Data from: Behaviors 3 and 6 weeks after caustic paste disbudding in dairy calves
Data files
Mar 19, 2026 version files 479.08 MB
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1_BehaviorData_BORISOutputs.xlsx
5.53 MB
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1_BehaviorData_Prep.pdf
210.88 KB
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1_BehaviorData_Prep.Rmd
11.38 KB
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2_BehaviorData_Numbness.xlsx
17.48 KB
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3_BehaviorData_SecondBySecond.xlsx
57.05 MB
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4_DisbuddingAndPharmacologicalManipulation.xlsx
20.47 KB
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5_BehaviorAnalysis_DisbuddingAndPharmacologicalManipulation.pdf
963.09 KB
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5_BehaviorAnalysis_DisbuddingAndPharmacologicalManipulation.Rmd
45.29 KB
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6_BehvaiorReliablity_Data.xlsx
28.75 KB
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7_BehaviorReliabilityAnalysis.pdf
737.88 KB
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7_BehaviorReliabilityAnalysis.Rmd
44.18 KB
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README.md
10.06 KB
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SupplementalTable.csv
4.04 KB
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SupplementalTable.pdf
152.25 KB
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Video_Examples.zip
414.26 MB
Abstract
Disbudding with caustic paste, which chemically destroys horn-producing tissue, is common on U.S. dairy farms. Research on behavioral changes in calves has predominantly focused on the 48 h after disbudding with a hot iron or caustic paste. In the weeks following the procedure, behavioral changes such as ear flicks, head shakes and other head and body movements have been evaluated primarily for hot-iron disbudding. Our objective was to quantify behaviors often associated with pain in calves for up to 6 wk after caustic paste disbudding compared with a sham procedure. Jersey and Holstein female calves were disbudded using caustic paste at 3 d of age with a local anesthetic (lidocaine) and an NSAID (meloxicam, n = 18), while control calves received a sham procedure (n = 15). To manipulate the calves’ experience, we measured behavior for both paste-disbudded and intact control calves under two conditions, either with the provision of lidocaine as a local anesthetic (Anesthesia observations) at 4 d, 3 and 6 wk of age, or without any pain relief (Baseline observations) at 3 and 6 wk. We predicted that caustic paste disbudded calves would exhibit more behavioral indicators of pain, through the presence of more spontaneous movements and less activity, than intact control calves during Baseline observations. We also predicted the behavioral differences would be reduced during Anesthesia observations when caustic paste-disbudded calves would experience pain relief. Ten behaviors were continuously measured from video recordings for 75 min/d as either total frequency (ear flicks, head shakes, head rubs, head scratches, tail flicks, and transitions between lying and standing) or duration (grooming, ruminating, lying with the head still, and non-nutritive oral manipulation). Unexpectedly, we found that the sensation loss from lidocaine did not persist for the entire 75-min period and therefore we chose to analyze only the Baseline observations. We found no evidence of significant differences between caustic paste-disbudded or intact control calves for any of the behaviors observed 3 and 6 wk after the procedure. Our results raise further methodological questions about how to best assess long-term pain in cattle. Future models could consider exploring 24-h observations or other pharmacological manipulations, such as NSAIDs or ring blocks.
Description of the data and file structure
1_BehaviorData_Prep.Rmd
This RMarkdown file uses the 1_Behavior Data_BORIS Outputs.xlsx and 2_2_Behavior Data_Numbness.xlsx file listed below to create the 3_Behavior Data_Second by Second.xlsx and 4_Disbudding and Pharmacological Manipulation.xlsx files. Rmd files can be downloaded and run in R. This file is annotated.
1_BehaviorData_Prep.pdf
This file is the PDF output of the corresponding RMarkdown file, and includes the code and output previews. This file is annotated.
1_BehaviorData_BORISOutputs.xlsx
The BORIS behavior output data was exported from BORIS observer software after continuous observation of the videos. Observation.id column shows Calf_YYMMDD_ObservationType(Baseline or LidocaineProbe) followed by a number indicating the video segment. These are then divided into the columns of "Calf", "Date_ymd", "Lido/Baseline", "VideoSegment", which indicate the calf ID, date, presence of lidocaine or baseline, and video segment #. Observation indicates the age (4 d, 3 wk, 6 wk) and presence of medication (Anesthesia) or not (Baseline). "BORIS date" indicates when the video was scored by the corresponding "Observer". "Media file" shows the path to video imported into BORIS, while "Total Length" shows the duration of that segment in seconds. Behavior represents what is being scored, the frequency (ear flicks, tail flicks, head shakes, head scratches, head rubs, transitions between lying and standing) or duration (grooming, ruminating, non-nutritive oral manipulation (NNOM), lying with the head still) were recorded during the 75-min observations. "Behavior type" shows "point" for frequency behaviors and "state" for duration ones. "Start (s)" and "Stop (s)" indicate the behavior start and stop time in seconds, while "Duration (s)" shows the total number of seconds a state behavior occurred for. The "Comments" allowed observers to note anything unusual.
The sheet "Starttimes" isolates when "Trial Start" was coded for the video in BORIS. The trial start time is used to format the data so all behaviors are on the same 75-min scale regardless of how long the video camera was running before the observation began.
2_BehaviorData_Numbness.xlsx
This file includes the calf individual identification number and disbudding treatment (paste or control). The observation column represents which of the 5 observations is presented (Baseline or Anesthesia and Age), while the observation type includes only the Baseline or Anesthesia information. Age_Wks shows the calf age in weeks for a given observation. During Anesthesia observations, pre pinpricks and post pinprick results are shown in their respective column by horn bud (left or right) or the sum by calf (left+right). A pinprick response of 0 indicates no behavioral responses occurred and the horn bud was completely numb, while 10 pinprick indicates full sensation on that side of the head. Before Baseline observations, a pinprick test using only 2 locations was completed as calves were assumed to have full sensation, which is supported by all calves showing 2 responses. "N/A" indicates the data was not collected. The "PinPrick_Disbudding" column shows the pinprick response for paste disbudded calves on the day of disbudding (3 d of age), and supports that all calves were completely numb at the time of the procedure.
3_BehaviorData_SecondBySecond.xlsx
This file presents the second by second scoring of behavior data for calves obtained via video observation. Calf represents the individual ID of each animal. Each behavior column (ear flicks, tail flicks, head shakes, head scratches, head rubs, transitions, grooming, ruminating, non-nutritive oral manipulation (NNOM), lying) indicate a 1 when the behavior is occurring, and 0 if it is not during the 75-min observations. If multiple occurrences of a behavior happened in the same second, the values will be summed, so that a 2 appears for that second. The "Standard Time" represents the 75 min in seconds. The observation column represents which of the 5 observations is presented (Baseline or Anesthesia and Age), while the observation type includes only the Baseline or Anesthesia information. Treatment designated if that calf was either disbudded with caustic paste, or a non-disbudded control. Breed indicates "J" for Jersey or "H" for Holstein. Age indicates when calves were 4 d, 3 wk, and 6 wk. Pinprick tests were conducted by the same individual and observed live. During Anesthesia observations, pre pinpricks and post pinprick results are shown in their respective column by horn bud (left or right) or the sum by calf (left+right). A pinprick response of 0 indicates no behavioral responses occurred and the horn bud was completely numb, while 10 pinprick indicates full sensation on that side of the head. Before Baseline observations, a pinprick test using only 2 locations was completed as calves were assumed to have full sensation, which is supported by all calves showing 2 responses. "N/A" indicates the data was not collected. The "PinPrick_Disbudding" column shows the pinprick response for paste disbudded calves on the day of disbudding (3 d of age), and supports that all calves were completely numb at the time of the procedure. One calf (3246) was missing data from the 4 d observation, which appears in the data set as a single row with N/A for the pinprick data and blank values for the behaviors.
4_DisbuddingAndPharmacologicalManipulation.xlsx
This file presents the summarized/totals of the behavior data for calves obtained via video observation. Calf represents the individual ID of each animal. The frequency (ear flicks, tail flicks, head shakes, head scratches, head rubs, transitions between lying and standing) or duration (grooming, ruminating, non-nutritive oral manipulation (NNOM), lying with the head still) of behaviors observed during the 75-min observations are represented in their respective column. The observation column represents which of the 5 observations is presented (Baseline or Anesthesia and Age) while the observation type includes only the Baseline or Anesthesia information. Treatment designated if that calf was either disbudded with caustic paste, or a non-disbudded control. Breed indicates "J" for Jersey or "H" for Holstein. Age_Wks represents the weeks of age for the calf during that observation, 0 represents calves that were 4 days old. Pinprick tests were conducted by the same individual and observed live. During Anesthesia observations, pre pinpricks and post pinprick results are shown in their respective column by horn bud (left or right) or the sum by calf (left+right). A pinprick response of 0 indicates no behavioral responses occurred and the horn bud was completely numb, while 10 pinprick indicates full sensation on that side of the head. Before Baseline observations, a pinprick test using only 2 locations was completed as calves were assumed to have full sensation, which is supported by all calves showing 2 responses. "N/A" indicates the data was not collected. The "PinPrick_Disbudding" column shows the pinprick response for paste disbudded calves on the day of disbudding (3 d of age), and supports that all calves were completely numb at the time of the procedure.
5_BehaviorAnalysis_DisbuddingAndPharmacologicalManipulation.Rmd
This RMarkdown file uses the 4_Disbudding and Pharmacological Manipulation.xlsx file listed above to build and validate models to describe the effects of treatment (Control and Paste) on the 10 behaviors observed and produce the model results used in the corresponding paper. Rmd files can be downloaded and run in R. This file is annotated.
5_BehaviorAnalysis_DisbuddingAndPharmacologicalManipulation.pdf; This file is the PDF output of the corresponding RMarkdown file, and includes the code and output previews. This file is annotated.
6_BehvaiorReliablity_Data.xlsx
This file presents the behavior data used to evaluate interobserver reliability before data collection began. The "Video" column shows the video segment that was scored to determine reliability. "Behavior" shows which of the 10 scored behaviors, described above, are shown in the respective row. The remaining columns show the count and duration data for the behaviors for 11 observers labeled as Gold and Intern 1 through 10. Data in the duration columns are presented in seconds.
7_BehaviorReliabilityAnalysis.Rmd
This RMarkdown file uses the 6_BehvaiorReliablity_Data.xlsx file listed above to evaluate inter-observer reliability for 10 observers in comparison to the Gold Standard for each the 10 behaviors recorded. Rmd files can be downloaded and run in R. This file is annotated.
7_BehaviorReliabilityAnalysis.pdf; This file is the PDF output of the corresponding RMarkdown file, and includes the code and output previews. This file is annotated.
SupplementalTable.pdf, SupplementalTable.csv
This file presents a supplemental table (Supplemental Table S1) with the behavior model outputs and test statistics, along with a table (Supplemental Table S2) presenting the means, SE, and 95% CI for all behaviors scored.
Videos:
Video_Examples.zip: A collection of short videos are available to demonstrate what each behavior, as defined in the corresponding paper, looked like. Videos include Ear Flick Example.mp4, Tail Flick Example.mp4, Head Shake Example.mp4, Head Scatch Example.mp4, Head Rub Example.mp4, Transition Example.mp4, Grooming Example.mp4, NNOM Example.mp4, Rumination Example.mp4, Lying Head Still Example.mp4
Code/Software
All analyses were run in R using RStudio. Software versions, including those for all packages used, are included in 1_BehaviorData_Prep.Rmd, 5_BehaviorAnalysis_DisbuddingAndPharmacologicalManipulation.Rmd, 7_BehaviorReliabilityAnalysis.Rmd and the associated PDF exports.
Data were collected from 33 heifers. Calves were assigned to 1 of 2 treatments: caustic paste disbudding (n = 18; 13 Holsteins and 5 Jerseys) or control (n = 15; 11 Holsteins and 4 Jerseys). On d 3 of life, pain relief was provided, and Dr. Naylor’s paste was rubbed into unshaved horn buds at 0.25 or 0.30 mL/per horn bud when calves had a birth weight of < 34 kg or ≥ 34 kg, respectively for disbudded calves. All calves were video recorded 5 times during the next 6 wk. To manipulate the level of pain experienced, we measured behavior under 2 conditions for all calves, first without pain relief (Baseline) and then with 7 mL of 2% lidocaine per horn bud (Anesthesia) at the same time of day (~0630h). Anesthesia observations occurred at 4 d of age, 3 and 6 wk, while Baseline observations occurred at 3 and 6 wk. Videos recording lasted for 75 min and were continuously observed for the frequency or duration of 10 behaviors. The 75 min videos were initially broken up into "segments" which the order on an observation are indicated by "Video_Segments". We will reformat the data so we can easily observe when behaviors are occurring across the 75 min, regardless of the video segment. To assess the the efficacy anesthesia, a pinprick test was conducted. A clean needle was used to gently prick 10 locations at the base of the horn bud or wound and behavioral responses were observed. Pinprick tests occurred on the Anesthesia days 10 min after the injection, before behavior was recorded, and at the end of observations, 85 min after the injection. On Baseline days, 2 pinpricks were used to show calves had sensation before video recording began. Files are numbered in the order we will follow to move from raw data through processing, summarizing, and then analyzing.
