dataesr/scientific-paragraphs-categorization huggingface dataset:
Note that multidecadal trends present in coral δ 18 O records from the eastern tropical Pacific may not be driven by temperature  13, 56, 57  possibly biasing the trend of this coral composite. The network of lake records is regionally constrained (Fig. 1 ), and that composite may contain multiple environmental influences beyond temperature. As a result, from the lake subset only, we cannot exclude the possibility of above-modern levels of warmth in the third century CE, though uncertainty bands for early centuries are wide, and the recent rate of warming is clearly unprecedented over the Common Era. The global composites derived from this dataset, despite their simplicity, supersede the composite-ofopportunity published in the last synthesis  11  , which was an average of regional indices obtained by very different means (hence not statistically homogeneous) and did not include the majority of the marine Figure  7.
Usage Notes Data Citation 1 gathers data records in multiple digital formats, as well as quality control dashboards for all PAGES 2k regions (Table  3 ). This collection is the cornerstone of current and future efforts by the PAGES 2k Consortium to better reconstruct surface temperature, attribute its variability to climate forcings, understand its relationship to other components of the climate system, and constrain model simulations. It is appropriate for many purposes, ranging from developing reconstructions of climate indices (e. g. , global mean surface temperature, NINO3. 4) and fields, to proxy-proxy and proxy-model comparisons, and it was designed to be functional and relatively inclusive so that appropriate records could be selected, depending on the intended purpose, of which some are presently unforeseen.
The 692 temperature-sensitive records described and validated in this manuscript were selected based on the criteria listed above. In addition to these records, Data Citation 1 contains 2,240 ancillary timeseries data from the same sites. Most (87%) are associated with tree-ring records from North America, including raw measurements, sample density and expressed population statistics; some are the native observations used to derive the temperature reconstructions included in the restricted group of 692 (e. g. , Mg/Ca of foraminifera for sea-surface temperature); others are not directly related to climate but represent environmental changes at the site that might be useful in interpreting the climatic significance of the record (e. g. , sedimentary magnetic susceptibility); some are proxy climate records that are sensitive to climate variables other than temperature.
These 2,240 records are all timeseries, in that the datasets are year/data pairs. These ancillary time series are provided 'as is'; the authors make no claims or guarantee as to their scientific usage. Within Data Citation 1, the 692 temperature-sensitive records that comprise v2. 0. 0 are each assigned a unique PAGES2k identifier, as listed in Table  1  (available online only) and Supplementary Table  1. The 2,240 ancillary records are not assigned PAGES2k identifiers. In addition, the 692 records are easily discoverable in Data Citation 1 (PAGES2k_v2. 0. 0_LiPD. zip, PAGES2k_v2. 0. 0. mat, PAGES2k_v2. 0. 0. RData, PAGES2k_v2. 0. 0-ts. pklz) by querying the metadata property 'paleoData_useInGlobalTemperatureAnalysis', which is set to 'TRUE' only for the 692 temperaturesensitive records described here.
Several factors stand in the way of the PAGES2k compilation being fully comprehensive: records are continuously being generated and published, while some existing records are not publicly archived. This synthesis represents a major community effort to compile data records and captures a substantial majority of relevant records; it is to be continuously expanded and curated by the PAGES2k community. In addition to Data Citation 1, the entire database will be made available as part of a more comprehensive, web-based data management platform (http://linked. earth). This cyberinfrastructure facilitates crowd curation, transparent discussions of proxy interpretations, tracking and versioning of paleo data, and is supported by the first paleoclimate ontology (http://linked. earth/projects/ontology).
In the near future, the current PAGES2k temperature dataset will be integrated with other paleoclimate datasets in this platform-for example, one dedicated to water isotopes (Iso2k 58 )-to enable the data-intensive studies of the last 2,000 years envisaged by the PAGES2k community  59. The LinkedEarth cyberinfrastructure will enable crowdsourced additions and edits to the database, allowing it to be a living entity, with careful versioning to ensure workflow reproducibility. Our versioning scheme is as follows: the version number for a data compilation is of the form C 1. C 2. C 3 , where C 1 is a counter associated with a publication of the dataset (e. g. , ref. 1), C 2 is a counter updated every time a record is added or removed, and C 3 is a counter updated every time a modification is made to the data or metadata in an individual record.
The dataset published here is thus v2. 0. 0 of the PAGES2k proxy temperature dataset. Future versions of the dataset, along with a change log that specifies the modifications associated with each new version, will be posted at http://wiki. linked. earth/ PAGES2k. This versioning applies only to the temperature-sensitive records in Data Citation 1; changes to ancillary time series are not tracked. In addition, an archival version of the dataset is available on the website of NCEI-Paleo/World Data Service for Paleoclimatology (https://www. ncdc. noaa. gov/paleo/study/21171), in both the LiPD format and the WDS ASCII template format developed in conjunction with the PAGES2k consortium, which will be updated and versioned as the dataset continues to evolve.
Acknowledgements PAGES, a core project of Future Earth, is supported by the  U. S. and Swiss National Science Foundations. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the  U. S. Government. Some of this work was conducted as part of the North America 2k Working Group supported by the  John Wesley Powell Center for Analysis and Synthesis , funded by the  U. S. Geological Survey. B. Bauer ,  W. Gross , and  E. Gille  ( NOAA National Centers for Environmental Information ) are gratefully acknowledged for helping assemble the data citations and creating the NCEI versions of the PAGES 2k data records. We thank all the investigators whose commitment to data sharing enables the open science ethos embodied by this project.
All these kinds of recommenders may expose (intentionally or not) web users to MITM attacks. Finally, any computer manufacturer may also manipulate the list of CAs (realizing tasks and ) before shipping the computers to their clients (e. g. ,  Dell). Trusting di erent lists of CAs (trust list) provided by di erent OS/browser editors can make the web users confused. Indeed for the same website, a web user may get di erent responses depending on the application (IE, FF, and Chrome)/platform (Windows, Linux, and Android) adopted by the user to access the website. On one hand the list of CAs is di erent from one application/platform to another. On the other hand, the quality of the validation process depends on the understanding of the application/platform developer to the related standards, even when the latter may not be clear about di erent points of validation [ ].
login. somesite. com and the second form allows the user to register by sending information to the server https://www. register. somesite. com. Before sending them personal or con dential data to either of these servers, the user's browser must retrieve the server's address and extract the certi cate that is used to determine if (s)he can trust the certi cate of the server for the speci c context. We have identi ed three di erent contexts of use for a user sending personal or con dential data to a web server: ( ) Connection login: the user will send a username and password to the web server and therea er will establish a secure session during which many di erent types of transaction may take place, for example, database access, le access, and online transaction. ( ) Registration: the user will send her personal information to the web server in order to create an account.
e browser extension tries to automatically determine the context of use based on the content of the personal data being requested. For example, when a single eld of type "password" exists in a web form, we assume the form is used to allow users to login to the server. When there are two elds of type "password," we assume the form is used for the registration of new users. When there is a eld of type credit card type or credit card number, we assume a payment is about to be made. However, we recognize that this is not always the case and that there are other cases where we cannot determine the intended use of the certi cate. Consequently, we have prepared a simple questionnaire (see Figure ) that appears when the user rst wants to send information to a server over a TLS connection. is allows the user to con rm or alter the automatically determined context of use.
In the current validation system, the roles that the intermediate entities should play are not clearly de ned. Any intermediate entity has the right to execute one or more of the obligations of web users. For example, Firefox has selected to achieve the four tasks whereas Google Chrome achieves only tasks (partially) and. If one web user uses Google Chrome on two di erent platforms (e. g. , Windows and Linux) (s)he may get di erent validation results for the same website because the trust list of Windows is not the same as Linux. On the other side, if one web user uses Firefox and Google Chrome on the same platform (e. g. , Windows) (s)he may get also two di erent validation results for the same website because the trust list of Mozilla is not the same as Windows. e -cornered trust model solves the aforementioned problems by creating a physical relation between the RP and the TB, who is a technical and legal expert in the domain of PKI.
Ligandbook is a public database and archive for force field parameters of small and drug-like molecules. It is a repository for parameter sets that are part of published work but are not easily available to the community otherwise. Parameter sets can be downloaded and immediately used in molecular dynamics simulations. The sets of parameters are versioned with full histories and carry unique identifiers to facilitate reproducible research. Text-based search on rich metadata and chemical substructure search allow precise identification of desired compounds or functional groups. Ligandbook enables the rapid set up of reproducible molecular dynamics simulations of ligands and protein-ligand complexes. Availability and Implementation: Ligandbook is available online at https://ligandbook. org and sup.
, 2005) , the R. E. DD. B. server  (Dupradeau et al. , 2008)  and Automated Topology Builder (ATB) and Repository  (Malde et al. , 2011). However, a reference repository for small molecule parameters generated by other means and especially for ones published in the literature is lacking. Such published parameters are valuable because they have typically been validated and can be easily used in new studies but they can be difficult to find and are often invisible to most searches, e. g. as part of supplementary information. Only a few, very specialized repositories for force field parameters exist: The Gromacs molecule & liquid database  (Fischer et al. , 2015; van der Spoel et al. , 2012)  contains about 500 parameter sets (OPLS-AA, AMBER/GAFF and CHARMM/CGenFF for Gromacs  (Abraham et al.
, 2015) ) for more than 150 organic molecules together with experimental liquid properties for validation purposes (as well as thermodynamic gas phase properties for about 3000 molecules  (Ghahremanpour et al. , 2016) ). Our own Lipidbook repository  (Doma nski et al. , 2010)  archives lipid and detergent force field parameters since 2009 and is a successful example for how a community-curated repository can be reliably maintained over many years. Our new Ligandbook site is a public database for force-field parameters of small and drug-like molecules for all major all-atom force fields, including the popular OPLS-AA, CHARMM/CGenFF and AMBER/GAFF varieties. Ligandbook aims to enable parameter re-use and simulation reproducibility by (i) facilitating the publication of force field parameters as open data; (ii) acting as an archive for parameter sets that are supplied and maintained by the community; (iii) making large, richly annotated parameter datasets easily available through human and machine accessible interfaces.
Repository architecture A set of parameters contained in the repository is called a package. For each tautomeric and ionization state of a molecule many packages can be created. A package contains a coordinate file and a topology file with the force field parameters. All files are versioned and each package-version pair has a unique and persistent package identification number. Metadata annotations as well as an abstract are stored to enable rich searching and filtering of packages. A package is linked to a user-supplied citation and carries a license. Ligandbook uses the CACTVS toolkit  (Ihlenfeldt et al. , 1994)  for the underlying cheminformatics functionality (see Implementation in Supplementary Information for details).
Capabilities Search and Download. The repository can be searched using either text-based or structure-based queries. Text queries can contain words, phrases, wildcards and groupings using boolean operators as well as the advanced Apache Lucene syntax. By default, the text search is performed across all annotation types (including compound names, synonyms and abstract words) but can be limited to a single attribute (for instance, a PDB ligand id or the packageId). For chemical exact structure or substructure search, the query can be drawn interactively in the CACTVS Sketcher  (Ihlenfeldt et al. , 2009)  or entered as a SMILES string. Each package is shown with all files in its history (with SHA1 checksums), chemical structure depictions and the meta data with links to other databases. Older versions are always available and provide a transparent history of changes so that studies can be reproduced with the exact same parameters.
A package can be downloaded as a zip file containing the files together with the license governing use of the parameters. References associated with the parameterizations are included so that users can ascertain appropriate use and cite the original authors appropriately. Additionally, if provided by the depositor, computed values and reference values for validation observables are shown as well as a subjective reliability score from 1 (not validated or not reliable) to 5 (very reliable); see Supplementary Information, Data structures and versioning. The database can also be queried directly with 3D coordinates. The input structure will be returned with the atoms reordered to match any found parameter files for immediate use in a simulation. Programmatic access. Results can be retrieved in YAML, XML and JSON formats for further automatic downstream processing through a RESTful API with URL-based queries.
Package deposition. Because packages are curated and owned by individual users, package creation requires free registration with a valid email address. Upon submission, the uploaded coordinate and topology files are processed, checked if they can be parsed by the Gromacs GROMPP input processor  (Abraham et al. , 2015) , and a preview of the data is shown to the user for approval or corrections. Most of the meta data are automatically derived from the chemical structure. Users may supply a description in the abstract field and link the parameters to publications, which can be automatically fetched via PubMed IDs, as well as submit computed and reference validation values and provide a subjective reliability rating together with a free-form justification. Users must accept the CC BY-SA (Creative Commons Attribution-ShareAlike) license for the parameters and the CC0 Public Domain Dedication for all meta data (see Supplementary Information, Licenses).
Initial content Currently the repository contains more than 2900 packages, formatted for use with GROMACS  (Abraham et al. , 2015). These include 455 parameter sets that were validated with hydration free energy calculations as part of the SAMPL challenges  (Beckstein and Iorga, 2012; Beckstein et al. , 2014; Kenney et al. , 2016) , parameters from some of our previous studies  (Simmons et al. , 2014) , and > 2000 packages with ligands from the PDB, parameterized with MOL2FF (manuscript in preparation). Because many common drugs are already included, users can easily set up simulations that probe protein-drug interactions (see Supplementary Information for an example). Coordinates are provided as PDB files. Topologies are always present as Gromacs ITP files  (Abraham et al. , 2015)  although files in other formats can be optionally deposited as supplementary data, such as CHARMM PRM files for CHARMM/CGenFF parameter sets.
If necessary, ITP files can be converted into or from other commonly used file formats (AMBER, CHARMM, Desmond, LAMMPS, etc. ) using open source tools such as INTERMOL (https://github. com/shirtsgroup/ InterMol), PARMED (https://github. com/ParmEd/ParmEd), or acpype (Sousa da Silva and Vranken, 2012).
In a context of growing demands for expert evaluation concerning medical, industrial and research facilities, the French Institute for radiation protection and nuclear safety (IRSN) considered necessary to acquire new software for efficient dimensioning calculations. The selected software is RayXpert ®. Before using this software in routine, exposure and transmission calculations for some basic configurations were validated. The validation was performed by the calculation of gamma dose constants and tenth value layers (TVL) for usual shielding materials and for radioisotopes most used in therapy. Calculated values were compared with results obtained using MCNPX as a reference code and with published values. The impact of different calculation parameters, such as the source emission rays considered for calculation and the use of biasing techniques, was evaluated.
Introduction For the past few years, demands for expert evaluation of medicine, industrial and research facilities dimensioning have been increasing. To respond to those requests, an efficient simulation tool is necessary. This tool should be easy to use and should offer a good compromise between calculation time and result accuracy. The software RayXpert has been selected for this purpose. Before using this software in routine, the impact of different calculation parameters was evaluated and basic configurations were validated. This article describes the validation of RayXpert for exposure and transmission calculations with the radionuclides most used in medicine for therapeutic purposes: Ir-192 and Co-60 in brachytherapy and I-131 in nuclear medicine. Preliminary results are presented.
RayXpert version 1. 3. 4. 0 The software RayXpert is developed by Tests and RADiations (TRAD, France). It uses Monte Carlo method implemented in GEANT 4 V10. 0 to simulate photon and electron transport for energies between 1 keV and 100 MeV. It is implemented on PC Windows and has the advantage of having a user-friendly interface that allows easy and rapid building of complex 3D geometries (Computer-Aided Design). RayXpert ® offers the possibility of considering radioactive sources of continuous electron or photon spectra (ie: for modelling conventional radiology or radiotherapy X-ray sources). Some important calculation parameters are automatically assessed by the software, such as the definition of the energy spectra of radionuclides' emission (database and selection of the rays), materials' composition, conversion coefficients, and the weights of the volumes for the Weight Windows variance reduction method.
This enables a straightforward use of the software. In this study, RayXpert version 1. 3. 4. 0 was used. Energy spectra of radionuclides' emission are extracted from the EAF-2010 decay data library (EASY-2010 system) or from the JEFF-3. 1/3. 1. 1 radioactive decay data sub-library  [1]. For this study, the EAF database was chosen as it is the default option. Calculations take into account the emission photon rays contributing to 99% of the emitted energy, with an automatic selection by the software ("RayXpert criterion"): ∑ ‫ܧ(ܲ‬ ‫ܧ)‬ _௦௨ ୀଵ = 0. 99 ∑ ‫ܧ(ܲ‬ ‫ܧ)‬ _௦௧௨ ୀଵ (1).
ICRS-13 & RPSD-2016 Where P(E i ) is the radiation intensity for a given ray i of energy E i , n_simul is the number of rays that are considered for the simulation and n_spectrum is the total number of rays of the spectrum extracted from the decay data library. The results are expressed in terms of ambient dose equivalent H*(10). The conversion coefficients from fluence to ambient dose equivalent, H*(10), are automatically applied by the software and are extracted from the publication 74 of ICRP  [2]. RayXpert proposes a database of materials, whose compositions correspond to the one given in the PNNL-15870 rev 1  [3]. The choice of a given material for a given volume automatically attributes that composition to the volume. In order to improve the convergence, different variance reduction methods are proposed as options: the Weight Windows, the thick target bremsstrahlung approximation (TTB) and distance or energy cut-off  [1].
MCNPX 2. 7. 0 MCNPX (Monte Carlo N-Particle eXtended) is developed and maintained by the Los Alamos National Laboratory  [4]. The code deals with transport of neutrons, gamma rays, and coupled transport, i. e. , transport of secondary gamma rays resulting from neutron interactions. The MCNPX code can also treat the transport of electrons, both primary source electrons and secondary electrons created in gamma-ray interactions. In this study, MCNPX version 2. 7. 0 was used. Energy spectrum of the source's radiation is defined by the user. For this study, energy spectra have been extracted from ICRP 107 [5] and a selection of the most contributive rays was performed to improve calculation times, according to a home defined reference method. The selection rule for a given ray i is as follows ("IRSN criterion"): (ா ) ∑ (ா ) ≥ 10 ିସ (2) Where P(Ei) is the radiation intensity for a given ray i (energy Ei) and Σ i P(Ei) is the sum of all intensities.
The emission photon rays that were considered for simulation using the different approaches are shown in figure  1. It can be seen that the RayXpert ® criterion (RXT) strongly reduces the number of rays considered for the simulation, irrespective of the emission spectrum (ICRP 107 or EAF-2010) or of the software (RayXpert ® or MCNPX). The removed rays correspond to the lowest energies or to the lowest intensities with intermediate energies. Emission photon rays that were considered for simulation using the different approaches. Further investigations have been performed with RayXpert ® , regarding the automatic energy distribution of the results. Indeed, the software distributes the calculated fluences as a histogram with energy bins automatically determined: the energy binning is logarithmic, with 10 steps per decade (default option).