dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank  Gregory Vegh  ( Université Libre de Bruxelles, Brussels, Belgium ) for technical assistance in w estern blot. We would like to acknowledge  Pr Denis Franchimont  for the review of this manuscript and  Sandy Field  (medical writer), PhD, to English-language editing of this manuscript. The present study was supported by the  Bourse du Conseil Médical de l'hôpital Erasme, Fonds E. et S. Jacobs and Novartis  grant (applicant: Pr Thierry Gustot).
To date, only a few cases of death caused by baclofen have been reported in the literature  [3] [4] [5]. Severe baclofen poisoning requires intensive supportive care. Treatment is symptomatic, with supportive care and mechanical ventilation if required. In patients with kidney failure, the half-life is enhanced significantly  [6]  and therefore potentially associated with a prolongation of the toxic of the molecule. While the place of renal replacement therapy (RRT) seems established to treat patients with renal failure, it remains controversial for poisoning in patients without kidney dysfunction  [7]. This study was based on retrospective biological data collected from patients hospitalised for suicidal ingestion of baclofen and aimed to define the effectiveness of RRT in the treatment of severely poisoned patients with normal kidney function.
Materials and methods We retrospectively collected baclofen poisoning cases reported to the Western Poison Control Centre (PCC) (Angers University Hospital, Angers, France), retrospectively. The Angers University Hospital ethics committee approved this study and waived the need for patient consent (approval number: 2015-89). In the West French region (corresponding to 12 million inhabitants), we identified all cases of oral intentional baclofen poisoning in patients with normal kidney function treated with RRT reported to the western PCC up to the 31 st of December 2015 from spontaneous reports. The cases between January 2012 and December 2015 were reviewed. Data used in this study came from phone declarations from all emergency departments and intensive care units of Western France to Western PCC.
Pharmacokinetic modelling All the pharmacokinetics profiles obtained from the 26 overdosed patients were analysed using the non-parametric adaptive grip approach implemented in a R-package (Pmetrics 1 version 1. 5. 0) [11]. The total data set was divided into development dataset (26 patients, 57 observations) and an independent validation dataset (2 external patients, 6 observations). Observations meant plasma concentration values of baclofen. Several structural models were assessed during the development process with and without absorption lag time (Tlag) and/or bioavailability (F). The analysis was based on a covariate-free mono-compartment open model: absorption of baclofen was modelled by the first process as described in Fig. 1. The model was parameterised in terms of F, absorption rate constant (Ka), elimination rate (Ke) and apparent central volume of distribution (Vd/F).
Isolation and Taxonomic Characterization of the Fungal Strain The endophytic fungus was isolated from both leaf and stem samples of V. amygdalina plant, which showed a colonization frequency (CF) of 90%. High CF was also recorded on previous studies on fungal endophytes communities such as in Puerto Rico and Sudan  [15, 34]. ITS sequences were deposited in GenBank and then compared using a BLAST search  [32]. The isolated fungus was identified as C. papendorfii with 99% identity (Genbank number KR673909) (Figure  1 ). Microorganisms 2020, 8, x FOR PEER REVIEW 6 of 20 The endophytic fungus was isolated from both leaf and stem samples of V. amygdalina plant, which showed a colonization frequency (CF) of 90%. High CF was also recorded on previous studies on fungal endophytes communities such as in Puerto Rico and Sudan  [15, 34].
ITS sequences were deposited in GenBank and then compared using a BLAST search  [32]. The isolated fungus was identified as C. papendorfii with 99% identity (Genbank number KR673909) (Figure  1 ). In this study, for the first time, C. papendorfii was reported as a fungal endophyte in V. amygdalina, collected in Sudan, although most Curvularia species occur as tropical and subtropical plant pathogens  [12, 35]. The genus Curvularia was also recovered from several plants as endophytes  [36, 37] , as endolichens  [38]  and as marine-derived fungus  [22, 23, 39].
Acknowledgments: The authors acknowledge: the  French Embassy in Khartoum  and the  Foreign Scholarships office at the Ministry of Higher Education and Scientific Research in Sudan  for the financial support of scholarship of A. K. ; the support of  "Laboratoire Lorrain de Chimie Moléculaire   L2CM UMR 7053 " by the " Impact Biomolecules" project of the "Lorraine Université d'Excellence" (Investissements d'avenir-ANR ); this research was also supported by the  MEAE  and  MESRI PHC   NAPATA  project (N •  43443YL ). François Dupire from Platform of Mass Spectrometry in UMR 7053-L2CM team,  Hervé Schohn  and  Tzvetomira Tzanova. R. S. acknowledges  Francoise Chrétien  and  Brigitte Fernette  for their help in identification of compound 1.
As this was an explorative study with no prior data to guide us as to effect size, we were not able to calculate power estimates prior to the study commencement. In order to be certain that we fully understood the FLG status of participants we only included children with 4 Irish grandparents. Children who had previously used topical corticosteroids stronger than 1% hydrocortisone or who had used topical tacrolimus were excluded. There were no other exclusion criteria. The study was conducted in accordance with the Declaration of Helsinki and was approved by the research ethics committee of Our Lady's Children's Hospital, Dublin. Written informed consent was obtained from all patients' parents. Stratum corneum trans-epidermal water loss measurement TEWL measurements were performed under standardized conditions (room temperature of 22-25 °C and humidity levels of 30-35%).
Clinical data Summary of demographic details of the investigated population is given in Table  2  (individual values are available as underlying data (Irvine, 2020)). Most of AD children had moderate to severe disease (SCORAD > 25)  (Kunz et al. , 1997). At least one FLG mutation was found to be carried in 15 children, while in the healthy controls there were two heterozygous carriers of FLG mutations. The skin barrier function, as assessed by TEWL on non-involved skin of the volar forearm, was significantly lower in AD patients when compared to healthy controls (P<0. 01).
Cell topography Corneocytes obtained with the seventh tape strip from the non-involved forearm skin were examined and their lower surface was recorded using AFM topography mode. Representative AFM images regarding disease status and FLG genotype are shown in Figure  2  (individual images are provided as underlying data (Irvine, 2020)). Clear-cut differences in cell surface morphology characterised by presence of numerous micro-protrusions were observed in AD patients, compared to healthy subjects. The slight variation between images recorded within the healthy and AD groups was also noted, according to the FLG genotype, but these differences were not quantified in the present study. Of note, cells from subjects that are heterozygous carriers of FLG-loss of function (LOF) mutations but did not develop AD, remained free of the surface alteration observed in AD.
Methods: Please add a more succinct description of how Ea is determined by stiffness tomography. Here follows a more succinct description: The methodological approach of AFM stiffness tomography of human SC corneocytes has been validated and fully described in the previous publication  (Milani et al. , 2018). In short, the Young modulus (Ea) is a measurement of relative elasticity/rigidity of the substrate probed with a tip of an AFM apparatus. Force curves reflecting the substrate's physical interactions with the tip are recorded and analysed using previously defined algorithms. As there are no restrictions on paper length we have not shortened the existing description which we believe makes it easier to replicate these experiments. Since the authors state that decreased cornified envelope stiffness in AD may be linked to imperfect corneocyte maturation, data on corneocyte maturation, related enzymes (e.
g. transglutaminase-1, 12R-lipoxygenase), and presence of mediators of inflammation (e. g. cytokines) would be helpful, if available (not required). We appreciate these comments and fully agree but unfortunately do not have these additional data points available This manuscript by Haftek et al. describes the changes in nano-mechanical properties found in cornified keratinocytes of children with atopic dermatitis. The authors study the skin of twenty AD patients and seven healthy children. Using adhesive tapes, cell stiffness and filaggrin degradation products named natural moisturizing factors were analyzed. In addition, transepidermal water loss (TEWL) was measured and disease severity was assessed using the SCORAD index. This data was complemented with FLG genotyping for the nine most common FLG mutations.
Three stacks of horizontal plane images (512 × 512 pixels corresponding to 119 × 119 μm) with a z-step of 1 μm were acquired for each biofilm at different areas in the well. Two independent experiments were performed for each strain. Image analyses of three-dimensional projections of biofilm structures were reconstructed with the Easy 3D function of the IMARIS 9. 3 software (Bitplane, Switzerland). The number of beads analyzed was equal to 10 for each incubation time. CPB_placebos were used as control.
ACKNOWLEDGEMENTS This work was funded by the  Regional Council of Bourgogne-Franche-Comté , the  "Fonds Européen de Développement Régional (FEDER)" the "Ministère de lʼEnseignement supérieur, de la Recherche et de lʼInnovation"  and the  "Société d'Accélération de Transfert Technologique (SATT )" SAYENS. The authors would like to thank  J. Deschamps ,  A. Bonnotte  and  C. Arnould  ( Microscopy Facility );  A. Geissler  and  A. Chlémaire  ( Histology Facility ),  S. Monier  ( Flow Cytometry Facility ),  A. Ducreux  ( Technical support ) and  Keith Hodson  (English text proofreading).
Flow cytometry. Up to four-color FACS staining was performed as described by  Gurniak and Witke, 2007. Briefly, single cell suspensions were filtered (30μm Filcons) and stained with the corresponding antibodies in FACS buffer (0. 5% FCS, 2mM EDTA in PBS) for 15 to 30min on ice, washed two times with FACS buffer and data were acquired on an Accuri C6 (Becton Dickinson (BD)). Actin measurements: To determine G-and F-actin levels by DNaseI and phalloidin staining, cells were fixed in 4% PFA/PBS for 10min washed with PBS and permeabilized for 15min with 0. 1% Triton X-100/PBS, both incubations at RT. Apoptosis staining: For apoptotic and dead cells the Annexin V-FITC Apoptosis Detection Kit (BD) was used in combination with propidium iodide, staining for CD4-PerCP and CD8-APC was performed simultaneously.
To determine spreading the number of extended cells were counted from phase contrast images. Statistics were performed by a two-tailed independent T-test and with SigmaPlot® 12 (Systat Software, Inc. ) using one-way Anova. Transwell assay: Two dimensional migration of thymocytes was measured by transwell migration using inserts with a pore size of 5µm (Corning Costar) as described by  Phee et al. , 2010 and Shiow et al. , 2008. Single cell suspensions were preincubated for 1h in migration medium (10mM HEPES pH 7. 2, 100U/ml penicillin/streptomycin, 0. 5% (v/v) BSA in RPMI 1640) at 37°C, 5% CO2, subsequently 3 x 10 5 cells were transferred to the top chamber of the respective transwell plates. Assays were set up in duplicates; the bottom chamber contained plain migration medium or one of the chemokines either SDF-1α (400ng/ml) or CCL25 (2.
Collagen-thymocyte mixtures were placed in custom-built chemotaxis chambers and incubated for 60min at 37°C, 5% CO2 to allow collagen polymerisation and cell recovery. Time-lapse imaging was conducted using a fully automated inverted microscope (Keyence) equipped with a 10x phase-contrast objective (Nikon) and a climate chamber (37°C; 5% CO2). Time-lapse images were recorded for 8h at 90s intervals; control and mutant thymocytes were simultaneously acquired at different coordinates. The ImageJ 1. 47q software (NIH) and the 'Manual Histology. Hematoxylin/Eosin (H&E) staining was carried out on 8µm cryo sections; after fixation with 4% PFA/PBS slides were incubated in 0. 05% Eosin (Sigma-Aldrich) and 20% Hematoxylin (Merck Millipore). Area measurements of thymic regions were performed manually on H&E stained sections using the area measurement plug-in of the Keyence BZ-II analyser software (version 1.
There is likely to be consensus across all societies that patients with ACLF grade 1 and 2 should be listed for LT. Even among patients who have recovered from an episode of ACLF, there is still an increased likelihood of developing a higher grade of ACLF in the future  (24)  and an inherent mortality at 6 months between 40% and 50%. (8) Therefore, evaluating and listing these patients for LT may build a "safety net" in the event of future deterioration and development of multiple organ failures. The presence of ACLF grade 3 should not be considered an absolute contraindication for LT. A large retrospective analysis of the United Network for Organ Sharing (UNOS) database with more than 50,000 patients very clearly shows that LT improves outcomes in these patients. (5) Similar results were obtained in different European countries evaluating retrospective and prospective cohorts.
(33) (36) (37)  A recent study identified a score associated with sustained use of alcohol after LT. (38)  The Sustained Alcohol Use Post-LT (SALT) score was composed by 4 variables: the drinking pattern of the patients at initial hospitalization (10 drinks per day: +4 points), prior rehabilitation attempts (multiple attempts: +4 points), alcohol-related legal issues (+2 points), and prior illicit substance abuse (+1 point). A SALT score of <5 had a 95% negative predictive value for sustained alcohol use after LT. (38)  Bacterial infection, which is the most frequent precipitating event in the recently conducted PREDICT study (NCT03056612), is also a common feature of ACLF in both the NASCELD and EASL-CLIF definitions. (1, 39) Interestingly, infections are not only precipitants, but also complications of ACLF.
(5) urther analysis of this database revealed even greater post-LT survival when transplantation occurred within 14 days, and furthermore, the survival benefit increased with a greater number of organ failures. Although patients with ACLF 2 did not see significant improvement when transplanted within 14 days of listing (90% versus 88%, P = 0. 053), greater post-LT survival was demonstrated among patients transplanted with 3 organ failures (86% versus 83%, P = 0. 012), 4 organ failures (81% versus 76%, P = 0. 007), and 5 organ failures (79% versus 67%, P < 0. 001). (52) owever, other studies have indicated that the benefits of transplanting a patient with ACLF as quickly as possible should be weighed against the benefits yielded by the recovery of 1 or more organ failures prior to transplantation.
Manual palpation Evaluation of the horses' spine was performed by a 20 years experienced licensed chiropractor (H. M), expert in the evaluation of joints and spinal related disorders  [18, 19] , who was not familiar with any of the horses beforehand. Manual palpation was performed from head to tail and the mobility of each vertebral site was tested (N = 51 vertebral sites: 7 cervical, 18 thoracic, 6 lumbar, 5 sacral and 15 coccigeal). Examination was based on bony and soft tissue manual palpation to localise regions of vertebral stiffness based on spinal mobilisation and palpable areas of muscle hypertonicity  [26, 27]. Comparisons of data from different practitioners in earlier studies (including H. M involved here) have shown high agreement and therefore repeatability (i. e. 94% of the vertebrae  [14, 22] ).
Examinations were performed outside the horses' working times, during the resting day, in each horse' s individual box. The examined horse was lightly restrained by one unknown (to the horses) experimenter (M. H). Horses were classified by the practitioner as totally unaffected, slightly affected (one affected vertebra) or severely affected (at least 2 affected vertebrae). Data included also the percentage of affected vertebrae per horse. As soon as a problem was detected at the level of a vertebra (stiffness or hypertonicity or both) the vertebral site was considered as affected.
Acknowledgements The authors thank the owner and staff of the riding schools for allowing us to work with their horses and for their understanding;  Hervé Menguy  for performing manual palpations;  Séverine Henry ,  Carol Sankey ,  Boris Weiss , and  Laure Prillieux  for their help during data collection;  Carol Sankey  for English corrections. This study was supported by the  Caisse Centrale de la Mutualité Sociale Agricole  and the  French Research Ministry. Received: 4 May 2012 Accepted: 11 October 2013 Published: 15 October 2013.
Metric data The wings were mounted between microscope slides and cover slips as described in  Schachter-Broide et al. (2004). Photographs of each pair of wings were taken using a digital camera (Sony MVC-CD300, US) and a stereo-microscope (Zeiss SV11, Germany). We used the 10 type-I landmarks (vein intersections) identified for T. infestans wings, according to  Bookstein (1990) , as described elsewhere  (Schachter-Broide et al. , 2004). Only right wings were included in the analyses to avoid pseudoreplication.
Acknowledgments We thank  Fundación Mundo Sano  for long-term support at the study site,  Jorge Nasir , the  Chagas Control Program of Chaco  and the National Vector Control Coordination for support in field operations; and  Judith Schachter-Broide ,  Ana Laura Carbajal de la Fuente ,  Romina Piccinali  and  Yael Provecho  for helpful advice. This study was supported by awards from the  International Development Research Center and Tropical Disease Research  ( UNICEF/PNUD/WB/WHO ) to R. E. G. , and by  National Institutes of Health/National Science Foundation Ecology of Infectious Disease program  award  R01 TW05836  funded by the  Fogarty International Center  and the  National Institute of Environmental Health Sciences  to U. K. , R. E. G. , and  Joel Cohen. This study was approved by IRB  00001678  ( National Institutes of Health registered ).
Every 10 s we recorded whether the quail had pecked vigorously at the mirror (aggressive pecks) or had pecked gently (less vigorous pecks, with non-aggressive posture)  [29]. Vigorous pecks were successive fast pecks sometimes associated with wing flapping and/or running or fast steps when approaching the mirror. This is intensive agonistic behavior  [29]. Threats (stiff body posture with feathers lifted) and retreats were recorded but, due to their low frequency, were not used in the analyses. Male and female quail were tested for aggressive behavior. However, only data from males were used in analyses as expression of aggressive behavior in females was very low. The number of aggressive or gentle pecks is referred to as AgrP or GentleP, respectively, in this study. Sexual motivation of the males (day 62).
Statistical analyses Normal distribution of the data was assessed by calculating the kurtosis and skewness parameters and by looking at the normal probability plot. As the distribution of several behavioral traits differed greatly from normality, non-parametric statistics were used. Phenotypic correlations between traits measured in the different tests were estimated by the Spearman Rank correlation using R software. The behavior of the HSR and LSR lines was compared using a Mann-Whitney U test with SYSTAT 8. 0 (SPSS Inc. , Chicago, IL, U. S. A. ). Body weights of HSR and LSR lines were compared using t-tests as the data distribution was normal. The methodology to estimate genetic parameters usually implies a normal distribution of traits which was the case for DistIso and the different production traits.
Acknowledgements We thank all the staff from the  INRA experimental unit PEAT  and particularly  Joël Dalaveau ,  Christophe Rat  for the incubation step,  Sandrine Rivière , for the care provided to the quail, mating management and recording the laying data, Philippe Servant and  Marc Vogel  for making the experimental devices. We also thank  Michel Couty  for managing the genetic lines and  Simon Constantin ,  Mathilde Bobet  and  Paul Constantin  for phenotyping quail behavior.
ncbi. nlm. nih. gov/genomes/static/Pipeline. html). The automated annotation identified 5,129 coding DNA sequences with 46 tRNA-and 3 rRNA-encoding genes. Genomic comparisons between isolate V06705 and the reference strain M. abscessus ATCC 19977 (CIP 104536 T )  (8)  show greater sequence homology than comparisons with other M. abscessus genomes  (9). ATCC 19977 is a rough strain that is hyperlethal to mice and contains the loss in function required to produce glycopeptidolipids  (10). Therefore, the genome sequence of V06075 makes an ideal candidate for identifying other regions containing high rates of mutation and transmissible genetic elements that contribute to virulence. Nucleotide sequence accession number. The M. abscessus strain V06705 genome sequence and annotation data have been deposited in NCBI GenBank under the accession no.
Pens and video recordings The barn had seven units (six units with 10 pens and one unit with six pens). Four units were used for this study. Within these units, 24 pens were randomly chosen for video recordings (six pens per unit). In total, 105 calves were observed (nine pens with five calves and 15 pens with four calves). Eighteen cameras (Type RC516BH, 600 TVL) were installed 2 days before the start of the study and were attached to the ceiling of the barn so that they would not be accessible to calves. One camera could film one or two pens and provided good-quality black and white digital videos. Pens were video recorded on 4 consecutive days from 0600 h to 2100 h (15 h). Data were stored for later observation. Observations for comparison of direct observation and observation from video recordings.
Statistical analyses All data were analysed with the SAS R statistical program (SAS R Institute Inc. version 9. 1). Data were expressed as percentages of calves performing a specific behaviour per scan, or as percentage of time spent on each behaviour by unit of time (either 60 min or 15 h), with the statistical unit being pen. In addition, the percentage of time the calves were in a standing posture by unit of time (either 60 min or 15 h) was analysed as an estimation of the activity level of calves. For comparison of the observation method, all behaviours in the ethogram were analysed. The observations from video were performed exactly at the same period as the direct observations performed for each pen. Therefore, for both methods of observation there were two times 30 min of observation periods.
For each pen, data from the two 30 min periods of observation were added up into one period of 60 min of observation. Means were calculated for the two types of observation and compared by a Wilcoxon matchedpairs signed-rank test for paired comparisons. Associations between the outcomes of the direct observations and the observation from video were calculated with Spearman's rank correlations (r s ), and the strength of the correlations was described according to  Martin and Bateson (1993). The behaviour of calves was assessed at day level (from 0600 to 2100 h). The percentage of time calves were standing, or spent on performing abnormal oral behaviour, and manipulating substrates were compared between days (without and with the presence of the observer). Means were calculated per day and compared with the Wilcoxon matched-pairs signed-rank test for paired comparisons and the Kruskall-Wallis test for overall comparison.