dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This study was supported by the generous donation of mustelid samples from across Europe; We thank all those who have assisted with post-mortem programmes across Europe, including  Cardiff University Otter Project  and the  Wildlife Veterinary Investigation Centre (England and Wales) R. Kuhn, Xavier Gremillet and Ludovic Fleury (France), G Loupal (Germany) ,  G Zaleśny  (Poland) and  E Fraser  (Scotland). Thanks also to  R Fusillo ,  M Bodner ,  I Dimov ,  N Ferrari ,  P Garcia Diaz ,  H Jansman  and  G Gorgadze  who were approached for samples in additional countries and were all very accommodating even though samples were unavailable. Thank you to  Dr. P Faria-Shayler  for the help with DNA extraction methods. Thank you to  Eileen Harris ,.
Background: Acetaminophen (APAP, paracetamol) mechanism for analgesic and antipyretic outcomes has been largely addressed, but APAP action on cognitive function has not been studied in humans. Animal studies have suggested an improved cognitive performance but the link with analgesic and antipyretic modes of action is incomplete. This study aims at exploring cognitive tests in healthy volunteers in the context of antinociception and temperature regulation. A double-blind randomized controlled study (NCT01390467) was carried out from May 30, 2011 to July 12, 2011. Methods: Forty healthy volunteers were included and analyzed. Nociceptive thresholds, core temperature (body temperature), and a battery of cognitive tests were recorded before and after oral APAP (2 g) or placebo: Information sampling task for predecisional processing, Stockings of Cambridge for spatial memory, reaction time, delayed matching of sample, and pattern recognition memory tests.
Materials and methods study This randomized, double-blind, crossover, controlled trial in healthy volunteers took place in the Clinical Investigation Centre/Clinical Pharmacology Centre, University Hospital of Clermont-Ferrand, France, from May 30, 2011 to July 12, 2011. The study was reviewed and approved by the French Institutional Review Board and the French Drug Agency. It followed standardized ethical and safety Good Clinical Practice Guidelines and procedures were in accordance with the Declaration of Helsinki. It was registered on ClinialTrials. gov (NCT01390467).
Volunteers Participants were recruited through the database of the Clinical Pharmacology Centre of the University Hospital of Clermont-Ferrand, France. Male volunteers (to avoid pain threshold variability due to menstrual cycle in females) were eligible if they were $18 years old, did not take analgesic or anti-inflammatory treatment in the last 7 days, and were nonsmokers. Exclusion criteria included: a known hypersensitivity to APAP, concomitant pathologies, contraindications to APAP, any abuse consumption of alcohol, addiction to drugs, or use of drugs of abuse. Eligible volunteers were informed about the protocol and provided a signed informed consent.
statistical analysis The sample size estimation for this study was done from the results of a previous APAP trial in healthy volunteers (ClinicalTrials. gov, NTC01053650) with the same methodology and where the Cantab psychometric test was used for cognitive assessment, but this previous study had no placebo group. Estimations were based on SOC test with 90% statistical power, two-sided type I error a=0. 05, expected difference 0. 8 (paired difference to be detected) for a standard deviation of 1. 68 (expected standard deviation of difference), and correlation coefficient due to crossover design r=0. N=40 subjects were analyzed in an intention to treat analysis. Statistical analysis was performed using Stata 13 software (StataCorp LP, College Station, TX, USA). The tests were two-sided, with a type I error set at a=0.
ACKNOWLEDGMENTS The work was conducted by  Evidera (formerly United BioSource)  and funded by  Pfizer Inc. Sonja Sorensen  and  Lael Cragin  are employees of Evidera, who were paid consultants to  Pfizer Inc  for the development of this manuscript. Editorial support was provided by  Leigh Prevost, BSc , of  PAREXEL , and was funded by  Pfizer Inc.
effectiveness analysis model inputs for base-case analysis FLU ITR POS VOR Source data Prophylaxis cost per day, € a 5. 49 2. 38 89. 87 71. 35 Portalfarma: Bot PLUS 2. 0 database 22 Duration of prophylaxis, days a 91 68 96 b 96 Marks et al. 15 Wingard et al. 18 Median probability of requiring OLAT, % 30. 7 29. 1 32. 2 22. 0 Derived from Bow et al. 14 Median probability of breakthrough IFI, % Candidaemia/IC 1. 5 0. 5 1. 4 1. 1 Bow et al. 14 IA 5. 9 4. 1 1. 9 2. 2 Other IFI 1. 0 1. 2 2. 7 0. 4 All treatments Source data Cost of treating breakthrough IFI, € Candidaemia/IC 18 354 IA 68 307 Olaechea et al. 23 Other IFI 68 307 c de la Camara et al. 24 Mortality rates (mean) for breakthrough IFI, % Candidaemia/IC 57. 1 Pagano et al. 25 IA 77. 2 Other IFI 40. 0 Non-IFI mortality d 20. 0 Martin-Pena et al.
Statistical analyses In the present study, measurements of N and energy balances, respiratory quotient, nutrient deposition and BW gain composition were taken on the same experimental subject (pig, n = 8) over time (stage, n = 2). To present least squares means the ANOVA was performed using mixed model procedure of SAS (PROC MIXED; SAS Institute, Cary, NC, USA) with nested design including fixed effects of stage and group within stage and the random effect of pig. Due to the fact that both experimental groups received the same treatment in stage 1, and thus the absence of difference between groups 1 and 2 in stage 1, the results (least squares means) for this stage are presented as their average values. To determine the changes between stage 1 and stage 2 due to combined effects of IC, growth and increased feed intake (IC/growth), the pigs on LF diet were compared in stage 1 and 2 (group 1 in stage 1 was contrasted to group 1 in stage 2).
Acknowledgements The present study was performed at  INRA ,  UMR 1348 Pegase, Saint-Gilles, France. Financial support was provided by  Slovenian Research Agency  (PhD scholarship of N. B. -L. , project  L4-5521  and programme  P4-0133 ),  Rennes Metropole  and Slovenian human resources developments and scholarship fund (PhD student mobility scholarship of N. B. -L. ). The authors would like to thank  J. Delamarre ,  Y. Jaguelin ,  R. Janvier ,  V. Piedvache ,  P. Roger  and  A. Starck  for their assistance in animal care and laboratory analysis.
, 2007]  and supported with independent datasets on lemurs  [Ganzhorn, 1992; Simmen et al. , 2012]  and howler monkeys  [Peres, 1997]. The biological relevance of this ratio has been questioned based on biochemical considerations, statistical issues around the use of ratios  [Wallis et al. , 2012] , and empirical grounds  [Gogarten et al. , 2012; Chapman et al. , 2014]  but it seems to retain some predictive capacity. Restricting the considerations to protein alone, several studies have shown that protein can be limiting with lasting effects on development and lifetime fitness [e. g. ,  Fleagle et al. , 1975; Elias & Samonds, 1977; Altmann, 1991 Altmann, , 1998;; Degabriel et al. , 2009]. However, the evidence that folivorous primates actually select leaves with high protein content is ambiguous.
Database The analyses presented here are based on published data from all primate radiations (except for apes; see below), supplemented by new data of folivorous primates from Madagascar, the New World and Nepal (Table  1 ). Analyses were restricted to forest dwelling species that have been classified as "folivores" because the majority of their food items were from photosynthetic material  [Kappeler & Heymann, 1996]. As more studies are conducted, it appears that the classification of species into specific feeding guilds does not reflect the species-specific variability of diet  [Hemingway & Bynum, 2005; Garber et al. , 2015]. Thus, we call those species "folivores" that are supposed to derive their protein from leaves and not insects according to  Kay's [1984]  hypothesis. Species that feed primarily on the leaves of grasses, bamboo (Hapalemur spp.
, Prolemur simus) and herbs (Gorilla spp. ) were not included, as grass and herbs have different physico-chemical properties than leaves from trees, such as different lignin, a general lack of tannins and incorporation of silica in grasses  [Robbins, 1983]. However, Hapalemur meridionalis from Mandena (south-eastern Madagascar) was included as these animals live in an area without bamboo and feed on grass and other leaves  [Eppley et al. , 2011]. For the current analysis we removed all grasses that were used as food and restricted the analysis to the proportion of their diet that consists of leaves from trees. We also included body mass in the database provided in Table  I. Data for primate body mass were taken from  Smith and Jungers [1997]  and  Mittermeier et al. [2010]  and averaged between sexes.
Food Types and Nutritional Analyses Foods included in the present analysis were leaves or flower buds from trees, shrubs or vines. We further restricted the analysis to concentrations of nitrogen (measured by the Kjeldahl method), or by a combustion procedure with subsequent analysis of elementary nitrogen (the Dumas method), or based on near infrared reflectance spectroscopy (NIRS) (calibrated against the Kjeldahl or Dumas method), soluble protein and acid detergent fiber (ADF). Data presented as "crude protein" (i. e. total nitrogen multiplied by 6. 25) was re-transformed to total nitrogen concentration as the biological significance of the conversion factor is presently debated and its biological meaning is unclear  (Milton & Dintzis, 1981; NRC, 2003;  for methodological reviews see  Ortmann et al.
, 2006; Rothman et al. , 2012). The Kjeldahl and Dumas methods yield almost identical results (regression between nitrogen measured by  Kjeldahl [y]  and by the Dumas method [x] forced through the origin: y = 0. 94x; R² = 0. 99; n = 90; Supplementary Material  [Terboven, 2014] ). Near infrared reflectance spectroscopy also provides accurate estimates for nitrogen concentrations when models were tested with truly independent data (Kjeldahl: y = 1. 06x, R² = 0. 97, N = 18; combustion: y = 0. 97x, R² = 0. 97; N = 18; Supplementary Material). Studies that published soluble protein concentrations (measured by the method outlined by  Bradford, [1976] ) but without estimates of crude protein were included in the analysis, when available. However, these two datasets were analyzed separately. "Available protein" would be a more biologically appropriate measure of protein than crude protein  [DeGabriel et al.
, 2008 [DeGabriel et al. , , 2014;; Wallis et al. , 2012]  and probably also than soluble protein as soluble protein concentrations are correlated with available protein in some studies but not in others  [Ganzhorn, unpubl. ]. To date, too few data exist for available protein to allow for comparative analyses. In primate studies, fiber concentrations are most commonly reported as acid detergent fiber (ADF). However, not all studies report exact details of the procedures (e. g. whether ADF is analyzed sequentially following isolation of neutral detergent fiber (NDF)). In addition, most studies do not specify whether ADF is reported on an ash-free basis or corrections are made for residual dry matter. Furthermore, there is little appreciation in primate literature that fiber residues can be contaminated with tannin-protein complexes  [Wallis et al.
Statistical Analyses Published data are based on the analysis of a single individual per plant species or averages based on several different individuals of the same plant species or on averages weighted by the frequency of abundance or the frequency of consumption. When possible, we base our analyses on unweighted means of plant species. Surprisingly, and despite the known temporal and inter-individual variation within plant species  [Ganzhorn & Wright 1994; Chapman et al. , 2003] , the variation between weighted and unweighted samples seems to average out in large samples (Table  II ). Statistical tests were made with SPSS 21. 0.
Selection of Leaves in Relation to the Average Concentrations of Nitrogen, Soluble Protein or ADF in a Given Forest Measures of nitrogen, soluble protein and ADF in representative samples of plant leaves were found for 19, 18 and 33 studies, respectively (Table  I ). Concentrations of the same components in food plants were found for 35, 22 and 41 studies. The data for soluble protein were unevenly distributed in the dataset, and were mainly available for foods of lemurs. Studies of the same species in different areas or during different times of the year were treated as independent units since the concentrations of chemical components vary significantly between sites and seasons. Selectivity for leaves containing high concentrations of nitrogen increased significantly with declining nitrogen concentrations in forests (r s = 0.
Acknowledgements We thank  Nicoletta Righini  for her invitation to contribute to this special volume of the American Journal of Primatology. Nicoletta Righini ,  Marcus Clauss  and an anonymous reviewer provided insightful comments on our manuscript, which we greatly appreciate. Funding was provided to MKC and AK by the  Alexander von Humboldt-Foundation , the  German Academic Exchange Service (DAAD) , and the  German Research Council (DFG) , to ID from DFG; to TE from the  American Society.
QTY AM ¼ QTY AM CUR þ QTY AM MONENSIN ð11Þ With: QTY AM MONENSIN ¼ N TRT Ã Quantity of monensin within one bolus ð12Þ The model was run using Scilab (version 5. 5. 1) open source software (www. scilab. org) with 10,000 iterations, and the 95% prediction intervals (PI) and 95% confidence intervals (CIs) were calculated. The PI makes it possible to predict the situation for the next farm with 95% probability, and the CI indicates the situation in 95 of 100 farms visited.
BCS ranges from 1 to 5 points (given in ¼ point increments) and cows with a BCS between 3. 75-4 points at calving are considered to be too fat and at risk for SCK  [11, 18, 19]. The literature included (S2 Table ) and the methods, results and discussion (S1 Text) of the meta-analysis are detailed in the supplementary files. The results of the meta-analysis showed it was difficult to precisely define RR SCK IF AT RISK. Two scenarios were then proposed, with RR SCK IF AT RISK defined through LN (0. 76,0. 60) or LN(1. 50,0. 62) (Table  1 ). EFF MONENSIN was evaluated from the report for the monensin bolus of the Committee for Medicinal Products for Veterinary Use from the European Medicines Agency (www. ema. europa. eu). Three other studies dealing with monensin in the form of a bolus or mixed in food were also included; however, the available data in the literature were limited compared to the Committee for Veterinary Medicinal Products data to define EFF MONENSIN (S3 Table ).
Methods The database of the bacteriological laboratory at the Bordeaux University Hospital was used to identify patients with isolation of NTM between January 2002 and December 2013. Only patients followed up at the Bordeaux University Hospital were included in the study. Demographic (gender, age) and clinical data (site of infection, underlying disease, impaired immunity, symptoms, radiographic results, treatment and outcome) were obtained from clinical records. Diagnosis criteria for NTM lung disease were those of the American Thoracic Society (ATS)/Infectious Diseases Society of America (IDSA) recommendations  [4). Patients with cystic fibrosis were excluded. Radiographic abnormalities (nodular, infiltrative or cavitary) were analyzed by chest radiography and/or CT scanning. We categorized extrapulmonary NTM disease cases as: skin and soft tissue; disseminated; lymphadenitis; bone and joint or catheter-related infections.
Economic model Using an economic model, the efficacy of VOR+ANI combination therapy was compared with VOR monotherapy for the treatment of IA in a hypothetical cohort of 1,000 galactomannan-positive patients. The model consisted of a decision tree (Figure  1 ) predicting outcomes after 6 weeks of therapy. The analysis considered the following variables: mortality or survival rate of the patient; probability of adverse events (AEs) occurring or not; probability of any AEs occurring being serious or mild-to-moderate; costs of antifungal therapy, AE-related costs, and costs of hospital stays (ward and intensive care unit [ICU]); and life expectancy in patients with HSCT who respond satisfactorily to antifungal therapy for IA. Efficacy and toxicity data were obtained from a clinical trial reporting on VOR+ANI combination therapy in 108 patients and VOR monotherapy in 110 patients (NCT00531479).
Drug acquisition costs The acquisition costs of VOR (Vfend ® ; Pfizer Inc. ) and ANI (Ecalta ® ) were obtained from the official manufacturer's sales prices in Spain, including the recently authorized mandatory discount of 7. 5% for ANI (Table  2 ). 13 We also considered the dosage schedules recommended in the Summary of Product Characteristics of both drugs  14, 15  and, in the case of VOR, the average body weight of adults in Spain (70. 0 kg; 95% confidence interval [CI]: 67. 8-76. 1 kg), obtained from Ministry of Health databases (Table  2 ). 16 Patients were assumed to receive treatment with ANI (200 mg on day 1, followed by 100 mg every subsequent day of treatment) for at least 2 weeks and no more than 4 weeks.
This was a theoretical model, which, by definition, was a simulation of real-world clinical practice. Additionally, efficacy and AE data were obtained from an explanatory double-blind, randomized clinical trial (NCT00531479),  9  as no data from pragmatic clinical trials were available. 32 Consequently, the results of the economic analysis are applicable only to patients with similar characteristics to those included in that clinical trial. Also, the lower mortality of the subgroup of patients who received VOR+ANI combination therapy for IA indicated by galactomannan testing in the trial reported by Marr et al  9  was determined by means of a post hoc analysis, with associated methodological limitations. 33 As noted by Marr et al,  9  further work is required to confirm the results obtained in the combination therapy subgroup; our economic model was, therefore, also dependent on such limitations.
As a consequence, we sequenced the complete 16S rRNA gene using a 3130-XL sequencer (Applied Biotechnologies, Villebon sur Yvette, France) and compared it to GenBank. The complete 16S rRNA gene of strain SN17 exhibited a sequence identity of 92. 67% with Clostridium sporosphaeroides strain DSM 1294 T (GenBank Accession number M59116), the phylogenetically closest species with standing in nomenclature (Fig. 1 ). Clostridium sporosphaeroides is an anaerobic bacterium isolated for the first time in 1948, and recently identified in biogas plants in Germany  [4]. Clostridium sporosphaeroides produces butyric acid, acetic acid and propionic acid from the fermentation of the biomass  [4]. Another closely related species, Clostridium leptum, has been proposed to play a role in the pathogenesis of inflammatory bowel diseases  [5]  as well as an immunomodulatory role in diseases such as asthma  [6].
The FACCE-JPI 'Global Network' project is an international initiative that intends, among other goals, to develop reliable and robust guidelines for generating and evaluating data from in vitro and in vivo experiments examining the potential to mitigate greenhouse gas (GHG) emissions from ruminant livestock systems. The present review is one output from the project that provides a critical evaluation of the key points for consideration when planning and performing in vitro studies and guidance for end users in the interpretation of experimental data from IVFT experiments. Major emphasis is placed on factors that influence microbial activity within in vitro systems typically used to assess CH 4 production, and how these can be balanced or accounted for, rather than simply providing a contrast and comparison of reports in the scientific literature.
Acknowledgements. 14 References. 14 Acknowledgements This review is part of the  FACCE-JPI 'Global Network ' project and the  'Feeding and Nutrition Network' of Livestock Research Group, in the Global Research Alliance for Agricultural Greenhouse Gases  (www. globalresearchalliance. org). Authors acknowledge national funding from  INIA (Spain , project  MIT01-GLOBALNET-EEZ ), the  Ministry of Economic Affairs  (The  Netherlands ; project  Global Research Alliance on Agricultural Greenhouses Gases ,  BO-20-007-006 ),  USDA-NIFA (USA) ,  French National Research Agency  through the program  FACCE-JPI program , the Irish contribution to this JPI- FACCE  project was funded by the  Agricultural GHG Research Initiative for Ireland (AGRI-I) ,  Department for Environment Food & Rural Affairs (UK) ,  BLW (Switzerland)  and  Academy of Finland, Helsinki, Finland  (Project  281337 ).
) is also an agricultural settlement dated to the transition between the Yangshao and Longshan cultures. During excavations in 2001, refuse pit H3 produced pig, hare and weasel bones, together with a nearly complete felid skeleton laid on its left side (S1 and S2 Figs). The left calcaneus has been directly dated using AMS 14 C to 5267-4871 cal BP (Table  1 ). Based on classical measurements (S2 Table ), the specimen was initially identified as Felis silvestris  [25]. Features of skull morphology (namely the shape of the tympanic bulla) allow us to exclude F. manul as a likely candidate. However, values for traditional cranial measurements all fall intermediate between our modern F. silvestris and P. bengalensis reference datasets. The site of Xiawanggang (Xichuan county, Henan prov. ) is a settlement occupied from the Late Yangshao culture through to the Han Dynasty  [26].
Identification of Chinese and Cypriot archaeological cats The fragmented nature of the Chinese archaeological mandibles required the use of a subset of landmarks and the computation of separate discriminant analyses for each archaeological specimen. Nonetheless, analyses show that all Chinese archaeological felid specimens were unambiguously identified as leopard cat (P. bengalensis) (Fig 2, S3 Table ). Their centroid size is relatively small, but within the range of current leopard cat specimens available in our dataset. The PPNB Cypriot cats were identified as F. silvestris, with probability ranging from 94% to 100% (S3 Table )-their size range being significantly higher than the Chinese archaeological cats (S4 Fig).
Data acquisition A total of 96 modern (S1 Table) mandibles, together with 5 Chinese and 5 Cypriot archaeological mandibles were analyzed using two-dimensional landmark based geometric morphometric approaches from standardized photographs taken from the vestibular view. With the help of small spirit levels, the mandibles were positioned in such a way that the plane between the lateral edge of first lower molar and the lateral face of the horizontal ramus at the level of the fourth/third lower premolar was horizontal; and the plane between the lateral edges of the ventral and anterior ridges of the vertical ramus was also horizontal. Coordinates of 11 landmarks were recorded (S5 Fig,  S5  Table) using TpsDig 2  [35]. Data from this study are available at Labarchives (doi: 10. 6070/H4NK3C1B).
Statistical analyses Differences in shape and size between the modern taxa were respectively tested using MAN-OVA and Kruskall-Wallis test. Shape proximities between the groups were visualised using a neighbour joining network computed from the Mahalanobis D 2 distances and differences in size variation between taxa were visualised using boxplots. Identifications of the nine archaeological mandibles (five from China and four from Cyprus) were made using predictive linear discriminant analyses (LDA) using Felis silvestris (including both subspecies) and P. bengalensis as the two alternatives. Results of discriminant analyses are known to be affected by the number of specimens by group. To limit the potential bias induced by our unbalanced dataset that included more F. silvestris than P. bengalensis, all the identifications were based on 100 random selections of specimens of F.