dataesr/scientific-paragraphs-categorization huggingface dataset:
The μ-PIXE spectra obtained at INFN LABEC were quantitatively analysed by means of GUPIXWIN (version 2. 2. 3) (Campbell 2010) using a set of reference standards: a sodalime container from NIST and thick pure elements from Goodfellow Cambridge Ltd. Instead, at AGLAE, the elemental quantification was subsequently obtained using the TRAUPIXE program  (Pichon 2015b ) with the pivot procedure normalisation between major and trace concentrations. This program is based upon the same GUPIXWIN version with processing parameters adjusted using the Dr-N (Diorite) geostandard.
On the contrary, finding altered pyrite crystals is a feature of all the Siberian rocks, observed even in fresh cut samples, and it is related to hydrothermal processes during the petrogenesis  (Re 2013; Angelici 2015). Also, the second strong marker excluding the Siberian provenance confirms the initial attribution. Actually, the strontium content in diopside crystals of all Siberian rocks in the database were always higher than 160 ± 40 ppm, with a maximum of 870 ± 30 ppm and a median of the distribution at about ppm  (Re 2015) , while the maximum strontium content measured in diopside crystals was 90 ± 40 and 140 ± 20 ppm in Afghan and Tajik rocks respectively. Diopside crystals in Egyptian objects suitable for trace element analysis were identified by means of ionoluminescence maps and on the basis of stoichiometry in order to avoid spurious signal from other phases, as we limited the analyses only to the crystals for which the stoichiometry was coincident within experimental errors to what was expected for this mineral phase.
In particular, 18 points of interest were selected on 8 out of 11 Egyptian objects; the measured strontium and other trace element concentrations useful for provenances study are reported in Table  2. When possible, for every object, more than one diopside crystal was analysed to take into account the variability in trace elements within the same sample. In Fig. 7  are also shown the box charts of the same values of Table  2  in comparison with rocks from our database  (Re 2015). The box charts represent the dispersion of the experimental points: each point is an individual μ-PIXE measurement, the boxes include 50% of analysed points (from 25 to 75%) and are separated in two parts by the median line, while the bars join the maximum and the minimum detected values. In this representation (called box and whisker plot), error bars are not reported to make the graphics more readable.
The square symbols in correspondence to the 0 value represent the numbers of measurements below the limit of detection (LOD). As shown in Table  2  and Figs   Although 21 samples are a sufficient starting point to attribute raw materials to a provenance, in the future, the analysis of further rocks could broad the boundary values found so far because of the natural heterogeneity of the sites. Moreover, it should be noted that all the samples used for our database were collected in the last century and although the proposed markers are characteristic for all the rocks of a district, small differences for quarries in the same area were observed. These differences are not discussed here but could be useful in future studies to distinguish among extraction sites in the same district and perhaps to identify the location of ancient quarries.
About the other trace elements interesting for provenance study in diopside crystals  (Re 2015) , it must be observed that almost all the 90 values in Table  2  are in the range expected for Afghan and Tajik rocks and only 2 data related to manganese are outside (which means about 2. 2% of the total). Moreover, it is interesting to observe that although the head of the Hathor Goddess (cat. 64) and the Bes God amulet (cat. 10316) are compatible with an Afghan or Tajik provenance, they seem to be slightly different from other objects due to the very low contents of all trace elements in diopside crystals. As in the case of strontium, this could be explained with a difference in the extraction site inside the same district. As already stated, the lapis lazuli used for these artefacts appears different in terms of colour from those used for the other artefacts; in particular, the Bes God amulet (cat.
Conclusions In this work, a protocol for determining the provenance of raw material used to carve lapis lazuli artefacts is described. Markers were obtained analysing 45 rocks of known provenance from 4 quarry districts: Badakhshan in Afghanistan, Liadjura-Dara in Tajikistan, Lake Baikal area in Siberia and Coquimbo region in Chile. To the best of our knowledge, for every provenance, the number of studied rocks is equal or higher than in any previous provenance study on lapis lazuli. The created database constitutes a sufficient starting point to attribute raw materials to a provenance, although in the future, its representativeness must be further augmented to increase the marker reliability or to revise them. Moreover, the database must be extended to rocks from other quarry districts. An important point is that all the markers are recognisable by means of Ion Beam Analysis.
7, 5 out of the 8 analysed Egyptian objects show a Sr content in diopside in the same range of Afghan and Tajikistan rocks, all other objects being also compatible within 2σ. Such results seem to exclude a Siberian provenance of the Egyptian artefacts, although it should be observed that the data distribution is slightly different from that expected for Afghan and Tajik samples. In particular, there are 4 analysed diopside crystals (i. e. 20% of analysed points) that have Sr contents between 160 and 200 ppm, slightly higher than those observed for these two provenances. Discrepancies could be due to the limited number of Afghan reference rocks in our database.
Acknowledgements Financial support by the Transnational Access to Research Infrastructures activity in the  Seventh Framework Program  of the  EU  ( CHARISMA Grant  Agreement n. 228330) is gratefully acknowledged. The authors warmly thank all the people participating and contributing to this provenance study during the last years. The authors wish to warmly thank CHNet, the  INFN  network of laboratories working in the  Cultural Heritage  field, for supporting this research, all in terms of instrumentation, competencies and grants. Moreover, the  INFN experiment CHNet -imaging is acknowledged with gratitude.
(Continued from previous page) Results: Inclusion of participants started in February 2007 and ended in December 2013. A total of 1721 index cases, 826 affected sisters, 599 unaffected sisters and 1419 controls were included. 98 % of participants completed the epidemiological questionnaire, 97 % provided a blood sample, and 76 % were able to provide mammograms. Index cases were on average 59 years old at inclusion, were born in 1950, and were 49. 7 years of age at breast cancer diagnosis. The mean age at diagnosis of affected sisters was slightly higher (51. 4 years). The representativeness of the control group was verified. Conclusions: The size of the study, the availability of biological specimens and the clinical data collection together with the detailed and complete epidemiological questionnaire make this a unique national resource for investigation of the missing heritability of breast cancer, by taking into account environmental and life style factors and stratifying data on endophenotypes to decrease genetic heterogeneity.
The CC organized the collection of blood samples from the index case and other participants by sending them a prescription for blood sampling, a letter for the medical analysis laboratory or the nurse who took the blood sample, and appropriate prepaid packaging for dispatch of the samples directly to the biological resource center at the Centre Léon Bérard (Lyon, France). The study was examined by the appropriate committees: ethics (CCP Ile-de-France III, 3 October 2006, agreement no. 2373) and by the data protection agency (CNIL, 22 May 2006, agreement no. 1170775), all of which approved the study.
Data collected All patients (index cases and affected sisters) and controls completed a questionnaire on environmental, lifestyle and reproductive factors and family history of cancer. This self-report questionnaire contained detailed questions concerning demographic data, alcohol and tobacco consumption, pregnancies, breastfeeding, contraception, hormone replacement, physical activity, personal medical history and exposure to irradiation at work and for medical purposes and pedigree, with detailed information on medical history for each first-and second-degree relative. Mammograms taken at the time of diagnosis or one to three years before diagnosis for the cases and most recent mammography for the controls and unaffected sisters at inclusion were collected. Craniocaudal and medio-lateral oblique views of both breasts were digitized.
A VIDAR DiagnosticPro Advantage scanner, with a resolution of 570 dpi, was used to record the information required for quantitative calculations of mammary density. The images obtained were recorded and the identity of the participant was erased from images with Adobe® Photoshop® software. The incidence and date of the mammograms were recorded on the images. Blood samples were collected from index cases, affected and unaffected sisters and controls. Viable lymphocytes from index cases were frozen if this had not already been done by the laboratory having carried out BRCA1/2 analyses. Part of each blood sample was frozen, while the rest was processed in order to obtain plasma, serum, and lymphocyte pellets, all of which were then frozen. DNA was subsequently extracted using the AutopureLS Instrument (Qiagen).
Study power These data will be used to study the missing heritability of BC by taking into account environmental factors. The power of the study depends on the study design and strategy employed for detecting BC susceptibility alleles. For instance, SNP genotyping, mutation screening of candidate genes or whole exome sequencing may be undertaken in all subjects or specific subset of participants, since stratifying data on endophenotypes may help decreasing genetic heterogeneity. Interaction effects according to the genes under study may also be investigated. A "simple" power calculation showed that a genetic association with an amplitude of 3 (relative risk associated with a susceptibility genotype) sought by a candidate gene approach in a case-control study design can be identified with a power of 80 % (alpha = 0.
Results Inclusion of participants started in February 2007 and ended in December 2013. Description of the GENESIS population is based on data available on 17 November 2014. Thus, the population may increase slightly when residual signed inform consents are received by the CC. Figure  1  shows the cumulative number of index cases over the time-course of inclusion, both for retrospective and prospective inclusions. 2543 patients qualified according to the study criteria were listed and invited to participate by 26 centers. 1669 women sent back a reply coupon to the CC for complete information about the study and 1315 agreed to participate (i. e. 52 % of patients invited). 539 additional cases, invited by 16 centers without being listed beforehand and meeting the inclusion criteria returned a reply coupon and 406 of them agreed to participate and were therefore included.
Therefore, we analyzed the pedigree of the 1411 unrelated controls by comparing the cancer incidences in these pedigrees (first degree of relationship) to the national incidences using SAS 9. 3 software (SAS Institute, Cary, NC) and the estimated national cancer incidences from 1975 to 2005  [22]. We observed a slight increased incidence of cancer within control families for all sites (Standardized Incidence Ratio (SIR): 1. 11 95%CI: 1. 02-1. 22), for breast cancer (SIR: 1. 21 95%CI: 1. 04-1. 39) and for ovarian cancer (SIR: 1. 16 95%CI: 0. 73-1. 76) and this should be taken into account in the further analyses.
Discussion The GENESIS study is a unique national resource to study the missing heritability of BC. This is a large study including over 6000 participants, and the biological, clinical and epidemiological data collected are detailed and complete. The rate of agreement to participate was moderate for each participant category, around 50 %. However, the constraint of asking the index cases to contact the other participants impaired assessment of the true agreement rates as for these people we relied on a list completed by the index cases. Indeed, people not listed beforehand were included (more than 11 % of the inclusions). Even though we have full confidence in the representativeness of the population of the included index cases and controls, it may be more effective in future studies to contact relatives and other participants directly.
Acknowledgments Financial support for GENESIS was provided by the  Ligue Nationale contre le Cancer  (3 grants:  PRE05/DSL ,  PRE07/DSL, PRE11/NA ), the  French National Institute of Cancer (INCa)  and the comprehensive cancer center SiRIC, ( Site de Recherche Intégrée sur le Cancer: Grant INCa-DGOS-4654 ). We wish to thank the genetic epidemiology platform (the  PIGE, Plateforme d'Investigation en Génétique et Epidémiologie :  S. Eon-Marchais ,  M. Marcou ,  D. Le Gal ,  L. Toulemonde ,  J. Beauvallet ,  N. Mebirouk ,  E. Cavaciuti ,  A. Fescia ), the biological resource center ( C. Verny-Pierre ,  L. Barjhoux ,  V. Sornin ) and all the  GENESIS collaborating cancer clinics (Clinique Sainte Catherine, Avignon :.
g. , ref. 27) and lower than the ratios found for pure aragonite (49 < Y/Ho < 217). Although the provenance of terrigenous sediment cannot be deduced from the LA-ICP-MS data alone, it likely derived from the Makran hinterland. During winter (NE) monsoons, enhanced river runoff transports loads of suspended sediment onto the shelf. Subsequently, terrigenous fines are transported farther down-slope by agitation and redeposition  12, 19. Remarkably, winter monsoon irrigation in the Makran hinterland increased within the past 1,000 years  28  , possibly impacting build-up growth within the OMZ. The baffling and binding effect of microbial mats covering the build-up is also apparent from biogenic fines on laminae surfaces. The most abundant constituents were coccoliths of surface-water dwelling calcareous nannoplankton species, including Gephyrocapsa oceanica, Emiliania huxleyi, Calcidiscus leptoporus, Umbilicosphaera sibogae (Supplementary Fig.
Data were calibrated against the NIST610 glass standard with contents reported by  31. Element contents were quantified with the Cetac GeoPro software, using 43 Ca as internal standard and assuming 40. 00 wt. -% Ca content of the analysed aragonite cement. Because of the high Sr content of the sample, the interference of 86 Sr 2+ on 43 Ca + + 43 Ca + was corrected using a factor derived from one measurement of a Sr-rich carbonate standard (MACS-3; data not shown; see ref. 32). Data quality was assessed by analysing USGS reference materials BCR2G and BHVO2G (basaltic glasses) along with the samples; the data are summarized in Supplementary Table  S3. Analytical procedures for U-Th measurements and isochron dating. Fragments of individual layers were sampled with a stainless steel tweezer and pulverized using agate mortar and pestle.
34 were used for calculations. Individual sample 230 Th/U ages were obtained with the 230Th/U Isoplot spreadsheet function (Table  1 ). Because the error of the isochron age using all activity ratios are unrealistically small, an error margin of ± 25% was applied which corresponds to the external U-Th isotopic measurement reproducibility obtained from repeated analyses of an in-house seep-carbonate standard (see refs 2, 35). Quantitative porosity measurements. Before cutting the build-up it was scanned using the medical X-ray computer tomography (CT) facility at the hospital Klinikum Bremen Mitte (Bremen, Germany). The X-ray source voltage was 120 kV at a current of 600 mA. Scan resolution was 1 mm in x-y-z directions. The CT data were processed with the Amira software (VGS, Burlington, U.
S. A. ). Two materials, i. e. pore space and carbonate, were defined by using the Amira semiautomatic grey-scale segmentation editor. Porosity was quantified for each CT-scan by calculating the percentile area of pore space per tomographic slice. High-resolution CT scan and gas flow simulation. A representative subsample was cut from the epoxy-resin embedded working half for high-resolution X-ray computer tomography (HRXCT) scanning with the CT-Alpha scanner (ProCon X-ray, Garbsen, Germany) at the Institute of Geosciences, Johannes-Gutenberg-University Mainz, Germany. The device is equipped with a micro focus X-ray tube featuring a diamond coated target and a 2048*2048 pixels detector. A three dimensional tomogram was assembled from multiple 2D projections with the Amira software. Based on the 3D tomograms the gas flow through a representative segment from the upper central part of the build-up towards the top was simulated using the GeoDict software.
Acknowledgements This study was funded through the  DFG-Research Center/Cluster of Excellence  "The Ocean in the Earth System" and by an  IFREMER  post doc grant (T. H. ). Analytical support by  Emmanuel Ponzevera  and  Yoan Germain  at the  Pôle Spectrométrie Océan  ( IFREMER, France ) is appreciated. Professional support at sea by the master and the crew of  R/V METEOR  and the team of the ROV 'MARUM-QUEST 4000 m' during expedition  M74/3  is acknowledged. Many thanks to  Sebastian Flotow  ( ZMT, Bremen ), and to  Vera Bender ,  Mariem Saavedra-Pellitero ,  Monika Segl ,  Petra Witte ,  Andreas Klügel ,  Patrick Monien , and  Christoph Vogt  (all  MARUM and Department of Geosciences University of Bremen ).
Image analysis of FDG-PET acquisitions Assessment of PET data was carried out by 2 nuclear medicine specialists (KB and FH), who were blinded to clinical and pathological findings. The diagnosis of GCA was based on the presence of high FDG uptake in the vascular wall of aortic segments, supra-aortic branches, and iliac-femoral territories with visual analysis of PET images. In addition, the intensity of FDG uptake was quantified in vascular regions with high FDG uptake using target to background ratio, the ratio between maximal standard uptake values (SUVmax) in the vascular wall, and SUVmean of blood. Unequivocal masked evaluation could be guaranteed because of the study design and controls' group selection.
Statistical analysis Data were compared between groups using x 2 test (or Fisher) for categorical variables and Wilcoxon rank-sum test for continuous variables. Statistical significance was defined as P < 0. 05. The diagnosis of GCA by CTA and PET was compared with the final diagnosis according to clinical judgment, TAB findings, and ACR criteria. Sensitivity and specificity as well as PPV and NPV were assessed. Statistical analysis was performed with GraphPad Prism 5. 01 software.
e. , IDP), as published in 2013, 1 on a standard, publicly available, dataset with a trusted reference standard. The purpose of the present study is to determine the sensitivity, specificity, and area under the operator receiving characteristics curve (AUC) of the device to referable DR (rDR), defined as moderate or severe nonproliferative DR (NPDR), proliferative DR (PDR), and/or macular edema (ME), and compare these with those published for the IDP at a similarly high sensitivity set point. IDx-DR X2. 1 also added a vision-threatening DR (vtDR) output, and so we also report performance of that to detect vision threatening DR, defined as severe NPDR, PDR, and/or ME. We used the same publicly available set of fundus images and the same previously reported consensus reference standard set by three US Board certified retinal specialists for comparison.
Subjects, Retinal Image Dataset, Reference Standard For the present study, we used the exact same dataset as in our 2013 publication. 1  In summary, the Messidor-2 dataset  25  consists of the digital retinal color images, one fovea-centered image per eye, of 874 subjects with diabetes, 1748 images. 1  Messidor-2 differs from the original Messidor dataset of 1200 images in that we ensured it has two images for each subject, one for each eye. As reported previously, subjects were pharmacologically dilated at two centers, and were not dilated at the third center, and then imaged using a color video 3CCD camera on a Topcon TRC NW6 non-mydriatic fundus camera (Topcon B. V. , Capelle A/D IJssel, The Netherlands) with a 458 field of view, centered on the fovea, at 1440*960, 2240*1488, or 2304*1536 pixels.
85 (95% confidence interval [CI]: 0. 81-0. 90), 1vs3 was 0. 82 (95% CI: 0. 78-0. 87), and 2vs3 was 0. 79 (95% CI: 0. 75-0. 84), average j was 0. 822. 1  Because IDx-DR X2. 1 requires two images per eye, and Messidor-2 only provides one fovea centered image per eye, all images were duplicated. The Messidor-2 dataset is in the public domain. The corresponding rDR reference standard is available for researchers in the public domain at http://www. medicine. uiowa. edu/ eye/abramoff.
IDx-DR X2. 1 IDx-DR X2. 1 ('the device') is an automated system for the detection of DR. It consists of two components, client software running at the point of care, which is not part of this study, and analysis software that is running on a server maintained and controlled by IDx, and which is evaluated in this study. In standard operation, the camera operator acquires four images, one optic disc and one macula centered for each eye, and submits them to IDx-DR. The analysis software provides four types of outputs: Negative: implying no or only mild DR present rDR: implying rDR is present vtDR: implying vtDR is present Low exam quality: implying either protocol errors or low quality of the individual images The device applies a set of CNN-based detectors to each of the images in the exam. These detectors are trained and optimized to detect normal anatomy, such as optic disc and fovea, as well as the lesions characteristic for DR, such as hemorrhages, exudates, and neovascularization.
Feature vectors formed from these likelihoods are fed into two fusion algorithms. The result of the first, the rDR index, represents the likelihood that a patient has rDR. The result of the second, the vtDR index, represents the likelihood that a patient has vtDR. The exam quality data is used to determine if the exam quality was sufficient for the system to make a diagnostic decision. These fusion classifiers were implemented as random forests, and trained on 25,000 complete exams of four images per subject annotated for their ICDR level by multiple experts. Obviously, none of the experts annotating the training images were involved in setting the previously reported reference standard for Messidor-2. Once available, the vtDR index is thresholded first. If the index is above or equal to the threshold, a positive output for vtDR is returned.
Modifications to IDx-DR to Create the IDx-DR X2. 1 Device As explained in the introduction, the IDP used only classical detector algorithms, and CNNs have been added as lesion/ anatomy detectors to the IDx-DR implementation studied here. In addition, the device had to be modified to support a retrospective dataset of only fovea centered images. Therefore, the device, as tested here, only allows access to the analysis software, the client software having been turned off. Because the image quality verifies that one disc-and one fovea-centered image are present for both a left and a right eye, and Messidor-2 does not contain the required disc centered images, the image quality algorithm had to be turned off. No other changes were made, nor was any component or CNN retrained for this IDx-DR version or this study.