dataesr/scientific-paragraphs-categorization huggingface dataset:
Comparing CMIP simulations with observations Another common use of CMIP results consist in comparing them with observations in order to assess the performance of the corresponding GCMs (86 papers in our set). A variety of observations can be used, such as station data, satellite data, proxy data or reanalysis data. However, this measure of performance of CMIP models raises another bunch of analytical problems. The first one is related to the fact that, in complex climate models, many parameters are poorly constrained by observations and are adjusted in order to satisfy key climate metrics.
Hourdin et al. (2017) provide an excellent overview of the tuning of parameters in GCMs and the epistemological problems it poses. As they explain, the agreement with observations can be improved by changing parameters not directly relevant for the problem at stake. For instance, they show that the global top-of-atmosphere energy balance can be adjusted by changing a parameter controlling the fall velocity of ice crystals, a parameter which, at first glance, seems far from the issue at hand. It is thus possible to get the right result for the wrong reasons -the agreement with observations may result from compensating errors and do not necessary prove that processes are well represented in the model. As noted by  Tebaldi and Knutti (2007) ,  Frisch (2019) , and others, this limitation is particularly strong if the same datasets are used to tune a model and to evaluate its performance.
Another issue concerns observations themselves. In our set of papers, the large majority of studies do not compare CMIP simulations with model-independent observations, but only with reanalysis. Since reanalysis models are based on numerical methods, assumptions, and parameterizations similar to those of real climate models, they all exhibit biases of various kinds  (Edwards, 2010). Even if the analysis is continually corrected by available obser-data, reanalysis models thus transmit part of their biases to reanalysis products. Therefore, an agreement between climate models and reanalysis data might just illustrate a common bias in both climate and reanalysis models. This problem gets worse for processes for which we have few observations, such as the hydrological cycle  (Tebaldi & Knutti, 2007 ) -the reanalysis is then loosely constrained by observations, but mainly model-derived.
350) In practice, these connections were made through different means: 1. First, CMIP made its data freely available from all over the world thanks to a distributed structure, the Earth System Grid Federation. It has also supported the development of technical tools to convert the output data of various modeling group into a format, making therefore their exchange easier. Nevertheless, in CMIP6 overview paper, the authors claim that CMIP has favored "scientific progress on the most pressing problems of climate variability and change"  (Eyring et al. , 2016 (Eyring et al. , , p. 1949)). Is it true? As an infrastructure, did CMIP succeed in making climate research more effective? Here, we think it is important distinguish between effectiveness and efficiency. Something is effective if it is adequate to achieve an objective.
In contrast, something is efficient if it works in the best possible way. In other words, being effective is about doing the right things, while being efficient is about doing things right. A process can thus be efficient -for instance, if it is fast or cheap -but ineffective -if it is not well suited to the objective we want to achieve. CMIP has certainly helped climate research to be more efficient. Indeed, it has pooled many time-consuming activities at the level of the research community, and therefore facilitated the work of climate scientists. For a single laboratory, building a simulation protocol is indeed a time-consuming and costly effort. Boundary conditions, forcings and the associated databases, output parameters and their format, as well as versions of the models involved have to be carefully defined.
Thanks to CMIP, climate laboratories have shared this burden. The use of standardized format for the output data has also simplified a lot the analyses based on the results of simulations, and in particular, the comparison with data from observations. As  Eyring et al. (2016)  explain: A key to the success of CMIP and one of the motivations for incorporating a wide variety of coordinated modeling activities under a single framework in a specific phase of CMIP (now CMIP6) is the desire to reduce duplication of effort, minimize operational and computational burdens, and establish common practices in producing and analysing large amounts of model output. (Eyring et al. , 2016)  We thus agree that the production and the analyses of GCMs simulations have been made as the best models in climate science  (Shackley et al.
, 1998)  and the most useful one to predict future climate change. However, this view has been challenged by  Bony et al. (2013) ;  Shackley et al. (1998) , and others. According to them, though valuable, GCMs should not be seen as the 'panacea" of climate science  (Bony et al. , 2013). Different models are useful for different purposes and simpler models can also provide valuable insights for understanding climate processes. They should therefore be more frequently used in complementary of more complex GCMs. Another issue comes from the fact that CMIP promoted the particular use of GCMs as black boxes. Since CMIP data are freely available, anybody can analyse them. As a consequence, the large majority of CMIP analyses are conducted by scientists who have not been involved in the development of the corresponding GCMs, and have therefore a poor knowledge of the content of the climate models at hand.
The previously reported MARINER trial (A Study of Rivaroxaban  on the Venous Thromboembolic Risk in Post-Hospital Discharge Patients) (NCT02111564)  (8) , randomized medically ill patients with additional risk factors for VTE to extendedduration rivaroxaban (10 mg once daily for 45 days or 7. 5 mg once daily for those with a creatinine clearance between 30 and 50 ml/min) or placebo after excluding those at high risk of bleeding. Although the trial did not demonstrate a reduction in the primary endpoint of symptomatic VTE and VTE-related death, key secondary efficacy endpoints revealed a 56% reduction in symptomatic VTE and a 27% reduction in symptomatic VTE and all-cause mortality. The lower 7. 5 mg dose of rivaroxaban used in patients with moderate renal insufficiency was found to be ineffective  (8) , unlike the dose of 10 mg, which had previously been demonstrated to be effective in the MAGELLAN (Venous Thromboembolic Event [VTE] Prophylaxis in Medically Ill Patients; NCT00571649) study of extended thromboprophylaxis in medically ill patients  (9).
95; 95% confidence interval: 0. 89 to 4. 27)  (11). The  (A) Time to first occurrence of composite: venous thromboembolism, myocardial infarction, nonhemorrhagic stroke, and cardiovascular death up to day 45 (rivaroxaban 10 mg daily vs. placebo; intention to treat). Includes all data from randomization to day 45 (inclusive). Patients who do not have events are censored on the minimum of last visit before or on death or day 45. (B) Time to first occurrence of major bleeding on-treatment (rivaroxaban 10 mg daily vs. placebo; safety population). On-treatment includes all data from randomization to 2 days after the last dose of the study drug (inclusive). Subjects who do not have events are censored on the minimum of last visit before or on death, or last dose þ2 days. CI ¼ confidence interval; HR ¼ hazard ratio.
authors concluded that arterial thrombotic events appeared to be under-reported in trials of venous thromboprophylaxis, and they recommended systematic monitoring of such events in future trials. In the MARINER study, data on arterial events were captured using a standardized data collection form, and all suspected events were centrally adjudicated using pre-specified criteria. Although exploratory, our analysis suggests that extended thromboprophylaxis with rivaroxaban in medically ill patients may lead to reductions in arterial thromboembolic events (primarily ischemic stroke) as well as a reduction in symptomatic VTE. Such a finding is in line with the results of the APEX trial  (12) , which in post hoc analyses revealed a w30% reduction in fatal and irreversible ischemic events (including PE, MI, nonfatal ischemic stroke, or CV death) without an increase in fatal or intracranial hemorrhage, and a w50% reduction in ischemic stroke with betrixaban compared with placebo  (6, 7).
Spyropoulos et al. The association between VTE and arterial thromboembolic disease has been well-established  (5, 14). Underlying common mechanisms of both VTE and arterial thromboembolism suggest that primary thromboprophylaxis using an established anticoagulant regimen, possibly against a background of antiplatelet therapy and given for a sufficient duration, can be effective in reducing both types of events. An analysis of MARINER data in the subset of patients receiving rivaroxaban plus aspirin, although not randomized for aspirin use and hypothesis generating, suggested greater efficacy with rivaroxaban plus aspirin in reducing symptomatic VTE and VTErelated death  (15). In the COMPASS (Rivaroxaban for the Prevention of Major Cardiovascular Events in Coronary or Peripheral Artery Disease; NCT01776424) trial, a very large study that compared 2.
ACKNOWLEDGMENTS The authors thank the patients who participated in the MARINER trial. The authors also thank  Traci Weber , who supported the writing of this manuscript. ADDRESS FOR CORRESPONDENCE:  Dr. Alex C. Spyropoulos , The Donald and  Barbara Zucker School of Medicine at Hofstra/Northwell , The  Feinstein Institute for Medical Research , and  Department of Medicine, Anticoagulation and Clinical Thrombosis Services ,  Northwell Health at Lenox Hill Hospital, 130 East 77th Street, New York, New York 10075. E-mail: aspyropoul@northwell. edu. Twitter:  @AlexSpyropoul.
SlDREBA4 Cloning and Phylogenetic Tree Construction The specific primer pSlDREBA4 (Table  S1 ) was designed based on the SlDREBA4 gene sequence. SlDREBA4 was cloned and sequenced using Microtom cDNA as the template. A phylogenetic tree was established by the Neighbor-Joining algorithm with 1,000 bootstrap replications using MEGA5 version 5. 05 software  (Sakuma et al. , 2002). Identification of Tissue-Specific Expression and Stress-Response Patterns of SlDREBA4 Using Real-Time Quantitative PCR (RT-qPCR) Microtom seeds were germinated and sown in vermiculite. After growing two true leaves, the plants were transplanted into Hoagland's nutrient solution. After seven to eight leaves were grown, plants were exposed to stresses. For the dehydration stress, hydroponic seedlings fixed in planting baskets were transferred from nutrient solution along with the basket to the filter paper.
HII(%) = S (plant numbers at each level Â level rank) Â 100=(highest level rank Â the total number of plants) The concentrations of indole-3-acetic acid (IAA), ABA, JA, SA, and 1-aminocyclopropane-1-carboxylic acid (ACC) were measured by HPLC-MS/MS using Agilent 1290 HPLC (Agilent Technologies Inc. , USA) and SCIEX-6500 Qtrap mass spectrometer (AB Sciex, USA)  (Pan et al. , 2010). Proline, malondialdehyde, soluble total sugar, soluble starch, peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT) were detected using an ELISA kit (Shanghai Enzyme-linked Biotechnology Co. , Ltd). Plasma membrane permeability was measured in terms of electrolyte leakage rate  (Kumar et al. , 1985). All the physiologic indices were measured in biological and technical triplicate. Biosynthetic genes in the JA, SA, and ETH pathways were searched against the DEGs data in the SlDREBA4-overexpressed and -silenced lines, and the expression profiles of these genes were validated using RT-qPCR by the 2 -DDCt method  (Zhao et al.
, 2013). All the primers are provided in Table  S1. The SlDREBA4-overexpressed and -silenced, and empty vector-transformed plants were selected to carry out transcriptome sequencing. Readcount for each gene was normalized to reads per kilobase per million mapped reads (RPKM). Prior to differential gene expression analysis for each sequenced library, the readcounts were adjusted using the edgeR program package through one scaling normalized factor  (Robinson et al. , 2010). Analyses of significant differences in gene expression were performed using DESeq2 and the R package  (Anders and Huber, 2010). Genes with a p adj < 0. 05 and |log 2 (foldchange)| >1 were selected as candidate genes. Based on the principles of hypergeometric distribution, clusterProfiler was used to perform a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs [p adj < 0.
8 It is largely based on the ongoing experience of TEI, EpiDoc, and EFES (EpiDoc Front-End Services) -a highly customisable platform for the online publication of ancient texts in EpiDoc XML, as will be illustrated in the examples below. 9 The developers plan to release version 1. 0 in the spring of 2021: a GitHub repository is already available with an in-progress version of 6 EpiDoc: Epigraphic Documents: https://epidoc. stoa. org/. For a list of projects related to inscriptions, coins, and papyri in Digital Humanities: https://wiki. digitalclassicist. org/Category:Projects (updated to 2016-05-31). 7 See https://www. doaks. org/resources/seals. 8 See Sopracasa, Filosa 2020; see also "Sunoikisis Digital Classics: Spring 2020. Session 5. EpiDoc 2: publishing and querying with EFES" (https://github.
com/Sunoiki-sisDC/SunoikisisDC-2019-2020/wiki/DC-Session-5-EpiDoc-2) and "Summer2020 Session 4. Text-Bearing Objects 2" (https://github. com/SunoikisisDC/Sunoikisis-DC-2019-2020/wiki/Summer2020-Session-4). the code 10 and a website (http://sigidoc. huma-num. fr/, empty for now) is ready to host documentation, guidelines, and general information about the project, as well as a test corpus consisting of a digitally enhanced version of a printed article (Sopracasa, Prigent 2017). SigiDoc 1. 0 will finally provide something that has been long awaited and discussed since 2006 amongst the community of Byzantine sigillographers, being something of a chimera for Byzantine studies at large, often announced but never seen. 11 However, we are aware that it can be improved and we have therefore tried to anticipate future developments and needs: a second round in SigiDoc's development is currently already seeking funding.
As the study of textbearing objects, sigillography utilises standards and criteria developed for editions of papyri and inscriptions, such as the Leiden conventions, whilst customising them to best suit the different kinds of material being treated. Finally, seals are also treated as images, both as digital facsimiles and as bearers of iconographic depictions. This paper, however, will only deal with the first two aspects. In addition, as a minor but relevant point, this paper will devote special attention to some aspects of the relationship between print and digital publication, whilst addressing the topic of the degree of digital enhancement of the discipline offered by the current state of SigiDoc. The Seal as an Object: The Metadata With regard to metadata on the EFES-generated webpage, 12 the structure of a SigiDoc edition will be similar to that of other Epi-Doc-based projects.
13 The digital edition appears more organised and better structured in comparison with the printed one, where the metadata are usually grouped, in a smaller font, under the main title of the seal, including a mention of the date (without dating criteria); the inventory number of the edited seal; its diameter (with no further measurements); a simple physical description, focusing mainly on the state of conservation of the seal; and, finally, a mention of its edition(s) and parallel(s), if applicable. As far as further metadata are concerned, these can be either found scattered within the commentary of the edition or are not registered by the editors at all. In SigiDoc, however, specific fields have been created to deal with these individual aspects of metadata. Examples of these include: Channel orientation and Axis, expressed with reference to the numbers on a clockface (e.
e. the information concerning the appearance of the letterforms on the seal, which is one of the key factors in the dating of a specimen. Further, in the digital edition, there will inevitably be some blank fields in which the information is replaced by, e. g. an em-dash or by the use of the phrase not applicable/not available. After much discussion with our colleagues -sigillographers and digital humanists alike -on whether to delete those fields with lack of information, we concluded that the lack of information is still information per se. 12 Metadata are, from a SigiDoc point of view, all information contained in the TEIheader. They concern appearance and physical description of the seal; its dating and dating criteria; its history -ancient and modern alike -spanning, therefore, from the time of the seal's issuer until the acquisition of the seal in a collection; a description of both sides of the seal, including a thorough description of the iconography; and bibliographical references to the seal and to its parallels, when applicable.
The font's effectiveness will be enhanced by its inclusion in SigiDoc: the epigraphy will be contextualised thanks to the other data available, such as dating, places, social milieu of the seal's issuer etc. , all materialising in a search form that takes all these factors into account. The main difference between Archetype's approach to the script and the one using Athena Ruby lies in their ultimate goal. Archetype provides a framework and methodology for palaeographical analysis that can be adapted to a wide range of alphabets, scripts, and decorative elements, based on the comparison of structured descriptions provided by specialists in their respective fields. Here the standardisation comes in the approach, methods, and tools, rather than in any specific vocabulary used for the distinct letter components.
EFES provides SigiDoc with two major assets: web visualisation and data valorisation, which is expressed in customisable, automated indices and faceted federated search. Knowing that EFES allows for the creation of a potentially unlimited number of indices, the developers of SigiDoc encourage its users to prepare a common set of indices, to ensure optimal cross-referencing across different corpora. The indices are generated on the basis of Authority Lists used in EFES, to which the markup points by using the attribute @ref. Here is an example of the legend of the seal in The Authority Lists will be shared among all SigiDoc-based projects, which will have the responsibility of supplementing them with new entries arising from their own materials. The approach used for indices is part of a broader objective of simplified data searchability, on the basis of developing a standard: creating a set of common and shared rules allowing for proper interoperability.
Such interoperability will be realised primarily through a centralised search interface, which will allow for a virtual unification of all the corpora encoded in SigiDoc, thus going beyond the indices themselves and single search forms of each EFES corpus. The functionality of this interface will be based on the shared application of the principles currently employed in the creation of indices and search forms for individual projects. The unified search interface is not yet available and represents the main goal of the next round of SigiDoc's development, currently seeking funding. If appropriate indices and search forms are effective with large amounts of data coming from large quantities of seals, the meaning of each seal needs to be fully explained in its commentary. In printed sigillographic editions, commentaries greatly differ in structure among publications, especially when it comes to a proper historical analysis connecting the seal to people, sources, and events related to the broader context of Byzantine history.
In EpiDoc-based projects this feature is not explored, and the rule is to have short references for the bibliographical apparatus or written in brackets inside the commentary. However, if one wants faithfully to transpose a printed publication into a digital form, one should find a place for footnotes: 54 the amount of information they convey might be too rich to be incorporated into the main text without jeopardising its legibility, as has been shown clearly by the experience in progress of transposing a journal article into digital form with SigiDoc (Sopracasa, Prigent 2017). Furthermore, thanks to the possibilities offered by EFES, the corpora encoded in SigiDoc will be multilingual by default. The accessibility of the data coming from seals will thereby be increased, reaching non-specialists, too: the user will find a multilingual version of the frame of the standard webpage, including the field names structuring the data, as well as the indices; however, the data themselves (including the text of the legend) and the plain text will have to be manually translated.
further development, however, it is crucial to release the project as soon as possible and let interested users experiment with it. We now have the first SigiDoc-based funded project, soon to be undertaken at the University of Oxford, on a collection of Sicilian signacula; this project provides a concrete use-case of a small corpus, and will produce more documentation, and the possibility for student training and contributions. 55 Testing on different material leads to improvements as the standard grows over time. 56 Moreover, thanks to its interaction with EpiDoc and EFES, SigiDoc allows the editors both to create accurate and reliable data and to take care of, and have control of, specific aspects of the online publication. In light of what has been analysed in this paper, we argue that widespread use of SigiDoc will enable the digital enhancement of Byzantine sigillography, thus permitting not only the conversion of analogue information into digital form, but also an extensive exploration of the possibilities provided by the Digital Humanities for the enhancement of the entire editorial process.
22 TEI Consortium (2020-02-13). TEI P5: Guidelines for Electronic Text Encoding and Interchange (Version v 4. 0. 0). Zenodo. http://doi. org/10. 5281/zenodo. 3667251, and the discussion: https://github. com/TEIC/TEI/issues/1835. 23 This discussion took place on the TEI-List on 2018-09-28, see https://listserv. brown. edu/cgi-bin/wa?A2=ind1810&L=TEI-L&P=72748. 24 See http://nomisma. org/. magazén e-ISSN 2724-3923 1, 1, 2020, 101-128 110.
Database of the Athena Ruby Glyphs (HTML): https://www. doaks. org/resources/athena-ruby/database-of-characters-in-html. 45 The font is now under the management of Colin Whiting at Dumbarton Oaks and periodical additions of new characters will henceforth take place (on a biannual rhythm) concurrently to the upcoming publications of seals in the Dumbarton Oaks collection -as Whiting told us per litteras.
EFES is a fork of the open source XML publishing platform Kiln developed by the Department of Digital Humanities at King's College London between 2012 and 2019. See https://github. com/kcl-ddh/kiln and https://kiln. readthedocs. io/en/latest/ for the documentation. For a thorough analysis of EFES and its potential, see most recently Bodard, Yordanova forthcoming.
44 Database of the Athena Ruby Glyphs (HTML): https://www. doaks. org/resources/athena-ruby/database-of-characters-in-html. 45 The font is now under the management of Colin Whiting at Dumbarton Oaks and periodical additions of new characters will henceforth take place (on a biannual rhythm) concurrently to the upcoming publications of seals in the Dumbarton Oaks collection -as Whiting told us per litteras.