dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We are grateful to the " Tiques et Maladies à Tiques " working group, which is part of the " Réseau Ecologie des Interactions Durables " for our shared discussions and their support. The modelling work was funded by the  Animal Health Department of the French National Institute for Agricultural Research  (http://www. inra. fr); the local government of Auvergne (http:// www. auvergnesciences. com); the  INRA   MEM metaprogramme  (the  Patho-Id  project); and  EU EDENext  grant  FP7-261504. It has been catalogued by the EDENext Steering Committee as EDENext360 (http://www. edenext. eu). This work was also supported by the  COST action TD1303  (EurNegVec). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the  European Commission.
Acknowledgments We thank  Jan Zoll ,  Ton Rijs ,  Hein van der Lee ,  Diane Lamers-Jansen , and  Birgit Brandt  for excellent technical assistance. We also thank  Monica Slavin ,  Orla Morrissey , and  Alison Campbell  for local site support. This work was supported in part by an unrestricted research grant through the  Investigator Initiated Studies Program (IISP)  of  Merck, Sharp & Dohme (MSD). We declare that we have no conflicts of interest related to this study. J. L. received travel grants from  Gilead  and MSD and honorarium as a speaker from  Pfizer. M. A. has received research grants, travel grants, and honorarium as a speaker or advisor from  Astellas ,  Gilead ,  MSD , and  Pfizer. A. W. received educational grants from  Pfizer ,  Gilead , and  MSD. K. L. received research grants from  Gilead ;  Pfizer ; and  MSD  and served on the speakers' bureau of  Pfizer  and MSD.
The aim of this work was to evaluate the plasmatic PCT concentration in healthy horses and those with acute GI diseases, in order to evaluate the differences between the two groups. Plasma PCT concentration was evaluated in 45 horses referred to three different University Teaching Hospitals, and in 16 healthy horses that underwent similar management conditions. The following data were recorded in order to divide horses in healthy (N = 16), less than two criteria met, and clinical endotoxemic horses' group (N = 45), two or more criteria met: neutropenia and/or toxic changes, increased PCV and TP, tachycardia, tachypnea, abnormal mucous membrane status and capillary refill time. Plasma PCT concentrations were measured with an equine PCT ELISA assay. Results were expressed as mean and standard deviation.
T-test for unpaired data was performed between healthy and suspected endotoxemic horses' group. PCT concentration in healthy and clinical endotoxemic horses' group was 22. 3 AE 21. 4 and 182. 5 AE 83. 9 pg/mL, respectively. T-test showed differences between the two groups (P < 0. 0001). Our results showed an increase in plasma PCT concentration in clinical endotoxemic horses as reported in human medicine. PCT could be used in the equine practice for early therapy planning, in order to improve prognosis and restrain therapy costs. The main objective of this study was to evaluate the association between the antemortem hemostatic profile and the presence of fibrin deposition in postmortem tissues of horses with gastrointestinal disorders. Thus, hemostatic clinicopathological data (D-dimer, prothrombin time, activated partial thromboplastin time, antithrombin) collected 0-24 h before death/ euthanasia and postmortem tissue-organ samples (kidney, lung, liver) from 48 horses with colic symptoms were retrospectively compared.
Clinicopathological evidence of DIC was determined from available hemostatic data (≥3 abnormalities). Phosphotungstic acid hematoxylin (PTAH) and immunohistochemical (IMC) methods were used for histological examination. A fibrin score was established for each technique, tissue and horse, as well as the presence of histopathological DIC, defined as microthrombi present in ≥2 organs. The relationship was assessed by estimating odds ratios and 95% confidence intervals from logistic regression models.
0006 Clinicopathological evidence of DIC was found in 11/48 horses whereas 9/48 (PTHA) and 7/48 (IMC) were considered to have histopathological DIC. No association was found between clinicopathological classification of DIC and postmortem classification based on tissue fibrin deposition. None of the measured hemostatic parameters was significantly different between horses with or without histopathological DIC. In conclusion, routine hemostatic abnormalities do not seem to help in predicting histological evidence of DIC found at necropsy in horses with gastrointestinal disorders. (This report represents a part of the thesis submitted by C. Cesarini to the Faculty of Veterinary Medicine, Universitat Aut onoma de Barcelona, Spain, as required for the PhD degree. ) Purpose of the study: Evaluate whether recent NSAIDs, antimicrobial or corticosteroid treatment was more common in horses with diarrhoea (cases) than practice and date matched horses without diarrhoea (controls) Material and Methods: This retrospective multicentre study used a database of electronic patient records (EPR) from 225,777 horses from North America.
Using a validated text-mining technique the database was searched for records reporting the clinical sign diarrhoea and for NSAIDs, antimicrobials and corticosteroids treatment. Cases and controls were compared using conditional logistic regression (significance: P < 0. 05). Results: Five thousand and six hundred eighteen cases of diarrhoea were identified and prevalence (AE95%CIs) was determined (2. 5%; 95%CIs: 2. 4-2. 6). Univariate analysis indicated recent NSAIDs (OR: 1. 4; 95%CIs: 1. 3-1. 5; P > 0. 001) or antimicrobial (OR: 1. 5; 95%CIs: 1. 4-1. 7; P > 0. 001) treatment or their combination (OR: 1. 7; 95%CIs: 1. 5-1. 9; P > 0. 001) were significantly more common in horses with diarrhoea. Recent corticosteroids treatment (OR: 0. 6; 95%CIs: 0. 5-0. 7; P > 0. 001) was more common in control horses.
8 IU/l and 53. 5 IU/l respectively and 13 cases had diverse causes of acute abdominal pain with average lipase level of 194. 4 IU/l and amylase level of 13. 5 IU/l, all with high standard deviations. Fisher's exact test was used to verify that the lipase and amylase levels are useful in separating AP/PE from RDD or either of these from other diseases. The data suggest that extreme values could be very strong predictors, but larger sample would be needed for quantitative results in this direction. Barium contrast function testing is considered the gold standard for assessment of oesophageal motility, whether by radiography or fluoroscopy; however, these techniques carry the risk of radiation exposure to personnel, and availability of fluoroscopy is limited. Endoscopic examination of the oesophagus is also commonly performed; whilst this technique is useful in the detection of anatomical abnormalities, it does not allow for the horse to be fed at the same time and the passage of the scope and the insufflation of air can alter oesophageal motility.
0011 A single centre retrospective observational study was performed. Case records of all horses admitted to the Dick Vet Equine Hospital between 1998 and 2013 for management of CGS were analysed. Signalment, survival status, indication(s) for euthanasia, duration of disease at hospitalisation, and body weights were analysed, and data for survivors and non-survivors compared. Two hundred and fourteen horses were included in the study, including 114 survivors to hospital discharge and 100 non-survivors. A non-linear model was fitted to each horse's weight records. Using parameters from the model we estimated the initial mean weight loss in non-surviving horses to be 0. 85% per day and 0. 59% in survivors. By the 30th day of disease the mean daily weight loss had increased to 2. 76% in non-survivors and was negligible in survivors.
0013 ADMISSION SEVERE HYPONATRAEMIA IN HOSPITA-LISED FOALS. N. M. Collins 1 , J. E. Axon 1 , J. B. Carrick 1 , C. Russell 1 , P. Dow 1 , J. E. Palmer 2. 1 Scone Equine Hospital, Scone, Australia, 2 University of Pennsylvania, Kenneth Square, USA Purpose of the study: To establish the prevalence of severe hyponatraemia in hospitalised foals on admission to an ICU and to document the diagnosis, treatment and outcome of these foals. Methods: Records from foals aged <3 months presenting to the ICU (2002-2012) were reviewed and foals with severe hyponatraemia (serum sodium<122 mmol/l) on admission laboratory data were identified and further evaluated. Data analysed included signalment, clinical and laboratory parameters, diagnosis, treatment and outcome. Results: Admission severe hyponatraemia was identified in 4% of foals (69/1718).
Image Pro software was used to quantify PSR staining; ten areas were selected by computer program at random and the adipocyte size measured by an observer blinded to the group. The number of blood vessels within a designated area was quantified by a blinded observer. There was increased fibrosis in horses with EMS (13. 87 AE 5. 70) and PPID (20. 43 AE 15. 39) versus healthy controls (5. 26 AE 2. 97) but this did not reach statistical significance (P = 0. 06). Adipocyte size and vessel number were not different between the groups. Vessel number was negatively correlated with body condition score (P = 0. 02). This study suggests that EMS and PPID may be associated with abnormal adipose tissue. Further work is necessary to further elucidate the role of WAT in equine endocrine disease. The majority of cases of laminitis result from endocrine disease, either Pituitary Pars Intermedia Dysfunction(PPID) or Equine Metabolic Syndrome(EMS).
In human medicine, procalcitonin (PCT) is accepted as a highly specific and early marker for microbial infections and sepsis. The aim of this study was to compare plasma PCT concentrations in horses questionable of sepsis to healthy individuals using a newly validated sandwich-ELISA for the detection of equine PCT. Plasma samples of 24 healthy horses and five horses with clinical signs of sepsis were tested. All horses were classified according to a sepsis-score adapted from Breuer et al. (  2012 ) including data from clinical examination and laboratory data at the time of first presentation as positive for sepsis (group A, ≥ 7 score points), questionable (group B, 4-6 score points), or negative for sepsis (group C, ≤ 3 score points).
Acknowledgements -Coral Winslow-Llewellyn and Algotec Research and Development for technical expertise and equipment and  The Langford Trust for Animal Health and Welfare  for funding. 0037  INFLUENCES OF AGE AND SEX ON LEUKOCYTES OF HEALTHY HORSES AND THEIR EX VIVO CYTOKINE RELEASE. C. L. Schnabel 1 , P. Steinig 1 , H. -J. Schuberth 2 , M. Koy 2 , B. Wagner 3 , B. Wittig 4 , C. Juhls 5 , S. Willenbrock 6 , H. Murua Escobar 6,7 , P. Jaehnig 8 , I. Nolte 6 , C. Pfarrer 9 , K. Feige 1 ,  J. -M. V. Cavalleri  1. 1 Foundation, University of  Veterinary Medicine Hannover, Clinic for Horses, B€ unteweg 9, 30559, Hannover, Germany, 2 Foundation, Immunology Unit, University of Veterinary Medicine, Bischofsholer Damm 15, 30173, Hannover, Germany, 3 Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University College of Veterinary Medicine, 240 Farrier Rd, Ithaca, New York, 14853, USA, 4 Foundation Institute Molecular Biology and Bioinformatics, Freie Universitaet Berlin, Berlin, Germany, 5 Mologen AG, Fabeckstraße 30, 14195 Berlin, Germany, 6 University of Veterinary Medicine Hannover, Foundation, Small Animal Clinic, B€ unteweg 9, 30559 Hannover, Germany, 7 University of Rostock, Division of Medicine, Clinic III, Hematology, Oncology and Palliative Medicine, 18057 Rostock, Germany, 8 pj statistics, Niedstr.
Acknowledgements. The authors wish to thank  M. Didier Geffard-Kuriyama  ( Muséum National d'Histoire Naturelle, Paris, France ) for the drawings and edition of the figures, and  Ms. Deborah Lynn Kay  for the English revision. Thanks are extended to  Dr David Spratt  ( CSIRO, Australia ) and two anonymous reviewers for valuable comments and suggestions on earlier versions of the manuscript.
The newly available genome sequences of some helminths combined with large EST libraries should facilitate future work in this area enormously; for example, a bioinformatic analysis of the genome sequence dataset along with proteomic and microarray data will accelerate the identification of more serine proteases. Useful tools to characterize helminth serine protease function such as development regulation, fertilization, invasion of host tissues, and immune evasion include crystallography for the determination of the 3D structure, RNA interference for the silencing of gene expression, and monoclonal antibodies for the inhibition of protease activity as well as colocalization studies to validate an association between a particular serine protease and a putative substrate. This comprehensive analysis not only expands the growing knowledge base regarding helminth serine proteases but also provides a platform for the exploration of their biological functions and potential as targets of effective chemotherapeutic or immunological treatments.
Traditionally, the establishment of a safe level of exposure (called hazard characterization) has been based on toxicological studies conducted according to internationally recognized regulatory guidelines addressing an array of endpoints (e. g. subchronic/chronic toxicity, reproductive toxicity, teratogenicity and carcinogenicity). It is important to note that DNT studies are rarely available in classical regulatory toxicological databases, therefore raising the question of the adequacy of currently used health-based guidance values to cover this specific endpoint. As discussed above ("Regulatory perspectives on current DNT testing" section), new in vitro DNT methods (including in vitro human stem cell-derived models) hold great promise in generating mechanistic data for the thousands of untested chemicals  (Crofton et al.
2012). Furthermore, these DNT specific measurements can be performed using neuronal/ glial models derived from human pluripotent stem cells (embryonic or induced), circumventing the complex issues of species specificity (Fritsche 2014;  Buzanska et al. 2009 ). • To establish DNT as pivotal effect by determination of the sensitivity of developing neuronal cells in comparison with other cell types. • Higher sensitivity/vulnerability of neurons than other cell types would either trigger the need for in vivo DNT data or justify the application of an additional uncer-tainty/safety factor on an existing health-based guidance value derived from a traditional animal database not covering neurodevelopmental studies. The application of a factor to address uncertainty regarding DNT potential would bring confidence regarding the suitability of the health-based guidance value to protect infant health.
When positioned within the AOP context, the usefulness of each assay is determined relatively to its place in the series of key events within an AOP. This approach offers the opportunity to verify that the in vitro method is part of a signalling pathway related to measurable KEs. For example, a pathway present, active and responsible for a KE in vivo should also be similarly responsive in an in vitro assay reflecting the same KE. Thus, the approach of placing in vitro methods into individual AOP contexts will increase the reliability of results from such well-characterized alternative assays because data are obtained on a sound knowledge base with clear determination of individual assay's biological application domains. The criteria for establishing correlative and causative linkages in AOPs can be especially challenging in biological systems with high levels of biological complexity, such is the DNT.
However, a number of issues remain concerning application and predictability of such in vitro methods that must be addressed (Table  2 ). First and foremost of the remaining issues is the need to implement these test methods in order to develop data that will allow an assessment of their utility in screening for DNT. The state of the science for other areas of toxicology, such as developmental, reproductive and endocrine toxicity as well as carcinogenesis, has made immense progress. This includes the development of in vitro testing databases for hundreds of assays and thousands of chemicals in the ToxCast and Tox21 programs  (Attene-Ramos et al. 2013; Kavlock et al. 2012 ). This has fostered development of computational models predicative of in vivo adverse outcomes  (Martin et al. 2011; Rotroff et al.
Common process The taxonomic assignment performed by BLASTN (against the EMBL database) on the contigs (similar to those used for above in the control process) of each sample demonstrated the ability of this process to identify the two viruses. For the PEL sample, HHV-8 presence was obvious since it represents 41 % to 80 % of assignments in the RNA and DNA samples respectively, after filtering. The background of the analysis is minimal since the taxonomy "Rhadinovirus" represents 100 % of viral taxonomies (Additional file 1: Figures  S5  and S6 ). For ATL, HTLV-1 was represented by only a few number of small contigs, however, the analysis process also leads to the detection of its presence. Although viral taxonomies represent only 0. 08-0. 7 % of the assignments (Additional file 1: Figures  S7  and S8 ), in this viral branch, HTLV-1 represents 86-98 % of the reads (Additional file 1: Figures S9 and S10).
Although the percentage of filtered reads is high, the number of remaining reads for each sample were variable with a maximum range from 0. 3 × 10 5 reads for sample AT5 to 2 × 10 5 for sample AT1 (Table  3 ). An overall assembly of all these filtered reads allowed us to obtain 596 contigs (global assembly Table  3 ). Similarities between these contigs and the sequences of the EMBL database (http://www. ebi. ac. uk/ena/home) were searched for using blast. A total of 434 significant similarities led to a taxonomic assignment for the same number of contigs. These taxonomies, depicted by the krona software  [12]  were overwhelmingly eukaryotic (96 %) and more specifically hominidae (76 %) (Additional file 1: Figure  S11 ). The remaining sequences consist of contigs, shorter than 200 bases, with small similarities (30-40 bases) with sequences annotated as vectors (in green in Additional file 1: Figure  S11 ).
The taxonomic assignment provided by blastx against Uniprot databases (http://www. uniprot. org/) were almost identical (data not shown). For 16 contigs, all from the AT2 sample, taxonomic assignment obtained by similarities close to 100 % is unexpected. These taxonomies refer to sequences from Mus musculus and never described in human sequences. A total of 12 contigs covering the entire CDS and the 3′ untranslated region of a LINE-1 sequence (L1spa Acc  AF016099. 1, L1Md-tf23 Acc AF081110); three contigs partially overlap the Gag/pol region of an intracisternal A-particle sequence (MIA14, Acc M17551. 1) and one contig, the only one with high coverage, is identical to a sequence described as a major satellite repeat sequence (Acc EF028077). To our knowledge, these three sequences have not been interconnected in a database sequence or in a publication but all three are annotated as mobile elements.
Acknowledgements This program was supported by the  Institut Pasteur and Institut Gustave Roussy , sponsorship by the  Elisabeth Taub  award from the  Académie Nationale de Médecine and the Laboratory of Excellence, Integrative Biology of Emerging Infectious Diseases (LABEX). High throughput sequencing has been performed on the  Genomics Platform , member of " France Génomique " consortium ( ANR10-INBS-09-08 ). We thank the  PIRC (Pôle Intégré de Recherche Clinique) at the Institut Pasteur  for their help in the biomedical regulatory aspects of the project. We thank  Magali Tichit  for his technical help and  Heidi Lançon  for the English revision. The funders had no role in study design, data analysis or preparation of the manuscript.
All horses breathed spontaneously. Dobutamine requirements, respiratory rate (fR), heart rate (HR), mean arterial blood pressure, end-tidal CO2, inspired (i) and expired (e) tidal and minute volume (VT and V  E ), inspiratory time (IT), and the inspiratory gas flow (VTi/IT) were measured every 5 min. Data were averaged during four 15 min periods before (P1 and P2) and after the incision (P3 and P4). Serial bloodgas analyses were also performed. Recoveries were unassisted, video recorded, and scored by three anesthetists blinded to the treatment. The postoperative behavior of the horses (25 demeanors), HR, and fR were recorded at three time points before induction (T0-24 h, T0-12 h, and T0-2 h) and six time points after recovery (TR) (TR + 2, 4, 6, 12, 24, 48 h). Data were compared between groups using a Wilcoxon test and within groups using a Friedman test or a Kruskal-Wallis signed-rank test when applicable.
m. (Honikel, 1998). The day after slaughter, on each left-carcass side, a piece of loin was excised between the 9th and 12th dorsal vertebrae, partially trimmed of external fat and aged for 3 days at 4°C. Subsequently, they were de-boned, and the LM was vacuum-packed and stored at -20°C before meat texture measurements. After thawing, samples were cut into pieces of 8 × 4 cm parallel to the fibre axis, vacuum-packed and heated in a water bath (70°C, 50 min). After cooling at room temperature, rectangular meat sections of 1 cm 2 were sheared perpendicularly to the muscle fibres with a Warner-Bratzler cell fitted on an universal testing machine (Instron France S. A. S. , Guyancourt, France), according to the recommendations of  Honikel (1998). Breaking energy and maximal shear force were determined simultaneously on at least 14 sections of each LM sample, and the data were averaged.
Statistical analyses The SAS software (version 9. 4, 2013; SAS Institute, Cary, NC, USA) was used for statistical analyses. For all the analyses, animal was considered as the statistical unit. First, data were submitted to an ANOVA (GLM procedure), including the treatment (five levels) and replicate (two levels) as fixed effects to calculate residues of data. Normality of residues was checked using the Shapiro-Wilk test (P ⩾ 0. 05). When necessary, a log transformation was applied to reach a normal distribution of residues of data (plasma glucose, lactate, ACTH and cortisol, LM water, protein, collagen, IMF, lactate, free glucose +G-6-P concentrations, LM drip loss and collagen solubility proportions and breaking energy and shear force). Normality of the residues of transformed data was checked as described above.
Homogeneity of variance of raw or transformed data was also checked (Bartlett test: P ⩾ 0. 05). Subsequently, contrasts between breeds were determined from ANOVA using only A and C pigs from each breed to balance for production system between breeds. Within each breed, contrasts between rearing systems were also determined to evaluate the effects of A v. C system in the LW breed as well as A v. C and E v. C systems in the B breed. Means were calculated by treatment. As it was not possible to normalize residues of data for plasma CK, skin lesions and pHu and because of the heterogeneity of variance of raw data (Bartlett test: P ⩽ 0. 05), a non-parametric method (NPAR1WAY procedure, Kruskal-Wallis test) was used to determine the effects of breed and rearing system within breed. Medians, first and third quartiles were calculated by treatment.
Acknowledgements The authors thank the staff of  INRA  experimental farm, slaughterhouse and laboratories ( URM1348   PEGASE ,  F-35590 Saint-Gilles ,  UR370  QuaPA, Theix, F-63122  St-Genès-Champanelle, UE EASM ,  Le Magneraud , F-17700 Surgères; France) for excellent assistance, as well as the breeders and slaughterhouse staff of the Basque Pork chain involved in this study. The authors gratefully acknowledge the  European Community  financial participation under the  Sixth Framework Programme for Research ,.