Modeling the lowest-cost splitting of a herd of cows by optimizing a cost function

Animals live in groups to defend against predation and to obtain food. However, for some animals --- especially ones that spend long periods of time feeding --- there are costs if a group chooses to move on before their nutritional needs are satisfied. If the conflict between feeding and keeping up with a group becomes too large, it may be advantageous to some animals to split into subgroups of animals with similar nutritional needs. We model the costs and benefits of splitting by a herd of cows using a cost function (CF) that quantifies individual variation in hunger, desire to lie down, and predation risk. We model the costs associated with hunger and lying desire as the standard deviations of individuals within a group, and we model predation risk as an inverse exponential function of group size. We minimize the cost function over all plausible groups that can arise from a given herd and study the dynamics of group splitting. We explore our model using two examples: (1) we consider group switching and group fission in a herd of relatively homogeneous cows; and (2) we examine a herd with an equal number of adult males (larger animals) and adult females (smaller animals).Comment: 19 pages, 10 figure

Study of prevalence, risk factors, and lifetime impacts of infection with bovine leukemia virus in the Canadian dairy industry

The overall goal of the research described in this thesis was to lay a proper foundation for designing and conducting efficient control and eradication programs for infection with bovine leukemia virus (BLV) in the Canadian dairy industry. The objective in Chapter 2 was to identify potentially important risk factors for BLV infection in Canadian dairy herds. Of 272 study herds, from 8 provinces of Canada and tested during 1998-2003, 78% were BLV-positive. Over 15 management determinants for the infection were evaluated. Herds with clinical cases of leukosis during the 12 months prior to sampling, as well as herds which purchased animals with unknown BLV infection status in the last five years, had a significantly increased proportion of BLV-positive cows. Herds from eastern provinces and those not purchasing cows in the last five years were more likely to be free from BLV compared to western provinces and farms purchasing cows in the last five years. The objective in Chapter 3 was to determine the lifetime effects of BLV infection on milk production and longevity of dairy cows in Canada. Overall, 4052 cows from 348 herds were enrolled in a historical cohort study, based on test results from 1998-2003 and lactation and culling records post-testing until 2013. Positive cows to BLV had consistently greater probability of being culled (or dying) than the negative cows (over lifetime lactations 2-7). Only BLV-positive cows with short longevity (2 and 3 lifetime lactations) had a significantly lower lifetime milk production compared with their negative counterparts. As the cows lived longer (> 3 lactations), the difference in milk production between the two cohorts was no longer significant. The objectives of Chapter 4 were: 1) to assess the potential for carryover of antibodies against BLV in milk samples obtained from shared meters; and 2) to determine if adjustment of the diagnostic test cut-off value would improve the test characteristics for meter-collected milk ELISA results. The study included 236 paired milk samples from 8 dairy farms in Prince Edward Island collected in 2013. Two simultaneous milk samples, one hand-collected at the beginning of milking, and the other from the corresponding milk meter, were taken from all lactating cows that were milked at the selected meters. The sequence of cows using each meter was recorded. Carryover of BLV antibodies at shared milk meters was significant. For low-titer cows, the carryover effect was positively associated with the titer of the preceding cows. This could result in generating false-positive results in the BLV antibody-ELISA test on meter-collected samples from dairy herd improvement (DHI) procedures. Based on a new optimal cut-point, a suspicious category on the ELISA titers was defined, and a retest on the samples falling within this range was recommended to reduce the false positive rate. The objectives for Chapter 5 were: 1) to determine the prevalence of BLV infection at the herd level using a bulk-tank milk (BTM) antibody ELISA in the Maritime region of Canada ; and 2) to develop applied statistical models for predicting within-herd prevalence of BLV infection using the BTM antibody levels. To detect BLV infection and the antibody levels, a census was implemented on BTM samples from all dairy farms in the Maritime region in 2013 (3 monthly rounds of sampling on 623 farms). Another round of BTM sampling was coincided with individual cow sampling (all cows that contributed milk to the fourth BTM) in 90 selected herds. Herd-level prevalence of BLV in the Maritime region was 90.8%. In the individual testing, 30.4% of cows were positive. The statistical models developed in this study were able to predict true within-herd prevalence of BLV reasonably well based only on the BTM results. The model including all BTM tests (4 rounds of sampling) as the predictor had the best fit, although the models using 2 and 3 BTM tests provided similar results to 4 repeated tests. The focus for Chapter 6 was to assess the diagnostic performance of a commercially available ELISA for detecting BLV antibodies in BTM samples collected from dairy herds in Eastern Canada in 2013. Of 133 tested herds, 108 herds were found to be truly infected. At the resulting optimal cut-point, sensitivity and specificity of the BTM ELISA were estimated at 0.972 (0.921 – 0.994) and 1 (0.863 – 1), respectively. With the high prevalence of BLV infection across Canada and its detrimental economic impacts, pursuing broad-based control programs is necessary. All of the findings in the present research could contribute to designing and conducting efficient BLV control programs

Evaluation of MEMS NIR Spectrometers for On-Farm Analysis of Raw Milk Composition

Today, measurement of raw milk quality and composition relies on Fourier transform infrared spectroscopy to monitor and improve dairy production and cow health. However, these laboratory analyzers are bulky, expensive and can only be used by experts. Moreover, the sample logistics and data transfer delay the information on product quality, and the measures taken to optimize the care and feeding of the cattle render them less suitable for real-time monitoring. An on-farm spectrometer with compact size and affordable cost could bring a solution for this discrepancy. This paper evaluates the performance of microelectromechanical system (MEMS)-based near-infrared (NIR) spectrometers as on-farm milk analyzers. These spectrometers use Fabry–Pérot interferometers for wavelength tuning, giving them the advantage of very compact size and affordable price. This study discusses the ability of MEMS spectrometers to reach the accuracy limits set by the International Committee for Animal Recording (ICAR) for at-line analyzers of the milk content regarding fat, protein and lactose. According to the achieved results, the transmission measurements with the NIRONE 2.5 spectrometer perform best, with an acceptable root mean squared error of prediction (RMSEP = 0.21% w/w) for the measurement of milk fat and excellent performance (RMSEP ≤ 0.11% w/w) for protein and lactose. In addition, the transmission measurements using the NIRONE 2.0 module give similar results for fat and lactose (RMSEP of 0.21 and 0.10% w/w respectively), while the prediction of protein is slightly deteriorated (RMSEP = 0.15% w/w). These results show that the MEMS spectrometers can reach sufficient prediction accuracy compared to ICAR standard values for at-line and in-line fat, protein and lactose prediction.202

Modeling Greenhouse Gas Emissions from Spanish Dairy and Beef farms: Mitigation Strategies

ABSTRACT Greenhouse gas (GHG) emissions and their potential effect on the environment has become an important national and international issue. Dairy and beef production, along with all other types of animal agriculture, are recognized sources of GHG emissions, but little information exists on the net emissions from dairy and beef farms. Component models for predicting all important sources of CH4, N2O, and CO2 from primary and secondary sources in dairy production were integrated in a software tool called the Integrate Farm System Model (IFSM). This tool calculates the carbon footprint of dairy and beef production as the net exchange of all GHG in CO2 equivalent units per unit of energy-corrected milk (ECM) produced or kg body weight (BW). The IFSM and Cornell Net Carbohydrate and Protein System (CNCPS) were used during this study to evaluate typical Spanish dairy farms for GHG emissions calculation and diet evaluation for methane production, respectively. The Three most important regions of dairy cattle production in Spain were selected Mediterranean (Catalonia, Valencia and Murcia), Cantabric Area (Galicia, Asturias and Cantabria) and Central zone (Castilla-La Mancha, Castilla-Leon, Madrid and Aragon), in addition to two other farms (one organic and one from Baleares Island). The average carbon footprint of all evaluated farms was 0.83 kg of CO2 equivalent units/ kg of ECM. Mediterranean farms have the highest Carbon footprint (average 0.98 kg CO2e/kg of ECM), while Cental Zone was 0.84 and the lowest was in Cantabric farms which (0.67). Two extreme farms were selected the first one had the highest carbon footprint and non-enteric methane (197MA), while the second had the lowest carbon footprint and the highest enteric methane (64CA), the first one was simulated by the IFSM model using different management change scenarios, while the second was simulated with CNCPS model using different dietary change strategies. We found that the management change reduced methane emission up to 30% while dietary change reduced it up to 5%. Three representative feedlot beef Spanish farms (two farms without corn silage; one Holstein and another mixed breed, and the third with corn silage) were used to simulate GHG emissions using the same models. The carbon footprint values ranged from 6.38 to 7.03 kg with an average value of 6.86 CO2e per kg BW. The feedlot farm with corn silage had an average carbon footprint value of 6.98 Kg CO2e/ Kg BW while without corn silage was 6.90 Kg CO2e/ Kg BW. It was concluded that both the Spanish dairy and beef sector has a lower carbon footprint and the management strategies provide a greater potential to reduce methane emissions as compared with dietary scenarios changes

Proceedings: beef cow efficiency forum

Held at Michigan State University on May 29-30, 1984 and at Colorado State University from May 31-June 1, 1984.Cover title

Leveraging Social Network Analysis for Characterizing Cohesion of Human-Managed Animals

peer-reviewedSocial network analysis (SNA) is a technique to study behavioral dynamics within a social group. In SNA, it is an open question whether it is possible to characterize animal-level behaviors by using group-level information. Also, it was believed that the combined use of SNA would provide a more comprehensive understanding of social dynamics. In light of these two factors, here we explain an approach to evaluate animal importance to a group by considering the variability in group-level structural information, which is computed by joining the animal- and group-level SNA measures node centrality and network entropy, respectively. Moreover, two other metrics, animal social interaction range and nearest-neighbor frequency matrix, which represent a social affiliation of each animal within the group, are computed to help address the general challenges in graph-based SNA and, thereby, improve the precision of animal importance measures. Finally, we derive the joint distribution of animal importance of the group in detecting atypical social behaviors. The approach is tested using tracking data of dairy cows. The reliability of the derived animal importance was superior to the already existing animal importance measures. To illustrate the usability of the animal importance metric, a simulation study was conducted to identify sick and estrus animals in a group. The social affiliation of sick cows was less when compared to healthy cows. Also, their individual distributions of animal importance were shifted toward the left of the mean of the animal importance distributions of healthy cows. Consequently, the joint distribution of animal importance of the group exhibited a bimodal distribution with a left tailored shape. The behavior of cows in estrus was opposite to that of sick cows. Moreover, with the increasing number of sick and estrus cows in the group, respectively, the group entropy decreased with larger variance and slightly increased with less variance. Therefore, the entropy-based animal importance metric has superior performances when evaluating animal importance to the group compared to the existing metrics. It can be used for generating alerts for the early detection of atypical social behaviors associated with, for instance, animal health, veterinary, and welfare.Science Foundation Irelan

Exploring the biological basis of residual feed intake in beef cattle using multi-Omics analysis.

Efficient feed utilization is critical for both economic sustainability and environmental responsibility in modern livestock production. While there has been extensive research, the multifaceted nature of feed efficiency remains complex, with many biological factors still unexplored. This dissertation examines the physiological foundations of feed efficiency by elucidating some of the complex biological mechanisms associated with residual feed intake (RFI) phenotype in beef cattle, using a range of Omics approaches. We hypothesized that metabolites related to amino acids, carbohydrates, and fatty acids could act as potential biomarkers for RFI. Through a chemical group-based metabolomics method, we identified enriched pathways in feed-efficient steers, notably in arginine biosynthesis and histidine metabolism. This led to the identification of five potential metabolite biomarkers mainly linked to amino acid metabolism, emphasizing a relationship between blood amino acid profiles and RFI. This led us to investigate the expression of genes and associated pathways related to nutrient and energy metabolism, especially in liver tissue, where hepatic metabolism is driven by transcriptional regulation. Low-RFI steers showed upregulation of genes involved in fatty acid transport, β-oxidation, and mitochondrial ATP production. In contrast, a crucial gene in amino acid metabolism responsible for aminoadipate aminotransferase activity exhibited a significant decrease in expression in low-RFI steers. These results indicate that alteration in expression of hepatic genes regulating lipid and amino acid metabolism, and mitochondrial ATP generation is associated with RFI phenotype. We also investigated potential differences in the rumen microbiome and immune gene expression of beef steers with low or high RFI. We observed increased mRNA expression of immune-related genes in both blood and liver tissues of low-RFI beef steers, especially those linked to pathogen detection and phagocytosis. Low-RFI steers also displayed variation in the relative abundance of microbial taxa compared to high-RFI. Lastly, detailed statistical analysis indicated that plasma amino acids such as tyrosine, glycine, and dimethyl sulfone may be promising economic prospects as cost-efficient predictors of RFI in beef cattle. In conclusion, this dissertation provides invaluable insights into some of the intricate biological processes associated with RFI in crossbred beef cattle, enhancing our grasp of the involved biological mechanisms and laying the groundwork for refining feed utilization in the beef cattle sector of livestock production

Proceedings...

Anais e resumos dos trabalhos apresentados na II SIGEE.bitstream/item/152904/1/Second-International-Symposium-II-SIGEE.pdfCoordenador: Roberto Giolo de Almeida. Organizadores: Patrícia Perondi Anchão Oliveira; Maurício Saito; Cleber Oliveira Soares; Lucas Galvan; Lucimara Chiari; Fabiana Villa Alves; Davi José Bungenstab

Eesti piimalehmade praakimine ja eluiga – loomapõhised, karja nakkuslikud ja loomapidajaga seotud riskitegurid

A Thesis for applying for the degree of Doctor of Philosophy in Veterinary Science.Väitekiri filosoofiadoktori kraadi taotlemiseks loomaarstiteaduse erialal.The milk production of the cows increases every year with an accompanying decrease in their lifespan both in Estonia and other countries around the world. These trends are especially apparent in larger production farms. Intensive culling and early exit from the herd reflect poor cow health and decreased welfare but may also be related to the production goals and attitudes of the farmers. The short productive life of the cows is associated with greater environmental impact and also does not meet consumer expectations. In this thesis the effect of different factors on dairy cow culling and lifespan were analyzed. The animal-based risk, herd infectious and farmer-related risk factors of culling were investigated in Estonian large dairy farms. In the current study we found that the culling rate and longevity of cows in Estonian dairy herds are similar to results of other high production countries. The highest culling risk was related to calving problems and early post-partum period. Also, the risk of culling increased with an age of the dairy cow. The four most common reasons for culling in this study were feet and claw disorders, udder disorders, metabolic and digestive disorders, and fertility problems. Estonian large dairy herds were endemically infected with many cattle pathogens having significant impact on culling and longevity by impairing cattle health, fertility, and production. In this research was found that farm managers are generally not satisfied with the culling rate and longevity of cows. Also, the culling rate was the highest and the longevity of the cows was the shortest precisely in those dairy farms where the farm managers prioritized the achievement of high milk production more than the long life of the cows. A better understanding of the economic return of dairy cow longevity and finding the compromise between milk yields and cow health would be important for the sustainability.Nii Eestis kui mujal maailmas suureneb lehmade piimatoodang igal aastal, kuid samaaegselt väheneb nende eluiga. Eriti märgatavad on need trendid suuremates tootmisfarmides. Intensiivne praakimine ja varajane karjast väljaminek kajastavad lehmade habrast tervist ja vähenenud heaolu, samas võib see olla ka seotud loomapidajate tootmiseesmärkide ja suhtumisega. Lehmade lühike produktiivne eluiga on seotud suuremate keskkonnamõjudega ega vasta ka tarbijate ootustele. Käesoleva väitekirja eesmärk oli analüüsida, millised tegurid mõjutavad lehmade praakimist ja eluiga. Uurisime nii praakimise loomapõhiseid ohutegureid Eesti piimaveise populatsioonis, samuti nakkushaiguste leviku ning loomapidajaga seotud riskitegureid peamiselt suurtes tootmisfarmides. Tuvastasime, et Eesti piimakarjades on lehmade praakimiskordaja ja eluea pikkus sarnane teistele kõrgetoodanguliste riikide näitajatele. Lehmade praakimisrisk oli kõige kõrgem poegimisprobleemide korral. Praakimise tõenäosus oli suurim vahetult pärast poegimist, samuti suurenes see oluliselt vanuse kasvades. Peamisteks Eesti lehmade praakimispõhjusteks on sõra- ja jäsemehaigused, udarahaigused, ainevahetus- ja seedeelundkonna haigused ning sigimisprobleemid. Eesti suured piimakarjad on endeemselt nakatunud mitmete oluliste veiste nakkushaigustega, millest mõnedel on märkimisväärne mõju lehmade praakimisriskile ja eluea pikkusele. Uuringus leidsime, et farmijuhatajad ei ole üldiselt rahul lehmade praakimismäära ja eluea pikkusega. Samas oli praakimiskordaja suurim ja lehmade eluea pikkus lühim just neis ettevõtetes, kus loomapidajad tähtsustasid kõrge piimatoodangu saavutamist enam kui lehmade pikka eluiga. Lehmade karjaspüsivuse parendamiseks tuleks enam panustada karja tervise edendamisse, samuti on vajalik selgitada lehmade pikema eluea majanduslikku kasumlikkust ning leida kompromiss lehmade väljalüpsi ja karjaspüsimise vahel.The publication of this dissertation is granted by the Graduate School in Biomedicine and Biotechnology and by the Estonian University of Life Sciences