Evaluation of a gait scoring system for cattle by using cluster analysis and Krippendorff’s α reliability

2018 ◽  
Vol 184 (7) ◽  
pp. 220-220 ◽  
Author(s):  
Nina Volkmann ◽  
Jenny Stracke ◽  
Nicole Kemper
Keyword(s):  
Cluster Analysis ◽  
Dairy Cows ◽  
Scoring System ◽  
Partial Agreement ◽  
Claw Lesions ◽  
Cluster 2 ◽  
Locomotion Score

The aim of the presented study was to validate a three-point locomotion score (LS) classifying lameness in dairy cows. Therefore, locomotion of 144 cows was scored and data on claw lesions were collected during hoof trimming. Based on latter data a cluster analysis was performed to objectively classify cows into three groups (Cluster 1–3). Finally, the congruence between scoring system and clustering was tested using Krippendorff’s α reliability. In total, 63 cows (43.7 per cent) were classified as non-lame (LS1), 38 (26.4 per cent) were rated as LS2 with an uneven gait and 43 (29.9 per cent) cows were ranked as clearly lame (LS3). In comparison, hoof-trimming data revealed 64 cows (44.4 per cent) to show no diagnosis, 37 (25.7 per cent) one diagnosis, 33 animals (22.9 per cent) two diagnoses and 10 (7.0 per cent) more than two. Comparing the respective categorisation received by either the cluster analysis or LS in between groups, a high correspondence (79.4 per cent and 83.7 per cent) could be found for LS1 and cluster 1 as well as for LS3 and cluster 3. Only LS2 had partial agreement (21.1 per cent) to cluster 2. However, Krippendorff’s α was 0.75 (95 per cent CI 0.68 to 0.81), indicating a good degree of reliability. Therefore, the results of this study suggested that the presented LS is suitable for classifying the cows’ state of lameness representing their claw diseases.

The effect of diet and housing on the development of sole haemorrhages, white line haemorrhages and heel erosions in Holstein heifers

1998 ◽  
Vol 67 (1) ◽  
pp. 9-16 ◽  
Author(s):  
C. T. Livesey ◽  
T. Harrington ◽  
A. M. Johnston ◽  
S. A. May ◽  
J. A. Metcalf
Keyword(s):  
Statistical Analysis ◽  
Dairy Cows ◽  
Scoring System ◽  
Post Partum ◽  
Early Lactation ◽  
Lesion Score ◽  
White Line ◽  
Analysis Of Results ◽  
Foot Lesions ◽  
Locomotion Score

AbstractHaemorrhagic lesions, heel erosions and changes in foot conformation have been associated with husbandry, underfoot conditions and nutrition of dairy cows.These characteristics were monitored in 40 heifers in a 2 × 2 factorial design starting in the last trimester of pregnancy and continuing until 12 weeks post partum. Primary treatments were housing in straw yards or cubicles and secondary treatments were alternative complete diets given during lactation which differed in concentrate: forage ratio. A scoring system was developed for each of the foot lesions to allow statistical analysis of results. Locomotion scoring was carried out weekly.White line haemorrhages, sole haemorrhages and heel erosions were all present before calving. White line haemorrhages were exacerbated by housing in cubicle yards and alleviated by housing in straw yards (P < 0·001) with an interaction between diet and housing around calving (P < 0·05). Sole haemorrhages were exacerbated both by housing in cubicle yards (P < 0·01) and the high concentrate diet (P < 0·01) with an interaction between diet and housing around calving (P < 0·05). Heel erosions were exacerbated (P < 0·05) by housing in straw yards but not affected by diet. Sole haemorrhage and heel erosion scores generally increased during early lactation (P < 0·001) independent of the treatments. There was evidence that these foot lesions were not caused by laminitis. There was a higher incidence of lameness for heifers given the high concentrate diet but no correlation between locomotion score and the type of lesion or lesion score.

scholarly journals Effect of Parity on Claw Horn Lesions in Holstein Dairy Cows: Clinical and Radiological Study

2019 ◽  
Vol 19 (1) ◽  
pp. 147-158 ◽  
Author(s):  
Enrico Fiore ◽  
Laura Perillo ◽  
Giorgio Marchesini ◽  
Giuseppe Piccione ◽  
Elisabetta Giudice ◽  
...  
Keyword(s):  
Dairy Cows ◽  
Correlation Coefficient ◽  
Radiographic Images ◽  
Pearson’S Correlation Coefficient ◽  
Pearson's Correlation ◽  
Group 3 ◽  
Claw Lesions ◽  
Locomotion Score ◽  
Group 1 ◽  
Holstein Dairy Cows

AbstractThe aim of this study was to estimate the effect of parity on claw lesions prevalence in Holstein dairy cows through clinical and radiological observations. Ninety-seven cows were examined two months after calving to record body condition score, locomotion score, feet diagnostic imaging (X-ray), hoof trimming and clinical evaluation. According to the lactation, the cows were divided into three groups: first parity (Group 1, n=40), second parity (Group 2, n= 29) and third or more parity (Group 3, n=28). Several claw lesions were found. One-way analysis of variance was applied along with Pearson’s correlation coefficient. Significant effect of groups was evidenced on radiographic images. In particular, the radiographic images showed a significant increase of osteolysis from Group 1 to Group 3. The application of Pearson’s correlation coefficient showed a significantly positive correlation between locomotion score and some claw lesions in all groups. In conclusion, this study provides an overview of claw lesions in dairy cow through clinical and radiological observations.

scholarly journals Echocardiographic phenotypes of patients with sickle cell disease. An unsupervised analysis based on etendard cohort

2021 ◽  
Vol 22 (Supplement_1) ◽  
Author(s):  
T D"humieres ◽  
J Inamo ◽  
S Deswarte ◽  
T Damy ◽  
G Loko ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Cardiac Output ◽  
Sickle Cell Disease ◽  
Diastolic Function ◽  
Sickle Cell ◽  
Left Ventricular ◽  
Integrative Approach ◽  
Cell Disease ◽  
Clinical Profiles ◽  
Cluster 2

Abstract Funding Acknowledgements Type of funding sources: Public grant(s) – National budget only. Main funding source(s): PHRC Backgroung Echocardiography is the cornerstone in the diagnosis of cardiopulmonary involvement in sickle cell disease (SCD). However, given the unique pathophysiology of SCD associating high cardiac output, and various degrees of peripheral vasculopathy, differentiate the pathological from the physiological using echocardiography can be particularly challenging. Purpose This study sought to link cardiac phenotypes in homozygous SCD patients with clinical profiles and outcomes using cluster analysis. Methods We analyzed data of 379 patients with a sufficient echographic dataset included in the French Etendard Cohort, a prospective cohort initially designed to assess the prevalence of pulmonary hypertension. A cluster analysis was performed on echocardiographic variables, and the association between clusters and clinical profiles and outcomes was assessed. Results Three clusters were identified. Cluster 1 (N = 122) patients had the lowest cardiac output, only mild left cavities remodeling, diastolic dysfunction, and high tricuspid regurgitation velocity (TRV). They were predominantly female, as old as cluster 2, and displayed the most severe functional limitation. Cluster 2 (N = 103) patients had the highest cardiac output, left ventricular mass and a severely dilated left atrium. Diastolic function and TRV were similar to cluster 1. These patients had a higher blood pressure and a severe hemolytic anemia. Cluster 3 (N = 154) patients had mild left cavities remodeling, the best diastolic function and the lowest TRV. They were younger patients with the highest hemoglobin and lowest hemolytic markers. Right heart catheterization was performed in 94 patients. Cluster 1 gathered the majority of precapillary PH while cluster 2 gathered postcapillary PH and no PH was found in cluster 3. After a follow-up of 9.9 years (IQR: 9.3 to 10.5 years) death occurred in 38 patients (10%). Clusters 2 had the worst prognosis with 18% mortality rate vs. 12% in cluster 2 and 5% in cluster 1 (P log-rank = 0,02). Results are summarized in the central illustration. Conclusions Cluster analysis of echocardiographic variables identified 3 phenotypes among SCD patients, each associated with different clinical features and outcome. These findings underlines the necessity to rethink echocardiographic evaluation of SCD patients, with an integrative approach based on simultaneous evaluation of TRV along with left cavities remodeling and diastolic parameters. Abstract Figure.

23 Effects of Rubber Matting on Cattle Locomotion Scores in Slatted Facilities

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 23-23
Author(s):  
Cody Dawson ◽  
Parker Henley ◽  
Adam Schroeder ◽  
Courtney Hayes ◽  
Tara Felix ◽  
...  
Keyword(s):  
Scoring System ◽  
Stocking Density ◽  
Feedlot Steers ◽  
Cattle Feeding ◽  
Trained Staff ◽  
Eden Prairie ◽  
Locomotion Score ◽  
Over Time

Abstract The objective was to determine effects of interlocking rubber floor matting in slatted indoor cattle feeding facilities on cattle locomotion. In experiment 1, Fall-born Angus × Simmental steers (N = 206; BW = 228 ± 34 kg) were blocked by weight and assigned to 32 pens. Pens were randomly assigned to 1 of 4 treatments: new Max Grip Animat matting (MG), new Animat Pebble matting (PEB), old Animat Pebble matting (OLD), and no matting/concrete slating (CONC). Steers were fed a common diet for 209 d with an average stocking density of 3.70 m2 per steer. Locomotion scores were assigned by two trained staff using a 0–3 scale of the Step-Up® Locomotion Scoring System (Zinpro, Eden Prairie, MN) throughout both experiments. There was no treatment by day interaction (P = 0.88) observed. Treatment affected (P &lt; 0.01) locomotion scores with CONC being the greatest and MG, PEB, and OLD being lesser and not different from each other. Locomotion scores also increased (P &lt; 0.01) over time. In experiment 2, Fall-born Angus × Simmental steers (n = 189; BW = 352 ± 43 kg) were blocked by weight and assigned to 21 pens. Pens were randomly assigned to 1 of 3 treatments: new Animat Pebble matting (PEB2), old Animat Pebble matting (OLD2), or no matting/concrete slating (CONC2). Steers were fed a common diet for 152 d with an average stocking density of 2.64 m2 per steer. There was no treatment by day interaction (P = 0.42) observed. However, both treatment and day affected (P ≤ 0.02) locomotion scores. Steers on CONC2 had the greatest locomotion score, while PEB2 and OLD2 were not different from each other. Locomotion scores were the greatest on d 152. Overall, results suggest new and old rubber floor matting improved locomotion scores of feedlot steers in slatted indoor cattle feeding facilities.

scholarly journals Identification of Novel Classes for Patients With Lupus Nephritis Using Two-step Cluster Model

2021 ◽  
Author(s):  
Ting Huang ◽  
Shasha Xie ◽  
Liqing Ding ◽  
Hui Luo
Keyword(s):  
Cluster Analysis ◽  
Evaluation System ◽  
Demographic Data ◽  
White Blood Cells ◽  
Damage Index ◽  
Cross Sectional Study ◽  
Laboratory Findings ◽  
Cross Sectional ◽  
Mild Disease ◽  
Cluster 2

Abstract Objectives: To identify and reclassify the patients in the LN cohort, and to further analyze the prominent clinical features and clinical significance of each cluster of patients.Methods: This is a cross-sectional study of a cohort of 635 LN patients from the Rheumatology Department of Xiangya Hospital of Central South University. Demographic data, laboratory findings and clinical evaluation system include physician’s global assessment and the SLICC/ACR Damage Index were collected. Using two-step cluster analysis, patients with similar clinical property were identified and compared.Results: Among the 635 LN patients, 599 patients (94.3%) were female. The mean age of the patients were 33.8 ± 10.4 years. Three subgroups were identified by two-step cluster analysis. Cluster 1 included 130 (20.5%) patients, Cluster 2 included 132(20.8%) patients and Cluster 3 included 373 (58.7%) patients. Cluster 3 was the largest group of mild disease activity, patients in this cluster had lower white blood cells, neutrophils, lymphocytes and mean SDI scores compared to those in the other two clusters. Cluster 1 was the smallest group of severe damage, patients in this cluster had multiple positive auto-antibodies, higher SDI scores and lower complement level. Patients of cluster 2 had the highest levels of granulocytes, but the results of other laboratory tests were roughly between the cluster 1 and cluster 3.Conclusions: This study reclassified three groups of LN patients in a large cohort. Our research shows that the multiple positive ANA antibody may be related to the high SDI score of LN patients. Clinicians can identify patients at different stages through cluster analysis to better implement prognosis.

scholarly journals Cluster Analysis of Micronutrients in Raw and Minimally Processed Plant Foods (P24-049-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Ying Li ◽  
Jaspreet Ahuja ◽  
Rahul Bahadur ◽  
Pamela Pehrsson
Keyword(s):  
Vitamin D ◽  
Cluster Analysis ◽  
Fruits And Vegetables ◽  
Pantothenic Acid ◽  
Food Composition ◽  
Dietary Quality ◽  
Minimally Processed ◽  
Plant Foods ◽  
Funding Sources ◽  
Cluster 2

Abstract Objectives This study aims to determine groups of unprocessed plant-based foods that have similar micronutrient profiles. Methods Raw and minimally processed plant foods (fruits, fruit juices, vegetables, nuts and seeds, legumes, cereal grains and pasta) were identified from the USDA National Nutrient Database for Standard Reference Legacy (2018). A dataset of concentrations of selected micronutrients per 100 g of the food was prepared. These micronutrients included calcium (Ca), iron (Fe), magnesium (Mg), phosphorus (P), potassium (K), sodium (Na), zinc (Zn), copper (Cu), manganese (Mn), selenium (Se), vitamin A, vitamin D, vitamin C, thiamin, riboflavin, niacin, pantothenic acid, vitamin B6, vitamin B12 and folate. The micronutrient concentrations were standardized ranging from 0 to 1, and analyzed using hierarchical clustering analysis (Ward's method). Squared euclidean distance was used for dissimilarity measure, and agglomeration schedule was used for determine the optimal clusters. Dendograms were plotted to visualize the clusters. Results The selected foods can be grouped into 4 clusters according to the result of agglomeration schedule. Dendrogram showed that cluster 1 (44 foods) contained 26 grains like cornmeal, rice and sorghum, 11 nut and seeds like walnuts and almond, 4 legumes and 3 vegetables. Cluster 2 (293 foods) was mainly fresh fruits and vegetables (277 foods), 9 grains like degermed cornmeal, 5 nuts and 2 legumes. Cluster 3 were 28 legumes. Cluster 4 (36 foods) contained 16 dried vegetables like dehydrated carrot and dried onions, 9 nuts, 8 legumes and 3 grains. Each cluster had distinct micronutrient profiles. On a 100 g basis, cluster 4 had almost the highest levels of all nutrients except vitamin D and B-12. Cluster 1 and 3 were rich in P, K, Zn, thiamin and cluster, but cluster 1 also had high amount of Fe and folate. Cluster 2 had the highest amount of vitamin D. Conclusions The cluster analysis on micronutrients of raw and minimally processed foods provides an alternate means to group foods based on nutrients. These results help identify foods of similar nutrients and can provide information to support dietetic practice and patient education for improving dietary quality and variety. Funding Sources USDA National Nutrient Databank for Food Composition (8040–52,000-064–00D).

Effects of behaviour on the development of claw lesions in early lactation dairy cows

2011 ◽  
Vol 134 (1-2) ◽  
pp. 16-22 ◽  
Author(s):  
Sabine Dippel ◽  
Cassandra B. Tucker ◽  
Christoph Winckler ◽  
Daniel M. Weary
Keyword(s):  
Dairy Cows ◽  
Early Lactation ◽  
Claw Lesions

Strengthening the Evidence of Relevant Somatic Mutations of Individual Patients By Pairing Sequencing Deduced Allelic Burden, Leukemic Blast Percent and Cluster Analysis

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2589-2589
Author(s):  
Marcus Celik Hansen ◽  
Sadudee Chotirat ◽  
Chirayu Udomsakdi Auewarakul ◽  
Peter Hokland
Keyword(s):  
Cluster Analysis ◽  
Exome Sequencing ◽  
Somatic Mutations ◽  
Signal To Noise Ratio ◽  
Tumor Burden ◽  
Clinical Settings ◽  
Leukemic Blast ◽  
Signal To Noise ◽  
Cluster 2 ◽  
Allelic Burden

Abstract Introduction Exome sequencing can detect somatic mutations at an unprecedented scale. However, high false-positive rates due to multiple technical contributors affecting signal-to-noise ratio is an unsolved inherent problem. Furthermore, the current literature does not consistently assess or report the allelic burden of detected and scrutinized mutations, potentially leading to focus on irrelevant mutations. We hypothesized that this issue can be addressed by a structured usage of allele frequencies in combination with detected mutations. Employing improved techniques to assess the molecular signature shortly after diagnosis could also result in improved risk stratification. Here, we present proof-of-principle that identification of relevant mutations, and extent of clonality, can be accomplished by pairing hypothetical allelic burden deduced from sequencing reads to leukemic burden in individual samples. Methods 7 samples were used for whole exome sequencing derived from bone marrow aspirated from two different patients. Of these, 4 were leukemia samples (diagnostic and two relapse samples of one T-cell/myeloid mixed-phenotype leukemia and a diagnostic from AML, M0), reflecting different clinical situations, and 3 samples served as controls (keratinocytes, and fibroblasts in the first, remission in the second) to include different clinical situations. Raw data processing, mutations analysis and downstream analysis of sequencing data was performed as described earlier (Hansen & al., MethodsX 2015, Hansen & al., Br J Haematol. 2015), following GATK Best Practice workflow and MuTect default parameters. Cluster analysis was utilized to mathematically divide somatic SNVs into read frequency clusters on the basis of squared Euclidean distance, thus enabling the retrieval of mean allelic burden and expected allele frequencies juxtaposed with flow cytometry-derived leukemic blast percent. The initial condition of the classification model was default set to accommodate separation of background (cluster 1: noise or low read), heterozygous mutations (cluster 2), and an outlier bin for possible homozygous mutations (cluster 3). Results and discussion In order to reference the leukemic burden of a given sample we employed data from immunophenotyping as a surrogate marker for malignancy. Without filtering of detected mutations by exome sequencing the partly stochastic nature of the signal is evident (fig. 1A). An exponential-like continuum of non-rejected mutations is found when these are sorted according to frequencies (black points), making it difficult to deduce any clonal nature of the malignancy, and to evaluate the validity of possibly relevant mutations found. Using a minimum depth of coverage threshold of 30 the signal-to-noise ratio is increased (fig. 1B), and, subsequently, two clones were resolved at diagnosis (fig. 1C) by cluster analysis. This resolution decreases at lower tumor burden showing expected sensitivity towards lower allelic reads (fig. 1D), although driver mutations of the persistent clone could be detected. At second relapse only one distinct sAML phenotyoe clone and, now homozygous, CDKN2 AR80* could be detected (fig. 1E) with the mutations of secondary clone present at diagnosis (cluster 2) lost due to selective pressure from treatment, i.e. FLT3D835Y. The observations are backed by another diagnostic sample from a patient with AML with NRAS and BCOR mutations (fig. 1F), also with a distinct clone. Here, too much emphasis could easily be given to NRASG12D if the frequency had not been assessed. Conclusion We have addressed the pertinent question regarding false positive observations arising from deep sequencing or emphasizing mutations found in the low allele frequency fractions. From this dataset we have, despite the low number of samples, accomplished to suggest a formalized approach for single sample mutational analysis. As a consequence, we can now show that malignant clones with high tumor burden can be resolved semi-spatially by sequencing, generally applicable to a wide range of clinical settings. We conclude that this approach is amenable in single patient situations. While further studies are needed to ultimately test the applicability of this approach in the clinical settings, the perspectives to this observation become evident as sequencing depth and cost continue to develop in an inversely correlated manner. Disclosures No relevant conflicts of interest to declare.

Autoantibodies in Pediatric Systemic Lupus Erythematosus: Ethnic Grouping, Cluster Analysis, and Clinical Correlations

2009 ◽  
Vol 36 (2) ◽  
pp. 416-421 ◽  
Author(s):  
ROMAN JURENCÁK ◽  
MARVIN FRITZLER ◽  
PASCAL TYRRELL ◽  
LINDA HIRAKI ◽  
SUSANNE BENSELER ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Cluster Analysis ◽  
Ethnic Groups ◽  
Ethnic Differences ◽  
Lupus Erythematosus ◽  
Systemic Lupus ◽  
Pediatric Systemic Lupus Erythematosus ◽  
Mild Disease ◽  
Cluster 2 ◽  
Autoantibody Profiles

Objective.(1) To evaluate the spectrum of serum autoantibodies in pediatric-onset systemic lupus erythematosus (pSLE) with a focus on ethnic differences; (2) using cluster analysis, to identify patients with similar autoantibody patterns and to determine their clinical associations.Methods.A single-center cohort study of all patients with newly diagnosed pSLE seen over an 8-year period was performed. Ethnicity, clinical, and serological data were prospectively collected from 156/169 patients (92%). The frequencies of 10 selected autoantibodies among ethnic groups were compared. Cluster analysis identified groups of patients with similar autoantibody profiles. Associations of these groups with clinical and laboratory features of pSLE were examined.Results.Among our 5 ethnic groups, there were differences only in the prevalence of anti-U1RNP and anti-Sm antibodies, which occurred more frequently in non-Caucasian patients (p < 0.0001, p < 0.01, respectively). Cluster analysis revealed 3 autoantibody clusters. Cluster 1 consisted of anti-dsDNA antibodies. Cluster 2 consisted of anti-dsDNA, antichromatin, antiribosomal P, anti-U1RNP, anti-Sm, anti-Ro and anti-La autoantibody. Cluster 3 consisted of anti-dsDNA, anti-RNP, and anti-Sm autoantibody. The highest proportion of Caucasians was in cluster 1 (p < 0.05), which was characterized by a mild disease with infrequent major organ involvement compared to cluster 2, which had the highest frequency of nephritis, renal failure, serositis, and hemolytic anemia, or cluster 3, which was characterized by frequent neuropsychiatric disease and nephritis.Conclusion.We observed ethnic differences in autoantibody profiles in pSLE. Autoantibodies tended to cluster together and these clusters were associated with different clinical courses.

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