dataesr/scientific-paragraphs-categorization huggingface dataset:
Lead isotopes and the convex hull strategy 124 The prevalent method of assessing provenance of silver artefacts is by means of Pb isotopes. 125 Contrary to the abundances of stable isotopes of other elements, such as Cu and Ag, which 126 vary with environmental conditions, the relative abundances of Pb isotopes vary 127 predominantly as a result of uranium and thorium radioactive decay and consequent lead 128 radiogenic ingrowth. Isotopic variations are controlled by the U/Pb and Th/Pb ratios of the 129 rock from which the Pb ore was born and by the time elapsed up to that point. Time (Pb 130 model age), U/Pb, and Th/Pb can be calculated from measured Pb isotopic compositions and 131 be used to deduce the tectonic context in which the ore appeared. In practice, however, 132 archeologists and numismatists simply manually compare the measured Pb isotopic 133 compositions of artefacts in pairs of 2-dimensional plots, such as 208 Pb/ 206 Pb vs 207 Pb/ 206 Pb and 204 Pb/ 206 Pb vs 207 Pb/ 206 Pb, with those of ores stored in a database until they find a match 135 that is acceptable.
The downside of the convex hull approach is that some ore districts are over-155 represented in the database with data variability at a given site being not specifically 156 considered. It is clear that the database contains an inordinate amount of Lavrion samples, yet 157 the hit maps are different for different samples  (Gentelli et al. 2021, and this work). The effect 158 of unequal sample representativeness for densely populated mine fields could be adjusted by 159 normalizing the number of hits to sample density, but such a correction would make little 160 sense for isolated ores with a very small number of samples, such as mines in Iran and North 161 Africa. Rather, careful manual examination of local densities of individual hits will limit such 162 potential bias as has been shown by a previous application of the convex hull method to 163 multiple Iron Age hacksilber hoards  (Gentelli et al.
2021 ) which showed no false-positive 164 identifications of bullion sources. Each Pb isotope datum extracted from a ca. 6700-entry 165 database on galena samples encompassing Europe, North Africa, and Western Asia is then 166 tested for inclusion in the convex hull. Data from major copper ore deposits, such as those 167 found in Cyprus and the Iberian Pyrite Belt, are unlikely to be significant Ag sources and database. An ore found to be included is considered a hit and therefore a potential Pb source, 170 whereas ores plotting outside the hull (considered a miss) can be safely excluded as potential 171 Pb sources. In order to minimize analytical errors and mass-dependent fractionation of Pb in 172 ores, we opted for using 206 Pb-standardized ratios, i. e. , 204.
Results and discussion 183 The coin Pb isotope data are listed in Table  S1  (Supplementary Information). Figure  3  shows 184 the distribution of Pb ores consistent with the present results on coins, i. e. , falling within the 185 convex hull of the data set, with histograms of model ages as insets. 186 187 First, cluster analysis was applied to the samples using techniques implemented by 188 commercial (Matlab) or public domain (R) packages  (Albarède et al. 2021 ) (Fig. 1c ). Each 189 coinage is satisfactorily accounted for by two clusters, which also stand out as separated 190 peaks in the histograms of model ages (Fig. 3 , insets), though one of the clusters identified by 191 sigloi has only two elements, which is not enough for a convex hull to be defined in the 3D 192 space of Pb isotope compositions.
6700-entry database on galenas which plot 519 within the convex hull. (c) The four steps used in this work to identify the ore deposits which 520 are 'hits' in the convex hulls defined by the samples. For purpose of illustration and 521 readability, this sketch of the different steps was drawn as a 2-dimensional representation 522 though all steps were carried out in three dimensions in the present work. The variables x and 523 y stand for any arbitrary Pb isotope ratios. Step 1: samples (yellow circles, e. g. , sigloi) are 524 plotted in an x-y representation; step 2: standard cluster analysis is carried out and, in this 525 case, identifies two groups shown within dotted contours; step 3: convex hulls are calculated 526 for each group with a small allowance (in grey) added for the fringe of each hull to take 527 analytical uncertainties into account; step 4: the position of each ore sample inside (hits 528 shown with green crosses) or outside (misses shown with red crosses) the convex hull is 529 determined numerically (fringe not shown).
Acknowledgments 344 This work is a contribution of Advanced Grant  741454-SILVER-ERC-2016 -ADG 'Silver 345 Isotopes and the  Rise of Money'  awarded to FA by the  European Research Council (ERC). 346 We thank  Marine Pinto ,  Chloé Malod-Dognin , and  Liesel Gentelli  for help with analytical 347 work and coin data compilation, and  Katrin Westner ,  Tzilla Eshel , and  Yigal Erel  for useful 348 discussions. Two anonymous reviewers are gratefully acknowledged for their constructive 349 comments and Editor  Yannis Bassiakos  for his efficient handling of our submission. 350 351.
The total number of hits is the 542 number of matches between coin and ore Pb isotopic compositions. The Pb ore database 543 consists of about 6700 European, North African, and Middle Eastern ores significantly 544 expanded and updated from a smaller core of data on Pb ores initially compiled in the 545 OXALID database (Stos-Gale and Gale 2009) after careful removal of artefacts, slags, and Cu 546.
The current study was based on data from the randomized SAFIR02-LUNG trial  [18]  (Essai intergroupe Unicancer 0105-1305/ IFCT1301 SAFIR02-LUNG -NCT02117167), including exhaustive clinical and molecular data on metastatic lung cancer patients, as well as clinical outcomes under various systemic first-line maintenance treatment regimens (chemotherapy, ICI, targeted therapies). The primary objective of this translational study was to compare the DNA mutational and copy-number profiles of NSCLC with or without BMs to establish a molecular signature associated with BMs. The secondary objective was to evaluate CNS outcome on various maintenance treatment regimens based on baseline BM status.
Bioinformatic analysis For NGS analysis, all variants passing the following thresholds were validated: depth of coverage > 100X, allelic ratio > 5%, and population frequency < 0. 1% in either 1000 g, ESP or gnomAD. All somatic mutations were annotated, sorted, and interpreted by an expert molecular biologist according to available databases (Cosmic, TumorPortal, TCGA, Cancer Hotspots, etc. ). Pathogenic variants were defined as follows: (i) for oncogenes, only mutations driving gain of function were considered (i. e. , hotspot missense mutations, in-frame insertions/deletions described as oncogenic in the literature), (ii) for tumor suppressor genes (TSGs), only mutations leading to loss of function were considered: that is, truncating alterations (nonsense mutations, frameshift insertions/ deletions/splicing) or missense mutations described as deleterious in the literature.
Regarding array-CGH analysis, copy number variations from Cyto-Scan and OncoScan were defined using the R package rCGH (v1. 16. 0 under R v3. 6. 3). Log 2 relative ratios were calculated before centralization of the profile to set the baseline from which copy number alterations were estimated (two copies being the neutral level). Break points in the log 2 relative ratio continuity were identified by profile segmentation. These segments were used to detect focal gene amplifications (log 2 ratio > 1. 58, i. e. , fold change > 6 DNA copies, and amplicon size < 10 Mb) or homozygous deletions (log 2 ratio < -1) and were discussed during the tumor board meeting. Focal amplifications and homozygous deletions were compared among the predefined groups, and a p-value < 0. 05 before adjustment was considered statistically significant.
Oncogenic driver evaluation among regions of interest relied on two different approaches. First, the candidate strategy presumed the oncogenic driver to have been described previously as a somatic alteration in lung cancer (among a 23-gene selection)  [19]. Second, every potential driver was assessed by the discovery strategy, which consisted of a screen among oncoKB and PubMed databases. Array-CGH analysis was focused on focal amplification and homozygous deletions because of their theragnostic impact.
Ethical framework The SAFIR02-LUNG trial was approved by the French ethics committee CPP Ile de France 2 on 09 November 2013 (2013-08-04) and the French health authorities ANSM on 17 October 2013 (130975A-12). The SAFIR02-LUNG study was conducted in accordance with the Declaration of Helsinki, current International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use guidelines, and all applicable regulatory and ethical requirements. Patients signed informed consent for biopsy, randomization, and use of their biological samples for research purposes. Concerning our study, all patients signed informed consent for the SAFIR02-LUNG trial and ancillary studies, and a license contract was established to frame the SAFIR02-LUNG trial data utilization by the investigators (RCAPHM14 0097).
Population Patients were enrolled between April 2014 and December 2018 at 37 centers in France. Among the 999 enrolled patients, CNS status at baseline was available for 785 patients, and 365 had sufficient genomic data quality to be included. Array-CGH data were collected from all 365 patients, and NGS data were collected from 360 of them (five were excluded because of insufficient tumor tissue sample quality). The population was first divided into two groups according to the baseline BM status, with 107 patients harboring BMs, including 67 patients with multiple brain lesions (two or more). Among the 107 BM-positive patients, 47 (44%) benefited from initial local brain radiation therapy. Patient characteristics, summarized in Table  1 , highlighted that a majority of the patients in the BM-positive group were active smokers (58.
Protein interaction analyses To explore the functional implications of our findings, we performed protein interaction analyses using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) molecular database. Among the 12 identified genes, only BCL2L1 and TNS1 proteins were found to interact directly (supported by co-expression, experimental data, and literature data). When the 12 adjacent gene products were added to the process, several interactions were identified (Fig. 2a ), centered on EGFR, but 13 gene products didn't show any interaction and were removed from the illustration. Finally, protein interactions were assessed between the 12 genes identified in our study and the 13-gene signature previously published by our team  [11]. As shown in Fig. 2b , additional protein interactions were observed with RUNX1T1, NCOR2, and LOR among the 13 genes identified in the pilot study.
CNS outcome during the maintenance phase Out of the 365 patients included in our study, 153 (41. 9%) were randomized, including 47 patients with baseline BMs and 106 without baseline BMs. Among them, 137 (89. 5%) experienced disease progression before radiological data cutoff, planned after 18 weeks of maintenance therapy. Forty out of 47 patients (85. 1%) with baseline BMs and 97 out of 106 (91. 5%) without BMs experienced disease progression. Brain evolution data were available for 124 out of the 137 patients who experienced disease progression. Brain progression was observed for 17 patients in the BM-positive group (44. 7%) and nine patients in the BMnegative group (10. 5%). The occurrence of brain progression per treatment arm is summarized in Fig. 4a. Among the 89 randomized patients in the experimental arm (arm A of both substudies 1 and 2), 20 patients (22.
Acknowledgements We thank the patients and their families, as well as all of the investigators and staff involved in the SAFIR02-LUNG trial. We are grateful to the members of the Independent Data Monitoring Committee:  Professor Nicholas Turner ,  Professor Sibylle Loibl ,  Dr Sylvia Novello ,  Dr Enriqueta Felip ,  Ms Saskia Litiere , and  Ms Delphine Beltram. We thank the  IFCT  for its expertise in and advice on thoracic oncology throughout the study.
Apical and basolateral compartments were collected 3 dpi and used to infect Vero E6 cells for 3 d. Infectivity was determined 3 dpi by endpoint titration, showing a median tissue culture infectious dose (TCID 50 ) between 5. 24 × 10 4 /mL and 1. 68 × 10 4 /mL (corresponding to 36,156 and 11,592 PFU/mL) for the apical compartment. Infectivity for the basolateral compartment was below the detection limit (20. 7 PFU/mL). These data demonstrated that SARS-CoV-2 actively replicates in reconstituted BE and that newly produced virions are released from the apical side 3 dpi. To detect virus-infected cells, we generated monoclonal antibodies against the SARS-CoV-2 nucleocapsid protein (N). Clone 3G9 was selected, which specifically recognized N (SI Appendix, Fig. S2A ) and stained infected cells (SI Appendix, Fig.
Transcriptomic Analysis (NanoString). Total RNA extracted from BE was used for 255 gene expression inflammation panel assays using NanoString technology. Multiplexed target enrichment was then performed with gene-specific primers from the "nCounter Inflammation panel" by following the manufacturer's recommendations (see SI Appendix for details). Imaging and Image Analysis. For antigen detection, BE were processed for IF analysis or EM as detailed in SI Appendix. Mounted samples were subsequently examined on an epifluorescence microscope (Leica inverted DMi6000 widefield microscope) at low magnification and at high magnification on a SP8 confocal microscope (Leica Microsystems at the Bordeaux Imagery Center). Image processing was done using Image J software or with Leica LAS-X software with task-adapted protocols (see SI Appendix for details).
ACKNOWLEDGMENTS. We thank the staff of the pathology and surgery departments of the  Bordeaux University Hospital , and  Isabelle Goasdoue ,  Virginie Niel , and  Marine Servat  from the clinical investigation center for technical assistance. Light and electron imaging was performed at the  Bordeaux Imaging Center (BIC) , member of the  FranceBioImaging national infrastructure  (grant  ANR-10-INBS-04 ). We thank the  BIC  for relentless support during the lockdown. We thank the  Agence Nationale de la Recherche  (grant  ANR-CE14-0015-01 , project  ROSAE ) and the  Fondation de France  (project  ANACONDA  ) for funding support. D. R. R. is funded by the  laboratoire d'excellence ParaFrap  (grant  ANR-11-LABX-0024 ). M. -L. B. was supported by the  R egion Nouvelle Aquitaine and UBReact, Bordeaux University.
The vegetation in the area is a dense semi-deciduous forest, with Sterculiaceae and Ulmaceae, which is subject to anthropogenic pressure  [33]. The river discharges of the Nyong (Olama and Mbalmayo) were obtained from two sources. The point of measurement, as well as the methods used for reading water levels and calculating discharges, however, remained the same for the sources. The series obtained and calculating discharges, however, remained the same for the sources. The series obtained from the Hydrological Research Center covers the period 1965-1987 (Olama) and  1951 -1987 (Mbalmayo) (Mbalmayo). This center manages a hydrometric database, mostly on a daily time step, which contains almost all the measurements carried out on Cameroonian territory since the beginning of the 1950s, for most of the stations.
No observation data were available on this watercourse between 1988 and 1997. Indeed, after 1987, due to budgetary constraints, the hydrological service could no longer sustain the continuity of observa-   [34]  were used in this study (Figure  2 ). These indices were collected at a monthly time step on the National Oceanic and Atmospheric Administration website (https://psl. noaa. gov/data/climateindices/list/). SOI, DMI and NAO were collected at the same intervals as the rainfall. The other indices have only been available since the beginning of the 1980s. The analysis of precipitation, average river discharge and runoff coefficients (at annual and seasonal time steps) was carried out using Pettitt  [35]  and Mann-Kendall  [36] [37] [38]  tests, at the 95% significance level. The Pettitt test seems to be the most suitable for the analysis of incomplete series such as ours because it can separate the series into two periods with an overall distinct behavior, which avoids the detection of false discontinuities which can sometimes be observed with other tests such as Hubert segmentation.
If the null hypothesis is rejected, an estimate of the date of discontinuity is given by defining the maximum in the absolute value of the variable Ut, N. In addition to the Pettitt test, the Mann-Kendall test was also used to analyze precipitation, average river discharge and runoff coefficients (at annual and seasonal time steps). This test is based on the test statistic "S" defined as follows: S = ∑ n-1 i=1 ∑ n j=i+1 sgn(xj -xi) where the xj are the sequential data values; n is the length of the data set; and sgn = (θ) if θ > 1, 0 if θ = 0 and -1 if θ < 0. There is no significant trend in the series analyzed when the calculated p-value is above the chosen significance level. To assess the behavior of extreme flows, the Indicators of Hydrologic Alteration (IHA) tool, version 7. 1, developed by The Nature Conservancy was used.
They affect all the images acquired by passive satellites including Landsat 4-5-7 and 8. With the downloaded Landsat images being orthorectified, the preprocessing involved the atmospheric correction of the images and reprojection into the local system (WGS_84_UTM_Zone_32N). For this, neo-channels were created, to increase the readability of the data by enhancing certain properties less obvious in the original image, thus showing more clearly the elements of the scene. Three indices are therefore created, namely: the Normalized Difference Vegetation Index (NDVI, Equation (  1 )), the Brightness Index (BI, Equation (  2 )) and the Normalized Difference Water Index (NDWI, Equation (  3 )). These indices respectively highlight vegetated surfaces, sterile (non-chlorophyllin) elements such as urban areas and water bodies.
Acknowledgments: The authors wish to thank the Cameroonian authorities and national services of  Meteorology and Hydrology , for providing data to the  Joint International Laboratory (LMI) DY-COFAC. The authors also thank the  National Observing System M-TROPICS (Multiscale TROPIcal CatchmentS) from France , which subsidizes observations in experimental tropical watersheds. The authors warmly thank the agents of the  IRD (Research Institute for Developing Countries ) representation in Cameroon, and the direction of the  LMI DYCOFAC, at Yaoundé , for their administrative and financial support.
HATS-18 b is a transiting planet with a large mass and a short orbital period, and is one of the best candidates for the detection of orbital decay induced by tidal effects. We present e xtensiv e photometry of HATS-18 from which we measure 27 times of mid-transit. Two further transit times were measured from data from the Transiting Exoplanet Survey Satellite ( TESS ) and three more taken from the literature. The transit timings were fitted with linear and quadratic ephemerides and an upper limit on orbital decay was determined. This corresponds to a lower limit on the modified stellar tidal quality factor of Q > 10 5. 11 ±0. 04. This is at the cusp of constraining the presence of enhanced tidal dissipation due to internal gravity waves. We also refine the measured physical properties of the HATS-18 system, place upper limits on the masses of third bodies, and compare the relative performance of TESS and the 1.
Of the 20 transits, 13 were good, five were affected by atmospheric cloud or haze (2017  May 13, 2017 June 13, 2018 May 25, 2018 June 20, 2021 June 14)  and two suffered from technical problems (2017 June 9, 2019  May 22). Data reduction was performed using the DEFOT pipeline  (Southworth et al. 2009a (Southworth et al. , 2014 ) ) , which in turn uses routines from the NASA ASTROLIB library 2  IDL 3  implementation of the APER routine from D AOPHO T  (Stetson 1987 ). Image motion was measured by cross-correlating each image with a reference image obtained near the midpoint of that observing sequence. The software apertures were placed by hand on the reference images and the radii of the aperture and sky annulus were chosen manually. No bias or flat-field calibrations were applied, as we found that these had little effect beyond increasing the scatter of the results.
Jongen Telescope Nine transits of HATS-18 were observed in the 2020 season using the Yves Jongen Telescope at Deep Sky Chile. This is a PlaneWave Corrected Dall-Kirkham telescope with an aperture of 430 mm, mounted on a L500 Plane Wave Mount, and equipped with a Moravian 4G CCD camera and EFW 4L-7 filter wheel. This setup has a field of view of 21. 0 arcmin ×15. 8 arcmin at a plate scale of 0. 63 arcsec per pixel. A Chroma imaging IR-UV filter was used, which has a high transmission between 370 and 700 nm. The data reduction was performed using the MUNIPACK 4  software. This comprised standard calibrations and brightness measurement using aperture photometry. Differential-magnitude light curves were calculated versus five nearby comparison stars.
Transiting Exoplanet Sur v ey Satellite TESS  (Ricker et al. 2015 )  observed HATS-18 in sectors 10 (2019 March 26 to 2019  April 22)  and 36 (2021 March 7 to 2021 April 2). In both sectors it was selected as a short-cadence target. One further observation of HATS-18 with TESS is currently scheduled, in sector 69 (2023 March). We downloaded the available observations from the Mikulski Archive for Space Telescopes (MAST) archive  5  and converted them into magnitude units. We decided to use the pre-search data conditioning (PDCSAP) light curves  (Jenkins et al. 2016  ) rather than the simple aperture photometry (SAP) observations, as the y hav e a slightly lower scatter. We retained only those data points with a QUALITY flag of zero: 15 390 in sector 10 and 15 449 in sector 36. We further rejected all data points more than 0.
P H Y S I C A L P RO P E RT I E S O F H AT S -1 8 The only existing measurement of the physical properties of the HATS-18 system is by  Penev et al. ( 2016 ) , who had access to only one high-quality transit light curve of the system. We have therefore redetermined the physical properties of HATS-18 using our e xtensiv e photometry and the methods from the Homo g eneous Studies project  (Southworth 2012 , and references therein). The measured parameters are useful in subsequent analyses. All modelling of the light curves of HATS-18 was done using version 42 of the JKTEBOP 6  code  (Southworth 2013 , and references therein). We first fitted each transit from the Danish Telescope individually, to check the level of scatter in the light curves. The fitted parameters were the transit midpoint ( T 0 ), the fractional radii of the two components ( r A = R A a and r b = R b a , where R A is the radius of the star, R b is the radius of the planet, and a is the semimajor axis of the relative orbit) expressed as their sum and ratio, and the orbital inclination ( i ).
Ho we ver, the quadratic and cubic ephemerides are not a significantly better fit to the data than the linear ephemeris, so we are only able to set upper limits on orbital period changes. Future monitoring of the system is needed to refine these limits and push the noise down below any real astrophysical signal. Finally, we used the PERIOD04 package  (Lenz & Breger 2005 )  to check for periodic variations in the residuals of the timings versus  the linear ephemeris. No significant signals were found, with the strongest being at 0. 0545 cycle -1 with a signal-to-noise ratio of 2. 9, well below the commonly used signal-to-noise ratio threshold of 4. 0  (Breger et al. 1993 ). We therefore find no evidence in our data for a periodic variation in the times of transit for HATS-18.