dataesr/scientific-paragraphs-categorization huggingface dataset:
A total of 81,092 records were obtained from the Czech Beef Breeders Association field database. The three traits were analysed as traits of the calf fitting a multivariate linear mixed model. All tested models included fixed effects of year of birth, age of dam, sex and breed of calf, whereas random effects included direct and maternal genetic effects, maternal permanent environment effect, contemporary group (herd × year × season) and residual error. Calving ease and birth weight were modelled as linear trait. The linear logit model was used for a analysis of calf survivability. Estimates of heritability (SE in brackets) for the direct genetic effects (CSd, CEd and Bwd) were 0. 04 (0. 03), 0. 12 (0. 01) and 0. 13 (0. 01) respectively, whereas the estimates for maternal genetic effects (CSm, CEm and BWm) were 0.
In order to assess these strategies in organic dairy farming we use a dataset from 2005 to 2010 of 70 voluntarily bookkeeping farms which show farm income per labour above the average. We apply cluster analysis to identify homogenous farm groups which differ in their strategies regarding intensity. Whereas this is done with data from 2010, we then compare the development of these groups over the time period 2005 to 2010. The cluster analysis identifies two out of six clusters which show the most different values in the used variables representing a high output strategy (n=14) and a low input strategy (n=8). First results show that these two clusters differ in milk yield per cow, total farm output and total farm input but are similar in utilised agricultural area and in farm income but. This leads to different developments during the time of volatile prices.
Eventing and showjumping are the main disciplines prioritised by breeders. Breeding values for showjumping ability have been estimated with a multi-trait animal model since 1995 but no international performance information was included. A study was carried out to investigate the inclusion of international performances of Irish Sport Horses in the genetic evaluation. Data used in the study included pedigree data on Irish Sport Horses (n=57,136) and a database of national and international performances constructed from FEI data, manually retrieved international performances and national performance data (n=1,119,770 The aim of this study was to estimate genetic parameters for type traits scored at adult age in the Italian Heavy Draught Horse and analyze genetic correlation with the same traits scored at younger age (i.
e. on 6 month-old foals), and used for selection. The initial databases consisted in 7,133 evaluations of adults and 15,945 of foals scored by 35 classifiers in 20 subsequent years (i. e. from 1992 to 2011) on 14 linear type traits with a 9 point scale system (from 1 to 5 including half points). After editing, 4,205 scores on adults and 8,490 scores on foals were retained for further analysis. Data were merged and 2,180 animals resulted scored at both ages. Bi-traits Gibbs Sampling analyses were carried out on a total of 10,515 records related to 15,649 animals in the pedigree. The model considered the following fixed effects: herd-year-classifier (1,855 classes for foals and 1,297 for adults), sex (2 classes), age at evaluations (9 classes for foals and 5 for adults), and age of mare at foaling (5 classes, for foal data only).
This work aimed to investigate the association between productive and reproductive traits of the dairy Sicilo-Sarde ewes. After edits, a database containing 5,935 lactation records collected during 6 successive years in 8 dairy flocks in the North of Tunisia was used. Total milked milk in the milking-only period (TMM) was retained as productive trait. The interval from the start of the mating period to the subsequent lambing (IML) and the status of pregnancy (SP) was designed as reproductive traits. Sicilo-Sarde ewes had an average TMM of 60. 93 L (±44. 12) milked during 132. 8 days (±46. 6) after a suckling period of 100. 4 days (±24. 9). Average IML was 165. 7 d. In a first step, the major factors influencing milk production and reproductive traits were determined. The significant sources of variation identified for TMM were: flock, month of lambing, year of lambing, parity, suckling length, litter size and milking-only length.
Impact of genetics and feeding on loin marbling levels of Since 2009, loin IMF predicted on live pigs using ultrasonic scanning has been included in the Canadian technician accreditation program and in the swine genetic evaluations for Duroc pigs. A research project involving 6,000 Duroc pigs scanned across Canada was designed to enlarge the live IMF database and confirm genetic parameters estimated in a previous study. Data collected in the project were also used for genetic evaluation and selection of Duroc boars with either low or high IMF EBVs to produce 1,350 commercial pigs tested in two research trials (in Western and Eastern Canada). Pigs were fed either a standard diet specific to the region, or a special diet formulated to increase marbling deposition. A total of 687 pigs were performance-tested from weaning to slaughter, and tracked at the packing plant for a full carcass and meat quality evaluation.
Generally, the records of longevity are not available when selection decision of replacement AI-boars is taken place. However, genomic selection opens new possibilities to improve longevity of sows. The aim of the current study was to estimate variance components of sow longevity traits using a multivariate competing risk model with discrete time to describe the number of parities. Culling was treated as three traits according to culling reason: leg weakness (L), fertility problems (F), or other reason (O). The data was collected from the database of Finnish breeding company Figen Ltd and contained records from 31,742 Finnish Landrace (LR) and 31,252 Finnish Yorkshire (FY) sows that were born between 2000 and 2010. The data included both complete (the culling date was available) and censored observations and was analyzed with the DMU program package using a multi trait sire model.
The DMU package using bi-variate and multitrait animal models was used to perform the genetic analyses. As expected, the two lameness traits (MOV and LEG) were highly correlated with a genetic correlation of 0. 88±0. 02. Due to relatively high standard error, correlation between lameness traits and reproductive traits in the first parity were not significantly different from 0. Lameness traits and WSI7 seem negatively correlated (r g =-0. 33±0. 21), meaning that sows with worse score of lameness tend to have longer weaning to service interval. In order to have a better conclusion about genetic association between lameness of the sow and her reproduction performance, further studies, including information on later parities will be performed.
The sequences were aligned to version 10. 2. 68 of the published pig genome using the software TopHat, and approximately 75% of the sequences were successfully aligned. The software HTSeq was used to register the number of sequences aligned to every known transcript of the pig genome. The R package edgeR was used to test for gene expression differences between animals with high DFI and low DFI. The reads were aligned to a total of 19. 334 different transcripts and 110 of the genes were found to be significantly differentially expressed (5% FDR) between samples with high/low % DFI. Several of the differentially expressed genes have previously been shown to be involved in traits such as fertility and semen quality in pigs or other species. The next step is to identify SNPs in differentially expressed genes to find putative genetic markers.
The dataset consisted of 1,282 boars (993 boars genotyped) from 184 groups of pen mates. After quality control, 46,421 SNPs were included in the model. Two models were fitted: the first model included the direct effect of the SNP of the individual and the second model included the indirect effect of the SNP effects of its pen mates. None of the SNPs (direct or indirect) were found to be genome-wide significant, but two QTL on SSC6 and SSC13 were detected chromosome-wide significant for the direct SNPs. A single association on SSC9 and a QTL on SSC14 were found for the indirect SNPs. A backwards elimination method and haplotypes were used to determine the variance explained by the SNPs. Using both methods, the QTL on SSC6 explained 2. 5% and 2. 1% of the phenotypic variance, and the QTL on SSC13 explained 6.
With a lower percentage of concentrate, P90 decreased because forage intake rate is lower than concentrate one. With a higher concentrate percentage, some of the goats increased their intake rate, but this increase was followed by a greater decrease in intake rate probably in order to face a rumen subacidosis. More work is needed to better understand the destructuration of feeding behavior in goats when facing rumen subacidosis. Session 30 Theatre 6 Session 30 Theatre 5 Interactions between milk amount and fat content of a starter feed on performance of Holstein calves G. Araujo 1 , M. Terré 1 and A. Bach Thirteen predictive equations of drinking water (DW) requirements of dairy cows were collected from the literature. These equations were established by multiple regression approach from datasets containing from 24 to 12821 individual measurements of DW intake on dry and lactating cows.
Included predictive parameters were related to animal, diet composition or meteorological conditions. A dataset of 71 observations of DW intake obtained from groups of cows given a same treatment was also constituted from 18 studies collected from the CAB with the keywords 'water intake' and 'dairy cows'. All the data that could have been used to establish one of the 13 compared equations were previously removed. The average daily dry matter intake, DW intake and diet dry matter content in the dataset were 17. 7 kg (±5. 35), 66. 5 l (±27. 52) and 54. 8% (±15. 18) respectively. The dataset included 75 observations on lactating cows, with an average milk yield of 28. 5 kg/d (±8. 40) and 54 observations in condition of ambient temperature exceeding 15 °C. The root mean square prediction error (MSPE) of DW intake ranged between 15.
4 and 25. 5 l/d with an average of 23. 0 l/d (±3. 56) and a relative RMSPE of 35% (±5. 4). For 2 equations, RMSPE were clearly lower, i. e. more than half of the initial RMSPE, when data obtained at ambient temperature exceeding 15 °C were removed, indicating that these equations should be preferred in thermoneutral conditions. For 4 of these equations, we observed a strong proportion of the MSPE explained by a bias on the average that could be explained by the difficulty to assess predictive parameters such as diet Na content or minimal daily temperature. This study shows that predictive performance of published equations is very variable. The choice of an equation should be driven by the relevance of the dataset from which it was obtained in relation with the type of variability that has to be predicted.
During 63 days of experimental period, egg weight, albumen weight, yolk weight, and shell weight was measured. And also Samples of the small intestinal and ceca contents of 4 quails from each replicate were collected in polymerase chain reaction (PCR) tubes. Bacterial load of Campylobacter, Closterdium perfringens and Lactobacillus were measured using Real time PCR. Rotorgene 6000 software, version 1. 7 used for variables and PCR setting. All analyses data were carried out with one way analysis of variance SPSS. Means were compared by using Duncan's test. Control group had the lower egg weight (P<0. 05) than the other groups. Yolk weight of control group and 2 and 3 treatments did not show significant difference whereas they were different with 4 th treatment (P<0. 05). Lactobacillus bacteria concentration as beneficial digestive bacteria was the highest in treatment 2 and then treatments 4 and 3 had the high concentration.
Sward variables (fill value, energy content, protein value, pre-and post-grazing grass heights, herbage mass and DHA), supplementation levels at pasture (concentrate and silage) and animal variables were introduced into the model. The mean actual GDMI of the database determined by differences between preand post-grazing grass heights (n=125) was 14. 2 kg DM/cow/day and GrazeIn predicted a mean GDMI for the database of 13. 8 kg DM/cow/day. The mean bias was -0. 4 kg DM/cow/day. GrazeIn predicted GDMI for the total database with a relative prediction error (RPE) of 12. 5% at herd level. The mean actual MY of the database (n=528) was 23. 2 kg/cow/day and GrazeIn predicted a MY for the database of 21. 8 kg/cow/ day. The mean bias was -1. 4 kg/cow/day. GrazeIn predicted MY for the total database with a mean RPE of 23.
Villalba, M. Tor, D. Cubiló, D. Babot and J. Álvarez-Rodríguez University of Lleida, Animal Production, Lleida, 25198 Lleida, Spain; dvillalba@prodan. udl. es  There is still a lack of information about the differences in quality between organic and conventional livestock products. The objective of the study was to compare intramuscular fatty acid (FA) composition from meat obtained in organic (ORG) and conventional (CON) systems. Meat samples from animals reared under ORG (EU regulation) or CON systems were obtained in the same slaughter conditions from beef (L. dorsi, 59 vs. 37, 2 vs. 3 farms), poultry (Semimembranous, 24 vs. 12, 2 vs. 1 farms) and pork (L. dorsi, 31 vs. 29, 2 vs. 3 farms) and they were analysed for fatty acids profile by gas chromatography. PROC GLM of SAS was used to compare the within species husbandry system effect on individual FA composition.
5 and 11. 1 birds/m for the MVB and NVB, respectively. The marketing age was 43 d and bedding consisted of dried coffee husks in its first time of use. Ventilation rates were calculated with the metabolic carbon dioxide mass balance method as elaborated by  CIGR (2002). Values of f NH3 were (0. 38±0. 12) g/bird/d and (0. 32±0. 08) g/bird/d for the MVB and NVB, respectively, and are in agreement to what was presented in other studies performed under similar conditions. Estimated f NH3 on yearly basis were 109 g/bird/year and 91 g/bird/year for the MVB and NVB, respectively. The results obtained with this study help providing reliable methodology for the determination of a solid database on NH 3 emission factors for tropical conditions that can be used for future inventories, when performed in a sufficient number of barns that is representative for Brazilian scenario.
Environmental burden of purchased feeds and piglets was estimated from database and was comprised in CF estimation as indirect carbon dioxide equivalent (CO 2 eq) emissions. Functional unit (FU) was 1 kg of body weight at the farm gate. The global warming potential (GWP) was expressed as kilograms of CO 2 eq; greenhouse gases (GHG) were CH 4 , N 2 O and CO 2 with a GWP of 25, 298 and 1 kg CO 2 eq respectively. The average CF was 3. 83 (±1. 07) kg CO 2 eq. The contribution of each emission source was: enteric CH 4 3. 34%, manure CH 4 17. 7%, manure N 2 O 1. 38%, direct soil N 2 O 6. 59%, indirect soil N 2 O 6. 39%, direct CO 2 1. 00%, indirect CO 2 63. 6% (comprising production of purchased feed and piglets, fossil fuel extraction and refing, electricity production, and transportations). In respect to other animal foods, such as milk, where the enteric fermentation is a main GHG source and the crop production is an important component of the system, this study showed that the main drivers of GHG production in growing and fattening phase of pork production chain are the off-farm feed production and transportation phase; on the contrary the activities within the system boundaries are of minor importance.
Milk composition (MIRS) was, in our population, a good indicator of ketosis status: a decision tree using C16:0 then fat/protein ratio makes possible a good prediction of the metabolic status of 26 cows. These results must be confirmed with bigger databases. Session 33 Theatre 5 Session 33 Theatre 4 Contributions of neighborhood and animal movements to Coxiella burnetii infection in cattle herds S. Nusinovici 1 , T. Hoch 1 , A. Joly 1 , J. Frössling 2 , S. Widgren 2 , A. Lindberg 2 and F. Beaudeau 1 1 Oniris, UMR1300 Biology, epidemiology and risk analysis in animal health, Atlanpole, La Chantrerie, BP 40706 Nantes, France, 2 National Veterinary Institute, Travvägen 20, 751 89 Uppsala, Sweden; simon. nusinovici@oniris-nantes. fr Coxiella burnetii infection occurs mainly after inhalation of aerosols contaminated by shedder ruminants.
The involved CPs partners have been visited by a team of experts to plan and design the interventions taking into account the requirements for high levels of animal welfare, sound systems of bio-security, work safety and efficiency of personnel and environmental sustainability. Co-financing procedures for CPs have been adopted by using analytical cost calculations based on official tariffs and price lists of equipment and building materials. To this end eight national databanks (IT, FR, ES, DE, PL, GR, HU, RO) of prices and tariffs of equipment have been constructed which serve as objective reference values for the final investment plans. An important achievement of the project has been also the production of a certification scheme, for CPs developed with an adequate involvement of relevant stakeholders represented by an appointed advisory board.
Session 33 Poster 11 Session 33 Theatre 10 The mortality of calves in French beef cattle farms: a national review B. Mounaix 1 , P. Roussel 1 and S. Assie 2 1 Institut de l'elevage, UMT Maitrise de la santé des troupeaux bovins, 149 rue de Bercy, 75595 Paris, France, 2 ONIRIS, INRA, UMR1300, UMT Maitrise de la santé des troupeaux bovins, CS 40706, 44307 Nantes, France; beatrice. mounaix@idele. fr The mortality of calves (up to 6 months old) in French beef cattle farms was analyzed from the national database of bovine identification to better understand its variability. Survival models (Proc Lifetest, SAS ® ) were elaborated from the individual dates of birth and death of 8. 6 million calves which were born in 33,982 beef cattle herds between 2005 and 2009. The average yearly mortality of calves within this period of time was 8.
0009). Differences were not detected for Ig M concentration or Ig A at days 14 or 28 of age. In conclusion, the form and dose of vitamin E supplementation to sows during gestation and lactation affects on the α-tocopherol concentration of colostrum and modifies the ig A concentration in piglets serum at day 2 of age. , 225, Jardim Elite, 13635-900, Pirassununga, SP, Brazil; mrmendes2010@gmail. com  The theme 'air quality' in rearing meat quail is still widely discussed in tropical and subtropical countries, such as Brazil, due to the lack of a database that relates productivity, thermal environment and air quality. For this reason, the aim of this research study was to evaluate the effect of different thermal environments on the quality of air inhaled by meat quails in the initial life cycle (1-21 d age).
Our objectives were to develop and compare fast BLUP models that can be applied at high frequency for routine estimation of breeding values, using SNP variances that are re-estimated at much lower frequency. Those objectives were investigated using both a simulated dataset and real dairy cattle data. The simulated data contained 2,000 reference and 3 generations of each 500 validation animals. The dairy cattle data contained 16,663 reference and 724 validation animals. The models used to estimate SNP variances were Bayesian Stochastic Search Variable Selection (BSSVS) and BayesC. The BLUP models were used to estimate breeding values, either using variances obtained from BSSVS (BLUP-SSVS) or BayesC (BLUP-C), or assuming that each SNP explained the same amount of genetic variance (RR-BLUP). Animals used for estimation of variance components were subsets of the animals used to estimate breeding values, comprising: (1) all animals; (2) a random subset; (3) the best 50% of the animals; or (4) the worst 50% of the animals.
Accuracies of BLUP-C and BLUP-SSVS in the simulated data decreased by 0. 03-0. 06 when SNP variances were estimated from a non-random subset of the data, but were unchanged when SNP variances were estimated from a random subset. All BLUP models converged very fast in the simulated data (i. e. within <10 iterations vs. ≥10,000 when SNP variances were estimated). These results will be compared with those from the Dutch cattle population. In conclusion, it appears that the BLUP models can be used to efficiently analyse rapidly growing datasets, while combined with separated estimation of SNP variances in a Bayesian model they are able to capture the same features as the variable selection methods used to estimate the SNP variances. Genomic selection was recognized to result in lower pedigree inbreeding compared to best linear unbiased prediction (BLUP).
Session 34 Theatre 12 Session 34 Theatre 11 In single-step genomic evaluation using best linear unbiased prediction (ssGBLUP), genomic predictions are calculated with a relationship matrix that combines pedigree and genomic information. For missing pedigrees, unknown selection processes, or inclusion of several populations, a BLUP model can include unknown-parent groups (UPG) in the animal effect. For ssGBLUP, UPG equations also involve contributions from genomic relationships. When those contributions are ignored, UPG solutions and genetic predictions can be biased. Several options exist to eliminate or reduce such biases. First, mixed model equations can be modified to include contributions to UPG elements from genomic relationships (greater software complexity). Second, UPG can be implemented as separate effects (higher cost of computing and data processing).
Preliminary results show that the technical efficiency is not significantly different between farms with individual housing and farms with group housing of sows. Nevertheless, sow farms with group housing use a significantly (P<0. 05) higher amount of feed per sow, have higher health and fixed costs per sow and a higher replacement rate. Cluster analysis using efficiency results of the 27 sow herds with group housing reveals that sow herds applying the same group housing system are situated among the different clusters. This indicates that the type of group housing system has no influence on the technical efficiency. An extended analysis using a larger dataset and considering more inputs (e. g. energy use) is planned to validate these findings. We compared the inter-and intra-observer repeatabilities (interOR, intraOR) of three locomotion scoring scales for sows: a tagged visual analogue scale (tVAS), a 5-point (5P) and a 2-point (2P) ordinal scale with identical descriptors.
Rabbit peripheral blood mononuclear cells (PBMCs) were isolated and either mock-stimulated or stimulated with lipopolysaccharide (LPS) or a mixture of phorbol myristate acetate (PMA) and ionomycin for 4 (T4) and 24 (T24) h. After statistical analyses using LIMMA package in R, we have shown that the number of differentially expressed genes after PMA/ionomycin stimulation was 20 and 24 times higher at T4 and T24, respectively, compared to the LPS stimulation at similar time points. At T4, LPS stimulation induced an over-expression (FDR<0. 05) of pro-inflammatory (IL23A) or regulatory (IL12A) cytokines and chemokine molecules (CXCL11), but a down-regulation of the LPS receptor CD14. At T24, IL1B, IL10, IL23A and IL36G were found over-expressed. At T4, PMA/ionomycin induced both Th1 (IL2 and IL10) and Th2 responses (IL4 and IL13).