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  • 1. 20 million data points can’t be wrong? Aur´lien e Madouasse 20 million data points can’t be wrong? Background Data Using milk recording data to make better decision on cow Milk health Production Somatic Cell Count Aur´lien Madouasse e Reproduction 10th March 2010
  • 2. Fifty Million Frenchmen Can’t Be Wrong 20 million data points can’t be They say the French are naughty wrong? They say the French are bad Aur´lien e Madouasse They all declare that over there The French are going mad. Background Data They have a reputation of being very gay Milk I just got back from Paris, and I just want to say: Production Somatic Cell ... Count Reproduction In Viva la France They’re full of romance You’ll find policemen with embroidery on their pants. And when they start to sing the Marseillaise They sing it forty different ways Fifty million Frenchmen can’t be wrong.
  • 3. Fifty Million Frenchmen Can’t Be Wrong 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 4. A cow’s life 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 5. What is Milk Recording? 20 million data points can’t be wrong? Aur´lien e Madouasse Milk recording is the regular collection of a milk sample from all lactating cows of a dairy herd Background What is measured: Data Milk Milk yield Production % butterfat, % protein, % lactose Somatic Cell Somatic cell count Count Reproduction Information collected Date of birth Date of calving Parity
  • 6. What is Milk Recording? 20 million data points can’t be wrong? Aur´lien e Madouasse Farmers pay for milk recording, in order to: Background Data Adapt management Identify cows likely to have mastitis Milk Production Identify the best producers Somatic Cell Count The information is also used for Reproduction Genetic evaluation Epidemiologic studies
  • 7. Dataset 20 million data points can’t be wrong? Aur´lien e Madouasse The National Milk Records: main provider of milk Background recording in England and Wales Data All the data collected by the NMR between January 2004 Milk and December 2006 were purchased: Production 19,893,093 recordings Somatic Cell Count 1,247,427 cows Reproduction 5,714 herds ⇒ Big!!!
  • 8. Dataset 20 million data points can’t be wrong? Aur´lien e Madouasse The National Milk Records: main provider of milk Background recording in England and Wales Data All the data collected by the NMR between January 2004 Milk and December 2006 were purchased: Production 19,893,093 recordings Somatic Cell Count 1,247,427 cows Reproduction 5,714 herds ⇒ Big!!!
  • 9. Data selection 20 million data points can’t be wrong? Aim: Obtain a homogeneous dataset and discard unreliable Aur´lien e data Madouasse Herds recording: Background For the 3 complete years Data On a monthly basis Milk At least 80 % of Holstein-Friesian cows Production Somatic Cell Milk samples collected on 2 consecutive milkings Count Reproduction
  • 10. Data selection 20 million data points can’t be wrong? Aim: Obtain a homogeneous dataset and discard unreliable Aur´lien e data Madouasse Herds recording: Background For the 3 complete years Data On a monthly basis Milk At least 80 % of Holstein-Friesian cows Production Somatic Cell Milk samples collected on 2 consecutive milkings Count Reproduction Final dataset 8,211,988 recordings 483,747 cows 2,128 herds ⇒ Reasonably big!!!
  • 11. Amelia’s problem 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 12. Amelia’s problem 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data 50 million Frenchmen Milk Production can’t be wrong! Somatic Cell What about one Count Reproduction Frenchman with a few million data points?
  • 13. Amelia’s problem 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 14. Milk Yield Variation 20 million data points can’t be wrong? Milk Yield Distribution Aur´lien e Madouasse Milk Yield Background Mean ∼ 27 kg/day Data Standard deviation ∼ 8.5 kg Milk Production Somatic Cell Count Reproduction 0 10 20 30 40 50 60 70 Milk Yield
  • 15. Milk Yield Variation 20 million data points can’t be wrong? Milk Yield Distribution Aur´lien e Madouasse Milk Yield Background Mean ∼ 27 kg/day Data Standard deviation ∼ 8.5 kg Milk Using a model notation we Production could write: Somatic Cell Count Yi = µ + i Reproduction Where µ = 27 kg 2 0 10 20 30 40 50 60 70 i ∼ Normal(0, 8.5 ) Milk Yield
  • 16. Milk Yield Variation 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data We can do better than that by Milk Production Somatic Cell incorporating other sources of Count Reproduction variation!!!
  • 17. Milk Yield Days in milk 20 million data points can’t be wrong? Yield increases from calving Aur´lien e until a peak and decreases 40 Madouasse Background afterwards 35 qqqqqq qq qqq qq q qqq qqqq qqqq qq Incorporating information on qq qq q qq qq q qq qq qq q qq q qq Data q q q q q q q q qq qq qq qq qq qq qq qq qq qq q q qq q qq qq q q qq qq q stage of lactation in Amelia’s q qq qq qq qq 30 q qq qq Mean Milk Yield Milk q q q qq qq qq qqq q qqqqq qq qq qq qqqq qq q Production q qqq qq qqq q qq q qq model should improve her q qq qqq qq qq qq qqq q qqqq qq qq qqq qqqq qq qq qq Somatic Cell qq qq qq 25 qq qq qq qq qqq qq prediction qq qq qq qqq Count qq qq q qq q q qq qq qq q qq qq qq qq qqq qq qqq qq q qqq qq q Reproduction qq qq q qq Using a model notation we q q qqq qq 20 q qq qq qq qq qqq qqq q q qqq qq q qq qq qq qq qq qq qq qq qq qqq qqq qq q qqq q qq qqq would write: qq qqq qq qqq qq qqq q q qqq q qqqqq q qq qq qqq qqq qqq qqqq q q qqq q q qqq q qqq qqq qq q 15 0 100 200 300 400 Yi = µ + β1 Dimi + β2 Dimi2 + ... Days in Milk + i
  • 18. Milk Yield Parity 20 million data points can’t be wrong? Aur´lien e 40 Madouasse qqq q q q qq q q qqqqqqqq qq q qq q q q q qq qqqq qq q qq qq q q qq qq q qqqqq qqqqq q qqqq q q q q qqqq q q q q q The lactation curve is lower and qqq q q qqq qq qqqqqq qqqq q qq qqqq q qq q qqq qq q q flatter for first lactation cows q q q q qq q q q qq qqqq q q qq qq q q qq qqqq qq qq qq q Background 35 qq q q q q q qq q q q q q q q qq q q q q qq q qq q qq q q qq q qqqqq qq qq qqq q qq q qqq q qq qqq q qq q q q qq qqq qq qqqq q qq qq q qq qqqqq q q q q qq q qqq qqqq q qqqq qqqqq qqq qq q qq qq qq q qq qq qq qqq qq qqq q q q q q qq q q qqqq qq qq q qq qqq qq qqqqq q qqq q q q qq qq qq qqqq Data q q q qq qq q q qqqq qq qqq q q qqqq q q qq The other parities can be q q qq qq qq q q q qqq qq qqqq q q q q q qq qqq qq q q q q q q qq qqqq qq q q q qq qq qq q q qqq q qqq qqqq qq qq qq q q qq qq q qqq qq qq qqq q qqq qqq q q qq qqq qq qq qqq qq q qq qqq qq q qqq qq qqqqq 30 qq qq q q q q q qqq Mean Milk Yield q qq qq q qq qq qq qq qqq q qqq q qq Milk q q qq q q q qq qq qq qqqqq q qqq q qqq qq qqq grouped together q qq qqq qqq qqqqq qqqqq qq qqqq qq q qq q qqq qq qq qqq q qq q qqqq qqq qqqqq qqq qqq qqqqq qq q Production q q q qq q q qq qq qqqqq q qqq qq qqq qq qq qqqqqqqqq q q qq qqqq q qq qqq q qqqqqq qq qq qqqq qqq q qq q q qq qq q qqq qqq q q qq qq qqqq q qqq qq qqqq q qqq qqq qq qq qq qq qq qqq q q qq qqq qq qqq qq qq qq q qq qq qqq q q qqq q qqq qq q qq q qqq qq qqq q q q q qqqqq qqqqq qq qq q q q qqq q q qqqq q q q q qq qqq qqq qqqq qq q qqq q q qq q q q qq qq q qq qqq qq qq q qqqqq qq q qqq qq qq qq q q qqq q qqq q q qq q q Using a model notation we q qqq q qqqq q q q qq q 25 qqqqq qq Somatic Cell q q q q q qqq q qqqqq qqqq qq q q qq qq q qq qq q qqqqq qq q qq qqqq q qq qq q qq qq qqqq qq qq qq qqq q qq q qq q qq qq qqqq qq q q q q q q q qq qq q qqq qq q qq qqq qqqq q qq qq q qq qq qqqq qq q qqqqq qq q q Count q q q qqqq qqqqqqq qqq qqq qqqqqqqq q q q qqq qq q qqq qq q q qqqq qqqq qqqq qqqq q q q q qq qq qqq qqq qqq qqq qqq qqq qq q qq qqq q qq q would write: qqq qq q qqq qqq qqq qq q qqqqqqq qqq qq q qqqq q qqqqq q q q q q q q qq qqqqq q qqqq q qq q qqqqq qq qqqq q qqqq q qqq qq qqq qq qq Reproduction q qq qq qq qq qq qqq qqqq qq qqq qqqq qqq q qqqq 20 qq q qq qq qq qqqqq q qqq q qq qqqqqq qq qq qqqqqqq q qqqqq qq qqqq qq q qq qqqqq q qq q qqq qq qq q qqqq qqqqqq q qqq q q qq qqqqqqqqqqq q qqqqq q qq q q qqq q qqqqq q qqqq Yi = µ + β1 Dimi + β2 Dimi2 + q qq q qq qqqq q q q qq qqq qqqqqqq qqq qq qq qqqqqqq qqqq q q qqqq q qq qqqqqq q qqq q q qqqqqqqqqq q qq qq q qqqqq q q qq q qqq q q qqq qq qqqqqqqq qqqqqq qqq qq q q q qqqqqqq q qqqqqq qqqqqqqqq q q q q qq qqq qqqq qq q q q qqqqqqqq q q q qq q q q qqq q qq qqqqq qq q qq qq qqq qqq qqqqq q qqqqqqqqqq qqqqqq qqq q qq qqqqqqqqqqq qq q qqqqqqqqqqqq qq qq q qqqqqqq qq qq q qq qqq q qqq qqq qqq q qq q qq qqq qqq q q q qq qq q qq qqqqqqq qq q q qq qqqq qq q q qqqq q q q qqq q q qq qq qqqqqqqq qqqqqq qq qq qqqq qq q q qq qqqqqqqqqq qq qq q q q qq q q qq qqq qq q q q qqq q q q qqq qqq q 15 q qq q q qq q q qqqqqqq q qq q qqqq ... + γParityi + q q q 0 100 200 300 400 i Days in Milk
  • 19. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 20. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 21. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 22. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 23. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 24. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 25. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 26. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 27. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 28. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 29. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 30. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 31. Milk Yield Season 20 million data points can’t be wrong? Parity 1 Parity > 1 Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 32. Solving the problem 20 million data points can’t be wrong? Aur´lien e Madouasse Summary values for milk production were extracted for Background groups of cows stratified by: Data Days in milk Milk Production Parity (1 vs. > 1) Somatic Cell Average herd production Count Month of calving Reproduction ⇒ 168 lactation curves were produced
  • 33. Amelia is happy 20 million data points can’t be wrong? Aur´lien e Madouasse Her model factored in Background details of variables such Data as the number of cows Milk calving and heifers Production Somatic Cell calving, cows to be dried Count off per month and cows in Reproduction milk exiting the herd The new model has an average accuracy rate of 96.83 %
  • 34. Amelia is happy 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 35. Somatic Cell Count 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 36. Somatic Cell Count Relation to mastitis 20 million data points can’t be wrong? Mastitis Aur´lien e Madouasse One of the biggest health problems in dairy herds Can be clinical or subclinical Background Causes an increase in milk somatic cell count (SCC) Data Milk Production Bulk Milk Somatic Cell Count Somatic Cell Reflects herd mastitis prevalence Count Penalty on milk price when it is too high Reproduction Contribution of individual cows to BMSCC Can we identify the contribution of different groups of cows to BMSCC?
  • 37. Somatic Cell Count Factors of variation 20 million data points can’t be wrong? Aur´lien e 300 q q q qq Madouasse q q q q q q q q q qq q q q qqq q qq q q q q q qq q qq q q q qqq qqq q qq q qq q q qq q q qq q q 250 qqq q q q q q qq q q q q qq q q qqq q qq Background qqq qq q qqq q q q qqq q q q q qq qq q q q qq q qq q qq qq q qq q q q q qq q q qq SCC varies with: qqq q qq q qq q q qq q q qq qqq qqq qqqqqq qq q qqq qq qq q q q q q qqqq qq Data qq qqq q q q qqqq qqq qq 200 q q qqq q qq q qq qqq q q q qq q q q q q qq q q q q qq qq q q q qq qq qqq q qqq q q q qq q q q q qqq q qq q q qq qq q qqq q q qqqqq q q q q Somatic Cell Count qq q Stage of lactation q qq qq qqq q q q q qqqq q q qq q qqqq q q qqqqq q qqq q q q q qq q qqq q qqq q Milk q q qqqqq q qq qqq q qqq q qq q q q q qq q qq q qq q q q q q q qq qq q qq q q qqq qqq q q q q q qqq qq q q q q qqq qqq Production qq qq qq qqq qq q q 150 q qq qqq q q qq q q q Parity q q qq q qqq q qq qq qq qqqqqq qq q q q qq q qq qq q qq qq q q q q qqq qq q q qqqq qqqq qq q q qqq q q q qq qq qq q qq q qq q qqqq qqqqq q q qq qq q qq qq qqqqq qqq qqq q q qqqq q qq q q q q q qq q qq q qqq q q q qq qq q q q qq qqq qq q qq q qqq q qqq qq q q q qqq q qqq q q qqqqq qq q qqq qqq q qq q q q q q qq q qq qqqqqq q q qq qqq q q q qqq q q qqq qq q q qqqqq q qq q Somatic Cell q q qqq q qq qqqq qqq qqqq q qqq q qqq q qqqqqq q qqq qq q q q q qqqqq qqq qq q q qq qqqq q qqqq q qq q q qq qqqq qqq q qq q qq q qqq q qqqqq qqqqq qq qq q q q q qq qqqqq qq qqqqq qq qqqq qqqq qqqqq qqq q qq q q q qq q qq q qqq q qqq 100 qqq q q q qqqq qq qq q q qqq qq q qq q qqq q Count qq q q q q q q q qq q q q qq q qq qqqq q qqqq q q q qq qqqq q qqqq q q q qq qqqqqq qq q q qqqq q qqqqq q qq qq qq qq qqqq qqq q q q q q q q q q qq qqqqqq qqqqq q q qq q q qqqq qqq q qqqq q q q q qqq qq qq q q qq q qq q qqqq qqq q qq q q qq qq qq qqq q qqqq q qq q q q q q q q q qq q q qqq qqqq q qqqq q q q q q q q q qq q q qqqqq q qqq qqqqq q qq q q qqq qqq qqq q qq qq qq q q qq qqq qqq q q qqqqqq q q qqqqqq q qqqqq qqq q q q qqqq q q qq qqqqqqqq qqqq q qq qq qqq qq qqq q q qq q q qq qqqqq qq q qqqqqq q qq qqqqqq qqq q q q q q qq q q q q q q qq q qqqqq q q qqq q qqq qq qqqqq qq qq qq qq q q qqqq q qqqqq qqqqq qq q qqqqqq q q q q q q qq q q q qqq qq qqq q qq q q qq q q qqqqqqqq qq qqqqq qqqqq qqqqq q qq q qqqqq qqqq q q q qqqq q qqqqqq q qq q qq q q q qqq q qq qq qqqqq qqqqq qqq qqqqq q qq q qqqqq qq qqqq q qq q qqq qq qqqqqq q qqqqq qq qqqqqqqqqqq Reproduction q q qq qqq qqqqq q qq q q qqqqqqqq qqq q q qq qq q qqq q qq qq q q qq qqqqq qqq q q qqqqqqq qqqqqqq q q qqqq qqqq q qqqq q q qqq q qqq qqqqqqqqq q qq qqq qqqq qqq qqq qq qq q q qq qq q qqq qqqqq q qqq qq q qqqqq q qqq qq qqqq q qqqqq qqqqqqq qqq q qqq qqq q qqqq q q qqqqqqqqqqqqq qqq qq qq qqqqqq qqqqqqqqqqqqqqqqqqqqq qqqqq q qqqqqqqqq qqqqq qq q qqqq q qqqq q q q q qqqqqqq q q q q qqqqqqqqqq q qq qqq q q qqqqqqqqqq q q q q qqqqqqqqq q q qq qqqqqqqq qq qqq qq qq q q qqqq qqq qqqqqq q qqq q qqqqqqqqqqq qq q q 50 q qqqqqq qqqqqqqq q qqqqqqqqqqqqqqqqqqqqq q qqqq q qqq qqqqqq q qqqqqqqqqqqqqqqqqqqq q q qqqq qqqqqq qqqqqqqqqq q qq qqqqqq q qq qqqqqqqqqqqq qqqq qq q qqq q q q 0 0 100 200 300 400 Days in Milk
  • 38. Somatic Cell Count Factors of variation 20 million data points can’t be wrong? Aur´lien e Madouasse 300 Background 250 Data SCC varies with: qqq qq qqq q qq Stage of lactation 200 qq qq q q qq q q q qq q q q qq q q q q q Milk qq q q q q Somatic Cell Count q qqqq qqq q qqq q qq qq qqqq q qqq q qq q qq qq q qqq q q q q q q Production qq qqq qq q Parity q q q qq q qq qq q qq qq qqq qq q qq 150 qq qq q qq qq q qq qq qqq q q qq q q qq qq qq qq q q q Somatic Cell q q q qq qq qq q qq qq q qq qq qqq q q qq q qq qq Parity 1 vs. > 1 qq q qq qq qq qq q q q q Count q qq qqq qq qq qq q q q q qqq q 100 q q q qq qq q qq q qq qq qqq q q q qq qq qq q q q qq q qqq q q q qqq qqq q qq q q qq q qqq q q q q qqq qq q qq q q q qq qqq qq q qqq q qq q q q q q q q qq q q q q qq q qq q q qq q q qq q q qqq q q q q qq qq q qq q q q qqq q qqq qqq qq qq qq qqqq q qq q qq q qq qq qq q qq q q q qqq q qqqqq qq q qq q qq qq qqq q q qq q qq q q q q qqq q qq q qqq q qq q qq qqq q q qq q q q qq q Reproduction q qq q qqq qq q q qq q q q qqqqq qq qq qq qqqqqqq qq q q qq qqqqqq q q qq qq q qq q q qq q qq qqq qqq qqqq qqqq qqq qq q qq qq qq q qqq qq q q qq q qq qq q q q qq qqq qq qqq q q q q qq qq qqq q q q qq qq q qq q q q q qq qq q q q q qqq q q qq qq q q q qq qq q qqq q q q qqq q q q qqqq q q qq q qq qqqq q q qqqq qqqqq q qqqqqqqq q qqqqqqqqqqq qq q q qqq qq qqq qq qqq q q qq qqq q q qq qqq q q qq q q qq qqq q qq q qq qq q q qq q q qqqqqqqqq q q 50 q q qq q qqq q q qqqq q qqqqqqqq qq q qqqqqq qqq q q qqqq qqqqq q q q q q q 0 0 100 200 300 400 Days in Milk
  • 39. Somatic Cell Count Factors of variation 20 million data points can’t be wrong? Aur´lien e Madouasse 300 Background 250 Data SCC varies with: qqq qq qqq q qq Stage of lactation 200 qq qq q q qq q q q qq q q q qq q q q q q Milk qq q q q q Somatic Cell Count q qqqq qqq q qqq q qq qq qqqq q qqq q qq q qq qq q qqq q q q q q q Production qq qqq qq q Parity q q q qq q qq qq q qq qq qqq qq q qq 150 qq qq q qq qq q qq qq qqq q q qq q q qq qq qq qq q q q Somatic Cell q q q qq qq qq q qq qq q qq qq qqq q q qq q qq qq Parity 1 vs. > 1 qq q qq qq qq qq q q q q Count q qq qqq qq qq qq q q q q qqq q 100 q q q qq qq q qq q qq qq qqq q q q qq qq qq q q q qq q qqq q q q qqq qqq q qq q q qq q qqq q q q q qqq qq q qq q q q qq qqq qq q qqq q qq q q q q q q q qq q q q q qq q qq q q qq q q qq q q qqq q q q q qq qq q qq q q q qqq q qqq qqq qq qq qq qqqq q qq q qq q qq qq qq q qq q q q qqq q qqqqq qq q qq q qq qq qqq q q qq q qq q q q q qqq q qq q qqq q qq q qq qqq q q qq q q q qq q Reproduction q q q qq qq qq q qqq qq q qqq qq qqq qq qqq q q qq qqq q q qq qqq q Early vs. late lactation q q qqq qqqq qqqq qqq qq q q qq qq q q q qq qq qq q q qq q q q qqqqq qqq qq q qqq q q q qqq q q q qqqq q q qq q qq qqqq q q qq qq qq qqqqqqq qq q q qq qqqqqq q qq q q q qqqq qqqqq q qqqqqqqq q qqqqqqqqqqq qq q qqq q q qq qq q qq q q qq qq qqq q q q qq qq q qq q q q q qq q qq qq q q q q q q qq q qq qq q q q qq qqq qq qqq q q qq q q qq qqq q qq q qq qq q q qq q q qqqqqqqqq q q 50 q q qq q qqq q q qqqq q qqqqqqqq qq q qqqqqq qqq q q qqqq qqqqq q q q q q q 0 0 100 200 300 400 Days in Milk
  • 40. Somatic Cell Count Splitting the data 20 million data points can’t be wrong? Aur´lien e Madouasse Two Consecutive Monthly Recordings Background Data Milk Production Somatic Cell Count Reproduction SCC
  • 41. Somatic Cell Count Splitting the data 20 million data points can’t be wrong? Aur´lien e Madouasse Two Consecutive Monthly Recordings Background Data Milk Production Somatic Cell Count Low Reproduction SCC High
  • 42. Somatic Cell Count Splitting the data 20 million data points can’t be wrong? Aur´lien e Madouasse Two Consecutive Monthly Recordings Background Data Milk Production Somatic Cell Low - Low Count Low Low - High Reproduction SCC High - Low High High - High
  • 43. Somatic Cell Count Splitting the data 20 million data points can’t be wrong? Aur´lien e Madouasse Two Consecutive Monthly Recordings Background Data Heifers Cows Milk Production Calving Lactating Dry Period Lactating Somatic Cell Low - Low Low - Low Low - Low Count Low Low Low Low Low - High Low - High Low - High Reproduction SCC SCC SCC SCC High - Low High - Low High - Low High High High High High - High High - High High - High
  • 44. Somatic Cell Count Dynamics 20 million data points can’t be wrong? Aur´lien e Heifers Calving Dry Period 100 100 Madouasse 80 q 80 Most heifers calve Low % of Cow Category % of Cow Category 60 60 Background 40 40 q q Lot of cows cured during Data the dry period 20 q 20 q q 0 0 Milk Low High Low−Low Low−High High−Low High−High Production High SCC more frequent Somatic Cell Count 100 Heifers Lactating 100 Cows Lactating in mulitparous cows q 80 80 Reproduction ⇒ Important variability % of Cow Category % of Cow Category q 60 60 40 20 40 20 q between herds: progress is 0 q q q 0 q q possible!!! Low−Low Low−High High−Low High−High Low−Low Low−High High−Low High−High
  • 45. Somatic Cell Count Dynamics 20 million data points can’t be Dry Period Heifers Lactating Cows Lactating wrong? 100 100 100 Aur´lien e 80 80 80 Madouasse q 60 60 60 % % % q Background 40 40 40 q Data 20 q 20 20 q q Milk 0 0 0 Production Dimin Rais Dimin Rais Dimin Rais Somatic Cell Count Reproduction
  • 46. Somatic Cell Count Dynamics 20 million data points can’t be Dry Period Heifers Lactating Cows Lactating wrong? 100 100 100 Aur´lien e 80 80 80 Madouasse q 60 60 60 % % % q Background 40 40 40 q Data 20 q 20 20 q q Milk 0 0 0 Production Dimin Rais Dimin Rais Dimin Rais Somatic Cell Count Reproduction Apparent cure rate At its highest during dry period More important in primiparous than in multiparous cows Apparent new infection rate Higher during the dry period
  • 47. Somatic Cell Count Contribution to BMSCC 20 million data points can’t be wrong? Aur´lien e 50 Madouasse q Chronically infected Background 40 lactating cows are the Median percentage of herd−years Data Milk 30 biggest contributors to Production BMSCC Somatic Cell Count 20 q Each % increase in cows Reproduction Heifers Lactating 10 q Cows Lactating calving High results in a q q massive increase in q q q −10 −5 0 0 5 q q q q 10 15 q q 20 BMSCC Heifers Calving Dry Period Increase in BMSCC (1,000 cells/mL) per % of increase in the herd
  • 48. Reproduction 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction
  • 49. Energy Balance in Early Lactation 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Start of lactation Milk Massive increase in energy demand Production Limited appetite Somatic Cell Count ⇒ Negative energy balance Reproduction
  • 50. Energy Balance in Early Lactation and Reproduction 20 million data points can’t be wrong? Aur´lien e Madouasse Background Later resumption of luteal activity in cows in NEB Data Milder estrus expression with increasing milk yield Milk Production Negative correlation between milk yield and calving Somatic Cell interval Count Genetic selection on yield and composition has been Reproduction accompanied by poorer reproduction
  • 51. Energy Balance and Milk Production 20 million data points can’t be wrong? Aur´lien e Madouasse Background Association between energy balance and milk composition Data at the start of lactation Milk Production NEB associated with: Somatic Cell Increase in butterfat % Count Decrease in protein % Reproduction Increase in the fat to protein ratio
  • 52. Aim of the study 20 million data points can’t be wrong? Most previous studies looked at: Aur´lien e Association between milk composition and an estimated Madouasse energy balance Background Association between energy balance and reproduction Data ⇒ The fat to protein ratio has become a widely used marker Milk of energy balance Production Somatic Cell ⇒ No study on the link between milk constituents and Count reproduction Reproduction Aim of the study Model the association between the calving to conception interval and milk quantity and constituents at the start of lactation
  • 53. Calving to Conception Intervals 20 million data points Calving to Conception Intervals estimated from recalving can’t be wrong? date Aur´lien e Gestation length: 280 days Madouasse 58.6 Background Percentage of cows that have conceived Data 46 38.7 Milk Production 29.3 Somatic Cell Count 17.9 Reproduction 7.3 0.5 0 20 61 82 103 124 145 200 Days in milk Intervals divided in 5 categories: [20-60]; [61-81]; [82-102]; [103-123]; [124-144]
  • 54. Model 20 million data points can’t be wrong? Aur´lien e Multilevel discrete time survival model Madouasse The probability of conception in each of the 5 intervals was Background modelled Data Accounting for herd variability Milk More clearly: Production Somatic Cell Count Reproduction
  • 55. Model 20 million data points can’t be wrong? Aur´lien e Multilevel discrete time survival model Madouasse The probability of conception in each of the 5 intervals was Background modelled Data Accounting for herd variability Milk More clearly: Production Somatic Cell Count Ytjk = Bernoulli(ptjk ) 5 Reproduction ptjk ln( 1−ptjk ) = Itjk (γt + δtk ) + Xjk β t=1 δtk ∼ MVN(0, Σδ )
  • 56. Model Results 20 million Interval 1 Interval 2 Interval 3 Interval 4 Interval 5 data points 0.2 0.15 can’t be Milk 2 0.1 wrong? 0.05 0.2 Aur´lien e 0.15 Madouasse Protein 2 0.1 0.05 0.2 Background 0.15 Lactose 1 0.1 Data 0.05 0.2 Milk 0.15 Protein 1 Production 0.1 0.05 Somatic Cell 0.2 Count SCC 2 0.15 0.1 Reproduction 0.05 0.2 0.15 SCC 1 0.1 0.05 0.2 0.15 Fat 1 0.1 0.05 −2 −1 0 1 2 −2 −1 0 1 2 −2 −1 0 1 2 −2 −1 0 1 2 −2 −1 0 1 2
  • 57. Model Results 20 million Interval 1 Interval 2 Interval 3 Interval 4 Interval 5 data points 0.2 0.15 can’t be Milk 2 0.1 wrong? 0.05 0.2 Aur´lien e 0.15 Madouasse Protein 2 0.1 0.05 0.2 Background 0.15 Lactose 1 0.1 Data 0.05 0.2 Milk 0.15 Protein 1 Production 0.1 0.05 Somatic Cell 0.2 Count SCC 2 0.15 0.1 Reproduction 0.05 0.2 0.15 SCC 1 0.1 0.05 0.2 0.15 Fat 1 0.1 0.05 −2 −1 0 1 2 −2 −1 0 1 2 −2 −1 0 1 2 −2 −1 0 1 2 −2 −1 0 1 2 Where is the fat to protein ratio?
  • 58. Is that of any use? Prediction of the calving to conception interval in new herds 20 million data points can’t be Interval 1 Interval 2 Interval 3 wrong? Aur´lien e 0.2 0.2 0.2 Madouasse Observed Observed Observed qq q q q q q qq q q qq q qq qqq q qq qq q q qq qq q qqqqq qqq q q qq qq q qq qqq q q qq qqq q q qq qqq q qq q q qqq q qq qq q 0.1 0.1 qqq q q qqq 0.1 qq qqq q q q qq qqqq q q q qqqq qqq qq q q qq Background qq q q qq qq q q qqq qq qq qq q q qq q qq q q qqq qq q qqq qq qq qq q qqqq qq q qqq qqq q q qq qq q qqqq qqqqq qq q qq qqq qqq q qq qq q qqq qq qq q q qq qqq qq qq qq q qq qq qq q qq qqq qq qq qq q Data q qq qq qqq qqq qq 0.0 0.0 0.0 Milk 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 Production Predicted Predicted Predicted Somatic Cell Count Interval 4 Interval 5 End of Interval 5 0.7 Reproduction 0.2 0.2 0.6 Observed Observed Observed 0.5 q q qq q qq qq qq q q q qq q q qq qq qqq qq qq qqq q qqqq qq q q q qq qq qqq 0.1 q qqqqq qqq q q q qqqq q q qqq q q 0.1 0.4 qq qq q q qqqq q qq q qq qqq q q q qq qqq q qq q q qqqqq q qq qqqq q q qq q qq q qq q qq qq qqq q qq q qq q qq q qq q qqqq qq q qqq q qq q qqq q q qqqqqq q qqq q qqq q q qq qq q q qqq qqqqq q qqqqqq q q qq qq qq qq qqq q qq qqqq q qqq q q q q q q qq qq q qq q qq 0.3 qqq q qq qq q q qq qq qq q q q 0.0 0.0 0.2 0.00 0.05 0.10 0.15 0.20 0.25 0.00 0.05 0.10 0.15 0.20 0.25 0.2 0.3 0.4 0.5 0.6 0.7 Predicted Predicted Predicted
  • 59. And now? 20 million data points can’t be wrong? Aur´lien e Madouasse Background The fat to protein ratio seems to be overrated! Data Possibility to implement the model in a herd management Milk software Production Somatic Cell ⇒ Identify cows that need to be looked after Count Reproduction ⇒ Maybe these cows are more at risk to get other health troubles
  • 60. 20 million data points can’t be wrong? Aur´lien e Madouasse Thank You Background Prof. Martin Green Data Dr Jon Huxley Milk Production Prof. William Browne Somatic Cell Count Dr Andrew Bradley Reproduction Prof. Ian Dryden r D Wendela Wapenaar The Postgraduates The Population Health and Welfare Group ...
  • 61. 20 million data points can’t be wrong? Aur´lien e Madouasse Background Data Milk Production Somatic Cell Count Reproduction

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