scarce. Fish have to adapt to these conditions of hyperthermia and hypoxia. Studies have already shown that it is possible to genetically improve these resistances in salmonids (e.g. Debes et al., 2021). However, current methods for phenotyping these resistances rely on exposing fish to extreme conditions until they lose equilibrium, which indicates that the animal experiences severe conditions and raises ethical and animal welfare concerns.

From the aforementioned, there is then a strong interest in using and identifying less invasive phenotypes, such as behavioural changes, that could serve as indicators of fish responses to hyperthermia and hypoxia. Some behaviours show promise in both wild (Campos et al., 2018) and farmed fish (Van Raaij et al., 1996). A former study by the authors of this manuscript suggests that some of these behaviours are sufficiently heritable to consider applying selection on them (Lagarde et al., 2023). Therefore, the main aim of the present study was to test whether behaviour can be used as an indirect selection criterion to improve the adaptation of rainbow trout to heat waves. To achieve this lofty goal, the responses of different isogenic lines of trout to hyperthermia and hypoxia were investigated using new criteria based on behavioural responses and the reference measure of loss of equilibrium.

The results suggest that certain behavioural traits, such as distance travelled and frequency of zone changes, are associated with resistance to these stresses. Moreover, moderate correlations were observed between certain behavioural variables and resistance to hyperthermia. Indeed, lines that were more resistant to hyperthermia had lower distance travelled and frequency of zone changes during the behavioural test. Other significant and positive correlations were observed between acute hypoxia resistance and certain behavioural variables, likely distance travelled, frequency of zone change and percentage of time spent moving.

These results pave the way for less invasive methods in assessing hyperthermia and hypoxia resistance based on behavioural observations, which could improve the resistance of farmed fish in response to climate change. The study further allows refining the measurements carried out on candidates for selection in order to improve their welfare during evaluation tests.

In conclusion, this study is commendable for its thematic relevance, originality and the potential application of its results to genetic selection of farmed fish.

 

References

Campos DF, Val AL, Almeida-Val VMF. 2018. The influence of lifestyle and swimming behavior on metabolic rate and thermal tolerance of twelve Amazon forest stream fish species. Journal of Thermal Biology 72:148–154. https://doi.org/10.1016/j.jtherbio.2018.02.002

Debes P V., Solberg MF, Matre IH, Dyrhovden L, Glover KA. 2021. Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon. Heredity 127:455–466. https://doi.org/10.1038/s41437-021-00469-y

Lagarde H, Phocas F, Pouil S, Goardon L, Bideau M, Guyvarc’h F, Labbé L, Dechamp N, Prchal M, Dupont-Nivet M, Lallias D. 2023. Are resistances to acute hyperthermia or hypoxia stress similar and consistent between early and late ages in rainbow trout using isogenic lines? Aquaculture 562:738800. https://doi.org/10.1016/j.aquaculture.2022.738800

Lagarde H, Lallias D, Phocas F, Goardon L, Bideau M, Guyvarc'h F, Labbé L, Dupont-Nivet M, Cousin X. 2025. Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic lines. bioRxiv, ver.4 peer-reviewed and recommended by PCI Animal Science https://doi.org/10.1101/2023.10.19.563047

Van Raaij MTM, Pit DSS, Balm PHM, Steffens AB, Van Den Thillart GEEJM. 1996. Behavioral strategy and the physiological stress response in rainbow trout exposed to severe hypoxia. Hormones and Behavior 30:85–92. https://doi.org/10.1006/hbeh.1996.0012

Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic linesHenri Lagarde, Delphine Lallias, Florence Phocas, Lionel Goardon, Marjorie Bideau, Fanch' Guyvarc'h, Laurent Labbé, Mathilde Dupont-Nivet, Xavier Cousin<p style="text-align: justify;">In the context of adaptation to climate change, acute hyperthermia and hypoxia resistance are traits of growing interest in aquaculture. The feasibility of genetic improvement of these resistance traits through sele...Animal behaviour , Animal geneticsNicolas Bedere2024-07-12 15:37:31 View
06 Jan 2025
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Understanding the implementation of antimicrobial resistance policies in Vietnam: a multilayer analysis of the veterinary drug value chain

Bridging the gap in antibiotic regulation within Vietnam's livestock sector

Recommended by ORCID_LOGO based on reviews by Rebecca Hibbard and 1 anonymous reviewer

The reduction of antibiotic use in livestock production, for the different species, has become a critical focus in national action plans across many countries, underscoring the urgent need to tackle this issue to preserve public health and combat antibiotic resistance (Xu et al., 2022; Jacobsen et al., 2023; Bava et al., 2024). Among these efforts, Vietnam's ambitious 2017 livestock plan is notable for its comprehensive regulatory framework aimed at controlling antibiotic use. This framework includes a phased ban on prophylactic antibiotics in animal feed and requires mandatory prescriptions for antibiotic access.

Despite these promising regulations, their actual implementation poses significant challenges, with limited data available on their practical application. A recent study led by Batie and collaborators attempts to fill this knowledge gap by examining how these regulations are understood, accepted, and applied by stakeholders in the veterinary drug value chain in both northern and southern Vietnam (Batie et al., 2024).

The study employed an interesting iterative stakeholder mapping and analysis approach, organizing a focus group in Hanoi with 12 participants and conducting 39 in-depth semi-structured interviews with a diverse range of stakeholders. These included government authorities, national research bodies, international partners, and private sector representatives. The qualitative analysis aimed to map the veterinary drug value chain, assess stakeholders' technical and social capital regarding regulations, and identify key factors influencing regulatory compliance.

This research convincingly unveiled a complex network of 30 stakeholder categories and identified ten crucial factors that affect the implementation of regulations. These factors include stakeholders’ perceptions and understanding of the regulations, the availability of technical guidance, economic conflicts of interest, management inconsistencies, and hurdles such as technical and financial constraints, informal distribution channels, international influence, and consumer demand for safety. Additionally, the collective drive to reduce antibiotic resistance emerged as an influential factor.

The comprehensive analysis reveals a pressing insight: although Vietnam's regulatory measures are essential for reducing antibiotic usage, their effectiveness is compromised by barriers such as inadequate local stakeholder involvement and various resource limitations. The study emphasizes the necessity for deeper engagement of local stakeholders in developing and refining these regulations. Furthermore, incorporating innovations from small producers into mainstream practices could be vital in overcoming current challenges.

Nonetheless, the study acknowledges several limitations. Most interviews were conducted online owing to the health crisis—a much-needed format for time and budget constraints, albeit with some drawbacks such as reduced direct observations and potential information loss (Namey et al., 2019). The sensitivity of the subject may have led participants to withhold their true opinions, although the researchers attempted to mitigate this bias by interviewing multiple respondents from each category and gathering diverse perspectives. Notably, the study struggled to engage informal stakeholders, which could have enriched the description of the informal value chain. Constraints of time and resources meant that only a single representative from some stakeholder categories was interviewed, suggesting that interviewing additional parties, such as another veterinary district station, might have clarified roles within the drug value chain. The stakeholder identification was initially influenced by the researchers’ familiarity with the Vietnamese context; however, the iterative process helped address this limitation by recruiting new participants based on existing participants' knowledge. Additionally, translation issues may have introduced misunderstandings, potentially leading to an incomplete representation of the veterinary drug value chain, which reflects the situation as of data collection in 2021.

For Vietnam to meet its policy objectives and contribute to the global endeavor against antibiotic resistance, it is crucial to reconcile stakeholder discrepancies and promote collaborative innovation. By fostering an inclusive environment for all parties, Vietnam can not only enhance regulatory adherence but also strengthen its commitment to sustainable and responsible livestock farming practices.

The study is thoughtfully designed and skillfully executed. Additionally, the authors have made further improvements based on feedback from the journal. Readers will find the article both informative and engaging, providing valuable insights. I highly recommend this original article on the regulatory framework for controlling antibiotic use in Vietnam's livestock production systems.

References

Batie, C., Duy, N. V., Khue, N. T. M., Peyre, M., Bordier, M., Dien, N. T., et al. (2024). Understanding the implementation of antimicrobial resistance policies in Vietnam: a multilayer analysis of the veterinary drug value chain. medRxiv, 2024.06.27.24309573, ver. 2 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2024.06.27.24309573   

Bava, R., Castagna, F., Lupia, C., Poerio, G., Liguori, G., Lombardi, R., et al. (2024). Antimicrobial Resistance in Livestock: A Serious Threat to Public Health. Antibiotics 13, 551. https://doi.org/10.3390/antibiotics13060551

Jacobsen, A. B. J. E., Ogden, J., and Ekiri, A. B. (2023). Antimicrobial resistance interventions in the animal sector: scoping review. Front. Antibiot. 2. https://doi.org/10.3389/frabi.2023.1233698 

Namey, E., Guest, G., O’Regan, A., Godwin, C. L., Taylor, J., and Martinez, A. (2019). How Does Mode of Qualitative Data Collection Affect Data and Cost? Findings from a Quasi-experimental Study. Field Methods. https://doi.org/10.1177/1525822X19886839 

Xu, C., Kong, L., Gao, H., Cheng, X., and Wang, X. (2022). A Review of Current Bacterial Resistance to Antibiotics in Food Animals. Front Microbiol 13, 822689. https://doi.org/10.3389/fmicb.2022.822689 

 

Understanding the implementation of antimicrobial resistance policies in Vietnam: a multilayer analysis of the veterinary drug value chainChloé Bâtie, Nguyen Van Duy, Nguyen Thi Minh Khue, Marisa Peyre, Marion Bordier, Nguyen Thi Dien, Vu Dinh Ton, Flavie Goutard<p>Reducing antibiotic use in livestock production has been a target for national action plans worldwide. The Vietnamese livestock plan issued in 2017 has, among other objectives, strengthened the regulatory framework for antibiotic use. While a p...Animal epidemiology, Animal health, Farming systems, Veterinary epidemiology , Veterinary scienceFrançois Meurens2024-07-15 10:47:33 View
14 Dec 2022
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Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stages

A focus on feed efficiency reproducibility and repeatability of dairy cows fed different diets over the lactation stage.

Recommended by based on reviews by Ioannis Kaimakamis, Angela Schwarm and 2 anonymous reviewers

The topic of feed efficiency is under discussion in the scientific community and several studies pointed out that lactation stage has to be accounted for when estimates of feed efficiency are carried out, especially for genetic ranking of animals and their performances, as highlighted by Li et al. (2017). Other researchers applied a latin square design to test dietary effects across lactation (Ipharraguerre et al. 2002) but this approach cannot be followed out of experimental conditions and particularly does not allow, nowadays, to valorize precision livestock farm data to get phenotypic information from individual animals at farm level. 

The current manuscript by Fischer, et al. (2022a) describes an experimental trial in which cows were first fed a high starch diet-low fibre then switched over to a low starch diet-high fibre and individually monitored over time. Data were analyzed with the objective to investigate effects within diets and across diets. Since all cows went through the same sequence at the same time it was not possible to completely separate the confounding effect of lactation stage and diet as stated by the authors. However, this manuscript adds methodological discussions and opens research questions especially to the matter of repeatability and reproducibility of feed efficiency of individual animals over the lactation stage. These variables are fundamental to evaluate nutritional traits and phenotypic performances of dairy cows at farm level, as highlighted by a paper of the same first author (Fischer, et al. 2022b) dealing to reproducibility and repeatability with a similar approach. My opinion is that this manuscript gives the opportunity to enlarge the scientific discussions on the calculation of repeatability and reproducibility of feed efficiency of individual animals over time. In particular, as in this study, specific mathematical approaches need to be carried out with the final goal to analyze and valorize precision livestock farm data for cow phenotyping and to propose new methods of feed efficiency evaluations. It also needs complete databases carried out under experimental conditions. In fact it has to be considered that this manuscript makes available to the scientific community all the data and the R code developed for data analysis giving the opportunity to replicate the calculations and propose new advancements in the feed efficiency evaluations of dairy cows.

References 

Fischer A, Gasnier P, Faverdin P (2022a) Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stages. bioRxiv, 2021.02.10.430560, ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2021.02.10.430560

Fischer A, Dai X, Kalscheur KF (2022b) Feed efficiency of lactating Holstein cows is repeatable within diet but less reproducible when changing dietary starch and forage concentrations. animal, 16, 100599. https://doi.org/10.1016/J.ANIMAL.2022.100599

Ipharraguerre IR, Ipharraguerre RR, Clark JH (2002) Performance of Lactating Dairy Cows Fed Varying Amounts of Soyhulls as a Replacement for Corn Grain. Journal of Dairy Science, 85, 2905–2912. https://doi.org/10.3168/JDS.S0022-0302(02)74378-6

Li B, Berglund B, Fikse WF, Lassen J, Lidauer MH, Mäntysaari P, Løvendahl P (2017) Neglect of lactation stage leads to naive assessment of residual feed intake in dairy cattle. Journal of Dairy Science, 100, 9076–9084. https://doi.org/10.3168/JDS.2017-12775

 

 

Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stagesAmelie Fischer, Philippe Gasnier, philippe faverdin<p>Background: Improving feed efficiency has become a common target for dairy farmers to<br>meet the requirement of producing more milk with fewer resources. To improve feed<br>efficiency, a prerequisite is to ensure that the cows identified as mo...Cattle production, Ruminant nutritionAlberto AtzoriAnonymous, Ioannis Kaimakamis, Giuseppe Conte, Angela Schwarm2021-02-11 08:43:59 View