dataesr/scientific-paragraphs-categorization huggingface dataset:
This is not to say that lower limits are unimportant, but their importance lies usually in a regulatory or legalistic context  (Kadachi and Al-Eshaikh 2012; Marguí et al. 2013 ). In the context of collaborative research databases for art and archaeology, the critical factor is that the result be reported with a reasonable estimate of the error associated with the prediction. It is knowledge of the error that allows an analyst to determine if a given result is useful for discrimination in a given context. To paraphrase  Lachance and Claisse (1995, 272) , a result of 0. 02% ± 0. 02% may be of little value if one is trying to discriminate between samples in a range of concentrations from 0 to 0. 1; however, if the range of concentrations being investigated is from 0 to 1. 0, the result (which has a R rel = 100%) may be of entirely satisfactory precision.
Several studies suggest strongly that reliance on the quantification methods provided by instrument manufacturers is not likely to yield results that are satisfactory for collaborative purposes  (Heginbotham et al. 2011; Goodale et al. 2012; Smith 2012; Shugar 2013 ). An unfortunate consequence of this circumstance is that many published quantitative ED-XRF results from heritage copper alloy artefacts are not reliably reproducible by other researchers, and thus cannot be used with confidence for comparative purposes. The reproducibility study presented here demonstrates that the CHARMed PyMca protocol is a useful tool to address these challenges in a manner that is rigorous, readily accessible and fully transparent. By using a shared set of standards, with free and open-source software, and a common calibration strategy, this protocol facilitates data sharing in a manner that is consistent with regards to the elements analysed, well characterized in terms of precision and demonstrably reproducible.
This is a significant improvement over the uncertainty values provided by most manufacturers' proprietary software for quantification, which typically rely on counting statistics and often reflect a measure of repeatability rather than true uncertainty. Realistic reproducibility and error estimations can help researchers make informed decisions about whether or not the degree of precision that they may expect from ED-XRF using the CHARMed PyMca protocol makes the protocol suitable for their specific purposes. The CHARMed PyMca protocol has been used recently in the development of a predictive machine-learning model designed to estimate the date of production of French gilt bronzes  (Heginbotham et al. 2018 ). These sumptuous objects, produced in large numbers from the late 17th century to the early 21st century, are notoriously difficult to date and authenticate (de  Bellaigue 1974, 1:35).
The dating model used a database (or 'training set'), compiled at the J. Paul Getty Museum, of 466 elemental compositions of securely dated French gilt bronzes. This database was assembled over the course of a decade from ED-XRF measurements made by five different instruments at three different institutions. The aggregation of data from disparate sources into a single database was possible because all the instruments had been calibrated according to the CHARMed PyMca protocol, assuring that the results for a common suite of 15 elements are reproducible between instruments, and are comparable with respect to both accuracy and precision.
ACKNOWLEDGEMENTS The authors thank  V. Armando Solé  for ongoing support and assistance with PyMca;  Nick Barbi of XGLabs  for arranging the loan of the Elio spectrometer to the  Getty Conservation Institute ;  Donna Corbin ,  Beth Price  and  Andrew Lins  at the  Philadelphia Museum of Art  for their generous support; and  Robert Van Langh  at the  Rijksmuseum, Amsterdam , his inspiration and for support. Part of the research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  ( FP7/2007-2013)/ERC grant agreement n°319209.
5406 Å radiation in a horizontally mounted INEL diffractometer with a quartz monochromator, a cylindrical position-sensitive detector (CPS-120) and the Debye-Scherrer geometry. NPG samples were introduced into a 0. 5-mmdiameter Lindemann capillary to minimize absorption, and the temperature was varied using a 600 series Oxford Cryostream Cooler. Using the Materials Studio software  58  , lattice parameters were determined by pattern matching using Pawley method for the cubic phase, and by Rietveld refinement for the monoclinic phase. Dilatometry was performed using a bespoke apparatus that operated up to 0. 3 GPa over ~193-433 K temperature range. Molten NPG samples of mass ~1 g were encapsulated inside stainless-steel containers to remove any residual air. Each container was then perforated by a stainless-steel piston, whose relative displacement with respect to a surrounding coil could be detected via measurement of electromotive force 59.
Acknowledgements This work was supported by the  MINECO  projects  MAT2016-75823-R  and  FIS2017-82625-P , the  DGU  project  2017SGR-42 , the  UK EPSRC  grant  EP/M003752/1 , and the  ERC Starting  grant no. 680032. We acknowledge  ALBA  for time on MSPD  BL04  under proposal 2016021701. E. S. -T. and X. M. are grateful for support from the  Royal Society.
Activities were determined by measuring the accumulation of the fluorogenic cleavage product (AMC) using a luminescence spectrometer FLX800 (Biotek) for 45 min at 380-nm excitation wavelength and 440-nm emission wavelength. Then, the activities were determined by calculating the difference between arbitrary fluorescence units recorded with or without MG132 in the reaction medium. The final data were corrected by the amount of protein. The time course for the accumulation of AMC after hydrolysis of the substrate was analyzed by linear regression to calculate activities, i. e. , the slopes of best fit of accumulation AMC vs. time.
Effect of immobilization and recovery on trypsin-like and chymotrypsin-like activities Muscle protein mass is controlled by the balance between rates of protein synthesis and breakdown. The proteasome system (UPS) is involved in the breakdown of the major contractile proteins in catabolic conditions, and we previously reported that the activation of the UPS pending immobilization was normalized 20 days after cast removal  [7]. Thus, the regulation of the UPS was assessed during immobilization (I8) and recovery until R20 by measurements of the main peptidase activities of the proteasomes, i. e. the chymotrypsin (CT)-and the trypsin (T)-like. The CT-and T-like activities of the proteasome were similar in muscles from animals either in the post absorptive or the post prandial state in all groups during the whole kinetic studied (data not shown).
Thus, data obtained in both the post absorptive and the post prandial state were pooled and analysed regarding the effect of the diet. The CT-and the T-like activities of the proteasomes did not change significantly in immobilized gastrocnemius of EXPERIMENTAL or CONTROL animals compared to the pair fed group (Figure  7 ). Only the CT-like activity of the proteasome increased at I8 in immobilized gastrocnemius of EXPERIMENTAL rats compared to the I0 group (+34. 7%, P<0. 05, Figure  7A ) and at R20 in remobilized gastrocnemius of EXPERIMENTAL and CONTROL animals compared to the pair fed group (+20. 5 and 29. 5%, respectively, P<0. 05, Figure  7A ).
Acknowledgements We would like to thank  G Williamson  ( University of Leeds ) for his valuable input in the protocol design,  A Cissoire ,  B Cohade ,  P Denis  and  P Lhoste  from the  IEN (INRA Clermont-Theix ) for their excellent assistance during animal experimentation and  X Blanc  for diets preparation. We also thank  F Bechereau ,  C Buffière F Glomot ,  N Hafnaoui  and  C Sornet  for their invaluable technical assistance at various steps of the samples preparation and assay.
Acknowledgments We thank  A. Dobson ,  D. Dowling ,  A. McTighe ,  R. Naylor ,  O. Otti  and  J. Rolff  for comments on the manuscript and technical help. Financial support was provided the VolkswagenFoundation ( 84-780 ),  NERC  ( NE/D009634/1 ), and a visitors' support scheme by the  Languedoc-Roussillon regional government  to K. R.
Purpose To determine the safety of fluconazole in neonates and other paediatric age groups by identifying adverse events (AEs) and drug interactions associated with treatment. Methods A search of EMBASE (1950-January 2012), MEDLINE (1946-January 2012), the Cochrane database for systematic reviews and the Cumulative Index to Nursing  and Allied Health Literature (1982-2012)  for any clinical study about fluconazole use that involved at least one paediatric patient (≤17 years) was performed. Only articles with sufficient quality of safety reporting after patients' exposure to fluconazole were included. Results We identified 90 articles, reporting on 4,209 patients, which met our inclusion criteria. In total, 794 AEs from 35 studies were recorded, with hepatotoxicity accounting for 378 (47. 6 %) of all AEs.
Search strategy We searched MEDLINE (1946-January 2012), EMBASE (1950-January 2012), the Cochrane database for systematic reviews, Cumulative Index to Nursing and Allied Health Literature (CINAHL1982-January 2012) and the Cochrane library (Cochrane Central Register of Controlled Trials, Cochrane database of systematic reviews, and Database of abstracts of reviews of effects) for any clinical study about fluconazole use that involved at least one paediatric patient (≤17 years). Any study with involvement of a paediatric age group participant taking at least a single dose of fluconazole was eligible. Only studies with a report of safety after exposure to fluconazole in the paediatric patients were included. There was no restriction on the language of publication of the articles as translations to extract relevant data were done; where translations were not possible, abstracts containing relevant data were used.
Also included in this review were any clinical study, whether comparative or non-comparative, randomised controlled trials (RCTs) or case reports and also letters to the editors that documented exposure of a paediatric patient to fluconazole and reported on safety. Included articles and extracted data were validated by two reviewers. Search terms comprised free text words and subject headings. These included terms relating to azole or imidazole or fluconazole, adverse effects or adverse drug reactions or side effects, pharmacokinetics and drug interactions.
Data collection The relevant data were extracted onto the data extraction form. Participants in the study were grouped into paediatric age groups of preterm neonates (<36 weeks gestation, 0-27 days), full-term neonates (0-27 days, >37 weeks gestation), infants and toddlers (28 days-23 months), children (2-11 years) and adolescents  (12-17 years). All reported AEs were pooled together from the various studies. The duration of treatment was grouped into <21, 21-42 and >42 days; the treatment dose was grouped into <3, 3-6 and >6 mg/kg; the route of administration was recorded as intravenous (IV), oral or IV and oral.
Design, expression and characterization of recombinant proteins Three recombinant proteins were produced in E. coli: bvPLA2 carrying the mutation H34Q, cancer/testis antigen NY-ESO-1 (referred to as NY(s)) and the fusion protein bvPLA2H34Q-NY-ESO-1 (referred to as PNY). To ensure strong binding to the membrane, bvPLA2m must be properly folded, especially its secondary structure, the α helix, which is involved in interfacial binding with membrane lipids. The secondary structure of each protein was investigated using far-UV CD spectroscopy. The spectra of bvPLA2 purified from bee venom and of recombinant bvPLA2m were similar (data not shown), corresponding to an approximate fraction of each secondary structure element calculated with K2D  [24] , 30% α helix, 12% β sheet and 57% random structure.
The DCs treated with inhibitors and pulsed with peptide NY 157-165 were used as controls. The inhibition efficiency was evaluated using the following formula: Regarding data from a statistical point of view, NY(s) crosspresentation was not significantly affected by the drug treatment. In contrast, the presentation of peptide derived from PNY was inhibited by BFA, a drug disassembling the Golgi apparatus and inhibiting newly synthesized MHC class I molecules. The drug treatment prevented 26% of peptide cross-presentation (p< 0. 001) (Figure  5 ). Unfused bvPLA2m was sensitive to clasto-Lactacystin β-lactone (p= 0. 029) and epoxomicin (p= 0. 016), two irreversible proteasome inhibitors which enhanced protein cross-presentation up to 50% more, and to BFA, which inhibited at least 50% of the peptide presentation (Figure  5 ).
After loading, the cells were washed and further incubated for up to 48 h. The results showed that three loadings of PNY were necessary for significant crosspresentation of peptides derived from proteins detected with the antibody (data not shown). For NY(s), peptide crosspresentation started after the second loading was complete (data not shown). In a second step, the same experiment was carried out to measure the MHC/peptide complexes appearing up to 96 h after the last loading. Reproducibility was evaluated using three PNY recombinant fusion proteins referred to as PNY1, PNY2 and PNY3, from three different E. Coli preparations. At the same time, the stability of HLA-A*02/ NY 157-165 complexes presented at the T1 cell surface was studied through analysis of their appearance and disappearance during the five-day experiment.
Dynamic light scattering (DLS) Each of the study proteins was characterized as being in a monomer or aggregate state using light scattering. Hydrodynamic diameters were measured at 25°C using a Malvern Nanosizer ZS instrument equipped with a 4 mW He-Ne solid-state laser operating at 633 nm. Backscattered light was detected at 173°, and the mean protein diameter was calculated from the quadratic fitting of the correlation function over 15 runs of 10 s. All measurements were performed in triplicate on proteins diluted to 0. 5 mg/ml in phosphate-buffered saline (PBS). The data were collected and analyzed using the Stokes-Einstein equation.
Acknowledgements We thank  Dr Hassane Zarour ,  Department of Medicine and the Melanoma Center, and Department of Immunology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213 , for providing the cell lines SK-MEL-37 and  UPCI-MEL-136. 1 , Aurélien Missonnier  and  Yannick Delcuze  for technical help,  Dr Roberto Mallone  for fruitful discussion and  Dr Agnès Hagège  for critical reading. This work is devoted to the memory of  Dr. André Ménez , President of the  French Natural History Museum , and world-renowned expert in the molecular and structural biology of animal toxins.
Figure. 9: Trajectory in the complex plan (s,h ,t) and projection in the plan (s,h) related to cd2. Based on the property of having a unique rotation center from the trembling and rambling trajectory either from detail wavelet coefficients trajectory, a specific parameter is defined; it is the area of the circle in which 95% of the data points are located  [4]. This feature is calculated for AP and ML directions, for the four measures situations (FO_EO, FO_EC, FT_EO, FT_EC) and for each of these components: trembling and rambling resulting from mCPA decomposition. These parameters (16 values of area) are labelled mPCA parameters. The feature is also calculated for AP and ML directions, for the four measures situations (FO_EO, FO_EC, FT_EO, FT_EC) and for each of these components: cd2, cd3 resulting from wavelet decomposition.
Data recorded The doses of midazolam and sufentanil were based on the RASS, with a target score between RASS -4 and -5. These drugs, which are commonly used in the ICU, do not alter the PMR  [6, 10]. PMR was measured with a 320 Lux flash of light using the Neurolight W (IDmed, Marseille, France). Three measurements per day were taken for a 48-hour period. BIS values also were recorded (BIS Vista W , Anandic Medical Systems, Feuerthalen, Switzerland). The data recorded by the pupillometric video comprised: variation of pupillary diameter (ΔPD), latency time (LT), and maximal speed of pupillary constriction (Vmax). These measurements were analyzed after classification of BIS values into three groups (<40 heavy sedation; 40 ≤ BIS ≤ 60 acceptable sedation; >60 light sedation)  [17]. All assessments of PMR, BIS, and RASS followed a standardized protocol for the study.
ANALYSIS OF DATA AND STATISTICS In many preparations, within a few tens of minutes, an intraluminal blockage due to the accumulation of remnants of digestive contents and mucosal secretion obstructed the anal output. In these cases, the intestinal lumen needed to be flushed to free the lumen thus disturbing the progress of the spontaneous CMMC activity. Data from these preparations were not included in this study. Cyclical, long-duration contractions which alternated with periods of relative quiescence and which were observed to occur at more than one recording site were considered to be CMMCs  (Fida et al. , 1997). The period, duration, area, and maximum amplitude of CMMCs were measured for all recording sites. To perform measurements, the starting and ending points of CMMCs were determined from the average baseline tension during the relative quiescence between CMMCs.
, 2001)  and in order to allow accurate comparisons between types of mice, in both groups analysis started at the same time-point from the beginning of the recording session and lasted for 20-50 min. Therefore, only preparations from which time-matched data were obtained were included in this study. Data are expressed as mean ± standard error of the mean (SEM). "n" refers to the number of preparations. Statistical analysis was performed using GraphPad Instat 3. 06 (GraphPad Software, San Diego, CA, USA). Student's two-tailed unpaired t tests or multiple comparison tests were used where appropriate. The site of origin of CMMCs was tested for significant changes between the two types of mice using a Fisher Exact test. P < 0. 05 was considered significant.
ACKNOWLEDGMENTS The authors would like to thank  François Maingret  and  John B. Furness  for critical comments of previous drafts of the manuscript,  Amandine Dufour  and  Axel Fernandez  for highly expert technical assistance and  Françoise Padilla. This work was supported by the  Centre National de la Recherche Scientifique (CNRS) ,  Aix Marseille Université  and by grants from the  ANR, FRM , and SFETD.
7 mM KCl, 4. 3 mM Na 2 HPO 4 , 1. 4 mM KH 2 PO 4 , pH 7. 4; 1 Â 10 6 cells per ml) and analysed using a LSRII Fortessa flow cytometer (Becton Dickinson, Allschwil, Switzerland) equipped for DsRed (561 nm laser excitation and 586/15 emission filter) detection and set to exclude dead cells and cell doublets. At least 10,000 cells were recorded per data set and analysed using FACSDiva (BD Biosciences, Franklin Lakes, NJ, USA, version no. 6. 1. 3. ). Blood fat levels. Blood cholesterol levels were profiled using a total cholesterol assay kit (Fluoro Cholesterol; Cell Technology, Mountain View, USA). In brief, 50 ml of appropriately ddH 2 O-diluted serum was added per well of a clear-bottom black 96-well plate containing 50 ml of freshly prepared reaction cocktail (20 ml resuspended enzyme mix, 20 ml resuspended cholesterol probe and 960 ml reaction buffer).
Acknowledgements We thank  Julian Sikorski  for providing pJWS17,  Tommy Schlumpf  for assistance with the Co-IP,  Marc Folcher  for visualizing microencapsulated cells in the peritoneal cavity, and  Pratik Saxena ,  Barbara Geering ,  Simon Ausla  ¨nder as well as  Henryk Zulewski  for critical comments on the manuscript. This work was supported by a  European Research.
Acknowledgments CH, GKJ, AK, and JR are employed by non-profit organisations with activities that focus on global efforts to address non-communicable diseases. MAH and PDG receive research grants and support for travel to meetings from food and pharmaceutical companies for work related to the developmental origins of health and disease. KH is employed by  Social and Scientific Systems , a government contractor that supported the logistics and technical writing for the workshop that initiated the development of this Comment. The  National Institute of Environmental.
Real-time quantitative PCR Opioid peptides and receptors were chosen according to the nomenclature of the International Union of Basic and Clinical Pharmacology (IUPHAR). The nucleotide primer sequences for PCR were selected with Oligo 6. 42 software (MedProbe, Oslo, Norway). The sequences of the primers used are described in Table  1. Gene expression was assessed by real-time quantitative PCR on the cDNA. Amplification was detected by SYBR s Green fluorescence on an ABI PRISMs 7900HT sequence detection system (Applied Biosystems, France). Thermocycling was carried out in a final volume of 20 ml containing 0. 5 mM of each of the primers used and 10 ml of Power SYBR s Green PCR Master Mix 2X (Applied Biosystems, France). We added 8 ml of diluted cDNA to this mixture. The thermal cycling conditions were as previously described  (Benturquia et al.
Data analysis All series of behavioural data were analysed with Statview 5. 0 software (SAS Institute Inc. , NC, USA). The data for real-time were analysed in a one-way ANOVA between subjects, followed by a Tukey test for post hoc comparisons. In the case of real-time PCR fold-change data, the S. D. was calculated as follows: S. D. ¼(mean of treated group) 2 /(mean of control group) 4 Â (S. E. M. of mean of control group) 2 +(S. E. M. of mean of treated group) 2 /(mean of control group) 2. The S. E. M. was calculated as: S. D. /√[(number of control animals+number of treated animals)-1]. Values of Po0. 05 were considered significant.
Limitations Our study population might not be representative of all HIVpositive patients initiating HAART in Burkina Faso as we essentially included patients living in the urban area of Ouagadougou. However, they might be quite representative of those living in the urban area of Ouagadougou as these three HIV clinics follow the great majority of HIV-positive people of this district. Some patients initially included in the study did not attend the subsequent follow-up visits. These patients might have presented a quite different of HRQOL during their follow-up, introducing potential biases in our PHS and MHS estimates. However, the comparisons of baseline characteristics of patients that attended the three following visits versus the ones that missed at least one visit did not show any significant differences in terms of age, baseline CD4 count and clinical stage (data not shown).
Acknowledgements We are indebted to all of the HIV-positive people in Ouagadougou who agreed to participate in this present study as well as to the health workers who performed the HRQOL assessments and data collection. We are also indebted to officials from the participating  HIV clinics in Ouagadougou [Hopital de jour, Medecine interne, Centre Hospitalier Universitaire de Yalgado Ouedraogo (CHU-YO), Centre medical associatif African Association Solidarity (AAS), Centre medical avec antenne chirurgicale de Pisssy ] for their positive implication in the present research project. We would also like to thank  Mrs Valerie Journot  and  Dr Bruno Spire  for their helpful advises during the study initiation.
Statistical analysis Data are presented as mean 6 SEM for n independent experiments. Statistical analysis was carried out using unpaired student's t-test (Microsoft Excel 2010) or one-way analysis of variance ANOVA analysis with Tukey post test (Graph pad Prism 5 Software). Densitometry analysis was performed with Image J Software. Statistical significance was denoted as p,0. 05. Hazard ratio for survival in the treated animal group versus the untreated group was calculated using GraphPad Prism software (San Diego, USA).