dataesr/scientific-paragraphs-categorization huggingface dataset:
This last point is key since longer reads will be available soon. They will much more likely incorporate not one, but several events -errors, mutations, splice junctions, etc. -and thus be harder to map. Whatever the class of required predictions, CRAC's sensitivity is always improved with longer reads. This is crucial for detecting multiple exons within single reads, and CRAC exhibits a better ability in this as exemplified by a transcript of TIMM50 gene (Figure  4c ). An issue in transcriptomics is to reliably extract the complete set of splice junctions with a minimal number of false positives  [24]. In this regard, our results (Table  2 ) demonstrate that k-mer profiling approaches (MapSplice and CRAC) profit greatly in sensitivity from longer reads, and that CRAC is the tool with the highest precision whatever the read length.
Figure2Comparison of mapping results by category for seven tools. The figure shows the mapping by event category on simulated RNA-seq against the human genome on datasets with short and long reads (left 42M, 75 nt; right 48M, 200 nt) for seven different mapping tools: Bowtie, Bowtie2, BWA/BWA-SW, CRAC, GASSST, GSNAP, and SOAP2. We consider six categories of reads depending on whether they contain an SNV, an insertion, a deletion, a junction, a sequence error, or a chimeric splice junction (a chimera). In each category, the bar is the percentage of those reads mapped at a unique location by the corresponding tool. The red tip at the top of the bar is the percentage of incorrectly mapped reads. With 75 nt reads, CRAC is better than the other tools, reaching a sensitivity >90% and a precision >95% whatever the category.
Acknowledgements The authors thank  Alban Mancheron  for help in packaging the CRAC software,  Gwenael Piganeau  for critically reading this manuscript. NP is supported by  Fondation ARC pour la Recherche sur le Cancer  (grant  PDF20101202345 ),  Ligue Contre le Cancer  (grant  JG/VP 8102 ). NP, TC, and ER are supported by a  CNRS INS2I  (grant  PEPS BFC: 66293 ), the  Institute of Computational Biology, Investissement d'Avenir. TC and ER acknowledge the support from the  Region Languedoc Roussillon  ( grant Chercheur d'Avenir, grant GEPETOS ). MS is partially supported by the  French   ANR-2010-COSI-004   MAPPI  Project. TC is supported by the  Ligue régionale contre le cancer  and the University of Montpellier 2. We acknowledge funding from  Agence Nationale de la Recherche  (grant  Colib 'read  ANR-12-BS02-008 ), from the  NUMEV Labex , and from the  CNRS   Mastodons Program.
The program is organised by Irish Cattle Breeding Federation (ICBF) under the brand name G€N€ IR€LAND. Within this organisational structure AI companies and private breeders can own bulls, with ICBF then responsible for the progeny testing of these bulls, including distribution of semen to targeted herds, collection of all relevant data and subsequent genetic evaluations. By taking a national perspective in the organisation of the breeding program, the Irish cattle breeding industry can more effectively manage: (1) the identification of elite animals (including provision of breeding program advice) through the use of the ICBF database; (2) the sharing of semen collection and progeny test resources across AI centres; and (3) the minimisation of risk to the breeding program, through maintenance of genetic diversity and monitoring traits of interest.
That called for a new way of cooperating at international level. In 2009 the European federation of BSW breeders set up a project, later called InterGenomics, with the goal of setting up a unique international system of genomic evaluation for the breed. In 2012 the service began to be provided routinely by Interbull The participants in the projects decided also to share the pool of genotypes used for prediction equation estimation in order to allow more scientific groups to work on the same database with the aim of improving continuously the quality of the service. Since the introduction of genomic evaluations the industry reacted very fast. The number of test made on candidates bulls increased exponentially, the rules for the introduction of 'proven' bulls on the market changed almost everywhere in some months.
The probability of successful pregnancy was fit with a logit model, with backwards stepwise selection of variables (P<0. 05) after the Wald test; a t-test was used to analyse follicle size at ovulation; and a simple linear regression was used to relate 'age of the mare' and 'follicle size at ovulation'. IBM SPSS ® Statistics 21 was the statistical package used in the analysis. There is an increase of 26. 4 in the odds ratio of pregnancy success per increased unit of UO, and therefore a positive relation between pregnancy success and UO is shown (P<0. 05). 'Follicle sizes at the time of ovulation' where found to be significantly different when hCG was used (P<0. 05). No significant differences for PGF 2α (P=0. 051), oxytocin (P>0. 05) and antibiotics (P>0. 05). Mean and 95% confidence interval with hCG treatment is 47.
Other factors are taste, environment and status of the animal (health, age, milk yield). Various attempts were made to include these theories into mechanistic models, but their prediction of voluntary feed intake for lactating dairy cattle is yet not accurate. Thus, models used to estimate feed intake are pragmatic, based on calibration datasets containing feed and animal characteristics, whereby the predicted feed intake results from a filling (satiety) index of the ration and a feed intake capacity of the animal. A selection of these models was evaluated, using an independent dataset. The behaviour of individual models was influenced by basic forage source (maize silage versus grass silage), forage:concentrate ratio, breed, genetic potential, parity and stage of lactation and gestation. It can be debated whether models including milk yield and bodyweight can be used to predict intake capacity because these animal characteristics may be highly correlated with nutrient intake.
Amongst the tested models, the mean square prediction error (MSPE) varied between 4. 0 and 14. 9. Results showed that accurate predictions are possible without inclusion of performance data. Random error as proportion of MSPE for individual cows was large across all models, suggesting that models are better suited for groups than for individual cows. French 'Systali project' to new feed units for energy and protein in ruminants D. Moreover, the respective weight of the main factors involved in the digestive interactions can be evaluated. The results for all the treatments are gathered and can be stored in databases for comparison with animal responses and thus validation of the system. The NorFor feed evaluation system H. Volden   Box 500, 1432 Ås, Norway; harald. volden@tine. no  Feed is one of the major expenses in modern cattle production.
In addition to feed prices, its overall costs are affected by the efficiency of feed utilization and the output of animal products to be marketed. Hence, there is a clear need to evaluate feed quality in order to maximise profitability. In Denmark, Iceland, Norway and Sweden, the NorFor feed evaluation was introduced for use in practise in 2007. The NorFor system is a semi-mechanistic, static and science-based model, which predicts nutrient supply and requirements for maintenance, milk production, growth and pregnancy in cattle. The model can be divided into five parts: (1) an input section describing characteristics of the animal and feeds available; (2) module simulating processes in the digestive tract and the intermediary metabolism; (3) a module predicting feed intake; (4) a module predicting the physical structure of the diet; and (5) an output section describing nutrient supply, nutrient balances and production responses.
In addition, NorFor has developed an IT and software system which is used can be used for ration formulation and economical optimization of diets. One of the major challenges in the NorFor system is the interactions and the non-linear relationships that are used to describe feed digestion and metabolism. This means that individual feeds do not have fixed feed values and that NorFor therefore must be considered as a ration evaluation system rather than a system used to evaluate individual feedstuffs.
Automatisms for phenotyping data gathering in animal farms J. -F. Bompa, E. Ricard and L. Bodin INRA, SAGA, Auzeville, 31326 Castanet Tolosan, France; jean-francois. bompa@toulouse. inra. fr  The INRA DGA has a great and long experience (since the 90s) in routinely phenotyping automatic measuring using electronic identification, in experimental farms. The goal was to develop the data collect reliability, to generate new data, to decrease the burden of this work in the field, to improve farm management and to introduce traceability for data. Each year, more than 10000 animals are electronically identified at birth, on different species on our different experimental farms. To manage this large data flow, a structured and centralized database is located on a specific server CTIG at Jouy en Josas (INRA).
Session 07 Poster 20 Session 07 Poster 19 The characterization and sustainability of cattle production in the communal areas of Namibia The objective of this study is to characterize the cattle production systems followed in the research area and identify those factors which impair the sustainability thereof. Experimental methods employed included rapid rural appraisal techniques, questionnaires and structured interviews. A total of 570 farmers formed part of this study. These farmers are all registered as cattle producers with the Meat Board of Namibia. Trained enumerators were deployed to gather the research data under the supervision of the researcher (second author) over a period of two months. Data were analyzed using the SPSS. Results indicate that the average herd size per household is 66 animals.
Additional sources of data outside of the farm include e. g. slaughter houses, and veterinary labs. On farm level huge amounts of data are increasingly available from automated and semi-automated milking-and management systems. In order to develop effective selection programs for new traits, the development of large databases is necessary. Session 10 Theatre 4 Session 10 Theatre 3 The optimal proportion of genomically selected young bulls in the herd AI mix A. P. W. De Roos CRV, P. O. Box 454, 6800 AL Arnhem, the Netherlands; sander. de. roos@crv4all. com  Dairy producers use artificial insemination to get their cows pregnant and improve the performance of their herd. Many dairy farmers use genomically selected young bulls as an alternative to daughter proven bulls, primarily because their breeding values or indexes are more attractive and they understand that this leads to greater genetic improvement.
Litters were standardized to 11 or 12 and piglets were weighed weekly until day 18. The MIXED procedure of SAS was used for statistical analyses with a univariate model. Body weight and backfat thickness of first-parity sows were lesser for TRT than CTL at the end of gestation (P<0. 01) and body weight was also lesser in late lactation (P<0. 05). There were no differences in piglet growth between CTL and TRT litters (P>0. 10), yet mammary development and mammary gene expression were affected. There was less parenchymal tissue (P<0. 01) at the end of gestation in TRT than CTL sows but its composition was not altered (P>0. 10). Relative abundance of IGF-1 (P<0. 05), ODC1 (P<0. 05), STAT5B (P<0. 05) and WAP (P<0. 01) genes in parenchyma at the end of gestation were lower in TRT than CTL sows and the effect on WAP was still present at the end of lactation (P<0.
The Beagle software was used for imputation, accuracy was assessed via five-fold cross validation. For the validation individuals all SNP were set to missing, except for SNP that occur on the Illumina BovineSNP50 or BovineHD arrays. Imputation accuracy was calculated as the correlation between observed and imputed genotypes. For BTA 29 and for the largest reference group imputation accuracy from BovineSNP50 to whole-genome sequence was on average 0. 37 and imputation accuracy from BovineHD was on average 0. 80. For SNP with minor allele frequency above 0. 25 the average imputation accuracy was 0. 89. For SNP with a lower minor allele frequency this decreased to 0. 13-0. 38 (depending on reference group size). When distance to nearest genotyped SNP increased to 5,000 base-pairs the average accuracy dropped from almost 1 to 0.
All of them were located in coding sequences, were non synonymous and had very damaging predicted effects. Previously reported causative mutations for Brachyspina and CVM were found with this approach. Finally we showed that some causative mutations were in the neighborhood of -but outside -these non homozygous regions, due to incomplete linkage disequilibrium. This study was funded by the ANR-10-GENM-0018 ANR-Apisgene Cartoseq project. The aim of this study is to compare the accuracy of the predicted breeding values obtained by genomic evaluation from various populations under different scenarios of marker densities, generations and type of divergence. An evolutionary process of 1000 generations of a population with effective size of 100 individuals was simulated. For each individual, 30,000 biallelic markers, evenly distributed throughout 20 chromosomes of 1 Morgan each, were simulated.
Two analysis-strategies were applied to calculate the accuracy of genomic predictions at an extremum of the environmental scale. (1) 100%, 80%, 50%, or 20% of phenotypes at THI 75 were deleted randomly, and the remaining dataset was used to predict the breeding value at THI 75 for non-phenotyped but genotyped cows. (2) Complete information (geno-and phenotypes) was available for 1600 cows, but phenotypes were missing for 400 genotyped cows at all THI levels. Without any phenotypic observations at THI 75, accuracy of prediction averaged over all scenarios was 0. 22. If 20% of cows had phenotypic records at THI 75, accuracies were moderate with values ~0. 60. Only a small proportion of phenotyped cows (i. e. 20%) in environments representing heat stress (=THI 75), is required to predict reliable genomic breeding values of cows without phenotypes at that environmental level.
Comparison results, including peculiarities and overlaps between the associations obtained from the two datasets with different statistical methods, are presented and discussed. A questionnaire was constructed with 49 main questions. 1039 questionnaires were received. With factor analysis no. of questions were reduced and cluster analysis was used to form farmer segments. On base of 10 strategies farmers indicated their 1 st , 2 nd and 3 th most important strategies for development of farm. Farmers' segments identified were: Independent and Cooperating diversifiers, Specializing growers, New starters, Cooperating and Chain oriented and Wait&see farmers. Differences between countries will be discussed. Also, farmers indicated how important farming goals were on a 7 point likert scale. Factors identified were sustainable quality, succession, enjoy work, good management and financial management.
Effects of the 2008 recession on aspects on the Session 18 Theatre 9 Session 18 Theatre 8 The REFErences network, an actor in the economic knowledge of the French horse industry X. Dornier 1 , P. ). This database is supplemented with surveys on businesses and horse buyers. Recent trends show a declining production of horses in France while buyers turn increasingly to foreign horses. In the meantime, betting and horse riding seems to stagnate after many years of growth, while employment is still progressing. The microeconomic approach aims at gaining a better understanding of the way that equine businesses are managed, both technically and economically. In order to collect data, 250 farms (breeding farms, equestrian establishments) are audited several times a year. Breeding enterprises turn out to be less economically efficient than equestrian centers (riding schools, livery yards, equestrian tourism centers) though businesses with complementary activities have better economic performance.
Session 21a Theatre 2 The French feed database: an efficient private-public partnership G. Tran AFZ (Association Française de Zootechnie), 16 rue Claude Bernard, 75231 Paris Cedex 05, France; gilles. tran@zootechnie. fr The French Feed Database is an information and expertise centre on the quality of feed materials, managed by the French Association for Animal Production (AFZ). Created in 1989, it is supported by a network of 16 member organisations including feed manufacturers, producers of raw materials, R&D institutes and trade organisations. Its core mission is to disseminate information about the chemical composition and nutritive value of feedstuffs. The database stores 1. 9 million composition and nutritional data for 2,500 feed materials and 800 parameters on more than 440,000 samples.
One major feature of the French Feed Database is that most of the data are provided by its members, who choose the nature, quantity and periodicity of the data they want to share. While the mostly private origin of the data imposes certain constraints on their nature (mostly chemical data), acquisition (delay) and dissemination (confidentiality), this gives the French Feed Database a unique overview of the nature and quality of feed ingredients actually used in feed manufacturing. Data from public sources (INRA, CIRAD and international literature) are present in smaller numbers in the database but are extremely valuable as they are usually derived from bioavailability assays. All the data are registered with the relevant information such as geographical origins, providers, methods of analysis, literature references, etc.
The main users of the database are its members, who have a privileged access to several tools (desktop database and on-line database) and services (requests for raw or processed data, literature reviews, consultancy in feed data management). For more than two decades, the French Feed Database has been serving the needs of the feed sector, by providing technical data to feed professionals, by assisting private organisations to develop feed data management systems and by helping public institutions to disseminate feed information (INRA-AFZ tables, Feedipedia…) and to take informed policy decisions about animal feeds. A number of factors have contributed to research interest in authentication of ruminant products from grassland based production systems. They include the increasing consumer demand for assurance about mode of production because of several food scares, the evidence that pasture-feeding can impart beneficial effects on meat and milk from a nutritional perspective and the interest in production practices which are environmentally sustainable.
Please refer to the pig genome paper for a full list of those who have contributed to the pig genome project. This research was funded by many sources, as acknowledged in the paper, including USDA, BBSRC and the EC-funded FP7 Project Quantomics-222664. A range of methods to locate the site of mutations causing autosomal recessive genetic diseases using SNP chip data have been suggested. This paper compared five methods with the recently proposed autozygosityby-difference (ABD) approach. These were chi-squared (CS), ASSHOM, ASSIST, HOMOYGOSITY MAPPER and the -homozyg option in PLINK. Data on the well-documented Lavender Foal Syndrome (LFS; a single base deletion at position 138,235,715 on ECA1, found using 6 cases and 30 controls) were analysed by all 6 methods. The original published position of this condition was located with a 3×2 SNP genotype-by-diseases status CS approach using Fisher's Exact Test (CSF) to a 10.
HOMOZYGOSITY MAPPER also located the same segment of ECA1. Technically 4 of the 6 methods compared here all found much the same segment of ECA1 containing the LFS mutation; the exceptions being ASSHOM and ASSIST. Both these methods, and the CSF method, rely on cases being monomorphic and controls being polymorphic at the mutation site, which was not the case in this dataset. The situations where specific methods may be preferable are outlined, using illustrations from other datasets, and the utility of the ABD method highlighted. One of the objectives of the NextGen EU project is to investigate vector-borne-disease resistance in Ugandan cattle. To date 915 animals have been collected from 52 grid cells covering the whole country. In total 9 populations belonging to Ankole (crossbred between Bos indicus and Bos taurus), Zebu and Ankole-Zebu crosses were sampled together with GPS data and health status information.
Session 25 Poster 21 Session 25 Poster 20 Effect of calving ease and calf mortality on functional longevity in Polish Holstein-Friesian cows M. Morek-Kopeć 1 and A. Maternal animal models are used for genetic evaluation of beef cattle. However, it is usual to report a strong negative genetic correlation between direct and maternal effects. In a previous study, we showed that the potential presence of non-considered paternally imprinted genetic effects may generate an inflation of the additive and maternal genetic variance components and produce a negative genetic correlation between them. In order to clarify this statement we analyse three datasets of weaning weight in Spanish Beef Cattle populations, Pirenaica (PI), Rubia Gallega (RG) and Avileña-Negra Ibérica (ANI). We used 17,106 weaning weight for PI, 41,248 for ANI and 55,631 for RG.
Session 25 Poster 41 Session 25 Poster 40 Comparison of mapping accuracy between methods predicting QTL allele identity using haplotypes L. J. Jacquin 1 , J. M. Elsen 1 and H. Detecting haplotypes in association with trait variability usually exploits local similarities between chromosomes: locally similar chromosomes have better chance to harbor identical QTL alleles than chromosomes showing local differences. Predictors of allelic identity based on 6 marker haplotypes were compared for their ability to correctly predict QTL allelic identity and for their mapping accuracy. The tested methods were: (1) identity by state (IBS) at each tested marker; (2) IBS between the haplotype pairs surrounding the tested position (IBS_hap); (3) a similarity score between haplotype pairs (SCORE); (4) an IBD probability between haplotype pairs derived from a coalescence process; (5) an identity predictor derived from local clustering between haplotypes pairs (BEAGLE); and (6) a predictor trained on the dataset (TP).
These predictions were collected in (2n×2n, n being the number of individuals) matrices M P id and compared to the actual QTL identity between the chromosomes assembled in a 2n×2n matrix M QTL , by calculating the normalized distances between matrices M P id and M QTL for each tested position. Secondly, mean square errors of the QTL position estimate, obtained from mixed models including a random haplotypic effect with covariance described by the MPid matrices, were computed. Algebraic developments were applied to the normalized distance between matrices to infer the predictors' ability to predict the allelic identity at the QTL depending on the local linkage disequilibrium (LD). Numerical comparisons were performed on simulated datasets based on a set of 235 porcine chromosomes and a 26 generations pedigree.
To validate the results the effects in Holstein cows were examined using raw phenotypes. Our study demonstrates the advantage of utilizing high density SNPs through imputation and provides more evidence on the path to identify the candidate genes underlying calving performance. Comparison on GWAS using different models and different markers data sets X. P. Wu Mastitis is the most common disease in dairy cattle causing substantial economic losses. The aim of this study was to compare the GWAS for refining the six previously detected QTL affecting mastitis, using two different models and three maker densities based on the 54K and imputed 770K (HD) marker data as well as genome sequence data. The dataset consisted of 4,496 Danish Holsteins. After quality control, there were a total of 790, 8,260 and 77,853 SNPs available within the six regions, respectively.