dataesr/scientific-paragraphs-categorization huggingface dataset:
Sequence Processing and Microbial Community Analyses Briefly, 16S rRNA gene sequences were processed and clustered using the mothur v. 1. 39. 3 standard operating procedure (SOP) designed for MiSeq data  (40) ; the mothur MiSeq SOP was accessed in August 2018. The SILVA-based bacterial reference alignment (version 132) was used to identify the taxonomy of OTUs at a cluster cutoff of 97% sequence identity. Measures of richness, evenness and diversity were determined in mothur. Richness can be defined as the number of OTUs per sample, evenness represents the uniformity of the distribution of an individual amongst a community over different species, while α-diversity is a concept combining both richness and evenness  (41). Richness and α-diversity were determined through the coverage, the number of OTUs observed, the Chao1, the ACE, the Shannon, the Simpson, the inverse Simpson estimators and β-diversity were calculated using the thetaYC distances as implemented in mothur.
No significant differences in any of the indicators considered were observed regarding the profiles of abomasum worm populations within kids (Fig. 4 ). The prolificacies of mature worms were 278, 4981, 502, 562, 6076 eggs for Leucaena leucocephala, Manihot esculenta, Cajanus cajan foliage, TRF blend and alfalfa respectively. Except for Manihot esculenta, the prolificacies tend to be similar (P < 0. 15) with the TRF compared with alfalfa. Data obtained from kids fed blended diets were consistent with those values obtained for each of the ingredients in the mixture, whatever the nutritional or health criterion.
Discussion The chemical compositions of feed provided to goat kids in experiments here are consistent with previously published data  6. The low intake and total tract digestibility values associated with kids provided Dichanthium spp hay was consistent with data showing its chemical composition, which indicated that it was poor quality hay. Estimates of the total tract digestibility of TRF and alfalfa, obtained by difference from that measured on Dichanthium spp hay when it was the only ingredient in the diets, seems relevant. This is especially true when referring to estimates of the total tract digestibility of alfalfa, for which values are available in the literature. However, an overestimation of the total tract digestibility of TRFs cannot be eliminated. Indeed, hay digestion could be improved in kids provided mixed diets because TRFs by promoting microbial activity in the rumen, increases its fibrolytic potential (described below).
Further, our data seem to indicate that the DM digestibility of TRF is highly variable (47. 9 to 63. 1%). None TRF-associated values reached values estimated for alfalfa, which was classified as high-value feed. Considering estimated total tract digestion of DM and CP, diet containing Cajanus cajanus was classified as low-value feed, and Leucaena leucocephala and Manihot esculenta were classified medium-value feed. When the protein value of TRF was assessed on the basis of the total digestibility of CP, the same classification of Cajanus cajanus, Leucaena leucocephala and Manihot esculenta was determined. These results are consistent with theoretical degradability (DT CP ) values of CP obtained in the laboratory using the same TRF. DT CP values of Leucaena leucocephala, Manihot esculenta and Cajanus cajan were 64.
25. NDF, ADF and ADL in the diets and faeces were determined using a sequential procedure (AOAC methods 200. 04 and 973. 18, respectively, for NDF and ADF + ADL). CTs were CT extracted and quantified as described in Laurent  27. Statistical analyses. Data were analysed to compare nutritional characteristics (intake, digestion, nitrogen balance, ADG, feed efficiency) of diets using the mixed SAS procedure  28. Differences between means were tested using the pdiff option. Significance was declared at probability levels ≤ 5%. Only data from the pre-infestation period and the first week post-infestation were considered in order to eliminate a possible effect of parasitism on the intake and digestion of the diets. The value one-week post-infection was considered since the impact of infestation remained low within that timeframe.
The statistical model used was as follows: = + + + + µ Y D T A e ( 1 ) ij i j k i jk where Y ij is the explained variable, µ is the mean, D i is the diet fixed effect (I = 1-6), T j is the time relative to the date of the artificial infestation (j = 1-2), A k is the random effect associated with the animal (k = 1-55) and e ijk is the residual term. For the nitrogen balance (faecal, urinary and retained nitrogen), the amount of nitrogen ingested was introduced as a covariate in the statistical analysis model. Animal responses (nutritional and heath indicators) to the infestation were analysed using the SAS mixed procedure (SAS, 2008). Nutritional indicators were analysed only before infection. PCVs and FECs were log-transformed (log (Eosinophils + 1), log (FEC + 1)) before analysis; however, only raw means are reported in data tables.
Acknowledgements The authors would like to thank  Lucien Philibert ,  Yoan Felicité ,  Xavier Godard ,  Fred Periacarpin ,  Christian Deloumeau ,  Claude Barbier  and  Frederic Pommier  for their technical assistance. This study was completed with the financial support of  INRA ,  Region Guadeloupe  and European funding:  FEDER  ( AgroEcoDiv  project),  FEADER (RITA TRANS'BOV).
B-Mode Ultrasonography-Prostate Gland During the first examination (Day 0, D0) the whole image of the prostate with margins and symmetry, as well as medial iliac lymph nodes and the presence of the periprostatic cysts were assessed. During each scanning four thematic categories, concerning B-mode prostate parenchyma appearance, were identified, and its particular aspects were described using exact, descriptive terminology  [14] : (1) background echo texture (normal, hyperechoic, hypoechoic); (2) parenchymal stippling (regular, increased, coarse); (3) general appearance (homo-and heterogenous); and (4) focal changes (cysts, mineralized opacities, focal hypoechoic lesions). To facilitate the evaluation of the results, all data found during each examination was tabulated (Table  1 ). Moreover, during each examination the length (L), depth (D), and width (W) of the prostate gland were measured, and the prostate volume (VP) was calculated using the formula published by Atalan et al.
Statistical Analysis Statistical analysis was carried out using the STATISTICA 10. 0 software (StatSoft, Kraków, Poland). Descriptive statistics, such as the mean and SDs, were calculated for each prostate measurement. The Shapiro-Wilk test was carried out to verify whether the parameters had a normal distribution. The values within the study groups with respect to D0 and the values between control and study groups were compared using the paired Student's t-test, or U Mann-Whitney test. The natural anatomical differences in prostatic and testicular sizes in individual dogs were addressed using percentage (%) instead of numeric values (cm 3 ), and the D0 volume was considered 100%  [20]. The relationship between prostate size and blood flow in the prostatic and testicular arteries in Group III and IV were assessed using Pearson's coefficient test.
Materials and Methods Medical records of cats presented to the Clinique Vétérinaire Aquivet during the period from 1st July 2016 to 1st May 2019 with a TCI that had been treated by open reduction and internal repair with concomitant temporary JAM-TESF were retrospectively reviewed. Inclusion criteria included patients with TCI, complete medical records, preoperative radio-graphs, postoperative radiographs and follow-up radiographs at 4 to 8 weeks. Collection of data was a minimum of 6 months after surgery ensuring adequate time for the development of complications. 18 Information collected included signalment, body weight, initiating trauma, type of TCI (medial, lateral or medial and lateral), other concomitant orthopaedic injuries, surgical approach, implants used, TESF configuration, time to TESF removal and complications (intra-and postoperative).
INTRODUCTION Hypercalcemia in cats may be associated with a variety of conditions which can be either parathyroid-dependent or, as in the majority of cases, parathyroid-independent  (1). Between the latter, idiopathic hypercalcemia is the one diagnosis considered exclusive of the feline species, and the diagnosis of which is made per exclusionem  (2). According to a review by de Brito Galvão and colleagues, idiopathic hypercalcemia should be addressed as main cause of hypercalcemia in cats  (2) , while recent analysis on the Cornell University's database  (2007) (2008) (2009) (2010) (2011) (2012) (2013) (2014) (2015) (2016) (2017)  suggests that malignancy and renal failure are more common causes  (3). Regardless of which place claims on the podium, being first or third in terms of frequency, it is clear that idiopathic hypercalcemia is one of the important diagnoses of hypercalcemia in cats.
Despite the etiopathogenesis is still not known, explanations for the development and maintenance of increased circulating calcium levels lie in a metabolic disorder of this mineral: enhanced bone resorption, augmented intestinal absorption, decreased renal excretion, or a combination of these  (4). Cats diagnosed with idiopathic hypercalcemia are typically middle-aged (mean, 5. 8-9. 8 years), with both sexes equally represented  (5, 6). Cats can be frequently asymptomatic  (6) , but when it is not the case, depending on literature source, either anorexia  (2)  or vomiting  (5)  are the most common signs, with lethargy, weight loss, constipation, dysuria, hematuria, polyuria, and polydipsia as other occurring symptoms  (2, 5, 6). To rule out the long list of potential causes of hypercalcemia, patient evaluation should start with a thorough history-taking and physical examination, followed by a minimum database comprising complete blood count, serum biochemistry, ionized calcium (iCa), PTH-measurement, urinalysis, imaging of chest and abdomen (radiography and ultrasonography)  (7).
Extended database may include serum 25-hydroxycholecalciferol (calcidiol), 1,25-dihydroxycholecalciferol (calcitriol), 24,25dihydroxycholecalciferol, concentrations of parathyroid hormone-related protein (PTHrP), ultrasonography of the neck, or exploratory surgery  (2). A typical cat with idiopathic hypercalcemia exhibits mild to moderate increases in total (tCa >2. 75 mmol/L) and ionized (iCa >1. 40 mmol/L) calcium serum levels  (1) , with normal serum albumin and usually accompanied by concentrations of calcemic hormones (parathyroid hormone and vitamin D metabolites) which are either low or perfectly within laboratory reference range  (1, 2). Dietary change is considered the first-line treatment in the management of the disease (2). Lack of published prospective studies, and conflicting results  (5, 8) , make it currently not possible to state which nutritional aspect is the most significant in the regulation of calcium homeostasis in this pathology.
Coproscopic analyses Since it was aimed to collect data about Anoplocephala and strongyle nematodes, optimised coproscopic analysis methods for both parasite groups were used. Faecal egg counts (FEC) were determined using mini-FLOTAC and a double centrifugation/combined sedimentationflotation technique in parallel. Prior to the mini-FLO-TAC  [31] , 5 g faecal samples were processed with the Fill-FLOTAC apparatus as described by Noel et al. [32] , with 45 ml of saturated saline solution (specific gravity 1. 2 (NaCl)) added. For each sample, two 1-ml flotation chambers of the mini-FLOTAC device were counted corresponding to a multiplication factor of 5 to convert raw counts into eggs per gram (epg) of faeces data. The double centrifugation/combined sedimentation-flotation technique was performed as described by Rehbein et al.
Data analyses Data were entered into a Microsoft Excel spreadsheet. Correlation analysis and all graphs were created using GraphPad Prism ® Version 5. 03. All other statistical analyses were performed with R 3. 4. 4 using RStudio version 1. 1. 456 for Windows. Confidence intervals for proportions were calculated as Wilson Score intervals with finite population correction in OpenEpi Version 3. 01  [33]. A mid-p exact test for differences between proportions was conducted using the tab2by2. test() function from the epitools package version 0. 5-10. A logistic regression analysis was performed to identify variables with potential influence on the odds of a horse in the study population to be positive for antibodies against Anoplocephala spp. in the serum-based tapeworm ELISA. The serum-based tapeworm ELISA was chosen here due to the fact that the saliva ELISA was not available in the beginning of the study and thus the dataset was smaller.
Discussion Cestode eggs were identified in only 0. 6% of the coproscopical examinations (farm level 6. 3%). Compared to other studies conducted in Germany using faecal sampling (Table  1 ), this is slightly below the expected frequency in the study population. A prevalence of 2. 0% (farm level 14. 3%) was observed by Hinney et al. [10]  and 3. 0% (farm level 35. 2%) by Behrens  [11]. In the present survey, the three Anoplocephala spp. positive faecal samples were detected in both mini-FLOTAC and combined sedimentation-flotation. The double centrifugation/ combined sedimentation-flotation technique is recommended for the coproscopical detection of Anoplocephala spp. eggs being relatively sensitive compared to flotation methods  [17, 18]. It is noteworthy that herein, no differences were found between the data obtained by the two faecal analysis methods.
Funding: NH obtained a PhD grant from the  Fondation Mediterranee Infection, Marseille, France. This work was supported by  Agence Nationale de la Recherche  ( ANR-17-CE35-0006-01 PRIME , http://www. agencenationale-recherche. fr/) and by the  French Government  under the  « Investissements d'Avenir » (Investments for the Future) program  managed by the  ANR  (reference: Mediterranee Infection  10-IAHU-03 ), as well as the  Agence Nationale de la Recherche  ( ANR-17-CE35-0006-01 PRIME , http://www. agencenationalerecherche. fr/). This work was supported by  Region Provence Alpes Cote d'Azur and European funding FEDER IHUBIOTK.
(1997). The MHP was then determined from the minimal value of O 2 consumption and CO 2 production over the 6 days of measurement. The data were then used to correct HP and energy retention for the difference in energy lost as AHP, considering an average AHP of 6% of ME intake. For each pig, a corrected AHP (AHP C ) was then defined and corrected TEF (TEF c ), HP (HP c ), RE (RE c ) and energy retained as fat were calculated. Finally, the signals of the force sensors were used to determine lying and standing positions  (Heetkamp et al. , 2007)  and total AHPc was partitioned between the different types of physical activity. The [U-13 C] glucose recovery as 13 CO 2 was calculated as the molar ratio between expired 13 C as 13 CO 2 above baseline and injected 13 C as [U-13 C] glucose during 24 h.
Data analyses Pigs were individually housed in an enclosure and considered as an experimental unit. A batch was constituted by three or four littermates that were successively measured during 1 week each. One level of DF and the three supplementation rates of aleurone were tested by batch. For the last batch, four littermates were used, fed with LF-NS, LF-S2, LF-S4 and HF-NS to balance number of pigs per treatment. Variables describing feeding and drinking behaviours were analysed using ANOVA test with the MIXED procedure of SAS (SAS Inst. Inc. , Cary, NC, USA). The level of DF, aleurone supplementation and day were considered as fixed factors with two levels for DF (low (LF) or high (HF)) and three levels for aleurone supplementation (non supplemented (NS), supplemented at 2 g/kg (S2) or supplemented at 4 g/kg (S4)).
Interaction between levels of DF and aleurone supplementation was tested. Batch was considered as a random factor for these analyses. Variables describing physical activity, digestibility, energy and nitrogen balances and glucose oxidation were analysed using ANOVA test with the GLM procedure of SAS (SAS Inst. Inc. ). Levels of DF and aleurone supplementation were considered as fixed factors. Interaction between levels of DF and aleurone supplementation was tested. Batch was considered as a random factor for these analyses. Period was added as a fixed effect to take into account the variability in BW. As a high variability was observed due to experimental diets but also to the experimental conditions, data were further analysed by multiple factorial analysis and hierarchical classification on principal components to discriminate clusters of pigs  (Husson et al.
, 2010, Supplementary Material S1). Three classes of variables were included: pre-meal plasma concentrations of metabolites and insulin, variables characterizing feeding behaviour over the previous days and the size of the first meal on the last day of measurement. This classification permitted to identify four profiles of responses  (Quemeneur et al. , 2019). After cluster identification using the R statistical package 'FactoMineR'  (Lê et al. , 2008) , data were further tested by ANOVA with GLM procedure of SAS using the cluster as main factor and replicate and period as random factors. Data were tested for normality according to Shapiro-Wilk's test of residuals. Data for feeding behaviour and time required to recover 50% of 13 C recovery in CO 2 were inversetransformed before ANOVA analyses.
We hypothesize that the physical effect of DF on anatomy of digestive tract permitted to maintain daily Three supplementation levels of wheat aleurone (GrainWise Wheat Aleurone; Horizon Milling) were tested: NS, supplementation at 2 g/kg (S2) and supplementation at 4 g/kg (S4). 3 Analysis of variance performed using Proc GLM (SAS) including the effect of dietary fibre (F) and aleurone supplementation (A) as main factor, and the interaction between DF and aleurone supplementation (non-significant). Effect of MS and duration since the last meal (D) were added as covariates. Data are presented in table as lsmeans unless stated otherwise. energy intake. Conversely, aleurone supplementation decreased meal frequency without effect on meal size that induced a decrease of daily feed intake and energy intake.
, 1996). The increase in meal duration Clusters were obtained by multiple factorial analysis and hierarchical classification on principal components (Supplementary Material S1) Three classes of variables were included: pre-meal plasma concentrations of metabolites and insulin, variables characterizing feeding behaviour over the previous days and the size of the first meal on the last day of measurement. 2 Analysis of variance performed using Proc GLM (SAS) including effects of clustering. Data are presented in table as lsmeans. 3 Two concentrations of dietary fibre (low fibre: LF (NDF = 10. 1%) and high fibre: HF (NDF = 14. 5%)) and three supplementation levels of wheat aleurone (NS, supplementation at 2 g/kg (S2) and supplementation at 4 g/kg (S4)) were tested. 4 Heat production due to the physical activity was corrected for inter-individual differences.
Acknowledgements The authors thank  G. Guillemois  and  J. F. Rouaud  for diets manufacturing,  A. Chauvin ,  J. Georges ,  F. Le Gouevec ,  M. H. Lohat  and  V. Piedvache  for animal care and  A. Marchais ,  G. Robin  and  C. Perrier  for laboratory analysis. Etienne Labussiere  0000-0003-1945-0741.
We previously reported  23  excellent in vivo efficacy in the S. mansoni murine model at 100 mg/kg. At that time, the stability of the compounds was yet unknown. Based on the stability results we obtained, it is entirely possible to attribute some activity of the derivatives to OXA itself, in addition to the derivatives' own bioactivity. Furthermore, we could infer that the factors of poor metabolic stability, solubility and permeability of the compound to the membrane contributed to the poor in vivo results. In order to have a better idea of the permeability of Ph-CH2-OXA (deemed the most stable candidate via stability testing), we proceeded to calculate the MW, logP value, number of Hydrogen bonds donors and Hydrogen bonds acceptors, using the software Molinspiration 32 to estimate its theoretical solubility and membrane permeability.
Computational studies Classical molecular dynamics simulations were performed of the target proteins, i. e. the sulfotransferase of S. mansoni (SmSULT) and of S. haematobium (ShSULT), in complex with OXA, Fc-CH2-OXA and Ph-CH2-OXA. Since the two enantiomers of OXA show different activities against schistosomes,  12, 46  we performed separate simulations for both enantiomeric forms of all molecules. To develop force field parameters for the drugs, the geometry of all compounds was optimized in the gas phase with the Gaussian 16 software package,  47  using DFT with B3LYP functional and a 6-31+G* basis set for non-metallic atoms and LANL2DZ pseudopotential for the iron atom. The initial geometries were taken from crystallized S-OXA complexed to SmSULT (PDB: 4MUB  11  ). Hess et al. crystallized in 2017 the R-enantiomer of Fc-CO-OXA  23  and we used this structure as a starting point for all R-isomers.
The electrostatic potential was computed with the same functional and basis set in order to estimate the effective atomic point charges through RESP fitting. 48 assical molecular dynamics simulations were performed using Amber16. 49 The protein was modelled using the FF14SB force field and the Generalized Amber Force Field 2 (gaff2) was used as a base for the ligands. The ferrocenyl group was modelled using the force field published by Doman et al. 50 To estimate the missing dihedral parameters between the ferrocenyl group and the rest of the molecule, we scanned the angles of interest and performed DFT single point energy calculations for all angles, using the same functional, basis set and pseudopotential as for the geometry optimization. We then used the software paramfit from AmberTools16  49  to estimate the parameters.
To prevent clashes between nuclei during the rotation, we performed these computations on subsystems containing solely atoms that are relevant for these parameters (e. g. Fc-CH2-NH2, Fc-CH2-N-(CH3)2, Fc-CO-NH2 and Fc-CO-N-(CH3)2). All parameters determined in this way accurately reproduce the corresponding ab initio energy profiles (Figure  S5 ). The crystallographic structures of SmSULT and ShSULT with OXA and the cofactor 3′phosphoadenosine-5′-phosphate (PAP) served as a starting point for our simulations (PDB: 4MUB and 5TIY, 46 respectively). OXA was replaced by its derivatives through alignment of their shared atomic groups. 3′-phosphoadenosine-5′-phosphosulfate (PAPS), the active version of PAP, was inserted in the same way by minimizing the distance between shared PAP atoms. Missing loops of the protein were added using the ModLoop web server.
Acknowledgements This work was financially supported by the  Swiss National Science Foundation  (Grant Sinergia  CRSII5_173718 ) and has received support under the program «Investissements d'Avenir» launched by the  French Government  and implemented by the  ANR  with the reference  ANR-10-IDEX-0001-02 PSL  (G. G. ). We are grateful for the loan of analytical instruments by  Agilent Technologies and CEA Saclay to Chimie ParisTech. V. B. is grateful to the  Swiss excellence scholarships  for financial support, scholarship number  2017. 0801.