dataesr/scientific-paragraphs-categorization huggingface dataset:
Heritability estimates for ABC index For the trait ABC, the heritability for the Pie NN line was consistent with that published by Revilla et al. (2022; 0. 03 ± 0. 016), but we found a slightly higher heritability in the Pie line (0. 09 ± 0. 03 vs. 0. 04 ± 0. 01). This difference is the result of a lower phenotypic variance in both lines compared with those reported by  Revilla et al. (2022). In the present study, the data were recorded during a different time period and an improved outlier detection procedure was used on the observations collected by AFS, which reduced the contribution of erroneous measures to the phenotypic variance, and consequently reduced the residual variance when estimating variance parameters.
Acknowledgments We acknowledge  Rafael Muñoz-Tamayo  for his constructive discussion on this project. We also acknowledge the technicians of AXIOM's testing station at  La Garenne  for their implication for data collection. We also thank the two anonymous reviewers for their critical review and helpful comments. This project was supported by  ANRT  ( Association Nationale Recherche Technologie)  with a  CIFRE Doctoral fellowship  ( 2019/0705 ).
Study design: Prospective blinded clinical study. Methods: Simultaneous ECGs were recorded with both systems in 49 healthy horses during exercise. High-intensity exercise (>40 km/h) was performed by 29 racehorses, and lower-intensity exercise for the remainder of the racehorses and show jumpers. Tracings were excluded if >10% artefact was present (duration of artefact relative to duration of exercise). For included ECGs, the duration of artefact was recorded and compared. ECGs were evaluated using Kubios premium software. Arrhythmia detection (yes/no) and arrhythmia classification (sinus arrhythmia, narrow complex of similar morphology to the sinus complexes or wide complex with a different morphology) were compared using Cohen's Kappa coefficient. Results: Nine Televet TM ECGs and 3 Equimetre TM ECGs were excluded due to artefact >10%.
| ECG analysis For the arrhythmia analysis, good-quality ECGs from the artefact analysis were used using the inclusion criteria defined above, 35 horses were, thus, included. A further three horses from a pilot study were also included for a total of 38 horses. The ECGs from the Equimetre TM were exported as csv files, compatible with Kubios. For the Televet TM , the files were converted to a csv file using the Televet TM software, which was then imported into Kubios. The ECGs were blinded and assigned a random number. This allowed the observers to be blinded to the animal and to the recording device. ECGs were analysed by two operators (F. t. W. and E. v. E. ) using the Kubios premium software (Kubios version 3. 2 for Windows; Kubios Oy, Finland). This software automatically detects and identifies R waves and creates a HR graph based on R-R intervals, on which premature R waves are readily identifiable as peaks on the curve.
| Data analysis Statistical analysis was performed using the Python (3. 6) programming language (Python Software Foundation, https://www. python. org). The exact binomial test was used to evaluate the agreement between the Televet TM and the Equimetre TM regarding the nondiagnostic (excluded) ECGs. Considering the small number of discordant pairs,  22  the hypothesised probability of success was set at 0. 95. For the diagnostic traces containing <10% artefact, an Intraclass Coefficient Correlation (ICC, two-way mixed, single measures, consistency) was used  23  to compare the proportion of artefact present in paired tracings. To compare the arrhythmia detection and classification between ECGs of both devices, a Cohen kappa coefficient was calculated. Statistical significance was set a P <.
This is similar to the method applied in other studies investigating equine exercising ECGs,  18, 19, 25, 28  although many other publications on this topic do not quantify how much artefact is accepted in the diagnostic ECGs. 12, 16, 20, 29 In two of our ECGs an arrhythmia was hidden in that small portion of noise, highlighting the risk of missing arrhythmias in ECGs even with very limited artefact duration at peak exercise. This suggests that for future studies more stringent cut-offs may be necessary. Kubios premium was the only available software allowing the visualisation and analysis of both Televet TM and Equimetre TM ECGs. Kubios was initially designed for heart rate variability analysis and not primarily for arrhythmia detection. It is generally more cumbersome to use for ECG analysis than the Televet TM software although recent updates have significantly improved the operator's ability to manipulate and correct any erroneous automated RR detection.
Nevertheless, it lacks two useful features, which are present in the Televet TM software: the identification of early or late complexes with a red line on the ECG and the ability to measure selected R-R intervals on the ECG. For the first feature, early or late complexes were not highlighted on the Kubios ECG but could clearly be seen on the heart rate trace (Figure  3  and Figures  S1-S3 ). Currently the Equimetre TM only records a single ECG lead in addition to GPS, speed, stride and environmental parameters. The use of a single lead can make distinction between atrial and ventricular arrhythmias difficult especially at high heart rates and was, therefore, not attempted in this study. This is also a problem when using a single modified base-apex configuration as was used here with Televet TM.
Data Collection and Laboratory Analysis At the end of the c-section, a composite colostrum (8 mL) sample coming from the four quarters (2 mL each) was collected by the investigator. This colostrum sample was analyzed on the farm using the same brix digital refractometer (Milwaukee model MA 887, Fotronic Corporation 99 Washington Street, Melrose, MA, USA). The results were expressed in Brix value. Twenty-four hours after the surgery, the investigator came back to the farm. A blood sample by jugular venipuncture was collected from the calf and the delay observed by the farmer between the end of the surgery and the calf first suckling was registered by the investigator (less than 2 h, between 2 and 6 h, more than 6 h). The sera of the blood samples were isolated and frozen on the sampling day until subsequent analysis of IgG concentration.
Experimental Schedule A prospective randomized crossover design was adopted. Trial 1 consisted of a 4-week long pre-treatment, 3-week long treatment and 4-week long post-treatment period. This protocol was repeated after a 9-week long washout period forming trial 2. In trial 1, five horses were randomly allocated to each treatment group (NAP or SAP) and groups were crossed over for trial 2. In both trials during pre-and posttreatment periods, lameness was recorded three times at a minimum weekly interval using a portable wireless inertial sensor-based system (PISBS; EquinosisQ, Lameness Locator, Columbia, Missouri, United States) and a digital video camera (Sony FDR-AX100E 4K, Tokyo, Japan). Data recording intervals were kept the same in both trials.
Quantitative Gait Analysis Vertical displacement data (mm) of accelerometers located on the horses' head and pelvis were automatically processed within the PISBS's software program and summary statistics for each trot-up episode retrieved: Average (D) and standard deviation (SD) of the differences between minimal head (pelvic) heights during the stance of the right forelimb (hindlimb) and the stance of the left forelimb (hindlimb); differences in minimum head height (DIFFMIN Head ) (differences in minimum pelvic height [DIFFMIN Pelvis ]) Table  1  Treatment protocol details. All acupuncture points listed were treated in every horse except for LI-1 and Yan Chi which were included in horses with perceived dominant fore or hindlimb lameness respectively. Point localization was performed in accordance with a core textbook.
g. ,  Oxtoby et al. 2017; Choy et al. 2020 ). To further improve our understanding of the importance of the various minerals, we then re-ran the PCA using only minerals that differed between recruitment groups (p < 0. 10 because of the small sample size) to see if a reduced data set could differentiate recruitment groups (vegan package;  Oksanen et al. 2016). Finally, to estimate thresholds in minerals levels of importance for muskox recruitment, we first used t-tests to compare the mineral levels between the two recruitment groups. For a more precise estimate of thresholds, we used linear regression to determine the mineral levels associated with a calf recruitment rate of 40% (see above). The number of wool samples in each year was included as a weighing factor, and we used robust variance estimation to relax assumptions of normal distribution.
Acknowledgements We thank the  Greenland Ecosystem Monitoring Programme  for access to ecosystem data from Zackenberg. The authors wish to thank  Frederic Candaudap  and  Aurélie Marquet  (both at the  ICP-MS platform at the Observatoirie Midi-Pyrenees, Toulouse France ) for assistance with the ICP-MS analyses. We are indebted to all the people who collected and donated wool samples over the years, and to  Dr Perry Barboza  and an anonymous reviewer for valuable comments to our manuscript.
Statistics All statistical analyses were performed using IBM SPSS 21 and R version 3. 6. 1. Variables recorded during the distal and displacement tests were analyzed either through linear mixed model (LMM, 'lmerTest', R package,  Kuznetsova et al. , 2017)  or generalized linear mixed-effects models (GLMM, 'lme4 ′ , R package,  Bates et al. , 2015)  fitted for Poisson or Negative Binomial error distribution. Normality of residuals and overdispersion were verified and corrected if necessary. The time spent pecking at the unreachable mealworms, during the persistency test, was compared between breeds using Mann-Whitney U tests. Fixed factors, and their interactions, included in the models were, for the training: breed (RJF vs. WL), and training day (D69 to D71, mean values for both training trials within days), and for testing: breed, test situation (distal vs.
Acknowledgments We thank  Jonathan Birch ,  Cormac Dickson ,  Steve Fleming ,  Liad Mudrik ,  Leon Deouell ,  Lucie Charles ,  Ian Phillips , and  Chaz Firestone  for their helpful comments, and  Bat-Sheva Mazor  for inspiring us to write this article. Authors appear in alphabetical order, except for  M. Mazor  and  N. Lubianiker , who cowrote the original version of this article. Notes 1. Our focus in this article is on consciousness as a term used in the scientific literature, in contrast to consciousness as a mental state or capacity. Thus, this definition is intended to be agnostic regarding different theoretical approaches to consciousness in the scientific literature. 2. We thank an anonymous reviewer for pointing out a third option: Animal models of psychiatric disorders may be both unethical (in that they cause suffering to animals) and invalid (in that they neglect to model the subjective experience itself; see Taschereau-Dumouchel et al.
Systematic review of albendazole pharmacokinetics literature Web of Science and PubMed databases were searched on 22 nd July 2022 with no limitations on date range using the keywords "albendazole" AND (treatment � OR dose � OR pharma � OR "half-life" OR "half life") in order to identify references containing temporally disaggregated data detailing the concentration of albendazole and/or albendazole sulfoxide in plasma following treatment with a single dose of the drug. A total of 6,855 unique records were identified through this search process, with 246 records retained for full text evaluation following Title and Abstract screening (Fig  1 ). Exclusion criteria comprised studies lacking the required information on plasma concentration levels over time; those that had been carried out in vitro or in non-human subjects, or were not in English.
Following this, a total of 36 references were included, yielding 113 time-series describing the evolution of plasma concentrations of albendazole and/or albendazole sulfoxide following treatment with a single dose. Of these, 19 timeseries contained information on both albendazole and albendazole sulfoxide levels, and 94 contained information on albendazole sulfoxide levels only. A total of 105 of these time-series  nd July 2022 using the keywords albendazole AND (treatment � OR dose � OR pharma � OR "half-life" OR "half life"). This produced a total of 6,855 results after duplicate removal, of which 246 were retained for full text screening. A total of 210 of the retained articles were subsequently excluded based on pre-defined exclusion criteria (see Systematic review of albendazole pharmacokinetics literature, in Methods), yielding 36 studies containing temporally disaggregated data on albendazole sulfoxide plasma concentrations following treatment with a single dose of albendazole.
These 36 references contained a total of 113 timeseries measuring albendazole and/or albendazole sulfoxide blood plasma concentrations over time in different groups. https://doi. org/10. 1371/journal. pntd. 0010497. g001 were studies in which only plasma albendazole sulfoxide concentrations following a single oral dose of albendazole were presented. In eight studies, measured plasma albendazole sulfoxide concentrations were presented that spanned a course of multiple doses, also containing information on albendazole plasma concentration levels immediately following the first dose. For these eight time-series, we extracted data following receipt of the first dose up until receipt of the second dose. For each time-series, we also extracted the data describing evolution of albendazole/albendazole sulfoxide plasma concentrations over time, as well as an array of metadata.
These included characteristics of the treatment regimen (dose, fasting state, co-administered drugs), as well as information and metadata on the patients receiving treatment (sex, age, infection status and weight). In the majority of instances, presented data were reported for a group of patients rather than individuals. In these instances, group averages for factors such as age, weight, etc. , were extracted. A full list of these references, as well as further information about each study and how the data were extracted are available in Text A in S1 File.
Uninformative priors were used for each of the parameters being subsequently related to the collected metadata. For each dataset, a total of 25,000 iterations were run, with the first 5,000 discarded as burn-in, leaving 20,000 samples available for parameter inference. The median value based on these (posterior) samples was then used as an input into the multiple linear regression analysis described below. Further information on the exact formulation of the model and the fitting process is available in Text B in S1 File.
Regression linking pharmacokinetic properties to patients' characteristics From the 113 fitted time-series, we extracted estimates of key pharmacokinetic parameters and regressed them onto the collected metadata (describing aspects of the patient group and treatment regimen received) to assess the influence of various factors on variation in albendazole and albendazole sulfoxide's pharmacokinetics. The pharmacokinetic parameters were k Albso (the clearance rate of albendazole sulfoxide, the reciprocal of which i. e. 1/k Albso is the albendazole sulfoxide half-life), the systemic availability of albendazole sulfoxide (the proportion of administered albendazole absorbed from the gut and detected in the plasma as albendazole sulfoxide), C Max (the peak concentration of albendazole sulfoxide in plasma), and AUC ("area under the curve", reflecting the total exposure to albendazole sulfoxide after administration of the dose, calculated over a time-period of 50 hours).
All significant associations described above were retained when conducting this subset sensitivity analysis (see estimates of k Albso , with the median clearance rate of albendazole sulfoxide 0. 15 per hour higher than in adults, corresponding to a half-life of 12. 4 hours in adults compared to only 7. 6 hours in children under the age of 18 years (p = 0. 01). We also observed significant associations between STH/LF/Giardiasis and both C Max400 and AUC 400 (increased by 198ng/ml and 1. 14-fold respectively, p = 0. 04 and p = 0. 02 respectively). We did not detect a significant effect of co-administered drugs on albendazole's pharmacokinetics, though it is important to note that the heterogeneous array of drugs co-administered across the collated dataset, and the comparative paucity of time-series featuring each of the drugs precluded a stratified analysis of each drug separately (as was possible with infectious agent).
Funding: C. W. acknowledges funding from the  Wellcome Trust  ( 224190/Z/21/Z ). C. W. and M. G. B. acknowledge funding from the  Medical Research Council (MRC)   Centre for Global Infectious Disease Analysis  ( MR/R015600/1 ), jointly funded by the  UK MRC  and the  UK Foreign, Commonwealth & Development Office (FCDO) , under the  MRC/FCDO  Concordat agreement and is also part of the  European and Developing Countries Clinical Trials Partnership  ( EDCTP2 ) programme supported by the  European Union. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
MiSeq Illumina sequencing data analysis The reading tool Trimmomatic was used to trim the MiSeq Illumina sequencing data for minimal trailing quality (Phred score: 30) and to filter for minimum read length by removing the Illumina sequencing adapters from read and adapter clippings  [37]. The resulting read pairs were aligned to the D. immitis reference genome nDi. 2. 2 (http:// www. nemat odes. org/ genom es/ dirofi laria_ immit is) using BWA-mem (http:// bio-bwa. sourc eforge. net/), resulting in binary alignment map (BAM) files  [38]. The alignments were processed with Picard (https:// broad insti tute. github. io/ picard) for the realignment of indels, mate fixing and marking of duplicate reads. BVA-Tools (https:// bitbu cket. org/ mugqic/ bvato ols/ src) was used to extract base frequencies for the DimPgp-11 SNP, and the read frequencies were assimilated to the allele frequencies.
Statistical analysis of DimPgp-11 constitutive expression The ddPCR results of DimPgp-11 constitutive expression were analyzed by normalizing copy numbers against the geometric mean of the copy numbers of the three reference genes: DimGAPDH, DimActin and Dimpmp-3. All experiments were performed in three biological replicates. All data are reported as mean fold change, with error bars corresponding to the standard deviation of three biological replicates. The replicates for the five isolates were prepared at a concentration of 100,000 mf. The known ML-susceptible Missouri isolate was used as the one-fold expression standard. The significance of the fold changes in constitutive expression were compared to the Missouri isolate by the parametric unpaired t-test with Welch correction, two-tailed P-value and 95% confidence interval using Prism 9.
Acknowledgements We thank  Kathy Keller  and  Cristina Ballesteros  for their guidance in the development of the protocols and sample preparation. We thank  Norma Bautista-Lopez  and  Ashish Jain  for training in confocal microscopy. We thank the  FR3  for providing the Missouri, MP3, and  Yazoo D. immitis isolates. We thank  Ray Kaplan  of the  University of Georgia  for providing the Metairie D. immitis isolate. We thank  TRS Lab. Inc. for providing the  Berkeley, Georgia II, Georgia III ,  Big Head ,  JYD-34  and  WildCat D. immitis isolates.
Availability of data and materials The data presented in this study is included within the article. Bioinformatic files for the Missouri, MP3, Yazoo, JYD-34 and Metairie Dirofilaria immitis isolates, i. e. SAMN28946274, SAMN28946275, SAMN28946276, SAMN28946277 and SAMN28946278, are openly available on the NCBI Sequence Read Archive as BAM files under BioProject PRJNA847600.
| Medical record review Data collected from the medical records included signalment (age, breed, sex, neuter status, and weight), clinical signs at admission (vomiting, regurgitation, diarrhea, cough, respiratory distress, and dysphagia), and whether surgical treatment (rhinoplasty and palatoplasty) was performed. Final diagnoses, treatments, and outcomes also were recorded when available. The study population was first divided into 2 groups: dogs with and without GLFH. These were then further categorized as the FB group (subgroup 1), non-FB brachycephalic dogs (subgroup 2), and the control group (all breeds excluding FB and brachycephalic dogs; subgroup 3). The breeds included in subgroup 2 included English Bulldog, Pug, Boston Terrier, Shih Tzu, Boxer, Dogue de Bordeaux, Cavalier King Charles Spaniel, and Brussels Griffon.
| Statistical analysis For descriptive statistics, continuous data were assessed for Gaussian distribution by histogram evaluation and the Shapiro-Wilk test (Gaussian if P >. 05). Gaussian data were presented using mean (standard deviation [SD]) and non-Gaussian data were presented using median (minimum-maximum). Categorical data were presented as the number of dogs (percentage). Because histopathologic findings, including HLOs and GLFH scores, were provided at the gastric body and antrum locations, each dog had 2 scores for each histopathologic variable. Thus, the associations between GLFH and gastric location, signalment, previous BAOS surgery, clinical signs, and endoscopic and histopathologic findings were assessed using univariate mixed effects ordered logistic regression, with the individual dog being the random factor.
Demographic data Three hundred and thirty cases were identified in the electronic veterinary medical database. Forty-two cases were excluded because of a final diagnosis of gastric foreign body or neoplasia, or because of incomplete data. The remaining 288 patients were included in the F I G U R E 1 Histopathological scoring of lymphofollicular hyperplasia (LFH) of HES-stained gastric biopsies. (A) normal, small lymphoid aggregates or follicles occupying <10% of the biopsy area, (B) mild LFH, mild hyperplasia with lymphoid aggregates or follicles occupying 10%-30% of the biopsy area, (C) moderate LFH, lymphoid aggregates or follicles occupying 30%-50% of the biopsy area, and (D) marked LFH, lymphoid aggregates or follicles occupying >50% of the biopsy area study. Of the included dogs, 143 (50%) were intact males, 19 (7%) were castrated males, 64 (22%) were intact females, and 61 (21%) were spayed females.
a b s t r a c t A dataset of 100 pigs, from the Piétrain NN Français line raised at the AXIOM boar testing station in 2020, was used. The farm was equipped with an automatic feeding system, recording individual weight and feed intake at each visit. We used a dynamic linear regression model to characterise the evolution of the energetic allocation factor (a t ) which represents the link between the cumulative net energy available (estimated from feed intake) and cumulative weight gain during the fattening period. The data were imported using an R script to estimate the allocation factor for a given animal. The dataset and R script are useful resources to study feed intake, growth dynamics and the relationship between these two variables. Ó 2022 The Author(s). Published by Elsevier B. V. on behalf of The Animal Consortium.
Data description The data for the 100 fattening pigs are available at https://doi. org/10. 5281/zenodo. 6626445. They are stored in one csv file (DataAxiom. csv) and structured as follows. ID: pig identification number; Fattening_group. Pen: fattening group and pen number for a given ID; t: time in days since the transfer to fattening group; Wt: median weight in kg at day t for a given ID; FIt: total feed intake in kg at day t for a given ID. The R script DLM_script. R includes the code with the implementation of the dynamic linear regression model for the estimation of the allocation factor.