Latest recommendations
Id | Title * | Authors * | Abstract * | Picture * | Thematic fields * ▲ | Recommender | Reviewers | Submission date | |
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14 Dec 2022
Feed efficiency of lactating Holstein cows was not as repeatable across diets as within diet over subsequent lactation stagesAmelie Fischer, Philippe Gasnier, philippe faverdin https://doi.org/10.1101/2021.02.10.430560A focus on feed efficiency reproducibility and repeatability of dairy cows fed different diets over the lactation stage.Recommended by Alberto Atzori based on reviews by Ioannis Kaimakamis, Angela Schwarm and 2 anonymous reviewersThe 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 stages | Amelie 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 nutrition | Alberto Atzori | Anonymous, Ioannis Kaimakamis, Giuseppe Conte, Angela Schwarm | 2021-02-11 08:43:59 | View | |
31 Jul 2023
The big challenge for livestock genomics is to make sequence data payMartin Johnsson https://doi.org/10.48550/arXiv.2302.01140The price of sequencing the livestock genomicsRecommended by Marcin Pszczoła based on reviews by Mario Calus and 1 anonymous reviewerUsing sequence data in livestock genomics has often been regarded as a solution to revolutionize livestock breeding (Meuwissen & Goddard, 2010). The main expected benefits were to enhance the accuracy of breeding values, achieve better persistence of the accuracy over generations, and enable across populations or breed predictions (Hickey, 2013). Despite the promised benefits, whole-genome sequencing has not yet been implemented in livestock breeding programs, replacing SNP arrays for routine evaluation. In this work, Johnsson (2023) thoroughly reviewed the literature regarding the implications of whole-genome sequencing and functional genomics for livestock breeding practice. The author discusses the potential applications and reasons for difficulties in their implementation. The author speculates that the main challenge for making using the sequence data profitable is to overcome the problem of the small dimensionality of the genetic data and proposes three potential ways to achieve this goal. The first approach is better modeling of genomic segments, the second inclusion of undetected genetic variation, and the third use of functional genomic information. The paper presents an original and interesting perspective on the current status of the use of sequence data in livestock breeding programs and perspectives for the future. References Hickey,J.M.,2013.Sequencing millions of animals for genomic selection 2.0. Journal of Animal Breeding and Genetics 130:331–332. https://doi.org/10.1111/jbg.12054 Johnsson, M., 2023. The big challenge for livestock genomics is to make sequence data pay. arXiv, 2302.01140, ver. 4 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.48550/arXiv.2302.01140 Meuwissen, T., Goddard, M.,2010. Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185:623–631. https://doi.org/10.1534/genetics.110.116590
| The big challenge for livestock genomics is to make sequence data pay | Martin Johnsson | <p>This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to consis... | Genomics, Genomic selection | Marcin Pszczoła | 2023-02-03 08:08:39 | View | ||
06 Sep 2019
Lactation curve model with explicit representation of perturbations as a phenotyping tool for dairy livestock precision farming.Ben Abdelkrim Ahmed, Puillet Laurence, Gomes Pierre, Martin Olivier https://doi.org/10.1101/661249Developing smart fitting algorithms to identify random perturbations in time-series dataRecommended by Luis Tedeschi based on reviews by Alberto Atzori, Jennifer Spencer and 1 anonymous reviewerThe ability to adequately characterize the lactation curve of livestock is important not only to ensure proper nutrition of the lactating animal but, among many other benefits, it can assist in diagnosing the incidence of diseases, predicting the quantity of milk production, and comparing animals within the herd for managerial strategies such as culling. Eventually, such smart fitting algorithms can lead to improved genetic selection of more productive animals after genetic-unrelated noises are removed from the data, systematically. References [1] Johansson, I. (1961). Genetic Aspects of Dairy Cattle Breeding. University of Illinois Press, Urbana, IL. [2] Nelder, J. A. (1966). Inverse polynomials, a useful group of multi-factor response functions. Biometrics. 22 (1):128-141. doi: 10.2307/2528220 | Lactation curve model with explicit representation of perturbations as a phenotyping tool for dairy livestock precision farming. | Ben Abdelkrim Ahmed, Puillet Laurence, Gomes Pierre, Martin Olivier | <p>Background Understanding the effects of environment on livestock provides valuable information on how farm animals express their production potential, and on their welfare. Ruminants are often confronted with perturbations that affect their per... | Lactation biology , Mathematical modelling, Precision livestock farming | Luis Tedeschi | 2019-06-07 09:38:26 | View | ||
14 Oct 2020
Determining insulin sensitivity from glucose tolerance tests in Iberian and Landrace pigsJ. M. Rodríguez-López, M. Lachica, L. González-Valero, I. Fernández-Fígares https://doi.org/10.1101/2019.12.20.884056Iberian pigs: more than excellent ham!Recommended by Jordi Estellé based on reviews by 2 anonymous reviewersIberian pigs represent a treasured resource that allows the maintenance of their “montanera” traditional breeding system and, thus, contributes to the socioeconomic sustainability of the rural areas in the south-western regions of Iberian Peninsula. While the excellence of Iberian meat products is widely recognized, the idea of using Iberian pigs as biomedical models is currently emerging. Interestingly, due to the particular fatty acid metabolism of this porcine breed, Iberian pigs have been proposed as models for type 2 diabetes (Torres-Rovira et al. 2012) or obesity-related renal disease (Rodríguez et a. 2020). In the present manuscript, Rodríguez-López et al. provide further insights on the particularities of “obese” Iberian pigs by comparing their insulin sensitivity in a glucose tolerance test with that of commercial “lean” Landrace pigs. The authors compared four Iberian pigs with five Landrace pigs in an intense time-series following an intra-arterial glucose tolerance test and measuring insulin, glucose, lactate, triglycerides, cholesterol, creatinine, albumin and urea plasma levels. Several of these parameters showed significant differences between both breeds, with some of them being compatible with an early stage of insulin resistance in Iberian pigs. These results are relevant from an animal production perspective, but provide also further evidence for considering the Iberian pigs as a suitable biomedical model for obesity-related disorders. References [1] Torres-Rovira, L., Astiz, S., Caro, A., Lopez-Bote, C., Ovilo, C., Pallares, P., Perez-Solana, M. L., Sanchez-Sanchez, R., & Gonzalez-Bulnes, A. (2012). Diet-induced swine model with obesity/leptin resistance for the study of metabolic syndrome and type 2 diabetes. The Scientific World Journal, 510149. https://doi.org/10.1100/2012/510149 | Determining insulin sensitivity from glucose tolerance tests in Iberian and Landrace pigs | J. M. Rodríguez-López, M. Lachica, L. González-Valero, I. Fernández-Fígares | <p>As insulin sensitivity may help to explain divergences in growth and body composition between native and modern breeds, metabolic responses to glucose infusion were measured using an intra-arterial glucose tolerance test (IAGTT). Iberian (n = 4... | Monogastrics, Physiology, Pig nutrition | Jordi Estellé | 2019-12-28 10:51:03 | View | ||
09 Apr 2022
The impact of housing conditions on porcine mesenchymal stromal/stem cell populations differ between adipose tissue and skeletal muscleAudrey Quéméner, Frédéric Dessauge, Marie-Hélène Perruchot, Nathalie Le Floc’h, Isabelle Louveau https://doi.org/10.1101/2021.06.08.447546Housing conditions affect cell populations in adipose and muscle tissues of pigsRecommended by Hervé Acloque based on reviews by 2 anonymous reviewersThe adaptability of livestock to changing environments is based in particular on their genetic characteristics but also on the farming conditions to which they are subjected. However, this last point is poorly documented and little is known about its contribution to environmental challenges. The study by Quéméner and colleagues [1] addresses this question by assessing the effect of two hygiene conditions (good vs poor) on the distribution of cell populations present in adipose and muscle tissues of pigs divergently selected for feed efficiency [2]. The working hypothesis is that degraded housing conditions would be at the origin of an hyper stimulation of the immune system that can influence the homeostasis of adipose tissue and skeletal muscle and consequently modulate the cellular content of these tissues. Cellular compositions are thus interesting intermediate phenotypes for quantifying complex traits. The study uses pigs divergently selected for residual feed intake (RFI+ and RFI-) to assess whether there is a genetic effect associated with the observed phenotypes. The study characterized different stromal cell populations based on the expression of surface markers: CD45 to separate hematopoietic lineages and markers associated with the stem properties of mesenchymal cells: CD56, CD34, CD38 and CD140a. The authors observed that certain subpopulations are differentially enriched according to the hygiene condition (good vs poor) in adipose and skeletal tissue (CD45-CD56-) sometimes with an associated (genetic) lineage effect. This pioneering study validates a number of tools for characterizing cell subpopulations present in porcine adipose and muscle tissue. It confirms that housing conditions can have an effect on intermediate phenotypes such as intra-tissue cell populations. This pioneering work will pave the way to better understand the effects of livestock systems on tissue biology and animal phenotypes and to characterize the nature and function of progenitor cells present in muscle and adipose tissue. [1] Quéméner A, Dessauge F, Perruchot MH, Le Floc’h N, Louveau I. 2022. The impact of housing conditions on porcine mesenchymal stromal/stem cell populations differ between adipose tissue and skeletal muscle. bioRxiv 2021.06.08.447546, ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2021.06.08.447546 [2] Gilbert H, Bidanel J-P, Gruand J, Caritez J-C, Billon Y, Guillouet P, Lagant H, Noblet J, Sellier P. 2007. Genetic parameters for residual feed intake in growing pigs, with emphasis on genetic relationships with carcass and meat quality traits. Journal of Animal Science 85:3182–3188. https://doi.org/10.2527/jas.2006-590. | The impact of housing conditions on porcine mesenchymal stromal/stem cell populations differ between adipose tissue and skeletal muscle | Audrey Quéméner, Frédéric Dessauge, Marie-Hélène Perruchot, Nathalie Le Floc’h, Isabelle Louveau | <p><strong>Background.</strong> In pigs, the ratio between lean mass and fat mass in the carcass determines production efficiency and is strongly influenced by the number and size of cells in tissues. During growth, the increase in the number of c... | Monogastrics, Physiology, Veterinary science | Hervé Acloque | 2021-06-08 17:34:54 | View | ||
24 May 2022
Identifying cattle with superior growth feed efficiency through their natural 15N abundance and plasma urea concentration: a meta-analysis.Gonzalo Cantalapiedra-Hijar, Isabelle Morel, Bernard Sepchat, Céline Chantelauze, Gemma A. Miller, Carol-Anne Duthie, Isabelle Ortigues-Marty, Richard J. Dewhurst https://doi.org/10.5281/zenodo.578396015N as a marker for feed efficiency in beef cattleRecommended by Marcos Marcondes based on reviews by Emilio Mauricio Ungerfeld and 1 anonymous reviewerIdentifying individuals with a more remarkable feed efficiency may positively affect the profitability and sustainability of the beef industry (Cruz et al., 2010; Basarab et al., 2013). However, although most international nutrient requirements systems predict animal feed efficiency, intake data is usually unavailable at the farm level, and ranking animals based on efficiency might be challenging. In this sense, using differences in the occurrence of isotopic N between animal and diet (Δ15Nanimal-diet) might become a natural biomarker to determine feed efficiency at the farm level. This methodology was firstly demonstrated by Guarnido-Lopez et al. (2021). In the present study by Cantalapiedra-Hijar et al. (2022), the authors evaluated the extent to which Δ15Nanimal-diet can be used as a marker for feed efficiency in beef animals. For this, a meta-analysis was conducted using a database including 759 individual records for performance and N isotopic discrimination measured in plasma or muscle (Δ15Nanimal-diet; n = 749) and plasma urea concentration (n = 659). The database was composed of 37% Charolais, 15% Simmental, and 40% of beef crossbreds. The results confirmed that Δ15Nanimal-diet could discriminate animals with at least 0.10 kg/kg difference in feed efficiency. Furthermore, the Δ15Nanimal-diet marker also successfully discriminated the feed efficiency of two animals from the same contemporary group if they differ by at least 0.06 kg/kg of FCE. However, when trying to predict feed efficiency, using the two candidate biomarkers did not improve estimates. Lastly, when data from biomarkers were combined with performance data, improvement in the predictions was observed. Nonetheless, the present results warrant more studies to evaluate the use of Δ15Nanimal-diet as a biomarker for feed efficiency since it could be used not only for feed efficiency discrimination but also in genetic selections.
References Cantalapiedra-Hijar G, Morel I, Sepchat B, Chantelauze C, Miller GA, Duthie CA, Ortigues-Marty I, Dewhurst RJ (2022). Identifying cattle with superior growth feed efficiency through their natural 15N abundance and plasma urea concentration: A meta-analysis. Zenodo, 5783960, ver. 3 peer-reviewed and recommended by Peer community in Animal Science. https://doi.org/10.5281/zenodo.5783960. Cruz GD, Rodríguez-Sánchez JA, Oltjen JW, Sainz RD (2010). Performance, residual feed intake, digestibility, carcass traits, and profitability of Angus-Hereford steers housed in individual or group pens. J. Anim. Sci. 88:324-329. https://doi.org/10.2527/jas.2009-1932. Basarab JA, Beauchemin KA, Baron VS, Ominski KH, Guan LL, Miller SP, Crowley JJ (2013). Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production. Animal 7:303-315. https://doi.org/10.1017/S1751731113000888. Guarnido-Lopez P, Ortigues-Marty I, Taussat S, Fossaert C, Renand G, Cantalapiedra-Hijar G (2021). Plasma proteins Δ15N vs. plasma urea as candidate biomarkers of between-animal variations of feed efficiency in beef cattle: Phenotypic and genetic evaluation. Animal 15:100318. https://doi.org/10.1016/j.animal.2021.100318.
| Identifying cattle with superior growth feed efficiency through their natural 15N abundance and plasma urea concentration: a meta-analysis. | Gonzalo Cantalapiedra-Hijar, Isabelle Morel, Bernard Sepchat, Céline Chantelauze, Gemma A. Miller, Carol-Anne Duthie, Isabelle Ortigues-Marty, Richard J. Dewhurst | <p>The objective of this study was to test two candidate biomarkers of feed efficiency in growing cattle. A database was built using performance data from 13 trials conducted with growing heifers, steers and young bulls and testing 34 dietary trea... | Physiology, Ruminant nutrition | Marcos Marcondes | 2021-12-07 15:24:15 | View | ||
10 Aug 2022
Decreasing the level of hemicelluloses in sow's lactation diet affects the milk composition and post-weaning performance of low birthweight piglets.Francesco Palumbo, Giuseppe Bee, Paolo Trevisi, Marion Girard https://doi.org/10.31220/agriRxiv.2022.00116Varying the hemicellulose content in the diet of lactating sows highlights the importance of early-life interventions for improving health and performance of small piglets during the post-weaning periodRecommended by Florence Gondret based on reviews by Hélène Quesnel and Myriam GrundyOne of the key questions in pig industry nowadays is how health and performance of piglets can be improved by sow nutrition and milk composition. The levels of dietary fibers in sow’s gestation diet have positive effects observed on the litters. However, the composition of dietary fibers and the organization of polysaccharides within the cell wall in the different plants determine their physicochemical properties and, thereby, their behaviour in the gut of the sows and the subsequent physiological response of the animals. Hemicelluloses are polysaccharides constituents of the cell walls of plants, which are fermented in the gut to produce volatile fatty acids (VFA). These VFA can serve as energy source for milk synthesis and can thereby influence the development of suckling piglets. Palumbo and colleagues (1) proposed an original experimental design to compare diets with similar fiber contents but different hemicellulose levels, thanks to varying the sources of fibers used in the dietary formulations. Effects were studied on performance and health of lactating sows and their piglets during suckling period and until post-weaning. The dietary treatments had no effect on the total number of piglets weaned and, consequently, on litter weight at weaning. Milk yield was not influenced by the dietary treatments, but milk composition (lactose content, copper and threonine proportions) was affected by the level of hemicellulose in the maternal diets. With a decreasing hemicellulose level in sow diet, milk lactose content linearly decreased, whereas the copper and threonine contents linearly increased. There was no effect on piglet performance during the lactation period. During the second week of post-weaning, a quadratic increase in the incidence of diarrhoea and the number of days with diarrhoea for suckling piglets was observed with decreasing hemicellulose level in diet. Interestingly, the observed effects were partly different for piglets born with a low body weight. Indeed, there was a linear decrease in the incidence of diarrhoea and days with diarrhoea with decreased hemicellulose level in the maternal diet for those piglets, together with increased growth performance from birth to two weeks post-weaning. The authors postulated that the improved growth performance and the lower incidence of diarrhoea observed in small piglets during post-weaning period may be related to the increased abundance of threonine and copper and increased concentration of total VFA in milk of sows fed a diet with reduced hemicellulose levels. This study confirms the importance of early-life interventions to improve the post-weaning development and health of this sub-population of piglets. Reference (1) Palumbo F, Bee G, Trevisi P, and Girard M. (2022). Decreasing the level of hemicelluloses in sow's lactation diet affects the milk composition and post-weaning performance of low birthweight piglets. agriRxiv 2022.00116, ver 4 (R3), peer-reviewed and recommended by PCI Animal Science. https://doi.org/10.31220/agriRxiv.2022.00116 | Decreasing the level of hemicelluloses in sow's lactation diet affects the milk composition and post-weaning performance of low birthweight piglets. | Francesco Palumbo, Giuseppe Bee, Paolo Trevisi, Marion Girard | <p>Hemicelluloses (HC) are polysaccharides constituents of the cell walls of plants. They are fermented in the gut to produce volatile fatty acids (VFA). The present study investigated the effects of decreasing HC level in sow's lactation diet on ... | Pig nutrition | Florence Gondret | 2022-01-21 12:00:22 | View | ||
07 Feb 2022
Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this traitFriggens, N. C., Adriaens, I., Boré, R., Cozzi, G., Jurquet, J., Kamphuis, C., Leiber, F., Lora, I., Sakowski, T., Statham, J. and De Haas, Y. https://doi.org/10.5281/zenodo.5215797Measuring resilience in farm animals: theoretical considerations and application to dairy cowsRecommended by Aurélien Madouasse based on reviews by Ian Colditz and 2 anonymous reviewersFarm animals differ in their ability to respond to the many environmental challenges they face. Such challenges include infectious diseases, metabolic diseases resulting from inadequate coverage of dietary needs, as well as the diverse consequences of climate change. Various concepts exist to characterise the responses of animals to different types of challenges. This article by Friggens et al. (2022) focuses on resilience, providing a conceptual definition and proposing a method to quantify resilience in dairy cows. The first part of the paper provides a definition of resilience and highlights its differences and relations with the related concepts of robustness, and, to a lesser extent, resistance and tolerance. In essence, resilience is the ability of an animal to bounce back quickly after a challenge of limited duration. On the other hand, robustness is the ability of an animal to cope with conditions that are overall unfavourable. From these conceptual and intuitive definitions, there are several difficulties precluding the design of concrete methods to measure resilience. First, there is some degree of overlap between the concepts of resilience, robustness, resistance and tolerance. Secondly, resilience is a multidimensional concept whereby resilience to a given perturbation does not imply resilience to other types of perturbation, e.g. resilience to a challenge by a specific pathogen does not imply resilience to a nutritional challenge. A further difficulty in the measure of resilience is the fact that different animals may be exposed to challenges that are different in nature and in number. The authors argue that although resilience cannot be measured directly (it should be seen as a latent construct), it is possible to quantify it indirectly through its consequences. In the second part of the paper, the authors propose a method to quantify resilience of individual dairy cows. The method is based on the premise that resilient animals should be kept longer in their herd than non-resilient animals. The main criterion in the evaluation is therefore the ability of cows to re-calve. Each cow that is calving receives a certain number of points, to which, in each lactation, bonus points are added for higher milk production and penalty points are removed for each insemination after the first one, for each disease event and for each day of calving interval above some herd specific value. Therefore, cows have a resilience score in each lactation. They also have a lifetime resilience score obtained by summing the scores for all the lactations, that gets bigger as the cow has more calves, and that also takes the age at first calving into account. In a previous study, Adriaens et al. (2020) showed that higher resilience scores were associated with fewer drops in milk yield and more stable activity dynamics. Starting from theoretical considerations on the notion of resilience, this paper describes a concrete method to quantify animal-level resilience on farm. Such quantification will be useful for breeding and culling decisions. Finally, the general framework to design resilience measures that is presented will be useful to researchers working on the quantification of farm animal resilience using new methods and data sources.
References Adriaens I, Friggens NC, Ouweltjes W, Scott H, Aernouts B and Statham J 2020. Productive life span and resilience rank can be predicted from on-farm first-parity sensor time series but not using a common equation, across farms. Journal of Dairy Science 103, 7155-7171.https://doi.org/10.3168/jds.2019-17826 Friggens, N.C. , Adriaens, I., Boré, R., Cozzi, G., Jurquet, J., Kamphuis, C., Leiber, F., Lora, I., Sakowski, T., Statham, J., De Haas, Y. (2022). Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this trait. Zenodo, 5215797, ver. 5 peer-reviewed and recommended by Peer community in Animal Science. https://dx.doi.org/10.5281/zenodo.5215797 | Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this trait | Friggens, N. C., Adriaens, I., Boré, R., Cozzi, G., Jurquet, J., Kamphuis, C., Leiber, F., Lora, I., Sakowski, T., Statham, J. and De Haas, Y. | <p style="text-align: justify;">Climate change, with its increasing frequency of environmental disturbances puts pressures on the livestock sector. To deal with these pressures, more complex traits such as resilience must be considered in our mana... | Precision livestock farming | Aurélien Madouasse | 2021-08-20 15:34:13 | View | ||
02 Sep 2021
A modelling framework for the prediction of the herd-level probability of infection from longitudinal dataAurélien Madouasse, Mathilde Mercat, Annika van Roon, David Graham, Maria Guelbenzu, Inge Santman Berends, Gerdien van Schaik, Mirjam Nielen, Jenny Frössling, Estelle Ågren, Roger Humphry, Jude Eze, George Gunn, Madeleine Henry, Jörn Gethmann, Simon J. More, Nils Toft, Christine Fourichon https://doi.org/10.1101/2020.07.10.197426Modelling freedom from disease - how do we compare between countries?Recommended by Rowland Raymond Kao based on reviews by Arata Hidano and 1 anonymous reviewerIn this paper, Madouasse et al. (2021) present a generalisable Bayesian method for calculating the probability that a herd is free from disease, based on its prior disease status, and using data (herd status over time over a sufficient number of herds to inform the model) and reasonable prior estimates of the sensitivity and specificity of tests being used to determine animal infection status. Where available, the modelling approach can also include relevant additional risk factors. By bringing all these factors together, it allows for most countries to use the same analytical approach on their data, with differences across datasets expressed in terms of the uncertainty around the central estimates. Having a single methodology that generates both a central estimate of disease freedom, and uncertainty thus provides the opportunity (given typically available data) to compare the probability of freedom across different systems. This is relevant in terms of the context of trade (since international trade of livestock in many cases depends on disease freedom). It is also important when evaluating, for example, transnational burdens of disease - and with different regulations in place in different countries, this is invaluable and can be used, for example, to assess risks of zoonotic infection including for zoonotic infection emergence. In the BVD example provided, the point is made that, since regular testing would probably pick up infection rapidly, the addition of risk factors is most valuable where testing is infrequent. This emphasizes the advantages of direct incorporation of risk factors into a single modelling framework. From a technical point of view, the analysis compares two different packages for the Markov Chain Monte Carlo (MCMC) implementation necesary to run the model. They show that, while there are some slight systematic differences, the estimates provided by the two methods are similar to each other; as one method is approximate but substantially more stable and generally much more computationally efficient, this is an important outcome. Both implementations are freely available and with relevant additional software made similarly available by the authors. This is extremely welcome and should encourage its general adoption across different countries. No single model can of course account for everything. In particular, the reliance on past data means that there is an implicit assumption common to all purely statistical methods that the underlying risks have not changed. Thus projections to altered circumstances (changing underlying risk factors or systematic changes in testing or test performance) cannot so easily be incorporated, since these factors are complicated by the dynamics of infection that lie outside the modelling approach. Of course the well known quote from George Box that "all models are wrong" applies here - the generality of approach, statistical robustness and open source philosophy adopted make this model very useful indeed. Madouasse A, Mercat M, van Roon A, Graham D, Guelbenzu M, Santman Berends I, van Schaik G, Nielen M, Frössling J, Ågren E, Humphry RW, Eze J, Gunn GJ, Henry MK, Gethmann J, More SJ, Toft N, Fourichon C (2021) A modelling framework for the prediction of the herd-level probability of infection from longitudinal data. bioRxiv, 2020.07.10.197426, ver. 6 peer-reviewed and recommended by PCI Animal Science. https://doi.org/10.1101/2020.07.10.197426
| A modelling framework for the prediction of the herd-level probability of infection from longitudinal data | Aurélien Madouasse, Mathilde Mercat, Annika van Roon, David Graham, Maria Guelbenzu, Inge Santman Berends, Gerdien van Schaik, Mirjam Nielen, Jenny Frössling, Estelle Ågren, Roger Humphry, Jude Eze, George Gunn, Madeleine Henry, Jörn Gethmann, Sim... | <p>The collective control programmes (CPs) that exist for many infectious diseases of farm animals rely on the application of diagnostic testing at regular time intervals for the identification of infected animals or herds. The diversity of these ... | TEST, Veterinary epidemiology | Rowland Raymond Kao | 2020-07-23 08:13:18 | View |
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