dataesr/scientific-paragraphs-categorization huggingface dataset:
The overall objective of the pilot project is to promote a trustworthy and credible dialogue and process for the sustainable development of dairy farming. Therefore, the tool will be put in practice on a large scale for the first time; its feasibility and recognition at all stages of the value chain will be checked; and furthermore, the tool will be further developed based on the knowledge gained. The resulting dataset is unique as it provides detailed information about relevant sustainability aspects of a large number of dairy farms. The concept, focusing specifically on the animal welfare criteria, will be presented at the conference. Session 01 Poster 10.
Values for these parameters were derived from data from commercial dairy farms that shorten or omit the dry period since 2010/2011. Other parameters were based on literature. Herds of 100 cows were simulated at cow level for 5 years following the change in dry period length (n=40 herds per scenario). Total herd milk yield in the first year was not different among different dry period lengths (ANOVA, P>0. 05), whereas a dry period of 28 days on average reduced yield by 2. 9% from the second year onwards (P<0. 05); and no dry period reduced yield by 7. 0% in the second year (P<0. 05), and by 3. 7% from the third year onwards (P<0. 05). At herd level, dry periods of 28 and 0 days in comparison with 56 days reduced net financial flows by €949 and €1,680 per year and resulted in similar greenhouse gas emissions per unit milk.
Manipulation and slaughter of American bison (Bison bison) in European farms Hilde Vervaecke Odisee University College, Agro-and Biotechnology, Belgium; hilde. vervaecke@odisee. be Approximately 6,000 American bison are bred on ranches in Europe for meat. Bison are wild non-domesticated animals that are kept extensively year-round but that require regular handling in order to comply with sanitary regulations. We surveyed the methods of manipulation and slaughter and the incidence of reported meat quality problems. The survey includes data on 18 ranches, in France (n=11), Belgium (n=3), Switzerland (n=2), the UK (n=1) and Poland (n=1). On average, each breeder had 72 adult bison (range=21-182) and slaughtered on average 16 bison per year (SD=10. 47), 75% males and 25% females, at an average age of 30 months (20-42 months).
The average cost to make them was $ 2. 1, and the average construction time by the farmer was ten minutes per cage. We prepared the total six nest designs by combining two floor designs (artificial turf floor or cage floor) and three surrounding designs (all side surrounding, one side surrounding, or no surrounding). We obtained six replicates by assigning a total 144 hens into each design (four hens/cage; 630 cm 2 /hen). We measured behaviour, physical condition, production and egg quality. The data were analysed using repeated measure ANOVA followed by Tukey-Kramer test. When compared the floor designs in nest, dust-bathing and litter-exploring were observed only in cages with artificial turf floor. The plumage damage and the proportion of eggs laid outside nest were also lower in cages with artificial turf floor than cage floor (P<0.
WAFL 2017 Assessing sustainability of welfare improvement in working equids in Petra, Jordan Ashleigh Brown Brooke, United Kingdom; ashleigh@thebrooke. org Brooke is an international charity aiming to sustainably improve working equine welfare. with milk production averaging 7,260±920 kg/lactation (±SD). Disease and culling data (slaughter/death) were extracted from on-farm computer herd management software. Only postcalving diseases that were consistently recorded across herds were considered, including retained placenta, mastitis, metritis and milk fever. Data were exported to SAS version 9. 1 (SAS Institute Inc. , Cary, NC) for statistical analysis. The effect of illness after calving on the number of cows culled (slaughter/death) was tested using a Chi-squared test. Overall, 17% of the cows studied developed at least one clinical disease during the first month after calving and the average culling rate was 7.
A unique case of an online submission of an interviewer's questionnaire to a slaughterhouse due to availability constraints during the data collection is included as well. Five farmers, two middlemen, three slaughterhouses, and four butchers, under condition of anonymity, provided insights of the current situation of the supply chain in regards of the use of the beta agonist. The choice of the units of analysis was based on their role within the supply chain and its access was through snowball sampling technique. Coding and analysis of the respondents' answers was aided by the software ATLAS. ti v7. A consensus was reached by all the respondents with the expressed needs of their customers for lean meat produced with clenbuterol, and no expressed needs for clenbuterol-free meat. Likewise, they all maintained an emphasis on production efficiency-related benefits of clenbuterol, lack of entrepreneurship for proactive differentiation and innovation of their offer, and mentioned the violability of the law against handling, possessing, and using this substance.
WAFL 2017 Social network analysis: opportunities and challenges for applications in wild and domestic animal populations Jens Krause University of Leeds, Faculty of Biological Sciences, United Kingdom; j. krause@leeds. ac. uk The field of social network analysis has rapidly developed in recent years. In most major taxonomic groups substantial progress has been made thanks to the tools and conceptual advances offered by social network analysis. In particular the arrival of reality mining (i. e. machine-collected data) has made it possible that huge datasets on the spatial and social dynamics of animals can be collected using standardized methods based on objective criteria. Nevertheless this opportunity has also created new challenges some of which I will discuss in this talk. In addition I will present a new approach to social networks using Markov chains which allows us to model the fission-fusion dynamics of populations.
Incidence of tail damage and growth performance were monitored. Behaviour of pigs was video-recorded for 6 h during daytime at 6 and 8 weeks of age, respectively. Videos were scanned at 10-min intervals to register pigs that were lying together (1) or not (0) in binary matrices. Pigs that were lying together were considered to be socially connected. Social network analysis was performed using the UCINET software. Non-littermates had greater network centralities (0. 95 vs 0. 65, SE=0. 02 for degree centrality (DC); 0. 86 vs 0. 44, SE=0. 03 for closeness centrality (CC); and 0. 99 vs 0. 45, SE=0. 05 for betweenness centrality (BC); P<0. 05 for all centralities), density (4. 91 vs 3. 27, SE=0. 36; P<0. 05), and clustering coefficient (4. 87 vs 3. 18, SE=0. 39; P<0. 05) than littermates indicating that non-littermates were more socially connected.
Fifteen litters of 5 day old piglets (n=80) were used and boar piglets within a litter were randomly assigned to one of eight possible treatments: 0. 4 mg/kg meloxicam-castrated, 0. 4 mg/kg meloxicam-uncastrated, 1. 0 mg/kg meloxicam-castrated, 1. 0 mg/kg meloxicam-uncastrated, 6. 0 mg/kg ketoprofencastrated, 6. 0 mg/kg ketoprofen-uncastrated, saline-castrated, or sham-castrated (n=10 piglets/ treatment group). Injections were given intramuscularly 20 mins prior to surgical castration. Piglets were video recorded for 1 h pre-procedure, immediately post-castration for 8 h and for another 1 h, 24 h post-procedure (10 h total). Twenty-one behaviours and postures were scored continuously for the first 15 mins of every hour by four observers blinded as to experimental time and piglet treatment using Observer software.
For HIT one of the following analgesic interventions was applied; Lignocaine administered to the tail at docking site, Tri-solfen applied post-surgically to the would site, tri-solfen and Lignocaine, or no analgesic intervention (as per standard industry practice). Rubber ring lambs were given lignocaine administered to the tail at docking site or no analgesic intervention. Baseline EEG data was recorded for 5 minutes prior to treatment, during the procedure and 5 minutes post-procedure. Data was manually scanned and movement and noise artefacts rejected from analysis. 10 second epochs were used to calculate total power (F Tot ) in mV 2 using specially written software in Matlab (Mathworksâ). Significant interactions between treatment and time (P<0. 001) were observed in all bandwidths for all treatments.
One major goal of the project was to apply standardised animal-based indicators to assess the welfare of dairy goats in Germany. The welfare assessment protocol was established according to literature sources. The AWIN-protocol for goats was not available at that time. Data acquisition was facilitated by programming an assessment tool using a relational database. On-farm assessment took a full workday including recording of animal-based and resource-based indicators, housing and gas concentration. Data analysis was performed using SAS 9. 4 to calculate prevalences for all indicators on farm level and for the reference population. The first assessment started in spring 2015 with 1,876 individually assessed lactating goats on 40 farms. The assessed goats were chosen as a representative sample according to Cochran from all herds using the milking order.
The frequency of spitting and tail-up were recorded as behaviour and posture; the frequency of humming, grumbling and screaming were recorded as vocalizations. Acoustic parameters were recorded with a microphone Sennheiser® ME-66/K6, connected to a digital recorder Tascam DR-100 MKII®. The audio files were analysed using the software Raven Pro® 1. 4. We measured duration and time to maximum amplitude (s) and spectral characteristics of acoustic signal, dominant frequency (Hz) and number of harmonics of acoustic signals. Friedman test was applied to compare behaviours between the three stages, and ANOVA was conducted to compare bioacoustics parameters. We found that only the frequency of humming was higher during handling than during painful stimuli (χ 2 =12. 25, P=0. 02). The frequency of grumbling, screaming, tail up and spitting was not affected by the painful stimuli (P>0.
WAFL 2017 Session Two types of software were used to analyse the microarray data; Genespring was used for statistical analysis and visualisation of transcriptomic data and Cytoscape was used to visualise molecular interaction networks between genes. Results indicated that panels of genes may identify a broad spectrum of infectious disease in chickens, whereas combinations of upregulated genes may be used as biomarkers of specific pathogens such as Escherichia coli or Eimeria. Pigs from two lines (RFI high and low) were kept in dirty environments which had the same bedding and clean environments which had fresh bedding. A greater difference was observed in the number of genes differentially expressed in the RFI high pigs than RFI low pigs. Pathway analysis from both chicken and pig experiments indicated that many networks were affected including those involved in regulating the immune-system.
WAFL 2017 Session 07 Theatre 1 Farmers' practices and attitudes towards artificial fed lambs and their mortality in meat systems X. Boivin Artificial rearing is a common practice in French sheep farming particularly for raising supernumerary lambs in prolific breeds. Mortality rates can reach more than 50% suggesting possible animal welfare and health issues. This prospective study aims to investigate a range of variable rearing conditions, practices, and farmer attitudes towards animals, contact with animals and working in this system, relating this diversity to declared mortality rates. This study was based on semi-directive interviews and questionnaires. As no database exists to identify farms with artificial feeding systems, a convenient sample of farms was built through a snowball process with the help of professional organisation networks in the central area of France.
In a first glance on European and German animal welfare assessment protocols regarding dairy cattle and their indicators, we hardly found animal-based indicators that are not only healthoriented but include aspects beyond that. For the Systematic Review we searched within five databases (CAB Direct, Google Scholar, Livivo, PubMed, Scopus) for peer-reviewed and non-indexed literature, using a strict protocol with English and German search terms. The outcome was limited to publications of the last five years, to dairy cattle as the species of interest and geographically to Europe, regarding the content of the studies. After the removal of all duplicates, we are now confronted with the abstract-screening and categorizing of 1,727 publications, separating peer-reviewed publications from Guidelines, Recommendations, Reviews and others.
However inspection is difficult because strict limits are not available. The aim of the project was to determine measures to assess climate in pig houses. This creates the possibility to enforce open standards on pig farms. In total 32 farms with finishing pigs and 64 farms with rearing piglets were assessed by the Dutch inspection service. On these farms a set of climate related measures was collected in six pens according to a newly developed protocol. The measures were animal and resource based measures and air quality. A simple assessment of the reliability, variation and correlation between measures reduced the dataset from 22 to 12 measures. With principal components analysis five of the measures within this set appeared to be the major measures and could be regarded as warning signals.
Claw health is an important indicator for dairy cattle welfare. The claw health status of a herd can be assessed by clinical observation of individual cows, which is time consuming and a challenge to obtain uniformity between observers. The objective of the study was to develop an empirical model on routinely collected herd data that could classify herds with a below or above average claw health. Two hundred dairy herds were visited to determine the proportion of lame cows, cows with visible hock or knee lesions and an overall grade for claw health. Routinely collected herd data were converted into cattle health parameters. Principal component analysis was used to combine claw health parameters into an observed claw health score. The dataset was randomly divided in a test group of 150 herds to develop a predictive model and a group of 50 herds for validation.
This is a so called 'open standard' which enables pig farmers to reach welfare goals with self-chosen measures. However inspection is difficult because strict limits are not available. The aim of the project was to determine measures to assess climate in pig houses. This creates the possibility to enforce open standards on pig farms. In total 32 farms with finishing pigs and 64 farms with rearing piglets were assessed by the Dutch inspection service. On these farms a set of climate related measures was collected in six pens according to a newly developed protocol. The measures were animal and resource based measures and air quality. A simple assessment of the reliability, variation and correlation between measures reduced the dataset from 22 to 12 measures. With principal components analysis five of the measures within this set appeared to be the major measures and could be regarded as warning signals.
To date, 100 diagnosis have been performed and show that 11% are in 'Excellent' grade; 77% 'Superior' , 12% ' Acceptable' and none 'notclassified'. Each diagnosis helps enrich the database and refine references and grading scale. In conclusion, BoviWell gives an accurate evaluation of animal welfare, comparable to Welfare Quality full evaluation, within only few hours. Identification of best practices and/or potential ways of improvement linked to technical indicators facilitates discussion and involvement of farmers. BoviWell is currently spread out in 1,600 farms in France.
The dataset was randomly divided in a test group of 150 herds to develop a predictive model and a group of 50 herds for validation. Multivariable linear regression with a backward elimination procedure was carried out on routine herd data of the test group to find the best predictive model for the observed claw health score. With the final predictive model, the claw health status of the 50 validation herds was estimated. Herds were classified as below or above average for claw health. Agreement between the predicted relative to observed claw health score was obtained and sensitivity and specificity of the model were determined using the veterinary observations during the herd visits as golden standard. The final model explained 27% of the variance in the observed claw health score. Dairy farming is widespread in the EU with milk the number one single product sector; in value 15% of agricultural output.
For self-monitoring of cattle welfare, in a first step 16 experts selected robust and feasible indicators which address the most important animal welfare problems in cattle. In a second step, detailed protocols for the implementation of self-monitoring in cattle farms were elaborated by a smaller expert group. Indicators consider already existing data (e. g. milk recording, cattle database) or should be assessed on-farm in defined intervals. The following sets of indicators have been recommended. Dairy cattle: Session 05 Poster 75 WAFL 2017.
Pulsed-Field Gel Electrophoresis (PFGE) and Analysis of Electrophoretic Profiles DNA preparation, restriction endonuclease digestion with the KpnI enzyme and PFGE were carried out as described by the Campynet protocol  (Rivoal et al. , 2005). One KpnI restriction profile was obtained for each isolate. Electrophoretic patterns were compared using BioNumerics v. 6. 5 software  (Applied Maths, Sint-Martens-Latem, Belgium). Similarities between profiles, based on band positions, were determined by calculating the Dice correlation coefficient, with a maximum position tolerance of 1%. A dendrogram based on the KpnI restriction profiles was constructed to represent the similarities between the isolates in the matrix. Isolates were clustered by the unweighted pair-group method using the arithmetic mean (UPGMA)  (Struelens, 1996).
Multilocus Sequence Typing (MLST) The seven housekeeping genes for MLST (aspA, glnA, gltA, glyA, pgm, tkt, and uncA) were amplified and sequenced according to previously developed experimental conditions  (Dingle et al. , 2001; Miller et al. , 2005). PCR products were cleaned up using the ExoSAP-IT treatment (GE Healthcare), and sequence extension reactions were carried out in BigDye Ready reaction mix according to the manufacturer's instructions. Unincorporated dye terminators were removed using an ethanol precipitation method before the products were analyzed on an ABI Prism 3130 sequencer (Applied Biosystems). The sequences were assembled using the assembler implemented in BioNumerics v. 6. 5 software. All allelic sequences were queried against the C. jejuni MLST database (http://pubmlst.
org/campylobacter). Alleles already present in the database were assigned the numbers given there; novel alleles and sequence types (STs) were submitted to the MLST database and assigned new numbers. STs were assigned into genetically related clusters called clonal complexes (CCs), based on the sharing of four or more alleles with the central genotype that had been identified in previous studies using the BURST algorithm and UPGMA cluster analysis  (Dingle et al. , 2002).
Some published primers were slightly modified (one or two bases added or removed) to obtain primers with the same (or very similar) melting temperature (indicated by * in Table  1 ). We used also the reverse sequence of the initial primer (virB11) published by  Bang et al. (2004). We designed eight primers from a sequence alignment using Multalin v. 5. 4. 1 (INRA, France) for the detection of the three cdt genes (GenBank accession numbers: AB562905, AB274801, AB274800, AB274799, AB274798, AB274797, AB274796, AB274795, AB274794, AB274793, AB182109) and the ciaB gene (GenBank accession numbers: HG326877, CP006702, AB433217, CP004066). The size of the PCR products was estimated by in silico PCR (FastPCR online v. 2. 07, PrimerDigital) and confirmed after electrophoresis on an agarose gel. Each PCR was carried out in a total volume of 25 µl with the mix SYBR R Green JumpStart TM Taq ReadyMix TM from Sigma-Aldrich, in which 1 µl of each primer at 10 µM was added.
FUNDING The sampling and isolation of isolates were conducted with the financial support of the  CORE Organic II Funding Bodies , partners of the  FP7 ERA-NET project ,  CORE Organic II (Coordination of European Transnational Research in Organic Food and Farming systems , project no. 249667 ). For further information, see www. coreorganic2. org. Characterization of the isolates was conducted with the financial support of  FranceAgrimer  (Contract number:  2013-0504 ).
(Fig. 3 ). ITS sequencing (using the following primers: forward: 5′-T CCGTAGGTGAACCTGCGG-3′: reverse 5′-TCCTC CGCTTATTGATATGC-3′ and the Genbank database) revealed F. pedrosoi. Minimal inhibitory concentrations of antifungal drugs could not be determined because of the impossibility to grow the fungus. Retrospective re-evaluation in our institution of the histological slides of the scalp lesion removed in Haiti eventually disclosed an aspect of chromomycosis. Chest and abdominopelvic computed tomography did not show any other infectious localization. In contrast, while the patient showed no neurologic sign, systematic cerebral magnetic resonance revealed a lesion of the peripheral left cerebellum, which was enhanced after gadolinium injection and which contained a necrotic centre (Fig. 4 ).
cardiorespiratory Variables Mean (±SD) HR was of 42 ± 9 bpm and mean (±SD) MAP was 75 ± 6 mmHg. Dobutamine was not required. Mean (±SD) PE'CO2 was 37 ± 1. 8 mmHg (4. 9 ± 0. 2 kPa) and PaCO2 (mean ± SD) was 48 ± 2 mmHg (6. 3 ± 0. 2 kPa). SpO2 was 84 ± 3% and PaO2 (mean ± SD) was 45 ± 1 mmHg (5. 9 ± 0. 1 kPa). All cardiorespiratory data are reported in Table  3. One single value of Qt was obtained at T35 indicating a cardiac index (CI) of 44 mL kg -1 min -1.
acKnOWleDgMenTs The authors would like to thank the interns and the technicians of VetAgro Sup, Campus Vétérinaire de Lyon, who have contributed to develop this trial. The authors would like to thank the LidCO Company for providing the LiDCO monitor. Conflict of Interest Statement: KS is the managing director of Vetronic Services Limited, who developed the modification of the equine anesthesia station for delivering xenon. The authors declare that this study received funding from Messer Group GmbH for providing xenon. The funder was not involved in the study design or collection, analysis, or interpretation of the data.
Methods Five clinically sound saddle horses (mean (SD): 9(3) years, 564(33) kg) were used. After trimming, the right fore and hind hooves were equipped with a dynamometric horseshoe (DHS), composed of 4 triaxial piezoelectric force sensors (9251A, Kistler) sandwiched between two aluminium plates  [Chateau et al. 2014 ]. The ground reaction force was calculated as the sum of forces applied on each sensor, with the normal component perpendicular to the hoof 's sole (positive downwards) and the parallel (longitudinal) component oriented palmaro-dorsally (positive forward). The DHS wires were connected to charge amplifiers (5073A411, Kistler) then to an analogue-to-digital converter (NI-USB 6218) plugged in a computer remotely controlled (Wi-Fi). Data were acquired at 7. 8 kHz. The horse's speed was measured and recorded by a global positioning system (GPS, Racelogic RLVBSS 100) the antenna of which was glued to the horse's croup.