Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Comparison of locomotion scoring for dairy cows by experienced and inexperienced raters using live or video observation methods.
    Schlageter-Tello, A. ; Bokkers, E.A.M. ; Groot Koerkamp, P.W.G. ; Hertem, T. van; Viazzi, S. ; Romanini, C.E.B. ; Halachmi, I. ; Bahr, C. ; Berckmans, D. ; Lokhorst, K. - \ 2015
    Animal Welfare 24 (2015). - ISSN 0962-7286 - p. 69 - 79.
    ensure high repeatability - training-program - milk-production - weighted kappa - holstein cows - risk-factors - lameness - cattle - agreement - reliability
    Lameness is considered a major problem in dairy production. Lameness is commonly detected with locomotion scores assigned to cows under farm conditions, but raters are often trained and assessed for reliability and agreement by using video recordings. The aim of this study was to evaluate intra- and inter-rater reliability and agreement of experienced and inexperienced raters for locomotion scoring performed live and from video, and to calculate the influence of raters and the method of observation (live or video) on the probability of classifying a cow as lame. Using a five-level locomotion score, cows were scored twice live and twice from video by three experienced and two inexperienced raters for three weeks. Every week different cows were scored. Intra- and inter-rater reliability (expressed as weighted kappa, ¿w)) and agreement (expressed as percentage of agreement, PA) for live/live, live/video and video/video comparisons were determined. A logistic regression was performed to estimate the influence of the rater and method of observation on the probability of classifying a cow as lame in live and video observation. Experienced raters had higher values for intra-rater reliability and agreement for video/video than for live/live and live/video comparison. Inexperienced raters, however, did not differ for intra- and inter-rater reliability and agreement for live/live, live/video and video/video comparisons. The logistic regression indicated that raters were responsible for the main effect and the method of observation (live or from video) had a minor effect on the probability for classifying a cow as lame (locomotion score =3). In conclusion, under the present experimental conditions, experienced raters performed better than unexperienced raters when locomotion scoring was done from video. Since video observation did not show any important influence in the probability of classifying a cow as lame, video observation seems to be an acceptable method for locomotion scoring and lameness assessment in dairy cows.
    Association between placentome size, measured using transrectal ultrasonography, and gestational age in cattle
    Adeyinka, F.D. ; Laven, R.A. ; Lawrence, K.E. ; Bosch, M. van den; Blankenvoorde, G. ; Parkinson, T.J. - \ 2014
    New Zealand Veterinary Journal 62 (2014)2. - ISSN 0048-0169 - p. 51 - 56.
    dairy-cows - bovine - pregnancy - agreement - fetometry
    AIM: The aim of this study was to estimate whether fetal age could be accurately estimated using placentome size. METHODS: Fifty-eight cows with confirmed conception dates in two herds were used for the study. The length of the long axis and cross-sectional area of placentomes close to the cervix were measured once every 10 days between approximately 60-130 days of gestation and once every 15 days between 130-160 days of gestation. Four to six placentomes were measured using transrectal ultrasonography in each uterine horn. A linear mixed model was used to establish the factors that were significantly associated with log mean placentome length and to create an equation to predict gestational age from mean placentome length. Limits of agreement analysis was then used to evaluate whether the predictions were sufficiently accurate for mean placentome length to be used, in practice, as a method of determining gestational age. RESULTS: Only age of gestation (p
    Technical note: Evaluation of an ear-attached movement sensor to record cow feeding behavior and activity
    Bikker, J.P. ; Laar, H. van; Rump, P. ; Doorenbos, J. ; Meurs, K. van; Griffioen, G.M. ; Dijkstra, J. - \ 2014
    Journal of Dairy Science 97 (2014)5. - ISSN 0022-0302 - p. 2974 - 2979.
    dairy-cattle - monitoring rumination - automatic system - coefficient - agreement - ovulation - time
    The ability to monitor dairy cow feeding behavior and activity could improve dairy herd management. A 3-dimensional accelerometer (SensOor; Agis Automatisering BV, Harmelen, the Netherlands) has been developed that can be attached to ear identification tags. Based on the principle that behavior can be identified by ear movements, a proprietary model classifies sensor data as “ruminating,” “eating,” “resting,” or “active.” The objective of the study was to evaluate this sensor on accuracy and precision. First, a pilot evaluation of agreement between 2 independent observers, recording behavior from 3 cows for a period of approximately 9 h each, was performed. Second, to evaluate the sensor, the behavior of 15 cows was monitored both visually (VIS) and with the sensor (SENS), with approximately 20 h of registration per cow, evenly distributed over a 24-h period, excluding milking. Cows were chosen from groups of animals in different lactation stages and parities. Each minute of SENS and VIS data was classified into 1 of 9 categories (8 behaviors and 1 transition behavior) and summarized into 4 behavioral groups, namely ruminating, eating, resting, or active, which were analyzed by calculating kappa (¿) values. For the pilot evaluation, a high level of agreement between observers was obtained, with ¿ values of =0.96 for all behavioral categories, indicating that visual observation provides a good standard. For the second trial, relationships between SENS and VIS were studied by ¿ values on a minute basis and Pearson correlation and concordance correlation coefficient analysis on behavior expressed as percentage of total registration time. Times spent ruminating, eating, resting, and active were 42.6, 15.9, 31.6, and 9.9% (SENS) respectively, and 42.1, 13.0, 30.0, and 14.9% (VIS), respectively. Overall ¿ for the comparison of SENS and VIS was substantial (0.78), with ¿ values of 0.85, 0.77, 0.86, and 0.47 for “ruminating,” “eating,” “resting,” and “active,” respectively. Pearson correlation and concordance correlation coefficients between SENS and VIS for “ruminating,” “eating,” “resting,” and “active” were 0.93, 0.88, 0.98, and 0.73, and 0.93, 0.75, 0.97, and 0.35, respectively. In conclusion, the results provide strong evidence that the present ear sensor technology can be used to monitor ruminating and resting behavior of freestall-housed dairy cattle. Our results also suggest that this technology shows promise for monitoring eating behavior, whereas more work is needed to determine its suitability to monitor activity of dairy cattle.
    Assessment time of the Welfare Quality protocol for dairy cattle
    Vries, M. de; Engel, B. ; Uijl, I. ; Schaik, G. van; Dijkstra, T. ; Boer, I.J.M. de; Bokkers, E.A.M. - \ 2013
    Animal Welfare 22 (2013)1. - ISSN 0962-7286 - p. 85 - 93.
    lying behavior - cows - reliability - lameness - imputation - indicator - agreement - variables - system
    The Welfare Quality® (WQ) protocols are increasingly used for assessing welfare of farm animals. These protocols are time consuming (about one day per farm) and, therefore, costly. Our aim was to assess the scope for reduction of on-farm assessment time of the WQ protocol for dairy cattle. Seven trained observers quantified animal-based indicators of the WQ protocol in 181 loose-housed and 13 tied Dutch dairy herds (herd size from 10 to 211 cows). Four assessment methods were used: avoidance distance at the feeding rack (ADF, 44 min); qualitative behaviour assessment (QBA, 25 min); behavioural observations (BO, 150 min); and clinical observations (CO, 132 min). To simulate reduction of on-farm assessment time, a set of WQ indicators belonging to one assessment method was omitted from the protocol. Observed values of omitted indicators were replaced by predictions based on WQ indicators of the remaining three assessment methods, resources checklist, and interview, thus mimicking the performance of the full WQ protocol. Agreement between predicted and observed values of WQ indicators, however, was low for ADF, moderate for QBA, slight to moderate for BO, and poor to moderate for CO. It was concluded that replacing animal-based WQ indicators by predictions based on remaining WQ indicators shows little scope for reduction of onfarm assessment time of the Welfare Quality® protocol for dairy cattle. Other ways to reduce on-farm assessment time of the WQ protocol for dairy cattle, such as the use of additional data or automated monitoring systems, should be investigated.
    The potential for integration of environmental data from regional stratifications into a European monitoring framework
    Ortega, M. ; Metzger, M.J. ; Bunce, R.G.H. ; Wrbka, T. ; Allard, A. ; Jongman, R.H.G. ; Rosselló, R.E. - \ 2012
    Journal of Environmental Planning and Management 55 (2012)1. - ISSN 0964-0568 - p. 39 - 57.
    strategic ecological survey - land classification - great-britain - climate-change - biodiversity - kappa - agreement - habitats - trends - cover
    The development of a co-ordinated system for monitoring European biodiversity that can provide policy makers with information to underpin the management of ecological resources requires an appropriate environmental stratification to facilitate sampling and data analysis. This paper quantifies the similarities between the European Environmental Stratification (EnS) and four regional stratifications to test whether the EnS is able to distinguish locally important environmental gradients. The results show that in general the EnS is comparable with regional stratifications, and resolves border effects where divergent environmental conditions are combined into dominant strata. However, some regional gradients are not discerned, illustrating the value of national stratifications to provide local detail within continental monitoring strata.
    Carbon nanoparticles as detection labels in antibody microarrays. Detection of genes encoding virulence factors in Shiga toxin-producing Escherichia coli.
    Noguera, P.S. ; Posthuma-Trumpie, G.A. ; Tuil, M. Van; Wal, F.J. van der; Boer, A. De; Moers, A.P.H.A. ; Amerongen, A. Van - \ 2011
    Analytical Chemistry 83 (2011)22. - ISSN 0003-2700 - p. 8531 - 8536.
    pathogen detection - dna microarray - bacteria - assay - quantification - optimization - immunoassay - statistics - agreement - tests
    The present study demonstrates that carbon nanoparticles (CNPs) can be used as labels in microarrays. CNPs were used in nucleic acid microarray immunoassays (NAMIAs) for the detection of different Shiga toxin-producing Escherichia coli (STEC) virulence factors: four genes specific for STEC (vt1, vt2, eae, and ehxA) and the gene for E. coli 16S (hui). Optimization was performed using a Box–Behnken design, and the limit of detection for each virulence factor was established. Finally, this NAMIA using CNPs was tested with DNA from 48 field strains originating from cattle feces, and its performance was evaluated by comparing results with those achieved by the reference method q-PCR. All factors tested gave sensitivity and specificity values higher than 0.80 and efficiency values higher than 0.92. Kappa coefficients showed an almost perfect agreement (k > 0.8) between NAMIA and the reference method used for vt1, eae, and ehxA, and a perfect agreement (k = 1) for vt2 and hui. The excellent agreement between the developed NAMIA and q-PCR demonstrates that the proposed analytical procedure is indeed fit for purpose, i.e., it is valuable for fast screening of amplified genetic material such as E. coli virulence factors. This also proves the applicability of CNPs in microarrays.
    Carbon nanoparticles in lateral flow methods to detect genes encoding virulence factors of Shiga toxin-producing Escherichia coli
    Noguera, P. ; Posthuma-Trumpie, G.A. ; Tuil, M. van; Wal, F.J. van der; Boer, A. de; Moers, A.P.H.A. ; Amerongen, A. van - \ 2011
    Analytical and Bioanalytical Chemistry 399 (2011)2. - ISSN 1618-2642 - p. 831 - 838.
    molecular diagnosis - pathogenic bacteria - immunoassay - biosensors - food - pcr - statistics - particles - agreement - samples
    The use of carbon nanoparticles is shown for the detection and identification of different Shiga toxin-producing Escherichia coli virulence factors (vt1, vt2, eae and ehxA) and a 16S control (specific for E. coli) based on the use of lateral flow strips (nucleic acid lateral flow immunoassay, NALFIA). Prior to the detection with NALFIA, a rapid amplification method with tagged primers was applied. In the evaluation of the optimised NALFIA strips, no cross-reactivity was found for any of the antibodies used. The limit of detection was higher than for quantitative PCR (q-PCR), in most cases between 104 and 105 colony forming units/mL or 0.1–0.9 ng/µL DNA. NALFIA strips were applied to 48 isolates from cattle faeces, and results were compared to those achieved by q-PCR. E. coli virulence factors identified by NALFIA were in very good agreement with those observed in q-PCR, showing in most cases sensitivity and specificity values of 1.0 and an almost perfect agreement between both methods (kappa coefficient larger than 0.9). The results demonstrate that the screening method developed is reliable, cost-effective and user-friendly, and that the procedure is fast as the total time required is
    Dietary non-heme iron bioavailability among children (5-8 years) in a rural, high anemia prevalent area in North India: comparison of algorithms.
    Rani, V.R. ; Trijsburg, L. ; Brouwer, I.D. ; Khetarpaul, N. - \ 2010
    Ecology of Food and Nutrition 49 (2010)4. - ISSN 0367-0244 - p. 262 - 278.
    absorption - prediction - agreement - foods - women
    Non-heme iron bioavailability of diet consumed by children (ages 5 to 8) in rural area of India was estimated by comparison of algorithms. A cross-sectional observational study was conducted among 232 children and consisted of a 24-hour recall on 2 nonconsecutive days. Four algorithms were chosen to estimate the non-heme iron bioavailability. Daily average non-heme iron bioavailability as calculated by different algorithms was low (between 3.2% and 4.6%). Correlations of bioavailable non-heme iron among different algorithms were strong, ranging from rs = 0.67 to rs = 0.85 (p = .01)
    Modelling catchment-scale erosion patterns in the East African Highlands
    Vigiak, O. ; Okoba, B.O. ; Sterk, G. ; Groenenberg, S. - \ 2005
    Earth Surface Processes and Landforms 30 (2005)2. - ISSN 0197-9337 - p. 183 - 196.
    soil-erosion - agreement - landscape
    Prompt location of areas exposed to high erosion is of the utmost importance for soil and water conservation planning. Erosion models can be useful tools to locate sources of sediment and areas of deposition within a catchment, but the reliability of model predictions of spatial patterns of erosion at catchment scale has seldom been validated against observations. This study aimed to evaluate the performance of a simple empirical model (Morgan, Morgan and Finney model, MMF) in predicting spatial patterns of erosion at two small catchments in the East African Highlands: Kwalei (Tanzania) and Gikuuri (Kenya). Erosion maps predicted by the MMF model were compared with erosion maps obtained by direct survey. In Kwalei, erosion features were especially frequent in fields of annual crops. In Gikuuri, slope was the critical erosion factor, with estimated erosion rates >10 kg m-2 a-1 on slopes >18 per cent. Predicted erosion rates were mainly transport-limited and ranged from
    Ability of veterinary pathologists to diagnose classical swine fever from clinical signs and gross pathological findings
    Elbers, A.R.W. ; Vos, J.H. de; Bouma, A. ; Stegeman, J.A. - \ 2004
    Preventive Veterinary Medicine 66 (2004)1-4. - ISSN 0167-5877 - p. 239 - 246.
    outbreaks - agreement
    Clinical signs recorded in a classical swine fever (CSF)-suspect situation and the results of the subsequent post-mortem examination (PME) from swine submitted to post-mortem during the 1997-1998 CSF epidemic in the Netherlands, were presented in an experiment as anonymous cases (without knowledge of the actual infection status of the submission) to five veterinary pathologists for their judgment: CSF-suspect or non-suspect. It was presented to them in two hypothetical situations: country was free of CSF for 5 years and CSF was detected in the country 2 weeks ago. Subsequently, their judgment was compared to the gold standard (infection status of the submission on the basis of an immunofluoresence assay on tissue samples) and the sensitivity (Se) and specificity (Sp) of clinical diagnosis was estimated. Furthermore, intra- and inter-pathologist agreement on pathological diagnosis was measured. Adding information on clinical signs to information on PME resulted in a significant increase in median Se and a significant decrease in median Sp for a clinical judgment by pathologists. Also, median Se was significantly higher-and Sp significantly lower-for a clinical judgment by pathologists in a situation in which CSF was detected 2 weeks ago in the country compared to the situation in which the country had been free of CSF for 5 years. Apparently, the internal threshold of pathologists is severely adjusted depending on the actual disease situation in a country. Intra-rater agreement ranged from fair to almost perfect for a clinical diagnosis on the basis of PME. There was considerable variation between pathologists, especially if clinical diagnosis was based on the combined information on PME and clinical signs observed in the herd. Inter-rater agreement was substantial for the diagnosis based on information on PME. Inter-rater agreement was considerably lower for the diagnosis based on the combined information on PME and clinical signs observed in the herd
    Updating cover type maps using sequential indicator simulation
    Magnussen, S. ; Bruin, S. de - \ 2003
    Remote Sensing of Environment 87 (2003)2-3. - ISSN 0034-4257 - p. 161 - 170.
    land-cover - accuracy assessment - classification - improve - prediction - agreement - imagery - volume - models - issues
    Maximum posterior probability (MAP) maps of forest inventory (FI) cover type classes were produced from a maximum likelihood (ML) classified TM image and 5% (2%) systematic reference sampling of actual cover types for of nine 2 x 2 kin study sites in New Brunswick, Canada. MAP cover type maps were obtained via sequential indicator simulation (SIS) using collocated indicator cokriging. A 5% reference sampling increased the coefficient of accuracy of MAP cover type maps by about 0.2 compared to the accuracy of the ML classified maps. MAP prediction errors were obtained for global and small area estimates of cover type extent. MAP-based cover type statistics of extent and precision were compatible with corresponding results for maximum likelihood bias-corrected estimates (MLE). Spatial autocorrelation of MAP prediction errors declined rapidly with distance and were near 0 for distances of more than 3-4 Landsat TM pixels. MAP cover type maps produced by SIS are attractive when both global and local estimates of precision of map-derived statistics are needed. (C) 2003 Published by Elsevier Inc.
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