dataesr/scientific-paragraphs-categorization huggingface dataset:
As a result of these calibrations the electron and photon reconstruction and identification performance at Run 2 are similar to that of Run 1, despite the increased pileup and radiation damage. The evident success of the dedicated Legacy calibration of 2017 data motivates a plan to pursue the same techniques for the 2016 and 2018 data. The ECAL timing resolution is crucial at CMS to suppress noncollision backgrounds, as well as to perform dedicated searches for delayed photons or jets predicted in several models of physics beyond the standard model. A global timing resolution of 200 ps is measured for electrons from Z decays with the full Run 2 collision data. Excellent performance in electron and photon reconstruction and identification has also been achieved in the case of lead-lead collisions at √ s NN = 5.
Figure10: Efficiency of HLT Ele32 WPTight Gsf (left) and HLT Ele23 Ele12 (right) trigger, with respect to an offline reconstructed electron, as a function of the number of reconstructed primary vertices, obtained for different η regions using the 2017 data set. Electron E T is required to be >50 GeV. The bottom panel shows the data-to-simulation ratio. The efficiency measurements combine the effects of the L1 and HLT triggers. The vertical bars on the markers represent combined statistical and systematic uncertainties. In 2017 the majority of the high-pileup data was recorded at the end of the year, the same time the pixel DC-DC convertors exhibited efficiency losses. Thus the efficiency loss versus number of vertices in the event is not solely due to the pileup. However the efficiency loss is significant only for 2.
Patient sample Exploratory cohort. Sixty children who underwent an allo-HSCT after myeloablative conditioning with BU/CY from 2001 to 2010 at CHU Saint-Justine, Montreal, Canada. This sample was used to genotype fifty-one chosen SNPs within seventeen DNA-repair genes. Extended cohort. The study was extended to n = 187 by including 122 children who had undergone allo-HSCT at five different centers (Supplementary Table  3 ). They were genotyped for those SNPs that showed a significant association within the exploratory sample after accounting for multiple testing correction (see Table  1  for the patient's characteristics). The Institutional Review Board at each center approved the study and all patients and/or parents provided informed consent. Details of inclusion criteria are available at Clinicaltrials.
gov site (NCT01257854) and the Australian New Zealand Clinical Trials registry (ACTRN12612000544875). Treatment: intravenous. BU (Busulfex ® , Otsuka Pharmaceuticals, Saint-Laurent, Montreal, QC, Canada or Busilvex ® , Pierre Fabre Laboratory, Paris, France) administration was given as a 2 h or 3 h infusion depending on whether the patients were given four times daily or once daily dose, respectively. BU first dose was either age or weight-based and pharmacokinetic (PK) guided dose adjustment was performed in order to obtain a cumulative AUC of 57. 6-86. 4 mg*h/L (Supplementary Table  1 ). Co-medication to BU, aGvHD prophylaxis and serotherapy are summarized in Table  1. All patients received non-manipulated grafts. Clinical outcomes: aGvHD was graded according to established grading criteria  [31]  and considered up to day 180 post HSCT  [32].
Seventeen genes in total were chosen for investigation (Table  2 ). We selected 17 candidate genes through a literature search from key protein-coding genes in simple demethylating repair pathways (MGMT, ALKBH1), BER pathway genes such as APEX1, LIG1, LIG4, and XRCC1 or double-strand break repair pathways mainly associated with DNA crosslinking by bifunctional alkylating agents such as BU (ATM, BRCA1, EXO1, FAN1, FANCD2, MRE11, NBN, RAD50, RAD51, RFC1). See Supplementary Material Methods for details on variant selection criteria. Statistics analysis: All statistical analyses were performed using SPSS software version 25 (IBM Corp) and R statistical software version 3. 6. 2. Association analysis was performed with individual polymorphisms that were in HWE and compared to the HapMap Caucasian population MAF data.
Univariate analysis: The SNPs were tested for association with aGVHD 2-4 in the exploratory cohort; using a X 2 test in a model (additive or dominant) that best fit the data according to genotype frequency among cases and controls. SNPs with a p value below a 0. 001 cut off were retained for further analysis according to the Bonferroni correction. Incidence of aGvHD 2-4 was estimated using cumulative incidence function within competing risk package (cmprsk) using R with death occurring before aGvHD as a competing risk and compared using Grays' test  [33]  for significant associations. Clinical characteristics tested in the univariate analysis in the extended cohort were HLA compatibility (matched related donor vs. other donors); stem-cell source (bone marrow; peripheral blood stem cells; cord blood); conditioning regimen (based on the number of alkylating agents, one versus 2 or more,); underlying disease (malignant; non-malignant); GSTA1 metabolic capacity based on diplotypes (classified as slow vs.
ACKNOWLEDGEMENTS We warmly thank the patients and their parents for consenting to participate in this study. We also thank  Mrs. L. Lesne ,  Mrs. M. Khoshbeen ,  Mr. D. Marino ,  Dr. Anuj Kumar Tyagi ,  Dr. Eva Choong ,  Ms. Pauline Mathot ,  Mr. R. Piccolo ,  Mrs. S. Mezziani ,  Mrs. M-F. Vachon , and  Mr. M. Cortier  for their help in this study as well as the  Swiss Pediatric Oncology Group. We thank  Pediatric Disease Working Party (PDWP)  of the  European Society for Blood and Marrow Transplantation (EBMT)  on behalf of which this scientific report has been realized with contribution from members  Marc Ansari ,  Christina Peters ,  Jean-Hugues Dalle , and  Selim Corbacioglu  (please see the main authors list). Others members of the  PDWP of EBMT includes Persis Amrolia ,  Adriana Balduzzi ,  Arnaud Dalassier ,  Cristina Hereda Diaz ,  Lawrence Faulkner ,  Tobias Feuchtinger ,  Franco Locatelli ,  Giovanna Lucchini ,  Josu de la Fuente ,  Jaques-Emmanuel Galimard ,  Marta Gonzalez Vincent ,  Rupert Handgretinger ,  Katharina Kleinschmidt ,  Anita Lawitschka ,  Antonio Perez Martinez ,  Vanderson Rocha ,  Annalisa Ruggeri ,  Petr Sedlacek ,  Peter Svec ,  Jacek Toporski , and  Akif Yesilipek.
Species identification and BIN assignment. Our integrative analyses combining morphology and DNA barcodes, identified a total of 157 species out of which 156 are described valid species belonging to six families (Andrenidae, Apidae, Colletidae, Halictidae, Megachilidae, Melittidae) and 28 genera (Tables 1, S4, Fig. 2 ). In addition, we found one specimen (MB00149) of an unnamed Andrena species whose BIN was new to BOLD. Seventy species (44. 6%) found in our study had not been reported before within the available regional species inventories. For instance, our barcode of Andrena avara liturata (Warncke) represent a first record for the studied area, and a new BIN in BOLD (Barcode of Life Data). Of the 157 species 156 were assigned to 172 BINs (results on 25 September 2020), sixteen (9. 30%) of them were new to BOLD.
The number of specimens sequenced per BIN ranged from 1 to 360 (for Lasioglossum morio (Fabricius)), averaging 17 specimens per BIN. Sixty-one BINs were represented by a single individual (singletons). Multiple BINS were associated with 14 species, with up to three BINS for some, including Andrena helvola (Linnaeus), Anthophora plumipes (Pallas), Lasioglossum laticeps (Schenck) and L. villosulum (Kirby) (Tables  2, S4 ). Two species pairs share the same BIN: Andrena carantonica (Pérez) and A. trimmerana (Kirby) (BOLD:AAD2472) and Halictus simplex (Blüthgen) and H. langobardicus (Blüthgen) (BOLD:AAD5869). The identification of those four species based on DNA barcode data is therefore uncertain. One species barcoded in our study (Lasioglossum mediterraneum (Blüthgen)) was new to BOLD but the sequence was too short to have a BIN assigned.
Barcode gap and haplotype diversity. The average genetic distance within species and genera in the dataset were 0. 23% and 15. 70% respectively (Table  3 ) with a maximum intraspecific distance of 9. 81% for Andrena lagopus (Table  S4 , Fig. 3a ). Intraspecific barcode divergence averaged 0. 23% whereas distance to the nearest-neighbour species averaged 9. 08%. When we considered only species with a number of records n ≥ 3, intraspecific divergence exceeded 2% in three species; Panurgus calcaratus (Scopoli) (2 BINs), Andrena bicolor (Fabricius) (2 BINs) and Andrena helvola (Linnaeus) (3 BINs) (Table  S4 , Fig. 3b ). The mean intraspecific distance (n ≥ 3) distribution ranged from 0 to 3. 78% and overlapped slightly with the distance to the nearest neighbour distribution (3. 64-19. 56%) (Fig.
Discussion DNA barcoding allows the unambiguous identification of over 96. 17% of the wild bee species found in our study. Among them species that are notoriously difficult to identify morphologically like: Bombus terrestris/ lucorum complex  51. Our barcode analysis revealed one interesting Andrena individual collected in the national reserve of Saint Mesmin, which was assigned to a BIN new to BOLD, and remains unnamed at the species level. By sequence homology, this individual belongs to the 'Andrena bicolor' group, and its nearest neighbour is Andrena allosa (Warncke). The Andrena bicolor species group has been recently revised to clarify the status of several alpine species  52  , the results suggest the existence of a substantial cryptic diversity in southern European Andrena (Euandrena).
In the present study in parallel to the new BIN attributed to this specimen (BOLD:ADZ3755), BINs BOLD:AAD0134 and BOLD:AAD0135 are also from the 'Andrena bicolor' group. Considering that two of these three BINs are represented by only one individual is very difficult to morphologically determine if these BINs represent different species or if they are representatives of subspecies of the 'Andrena bicolor' group that are not well represented so far in the BOLD database. Our specimen could indeed represent a new species or subspecies within this cryptic complex, but more specimens are needed to assess its taxonomic status. The two species pairs that shared a BIN Andrena trimmerana/A. carantonica and Halictus langobardicus/H. simplex are morphologically very similar. Indeed, females of Halictus simplex/langobardicus/compressus complex are morphologically indistinguishable  53.
70%) genetic divergence indicating the existence of a species barcode gap  65  in our dataset (Table  3 ). This low average intraspecific divergence has also been reported in Canadian wild bees  26. Here we report an 83. 07% success rate using SMRT sequencing compared to 70. 74% with Sanger sequencing using our newly designed primers. Sanger sequencing remains the gold standard in terms of quality and reliability for small projects of a few hundred samples. However, Sequel platform can greatly reduce sequencing costs and be more competitive for projects with thousands of samples  49. Our analyses revealed 14 species (9%) with multiple BINs (Table  2 ). A barcoding study on German bees found a similar level (11%) of species with multiple BINs 27. Among the 14 species that show deep mitochondrial splits, most belonged to Andrena (3 spp.
Conclusion Our DNA-based survey represents a major contribution to the barcoding of European wild bees  27, 31, 38  both at the inter and intraspecific levels. Our records were assigned to 172 BINs, 16 of which were new to BOLD. Of the 157 species reported in this study, only 67 of them had previously been barcoded from France. DNA barcoding using Sequel platform represents a helpful tool to process large numbers of bees to obtain not only species richness but also abundance data for further ecological analyses. Our study revealed fourteen species with multiple BINs without morphological differentiation suggesting the existence of cryptic diversity. We have found a relatively high species richness of bees in urban areas. Our DNA barcode reference library will help to streamline the identification of wild bees and assess the impact of anthropogenic disturbances such as urbanization.
Amplification was confirmed by agarose gel electrophoresis. PCR products were subsequently cleaned using the NucleoFast 96 PCR kit (Macherey-Nagel, Düren, Germany) and sequenced in both directions by the Sanger method using the ABI Prism BigDye Terminator v3. 1 Cycle Sequencing Kit (Thermo Fisher Scientific). Sequencing reactions were purified by ethanol precipitation, loaded on an Applied Biosystems 3500 Genetic Analyzer (Thermo Fisher Scientific). We used CodonCode (CodonCode Corporation, Centerville, MA) for primers trimming, contig assembly and sequence editing. Sequence alignment was straightforward in the absence of indels and the sequences along with corresponding trace files were uploaded to the Barcode of Life Data Systems (BOLD) (http://www. barco dingl ife. org)  81. A total of 3350 tissue samples (hind legs) were DNA barcoded using single-molecule real-time sequencing (SMRT  49  ) in the PacBio Sequel platform (Pacific Biosciences, Menlo Park, CA, USA) at the Canadian Centre for DNA Barcoding (CCDB), in the University of Guelph, Ontario, Canada).
Barcode DNA sequences were aligned in Geneious v. 8. 0. 3 (www. genei ous. com) through the MAFFT alignment tool  82  to verify the correct cox1 codon translation into proteins and check for potential presence of numts by looking for stop codons, insertions and deletions, errors and inconsistencies. We edited SEQUEL sequences with minor errors caused by the addition or deletion of a single nucleotide that initiated a reading frame shift and the introduction of stop codons. All sequences, along with the voucher data, images, and trace files, are deposited in BOLD and the sequences are deposited in GenBank (Table  S2 ). All data are available from the BOLD database, https ://doi. org/10. 5883/ DS-BEECO I. We used the Barcode Index Number system (BIN)  50  to delineate species using DNA barcode data.
BINs were assigned automatically to each record with a barcode longer than 500 bp based on the Refined Single Linkage (RESL) algorithm in BOLD 4. Sequence alignment generated by the amino acid-based (HMM) BOLD aligner was used to construct a Kimura 2 parameter 83 (K2P) Neighbour-joining tree (File S1) to provide a graphic representation of the species divergence and calculate genetic intra and interspecific distances through the BOLD analytical tools support  81. We constructed an approximately Maximum-Likelihood tree using Fast Tree2 with default settings  84  in Geneious v. 8. 0. 3 (www. genei ous. com) which was then used to represent species abundance, number of haplotypes and haplotype diversity values with the ITOL tree viewer  85. We used R ggplot2  86  to represent genetic intra and interspecific distances.
Acknowledgements This work is part of the  POLLEN  project ( 2016-00108486 ) funded by the  Region Centre Val de Loire (France). The authors are indebted to  Carl Moliard  and  Xabier Pineau  for technical assistance in the field and  Jeremy Dewaard  for providing useful information on taxon coverage of wild bee barcoding. We are thankful to students  Sarah Flamans  for DNA barcoding at URZF, Orléans;  Henri Sacoura Cissé  for curatorial work of the bee reference collection at IRBI, Tours and  Anaïs Garnier ,  Baptiste Ducros ,  Juliette Carpentier  and  Alexia Briandon  for help in bee collecting. We are very grateful to the entire team at the  Canadian Centre for DNA Barcoding (Guelph, Canada ), and in particular  Evgeny Zakharov  for his assistance with PacBio sequencing. We want to thank  Christian Cocquempot  for sharing with us its regional inventory of wild bees and  Bernard Lemesle  for his bibliographical contribution.
Data availability Dataset title: POLLEN DNA barcode reference library. Resource link: https ://doi. org/10. 5883/DS-BEECO I. Number of data sets: (1) Data set name: DS-BEECOI. Data format: xml, tsv, fasta, ab1. Description: The POLLEN library dataset could be accessed through the Workbench platform of BOLD, and all data files can be downloaded from the BOLD public portal in different formats depending on the dataset type. All records are also accessible within BOLD, using the search function of the database. An excel spreadsheet containing the library dataset information is included (Table  S5 ). Similarly, the fasta sequences of dataset barcodes are included as File S2. We compiled a checklist of the 157 species of bees found in our study (CL-BEE37 in BOLD) following the higher classification of TAXREF taxonomic repository.
The RaDiCo-ILD cohort RaDiCo-ILD is a national, multicentre, non-interventional cohort study in France. The majority of participating centres are part of the French national networks of reference and competence centres for rare respiratory diseases (OrphaLung and Rare Respiratory Diseases Healthcare Faculty [RespiFIL] networks). The full list of participating centres and investigators is included in Supplementary Table  S1. For the RaDiCo-ILD cohort, all incident and prevalent patients who met the following criteria could be included: (1) a diagnosis of IIP established on presenting history, clinical, radiological, functional and, if available, pathological findings (for full criteria see Supplementary Methods); and (2) patients affiliated to a public health insurance provider. The RaDiCo-ILD study was registered with ClinicalTrials.
IPF cohort The IPF cohort was a subgroup of patients included in the RaDiCo-ILD study. All patients in the IPF cohort who met the following criteria were included in the present study: (1) aged >18 years; (2) IPF diagnosed using the American Thoracic Society/European Respiratory Society (ATS/ERS) 2011 criteria  [1]  (until the revision of criteria in September 2018, which was subsequently used, allowing for the inclusion of patients with a diagnosis of probable IPF  [13] ); and (3) completion of a pulmonary function test (PFT) at inclusion visit. A multidisciplinary discussion was recommended to obtain a diagnosis, based on clinical signs, radiological investigation and surgical biopsy. The study data were collected and managed using Research Electronic Data Capture (REDCap) tools hosted at Inserm UMR S 933 RaDiCo.
Statistical analyses The analyses in this study were mainly descriptive and were performed with SAS ® 9. 4 software. The characteristics of patients with IPF were described. For continuous variables, the number, number of missing values, median (range) or mean (standard deviation) according to the normality of the distribution, and 95% confidence interval (CI) of the means were included. For categorical variables, the number, percentage and 95% CI of the proportion were included. Data including demographic characteristics, significant comorbidities, pulmonary function testing, chest imaging, health-related quality of life (HRQoL) and IPF treatment were collected at inclusion visit and described by gender. Comorbidities at inclusion were recorded by investigators as present or absent. HRCT scans were obtained and analysed in each reference centre by each investigator independently, according to ATS/ERS recommendations.
9, 24. 7) and 1. 0% (95% CI: 0. 0, 2. 9), respectively. The mean composite physiologic index (CPI) at inclusion for all patients was 47. 0, and this was higher for male patients than female patients (47. 6 [95% CI: 46. 4, 48. 8] and 43. 8 [95% CI: 41. 4, 46. 1], respectively). The estimated extent of emphysema predicted using the combined pulmonary fibrosis and emphysema (CPFE) index  [16]  was 5. 0%, and was higher in female patients than male patients (7. 1% [95% CI: 5. 6, 8. 5] and 4. 5% [95% CI: 4. 0, 5. 1], respectively). Further lung function data recorded at inclusion in RaDiCo-ILD are presented in Supplementary Results. The prominent markers of pulmonary functional impairment at inclusion to the cohort were significantly less severe for women than for men. At cohort inclusion, the mean SF-36 physical and mental scores for the whole population were 52.
Discussion We conducted an analysis of patients with IPF included in the multicentre RaDiCo-ILD registry in France over a 3-year period. In the present manuscript, we report a comprehensive summary of data recorded at inclusion from patients with IPF according to gender, in terms of demographics, clinical and radiological characteristics, HRQoL and treatment initiation at the time of study inclusion. The present study enrolled 724 patients with IPF, of whom 83% were male, representing a higher proportion than those seen across other IPF registries  [3, 8, 17, 10]. Patient gender bias at the time of IPF diagnosis is a topic of increasing interest, with a recent study by  Assayag et al. demonstrating that male patients are more likely to receive a diagnosis of IPF compared with females, after adjusting for age, smoking history, environmental exposures and autoantibodies.
This suggests that females may be under-diagnosed and males may be over-diagnosed with IPF  [18]. An indirect, observational study that used data from the French hospital discharge database presented a very different picture of the IPF diagnosis disparity between genders in France, with a male population of 56. 4% (n=3,650/6,467)  [19]. Other large, national, epidemiological studies based on hospital databases in countries such as Finland, Italy and Denmark also demonstrated lower percentages of male patients than the RaDiCo-ILD cohort  [20] [21] [22] [23]. Despite study limitations with regards to the use of International Classification of Diseases codes to identify populations with IPF  [19] , which may present a risk of disease misclassification, the differences in gender distribution suggest that female patients may be under-diagnosed in the RaDiCo-ILD cohort.
Glucocorticoids were prescribed to 13% of patients at diagnosis, which may represent the population with the most advanced disease, requiring palliation of symptoms. As with any observational study, several potential biases are possible. Data bias was limited by the French organisation of reference and competence centres, which agreed to diagnose IPF in accordance with international and national guidelines defining a common diagnosis algorithm. Our study does not include data on the proportion of patients who had lung biopsies at diagnosis or were diagnosed with definite or probable IPF due to challenges collecting such data in a real-life cohort and the change in ATS/ERS IPF diagnosis criteria during the course of patient inclusion. HRCT scans were obtained and analysed in each reference centre and were not systematically reviewed by a panel of radiologists; hence, it is possible that there are inconsistencies across centres.
Acknowledgements Medical writing assistance was supported financially by  RaDiCo and Boehringer Ingelheim  and provided by  Hannah Cook, PhD , of  MediTech Media , under the authors' conceptual direction and based on feedback from the authors. Boehringer Ingelheim is an industrial supporter of the RaDiCo-ILD cohort. A full list of investigators is included in the BC reports grants from  Astra Zeneca  and BI; personal fees from  Astra Zeneca ,  BI ,  Roche ,  Sanofi, Genzyme  and BMS; and non-financial support from  Astra Zeneca ,  BI ,  Roche ,  Sanofi, Genzyme  and  BMS , outside the submitted work. PB reports personal fees from  Roche, BI ,  Novartis ,  Teva  and  AstraZeneca. He has also received congress travel fees and/or speaker honoraria from  Roche, BI ,  Novartis ,  Chiesi ,  Stallergene  and  Sanofi , outside the submitted work.
Funding sources The RaDiCo-ILD cohort was implemented as part of the RaDiCo research programme, funded by the  French National Research Agency  under the  'cohorts' program of the Investissements d'Avenir (Investments for the Future)  ( ANR-10-COHO-0003 ) and coordinated by the  French national institute for Health and Medical Research  ( Inserm Unité UMR S933, Hôpital Trousseau ).