dataesr/scientific-paragraphs-categorization huggingface dataset:
Model validation Data extracted from the experiments are used as inputs or comparative outputs for numerical model validation. The pulse temporal profile ( ( )) and the laser wavelength ( ) are entered in the cell stacking of ESTHER as a solicitation on the external cell. Both internal and external cells are free to move. The velocity of the internal cell is recorded as nominal numerical FSV. Different simulations are run with ( ) -and ( ) + as input data, in order to generate numerical FSV curves representative of the energy source term uncertainty. For each shot, numerical and experimental FSV curves are then plotted together and compared. The shock generated by laser-matter interaction propagates through the target thickness and generates a fast increase of the FSV, followed by a slower decrease which characterizes the release wave coming out onto the target free surface.
An other numerical FSV curve has been generated with a 2D-axis-symmetrical simulation led with the same material models and the ablation pressure profile generated with ESTHER, introduced as source term. Despite some small discrepancies induced by focal spot edges-effects (i. e. for 350 < < 400 ), numerical FSV curves are very similar. Larger difference is observed for > 1000 , when 2D effects become dominants. ESTHER code with the associated numerical models is then validated for shock propagation modeling in the assembly presented here.
Our data suggest that iron acquisition systems differ between the NmY and NmW isolates in this sudy (Table  2 ). This may be linked to the different virulence observed in our mouse model, because the ability to use one of the systems of iron acquisition (the human transferrin) is scored. Interestingly, the haemoglobin receptor protein (HmbR) which has been reported to be linked with enhanced meningococcal virulence  [25] , was missing in NmY isolates but present in NmW. This gene was also missing in 98% of all NmY isolates in PubMLST. Fig. 4  Staining of immune cells in peritoneal wash from one representative N. meningitidis serogroup W (isolate PubMLST ID 57576) infected mouse, 3 h post-infection compared to a non-infected mouse. The defined immune cells are gated on the forward (FSC) and scattered (SSC) axis and are seen in red.
Differences in genes involved in apoptosis, inflammatory response, LOS, and iron acquisition Previously published WGS data  [33]  available on the PubMLST Neisseria database (www. pubMLST. org/neisseria) was used to investigate isolates genetically with N. meningitidis cgMLST v1. 0  [34]. Neighbour-net networks generated from the genomic comparisons were visualized using SplitsTree4 V4 (www. splitstree. org) [35]  (Additional Files 1 and 2). WGS data were also analysed and compared for specific genes known to be involved in inflammatory response and induction of apoptosis using a "gene-by-gene" approach available through the PubMLST Genome Comparator tool of the BIGSdb. The investigated genes were porB (NEIS2020), ponA (NEIS0414), penA (NEIS1753), iga (NEIS0651), genes involved in iron acquisition (NEIS1468, NEIS1469, NEIS1693, NEIS1691, NEIS1946, and NEIS1947), and the genes encoding LOS (NEIS0304, NEIS0657, NEIS1456, NEIS1618, NEIS1619, NEIS1812, NEIS1814, NEIS1900, NEIS1901, NEIS1986, NEIS2012, and NEIS2134).
The activities of the EUROfusion consortiums on the development of high quality nuclear data for fusion applications are presented. The activities, implemented in the Power Plant Physics and Technology (PPPT) programme of EUROfusion, include nuclear data evaluations for neutron and deuteron induced reactions and the production of related data libraries which satisfy the needs for nuclear analyses of the DEMO fusion power plant and the IFMIF-DONES neutron source. The activities are closely linked to the JEFF initiative of the NEA Data Bank. The evaluation work is complemented by extensive benchmark, sensitivity and uncertainty analyses to check the performance of the evaluated cross-section data and libraries against integral experiments.
Starting in 2017, the European activities on the development of nuclear data for fusion were integrated into the PPPT programme focusing on the needs of the PPPT neutronics supporting the development of the DEMO fusion power plant and the IFMIF-DONES neutron source. Transversal actions on Nuclear Data Evaluations (NDE) were implemented in the PPPT projects PMI (Plant Management and Integration), BB (Breeding Blanket), SAE (Safety and Environment), ENS (Early Neutron Source) and MAT (Materials). The NDE tasks include general purpose neutron cross section data evaluations (ENDF) up to 200 MeV incident neutron energy including co-variance data, special purpose nuclear data evaluations and libraries (neutron activation, displacement damage, gas production, deuteron cross-sections), specific method and tools developments, testing and benchmarking of the data by means of V&V (verification and validation) and S/U (sensitivity and uncertainty) analyses.
The tasks are conducted by Research Units (RU) of the European Union and Switzerland providing the expertise required for the different areas: CCFE (Culham, UK), IFIN-HH (Bucharest, Romania), JSI (Ljubljana, Slovenia), KIT (Karlsruhe, Germany), PSI (Würenlingen, Switzerland), TUW (Vienna, Austria), UNED (Madrid, Spain), and UU (University of Uppsala, Sweden). The data evaluations provided with these activities are fed into the JEFF (Joint Evaluated Fission and Fusion) nuclear data libraries, maintained and disseminated by the NEA Data Bank of the OECD, Paris  [3]. JEFF addresses the needs of the European nuclear fusion and fission communities and serves, among others, as reference data library for PPPT nuclear analyses.
Nuclear Data Evaluations -tasks and achievements The 2017/18 PPPT work programme included activities on the evaluation of general purpose neutron cross-section data for the 180,182,183,184,186 W, 56 Fe and 16 O. The W evaluations aimed at providing full ENDF data files with covariance data up to 200 MeV neutron energy for the later use in application calculations. The activities on 56 Fe and 16 O included the elaboration of advanced evaluation methodologies and nuclear models with the production of trial evaluations that can be used for testing purposes. 3. 1 180,182,183,184,186 W neutron cross-section data evaluations for general purpose applications These evaluations were performed by KIT applying a Bayesian approach taking into account experimental and nuclear model uncertainties  [4]. The evaluation procedure consists of the following steps: (i) the calculation of crosssections, angular distributions for elastic scattering, energy distributions of emitted particles, and the calculation of covariance matrices for cross-sections, (ii) the processing of the data into an ENDF data file, (iii) the selection and analysis of experimental data for the subsequent combination with the results of calculations, (iv) the evaluation using experimental data, results of model calculations, and covariance information, (v) recording of the final data in ENDF-6 format, and (vi) checking of the ENDF data file.
The nuclear model calculations were performed with a modified version of the TALYS code  [5]  which employs an improved description of the pre-equilibrium emission of particles and clusters  [6]. It is based on a modified version of Blann's geometry depend hybrid (GDH) model  [7]  and results in a better reproduction of the particle emission spectra  [8]. The model parameters were properly estimated using measured data for individual tungsten isotopes. Processing of the TALYS output data and preparation of the preliminary data in ENDF-6 format was performed with the TEFAL-1. 9 code  [9]. Resonance parameters were added at this stage from the JEFF-3. 3 data library. Covariance matrices were produced on the basis of the Unified Monte Carlo (UMC) approach proposed by D. Smith  [10]. The calculation includes the following steps: (i) choice of the best set of parameters for the selected nuclear models, (ii) assessment of uncertainties of model parameters, (iii) Monte Carlo sampling of input data sets, (iv) the execution of calculations for the input data files obtained in the previous step, and (v) the calculation of covariance matrices.
The evaluation of cross-sections using experimental data, results of model calculations, and covariance information was performed using the generalized least-squares (GLS) method  [11]  as implemented in KIT's BEKED code package  [12]. Fig. 1  shows, as an example, the neutron emission cross-section for natural W at 14 MeV incident neutron energy compared to available experimental data and evaluations from other data libraries. A comprehensive comparison is provided in Refs. [13]  and  [14]. The W evaluations are currently under intensive benchmarking and are thus subject to further modifications before the final data files are produced.
Hence a smooth transition between the two models is achieved enabling the generation of a complete evaluation of neutroninduced reaction data for 16 O up to 200 MeV. The 2017/18 works involved the following steps: (i) development of a module in TUW's GECCCOS code system to optimise the statistical model calculations with TALYS; (ii) retrieval of experimental neutron-induced reaction data of 16 O at incident neutron energies higher than 6 MeV; (iii) statistical model calculations to find an optimized model which describes the available experimental data between 11 MeV and 200 MeV; (iv) implementation of a more efficient fitting algorithm for the optimization of the R-matrix presentation; (v) optimization of the parameters of the R-matrix representation using the available experimental neutron-induced reaction data up to 13 MeV; (vi) combining the results of (iii) and (v) to generate the prior of the envisaged Bayesian evaluation procedure; (vii) development of a concept for a unified Bayesian evaluation procedure over the whole energy range (i.
This includes an extension of the Total Monte Carlo (TMC)  [17]  approach with the Bayesian MC (BMC) method to find the best final evaluation, and the use of Gaussian processes to take into account model defects  [18]. With the extended TMC approach not only model parameters are randomized but also nuclear models as implemented e. g. in the TALYS  [5]  and the EMPIRE  [19]  codes. In this work, 18,000 random files were produced for Fe-56 which then were subjected to a Bayesian selection process using the BMC/BFMC (Backward-Forward MC) method  [20]. Fig. 3  shows the example of the 56 Fe(n,2n) cross-section with prior and posterior, and the considered experimental data. Prior and posterior cross-section for the 56 Fe(n,2n)reaction evaluated on the basis of the BFMC method Such a procedure can be utilized for the evaluation of all neutron cross-section data resulting in an ENDF data file with co-variance data.
The results obtained with this procedure for the 56 Fe reaction cross-sections in the fast neutron energy domain up to 30 MeV were processed with the TEFAL code to produce the final ENDF data file including covariance matrices. Fig. 4  shows examples of produced 56 Fe neutron reaction cross-sections with uncertainties. Work is progressing to interface UU's model defect ansatz with PSI's extended TMC approach for the production of a full data evaluation with all uncertainty information and the final integration into a general purpose nuclear data library like JEFF. This is to be demonstrated for n+ 56 Fe neutron cross-section data up to 200 MeV.
The strategy in the PPPT programme is to adopt the TENDL data library  [25]  as source data library for activation cross-sections. Significant efforts were thus undertaken to ensure that TENDL can actually preserve or increase the quality of EAF-2010 by including the variety of validated cross-sections and improving deficient data. To this end, a dedicated effort is conducted in the PPPT programme to improve in TENDL reaction cross-sections of high importance for fusion activity inventory calculations. A set of 91 cross-sections, identified previously as deficient in the TENDL-2015 library  [26]  was thereby improved for the latest issue TENDL-2017  [27]. Fig. 6  shows the example of the 65 Cu(n,γ) 66 Cu activation crosssection which includes improved data in the resonance and the high energy range.
A dedicated activation data file was produced from TENDL-2017 by extracting and processing the activation cross-sections ("excitation functions") into the traditional EAF data format. This library was adopted as JEFF-3. 3 activation data library  [28]  and, with some changes applied for light mass nuclides and actinides, was then processed into a 211 group data library which can be used by any activation code compatible with the EAF data format. Comprehensive verification and validation (V&V) analyses were performed on both the activation data library in (groupwise) EAF format and the underlying TENDL-2017 data library. CCFE's validation data base was applied to this end including a wide range of differential and integral measurements, resonance integrals, thermal cross-sections, astrophysical data, and decay heat data  [29] ,  [30].
The V&V analyses were further complemented with statistical checks. Fig. 7  shows the C/E distribution of the integral checks performed on TENDL-2017 (ENDF format, 709 energy groups). It is concluded that TENDL-2017 provides superior agreement with experimental data and is thus recommended as basis for the activation data library in fusion applications. In repeating the benchmark exercise on the derived TENDL-2017 activation data library in EAF format (211 groups) an overall good agreement was obtained. A few inconsistencies were though detected which are being currently fixed. With another V&V analyses cycle successfully completed, the TENDL-2017 activation data library in EAF data format and 211 energy groups will be then ready to serve as (mandatory) reference library in the PPPT programme.
Deuteron induced cross-section data High quality cross-section data of deuteron induced reactions are required for design analyses of the IFMIF-DONES facility, developed as a neutron source for material irradiations within the ENS project of PPPT. The analyses include deuteron transport simulations, performed primarily with the MCUNED Monte Carlo code  [36]  and activation calculations for accelerator components subjected to deuteron beam losses and secondary neutron radiation resulting from deuteron-induced reactions. The TENDL deuteron data library is the current reference used in the ENS project. The quality of the TENDL deuteron cross-sections, however, is in general poor since they are largely based on automated calculations with the TALYS code which employs reaction models that are not wellsuited for these reactions.
This applies in particular to deuteron reactions on low mass nuclei. A dedicated effort has been therefore allocated in the PPPT programme to improve the deuteron crosssection data for transport simulations and activation calculations. An advanced modelling approach was developed by M. Avrigeanu, IFIN-HH Bucharest, Romania, which takes proper account of the contributions from all involved reaction mechanisms including breakup, stripping, pick-up, pre-equilibrium and evaporation processes  [37]. This was demonstrated with the recent evaluations of deuteron induced cross-sections for 27 Al, 50,52,53,54 Cr, 55 Mn, 54,56,57,58 Fe, 58,60,61,62,64 Ni, 63,65 Cu, 93 Nb up to 60 deuteron energy MeV  [38]. [38]  This deuteron reaction model was implemented in an ad-hoc modified TALYS version 1. 81. The strategy in the PPPT programme is to implement such a model in a future TALYS release and include improved deuteron crosssections in the next version of the TENDL data library.
Summary andd conclusions EUROfusion's activities on the development of high quality nuclear data, implemented in the PPPT programme, were presented in this paper. The activities include nuclear data evaluations for neutron and deuteron induced reactions, the production of related data libraries, suitable for transport simulations, activation and radiation damage calculations which satisfy the needs for nuclear analyses of the DEMO fusion power plant and the IFMIF-DONES neutron source. The activities are closely linked to the JEFF initative of the NEA Data Bank, to which the produced data evaluations and libraries are provided. The evaluation work is complemented by extensive benchmark, sensitivity and uncertainty analyses to check the performance of the evaluated cross-section data and libraries against integral experiments.
Acknowledgment This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training programme 2014-2018 and  2019-2020  under grant agreement No  633053. The views and opinions expressed herein do not necessarily reflect those of the  European Commission. The support by the  NEA Data Bank, Paris , in providing their services for the data file assembly and maintenance, and hosting the progress meetings, is gratefully acknowledged.
Tier 1 centres will be smaller centres, with at least 150 cancers per year, access to MDT working but may not have access to all reconstruction options or genetics clinics. It is hoped that tier 2 centres will offer specific breast surgery fellowships to offer such training and the BRESO website will maintain a database of such fellowships, searchable by country and language. The candidate will have to demonstrate their practical skills by means of a certified log book and evidence of ability to undertake key procedures to a good standard (axillary clearance (ANC), level 1 and 2 oncoplastic surgery (OCBS), wide local excision (WLE), mastectomy (Mx) and skin and nipple sparing mastectomy (SSM/ NSM) for example). They will also be expected to demonstrate they have attained knowledge in breast cancer management and more in depth expertise in surgical management, as set out in the knowledge curriculum (which will be attested to by the passing of the UEMS European Board of Surgery Qualification (EBSQ) in Breast Surgery exam or holding an approved higher degree or certificate of competence, in addition to attendance at certified/approved courses and attendance at a minimum of 1 international breast congress).
Computation of the contact probability as a function of genomic distance Contact probability as a function of genomic distance P c (s) was computed as described  (Muller et al. , 2018). Intra-chromosomal pairs of reads were selected and partitioned by chromosome arms. Pairs oriented toward different directions or separated by less than 1. 5 kb were discarded. For each chromosome, the remaining pairs were log-binned as a function of their genomic distance s using the formula: bin = [log1. 1(s)]. The number of read pairs in each bin was counted and weighed by the bin size 1. 1(1+bin), as well as the difference between the length of the chromosome and the genomic distance. Identification of cohesin binding-sites and generation of pile-up plots Data from  (Verzijlbergen et al. , 2014)  were used to generate Scc1 ChIP-Seq profiles with a 2kb resolution.
ACKNOWLEDGMENTS We thank  T. U. Tanaka ,  Kerstin Bystricky , and  K. Nasmyth  for sharing strains and  K. Shiahige  for the Smc3 antibody. We thank  Aurele Piazza ,  Dave Lane ,  Luis Aragon ,  Julien Mozziconacci ,  Christophe Chapard ,  Olivier Cuvier ,  Tony Marchal , and O. G. and R. K. teams for discussions and comments on the manuscript. L. D. was supported by  ARC  fellowships. L. L. S. was partially sup-ported by a fellowship from  Fondation pour la Recherche Medicale  ( SPE201801005113 ). This research was supported by funding to R. K. from the  European Research Council  under the  Horizon 2020 Program  ( ERC grant  agreement  260822 ).
DATA AND CODE AVAILABILITY The accession number for the sequencing reads reported in this paper is SRA: PRJNA528616. The accession number for the imaging data reported in this paper is Mendeley (https://data. mendeley. com/datasets): https://doi. org/10. 17632/pgwsf28v2d. Codes and functions used to generate the figures from the raw data are available online at https://github. com/koszullab/hicstuff.
STAR+METHODS KEY RESOURCES Hi-C library of LD127-20b (scc1-aid) arrested in metaphase (Cdc20 depleted) This study SAMN11233326 SAMN13558635 Hi-C library of FB133-49B (wpl1D) arrested in metaphase (Cdc20 depleted) This study SAMN11233327 SAMN13558637 Hi-C library of yLD118-1a (pds5-S81R) arrested in metaphase (Cdc20 depleted) This study SAMN11233328 Hi-C library of yLD121-1a (pds5-aid) arrested in metaphase (Cdc20 depleted) This study SAMN11233329 SAMN13558638 Hi-C library of FB133-20C (eco1-aid) arrested in metaphase (Cdc20 depleted) This study SAMN11233330 SAMN13558636 Hi-C library of FB133-1D (wpl1D eco1-aid) arrested in metaphase (Cdc20 depleted) This study SAMN11233331 (Continued on next page).
Expression of non-degradable Sic1 was induced 30min before release by addition of galactose (2% final) to the media. Cells were washed and released in YP supplemented with raffinose and galactose for 120min. Cells were placed on 2% agarose pads made of synthetic complete medium plus glucose. Live cell imaging was performed under a spinning disk Continued REAGENT or RESOURCE SOURCE IDENTIFIER Software and Algorithms Bowtie2 Langmead and Salzberg, 2012 http://bowtie-bio. sourceforge. net/bowtie2/ index. shtml SCN procedure Cournac et al. , 2012 https://github. com/koszullab/hicstuff. confocal system (Nipkow Revolution, Andor Technology) with an EM charge-coupled device (CCD) camera (DU 888; Andor Technology) mounted on an inverted microscope (IX-81; Olympus) featuring a CSU22 confocal spinning disk unit (Yokogawa Corporation of America).
Elemental mapping using STEM-HAADF-EDX confirmed the formation of NPs containing both Rh and Co, as exemplified for Co 80 Rh 20 @SILP in Figure  2c -e (See Figure  S7  in the Supporting Information for other examples). Interestingly, the elemental mapping revealed a higher concentration of sulfur around the NPs than on the rest of the support, suggesting a strong interaction between the ionic liquid (especially the S-containing anion) and the NPs. Overall, these data confirm the versatility of the organometallic approach in the controlled formation of bimetallic NPs on SILP. To characterize the oxidation state and alloying properties of the Co x Rh 100-x @SILP materials, a series of materials with x = 100, 80, 30, 25, and 0 were characterized using Co and Rh K-edge X-ray absorption spectroscopy (XAS).
The NP size and distribution was determined from the measurement of >150 spherical particles chosen in arbitrary areas of enlarged micrographs. Scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS) was performed on a JEOL JSM 7800F operated at 10 kV with a thermally assisted Schottky electron gun and equipped with a Bruker XFlash 6|60 detector (silicon drift detector technology), and on a Hitachi S-3500N using a 10 mm² Si(Li) detector (Oxford Instruments). Samples for SEM/EDS analysis were prepared by pressing powder of NPs@SILPs on carbon tape. BET was measured using a QuadraSorb station (7. 01). Powder X-ray diffraction was performed using a X'Pert PRO powder diffractometer (PANalytical) equipped with a copper X-ray source. The data collection was performed with the aid of X'Celerator detectors.
Acknowledgements The authors acknowledge financial support by the  Max Planck Society  and by the  Deutsche Forschungsgemeinschaft (DFG, German Research www. small-journal. comFoundation) under Germany's  Excellence Strategy -Exzellenzcluster 2186 "The Fuel Science Center " ID: 390919832. The authors thank  ERC Advanced Grant  ( MONACAT 2015-694159 ). Fruitful discussion on the dynamics of NP catalysts with  Prof. Robert Schlögl  is gratefully acknowledged by W. L. C. V. S. would like to thank the  IMPRS-RECHARGE  for funding. Use of the  Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , was supported by the  U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences  under Contract No. DE-AC02-76SF00515. For experiments performed at beamline 9-3 of SSRL, the authors would like to thank  Dr.