dataesr/scientific-paragraphs-categorization huggingface dataset:
Experimental design, materials, and methods The data collection was carried out in a textile company that is the market leader in Brazil, where the textured fibers bobbins process represents 15% of the total production of the factory. To ensure a satisfactory amount of data, the information can be divided into two measurement data collection. In accordance with the requirements suggested by the AIAG  [5] , in both studies, the measurements of ten distinct parts was collected for three different operators and three replicates were carried out, characterizing in a quantity satisfactory information for applications of measurement techniques. This data collection methodology is widely used in measurement system analysis studies, such as  [6, 7]. It is important to note that the collection was performed in a random manner.
From these data, the data of the scores of the principal components' scores were extracted. In the first data, the measurements of the original data are shown in Table  1  and the principal components' scores of these data are shown in Table  2. Table  3  presents the eigenvalues and eigenvector data of the components. In view of the second data collection, the Table  4  presents the original data of the bobbin's measurements. The dimensionless data for the components' scores are shown in Table  5. Table  6  describes the eigenvalue and eigenvector data for the scores, representing the second measurement data collection.
Methods Three jumping horses (geldings, mean (SD): 556 (55) kg) clinically sound were used. After trimming, the right forehoof of each horse was equipped with a DHS  (Crevier-Denoix et al. 2013). A horseshoe with matching height and weight was attached to the left fore, as well as to both hind hooves. Data were acquired at 7. 8 kHz. The acquisition system was placed in saddle-bags. The GRF was expressed in a local reference frame with the normal Z-axis perpendicular to the solar plane (positive downward). Reflective markers were stuck to the skin facing the elbow, distal radius and fetlock joint of the right forelimb. A T-square with 3 reflective markers was screwed on the right forehoof. A high-speed camera (1000 Hz, Phantom v5. 1, Vision Research), filming the right side of the horse, was placed on the side of the landing area, at a distance of about 7 m from the middle of the recording corridor.
Customised softwares developed in Matlab (MathWorks) were used to calculate stance duration as well as peak vertical force and vertical impulse (integral of force over time). Kinematic markers were semi-automatically tracked on each film using a custom program. The markers' 2-D coordinates were low-pass Butterworth filtered with a 50 Hz cut-off frequency. Fetlock joint angle, measured on the dorsal side, as well as the angle of the elbow-fetlock (limb) axis with respect to the track, were computed during stance. Angles at the beginning of stance, and minimal fetlock angle, were determined, and the area of the fetlock angle-time curve (reference value at landing) was calculated. Linear mixed-effects regression models (SAS v 9. 2) were used to test the association between kinetic or kinematic variables and fence's height, taken into account repetitions within a given horse, for each lead on one hand, for both leads together, adjusting for the lead, on the other hand (p < 0.
If the Nocardia PCR was positive, a second PCR targeting the hsp65 gene was performed to provide species identification. The hsp65 gene was selected because the 16S rRNA gene fragment amplified in the PCR described above is not considered polymorphic enough to allow accurate identification at the species level. For this purpose, TB11 (5'-ACCAACGATGGTGT GTCCAT-3') and TB12 (5'-CTTGTCGAACCGCATACCCT-3') primers were used to detect a 441-bp fragment of the hsp65 gene encoding the 65-kDa heat shock protein  [10]. PCR program and reaction mixture were carried out as described elsewhere  [11]. The positive PCR products were sequenced using Sanger technology (Biofidal). Sequences were compared with those stored in GenBank using blast alignment software (http://www. ncbi. nlm. nih. gov/ BLAST) and BIBI (Bio Informatic Bacteria Identification tool; http://umr5558-sud-str1.
Clinical data collected We collected demographic information (sex, age), transplant-related parameters (type of lung transplant, indication for transplantation, type of donation, CMV serostatus, occurrence of biopsy-proven acute rejection in the last six months), BAL-related characteristics (surveillance vs. clinically-indicated bronchoscopy, time from transplant to bronchoscopy, BAL fluid leukocyte count, microscopy and culture results, other microbiological findings), treatment details at time of bronchoscopy (immunosuppressive regimen, use of antibiotics), blood test findings (white blood cell count, C reactive protein concentration, kidney function, immunoglobulin G concentration), and outcome data (occurrence of nocardiosis, allograft rejection or death following bronchoscopy). Low-dose cotrimoxazole was defined as no more than 800/160 mg daily.
Statistical analysis The final analysis was performed after all data were verified. Categorical variables are presented as numbers and frequencies. Continuous variables are presented as medians (extreme values). Nocardia PCR sensitivity was calculated as the proportion of patients with pulmonary nocardiosis (see definition below) who had a positive PCR result. Specificity was calculated as the proportion of patients without pulmonary nocardiosis who had a negative PCR result. Diagnosis of pulmonary nocardiosis was based on the association of (1) presence of signs and/ or symptoms compatible with nocardiosis and (2) growth of Nocardia spp. from a respiratory sample.
BspL interacts with Herp, a key component of ERQC To gain insight into the function of BspL we set out to identify its interacting partners. A yeast two-hybrid screen identified 7 candidates: eukaryotic translation initiation factor 4A2 (EIF4A2), pyruvate dehydrogenase beta (PDHB), MTR 5-methyltetrahydrofolatehomocysteine methyltransferase, Bcl2-associated athanogene 6 (BAG6), ARMCX3 armadillo repeat containing protein (Alex3), homocysteine-inducible ER protein with ubiquitin like domain (Herpud or Herp) and Ubiquilin2 (Ubqln2). In view of our previous results for BspL showing ER localization and induction of UPR we decided to focus on Alex3, Herp and Ubiquilin2 which are rarely present or even absent in the database of false positives for this type of screen (http://crapome. org/). Alex3 is a mitochondrial outer membrane protein that has been implicated in regulation of mitochondrial trafficking  (Serrat et al.
05 % saponin, once in PBS and once in ultrapure water. Lastly, they were mounted on a slide with ProLongGold (Life Technologies). The coverslips were visualized with a Confocal Zeiss inverted laser-scanning microscope LSM800 and analyzed using ImageJ software. For Lamp1 immunostaining no pre-permeabilization and blocking were done and coverslips were directly incubated with antibody mix diluted in PBS containing 10% horse serum and 0. 5% saponin for 3h at room temperature. The remaining of the protocol was the same as described above.
Then cells were incubated with a provided substrate 3-(4-methoxyspiro [1,2-dioxetane-3,2'(5'-chloro)-tricyclo(3. 3. 1. 13,7) decane]-4yl)phenyl phosphate (CSPD) by SEAP reporter gene assay, chemiluminescent kit (Roche Applied Science). Chemiluminescence values were obtained with the use of a TECAN at 492 nm. Data are presented as the SEAP secretion index, which is a ratio of extracellular SEAP activity to intracellular SEAP activity.
Acknowledgements This work was funded by the  ERA-Net Pathogenomics   CELLPATH grant  ( ANR 2010-PATH-006 ), the FINOVI foundation under a  Young Researcher Starting Grant  and the  ANR charm-Ed  (grant n°  ANR-18-CE15-0003 ), both obtained by  SPS. JBL was supported by a doctoral contract from the  Région Rhônes-Alpes   ARC1   Santé. SPS is supported by an  INSERM  staff scientist contract. We are very grateful to  Linda Hendershot  ( St Judes Medical School, USA ) for sending us the pcDNA-TCRα and for all the help with setting up the ERAD assay and discussion of the results. We thank  Renée Tsolis  ( University of California at Davis, USA ) and  Jean Celli  ( Washington State University, USA ) with advice for the construction of the following plasmids  TEM1-VceC, HA-VceC, HA-BspB  and  HA-BspD , as the  French Agency ANSM  has prevented us from importing these vectors directly from them due to the size of the genes encoded.
Average ambient temperatures in farrowing rooms were similar in the two systems (P > 0. 10). They averaged 23. 8 ± 0. 2°C on the day of farrowing. Supplemental heating was provided to the piglets by means of two heat lamps in each crate until 24 h postpartum. Three successive batches of Landrace × Large White sows of mixed parity (1 to 12) were used. Sows of the two systems were inseminated with semen from the same Piétrain boars. On DG114, parturition was induced by an intramuscular injection of cloprostenol (2 ml of Planate ® ; MSD Santé Animale, Beaucouzé, France). After parturition, sows were injected with Sergotonine ® (5 ml, i. m. ; Mérial SAS Villeurbanne, France) and then Dynolytic ® (2 ml, i. m. ; Zoetis, Paris, France) 36 to 48 h afterwards to stimulate uterus emptying. Gestation and lactation data for all sows (n = 106) were provided in our companion paper  (Merlot et al.
Statistical analyses Numbers of piglets per litter, mortality rates and proportion of light or heavy piglets were analysed using the GENMOD procedure using a Poisson distribution and a logtransformation as the link function for numbers of piglets and a binomial error distribution and a logit-transformation for other criteria. Other data were analysed by ANOVA using the MIXED procedure of SAS (SAS Institute Inc. , Cary, NC, USA). The sow or the piglet represented the experimental unit. Models included the effects of the system (C or E) as main factor and the replicate (1, 2 or 3) as random factor. When performance or physiological data were recorded on several piglets per litter, the random effect of sow nested within system × replicate was included in the model to take into account the effect of the sow.
Piglet organs and tissue maturity at birth Organ weights relative to BW did not differ between C and E piglets (Table  5 ), with the exception of the gut which was  Effect of system. Data are expressed as least-squares means and the greatest SEM when analysed using the MIXED procedure and as raw data when analysed using the GENMOD procedure. 2 GENMOD procedure. 3 Stillbirth: the number of stillborn piglets was calculated relatively to the total number of piglets. Between birth and 12 h pp, early and late mortality rates were calculated relatively to the number of piglets born alive. Overall mortality included stillborn piglets and piglets born alive that died before weaning, relatively to total born piglets. lighter, relative to BW, in C than in E piglets (-11%, P = 0. 01). Glycogen content, the main energy reserve of the neonate, was reduced in longissimus muscle of C piglets when compared with E piglets (-8.
Acknowledgements The authors thank  C. Calvar  and  B. Le Bris  ( Chambre d'Agriculture de Bretagne -CRAB, France ) and the staff of Crécom (CRAB,  B. Le Guilcher ,  P. Lirzin ,  D. Lesaicherre ,  M. Gautier ) for animal care and data collection and the technical staff of  UMR1348   PEGASE  ( S. Tacher ,  S. Daré ,  N. Bonhomme ,  C. Tréfeu ,  R. Comte ,  F. Thomas ,  F. Mayeur ,  M. Lefebvre ) for sample and data collection and for expert technical assistance. They also thank  F. Robert ,  A. Hamard  and  T. Pinard  from  Deltavit CCPA group. Research received funding from the  EU   FP7   Prohealth  project (no. 613574 ).
Bioinformatics analysis Bioinformatics analyses followed previous study  (Li et al. 2016). Briefly, the raw sequences were analysed using QIIME Pipeline-ver. 1. 7. 0 (http://qiime. org/tutorials/tuto rial. html). All sequences were trimmed and assigned to each sample based on their unique barcodes (barcode mismatches = 0). The overlapping paired-end reads were merged using the FLASH-1. 2. 8 software  (Caporaso et al. 2012). The merged sequences with high quality (read length >300 bp, without an ambiguous base 'N' and an average base quality score >30) were used for further analysis. The aligned 16S rRNA gene sequences were used for a chimera check using the Uchime algorithm  (Edgar et al. 2011). Operational taxonomic units (OTUs) were clustered at a 97% identity threshold using CD-HIT  (Li and Godzik 2006).
Singleton OTUs were filtered out. Each sample was rarefied to the same number of reads (8467). The most abundant sequences within each OTU were designated as 'representative sequences' and aligned against the core set of Greengenes 13_8 reference database  (DeSantis et al. 2006)  using the PyNAST tool. The representative sequences were taxonomically classified using the Ribosomal Database Project classifier in the QIIME platform  (Wang et al. 2007 ). The alpha diversity indices, including observed species and Shannon diversity, were calculated. The rarefaction curves of all samples were generated from the observed OTUs at the OTU level. To assess the beta diversity, the weighted UniFrac distance metrics, which use phylogenetic information to calculate community similarity  (Lozupone and Knight 2005) , were produced through the QIIME pipeline.
Statistical analysis An analysis of similarity (ANOSIM) was used to reveal whether the beta diversity was significantly different across the pregnancy and parturition stages based on the weighted UniFrac matrices using the 'vegan' package in the R program  (Li et al. 2017). The effects of the different stages on backfat thickness, plasma biochemical parameters, the apparent relative abundances of communities at the phylum and genus level and the alpha diversity indices were analysed using a one-way analysis of variance with LSD post hoc test in SAS (SAS Institute, Inc. , Cary, NC). P-values <0Á05 were considered to indicate statistical significance and P-values: 0Á05 ≤ P < 0Á10 were considered to indicate a trend. Linear discriminant analysis effect size (LEfSe) was used to identify bacterial biomarkers at the different stages, based on P-values < 0Á05 and LDA scores >2Á0.
Acknowledgements The present work was jointly supported by grants from the  National Key R&D Program  ( 2017YFD0500503 ), the  National Nature Science Foundation of China  ( 31572421 ,  31772613 ) and the  Key Research Program of the Chinese Academy of Sciences  ( KFZD-SW-219-2-3 ). All authors have read and approved the final version of the manuscript and have declared that no competing interests exist. We would like to thank Editage (http://online. editage. cn/) for English language editing.
Positive samples were examined by a modified McMaster technique adapted to small amounts of samples to quantify the number of oocysts per gram of faeces (OpG)  [15]. Results (body weight development, faecal consistency/diarrhoea, oocyst excretion) were compared by a Kruskal-Wallis test, and in cases of significant differences, groups were compared by Mann-Whitney U-test using GraphPad ® Prism v. 5. 04 for Windows (GraphPad ® Software, La Jolla, CA, USA). Significance was assumed for P < 0. 05. To evaluate the presence of other entero-pathogens in the litters, sows were sampled individually ante partum and examined for the presence of bacterial enteropathogens. On the first day of sampling (5th dol) a pooled faecal sample from each litter was examined for determination of bacterial causes of diarrhoea (E.
The loggers are measuring voltage differences with two 40-mm distant electrodes in a 256-Hz sampling rate. The raw electrocardiogram data are continuously processed into interbeat intervals and further into a 2-min mean HR in bpm that is saved on the logger's memory. The memory capacity is 1 year and data were retrieved using a non-invasive transcutaneous telemetry system (CareLink Model 2090 Programmer, Medtronic Inc. , Minneapolis, MN, USA) during captures once per year (April to June). All animal captures and handling were approved by the Ethical Committee on Animal.
Data were available from 15 bears, eight males and seven females. Four females had cubs-of-the-year in 2016 and one in 2017. Body mass was weighed at capture and age (for bears not followed from birth) was determined by counting the annuli of a cross section of the premolar roots  [8]. A body mass < 60 kg was considered small (n = 8), medium between 60 and 120 kg (n = 11) and large for > 120 kg (n = 4). An age < 5 years was considered young (n = 11), middle-aged between 5 and 15 years (n = 3) and old when > 15 years (n = 9). Bears travelled long distances when the movement distance exceeded 50 m in an hour, as previously validated with 25 m in half an hour  [2].
Correlation coefficients (r) between HR and distance travelled were obtained by parametric Pearson tests. Distance travelled was log transformed to improve model performance and to avoid over-dispersion of the deviance. We found a bimodal distribution of the logarithmic distance travelled corresponding to short and long distances travelled by bears. We separated the data set into short and long distances travelled with 50 m as the cut-off value. All statistical analyses were done using R  [42]  version 3. 5. 1, R-studio  [43]  version 1. 1. 463 and relevant packages. All data (GPS and HR) were stored in the WRAM (Wireless Remote Animal Monitoring,  [44] ) database.
Acknowledgements Holger Dettki  at the WRAM database in Sweden made this study, with millions of data points, feasible. Field technicians  Sven Brunberg ,  David Ahlquist ,  Andrea Friebe  and veterinarian  Anne Randi Graesli  contributed to capturing the bears and collection and storage of data. Olivier Devineau at  Inland Norway University of Applied Sciences  provided statistical advising. This is scientific paper no. 282  from the  Scandinavian Brown Bear Research Project.
We first assessed the DNA binding capacity of the purified C-terminally His-tagged fusion protein (ComH-His 6 ) (Supplementary Fig. 3a ) by electrophoretic mobility shift assays (EMSA). ComH-His 6 formed discrete nucleoprotein complexes with an 18 bp dsDNA in a concentration dependent manner while no binding to ssDNA (18-mer) was detectable (Fig. 3a ). The same preference for dsDNA over ssDNA was observed when Surface Plasmon Resonance (SPR) was used to characterise the DNA interaction properties of the ComH-His 6. The binding sensorgrams show that ComH-His 6 protein bound dsDNA with high affinity while only residual binding was detected when ssDNA was used as substrate (Fig. 3b ). Neither the Langmuir isotherm nor the equilibrium approach using the Proteon Manager software gave satisfactory fittings for the calculation of affinity constants.
6a, b ). In order to obtain quantitative data on the relative binding affinity of full-length ComH versus the N-and C-terminal domains for dsDNA, the interactions of the His 6 -tagged domains were analysed by MST. The Kd obtained for ComH-CTD was 3. 4 ± 1. 7 µM (Fig. 4d ). While this value reflects a lower affinity than the full-length protein, the ComH-NTD had a much weaker affinity (Kd > 40 µM) (Supplementary Fig. 6c ) in agreement with the EMSA analyses. Finally, we addressed the question of whether ComH needed free DNA ends for loading using His 6 tagged constructs. Both, ComH-His 6 and ComH-CTD-His 6 displayed concentration dependent binding to linear and covalently closed supercoiled plasmid DNA irrespective of their topology (Supplementary Fig. 7a, b ). In conclusion, the DNA binding properties of the truncated version of ComH suggest that the CTD harbours a novel DNA binding motif responsible for the affinity of ComH for dsDNA.
0 at 600 nm) were incubated with isogenic streptomycin resistance total chromosomal DNA (200 ng) on Blood Agar Base (BAB) plates for 24 h at 37 °C. Next day, serial dilutions of H. pylori cells were plated on BAB plates with or without streptomycin (10 μg/ml) and incubated for 4-5 days at 37 °C. The recombination frequencies were calculated as the number of streptomycin resistance colonies per recipient colony-forming unit. P values were calculated using the Mann-Whitney U test on GraphPad Prism software. Determination of spontaneous mutation frequencies. Exponentially growing H. pylori cells (optical density of 4. 0 at 600 nm) were spotted on Blood Agar Base (BAB) plates for 24 h at 37 °C (no exogenous DNA was added). Next day, the spots were collected in peptone water. 200 µl of non-diluted sample was directly plated on BAB plates with streptomycin (10 μg/ml).
The electroporation was performed at 2. 5 kV cm -1 , and 25 µF. Immediately, 100 µl BHI was added and 50 µl cells were spotted on BAB plates. Next day, serial dilutions of H. pylori cells were plated on BAB plates with or without streptomycin (10 μg/ml) and incubated for 4-5 days at 37 °C. The recombination frequencies were calculated as the number of streptomycin resistance colonies per recipient colony-forming unit. P values were calculated using the Mann-Whitney U test on GraphPad Prism software. Subcellular fractionation. To obtain the subcellular fractions, 20 ml of bacterial cultures at OD 600 1. 5 were pelleted, washed in PBS and resuspended in 2 ml buffer C (20% Sucrose, 1 mM EDTA, 30 mM Tris-HCl, pH8) and further incubated for 10 min at room temperature and centrifuged at 5700 × g.
To monitor in vivo co-localisation of ComH-mCherry with DNA, 1 µg of ATTO-488-dUTP labelled dsDNA (2 kb) was incubated with exponentially growing H. pylori cells for 90 min at 37 °C under microaerophilic conditions. The bacteria harvested by centrifugation (323 g for 3 min) were subjected to DNaseI (50 U/ml) treatment at 37 °C for 5 min followed by 1× PBS wash before fixation with formaldehyde (4%). All the images were captured with a 60x objective using inverted Nikon A1R confocal laser scanning microscope system equipped with an environmental chamber. The images were processed and analysed using NIS-element software (Nikon Corp. , Tokyo, Japan) and ImageJ software. The bacteria that formed DNA and ComH-mCherry foci were counted manually. The volumes of internalised DNA were calculated by 3-D image analysis performed using Volocity software (Perkin Elmer, Waltham, USA).
Acknowledgements We thank  Didier Busso  for providing the plasmids used for cloning. We thank  IRCM Microscopy and Molecular Biology (CIGEX)  facilities for technical assistance and  Anna Campalans  for her help with cell imaging. We thank  Audrey Comte  for her help with biophysical measurements and  Hilde De Reuse  ( Institut Pasteur ) for antibodies against MotB and  NikR. Financial  support for this work was provided by the  CEA, INSERM  and grants from the  Indo-French Centre for Promotion of Advanced Research (CEFIPRA  grant  n°5203-5 ). DNR acknowledges  DST for JC Bose Fellowship. Biophysical measurements were performed on I2BC platform PIM that is supported by the  French Infrastructure for Integrated Structural Biology (FRISBI)   ANR-10-INBS-05. P. P. D. was supported by grants from  Enhanced Eurotalents fellowship programme (CEA/EU) ,  CEFIPRA  and the  Région Ile de France  ( DIM1Health ).
Domestication has changed the natural evolutionary trajectory of horses by favoring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago. To identify the factors underlying this trajectory, we gather an extensive dataset consisting of 175 modern and 153 ancient genomes previously published, and carry out the most comprehensive characterization of deleterious mutations in horses. We confirm that deleterious variants segregated at low frequencies during the last 3500 years, and only spread and incremented their occurrence in the homozygous state during modern times, owing to inbreeding.