dataesr/scientific-paragraphs-categorization huggingface dataset:
Integration at a global level As already described, the use of ontologies, nomenclatures and data exchange formats should be viewed in a more global context. In fact, this dimension has already been addressed by the ELIXIR hCNV Community's partners who have identified international projects and organizations with which relationships will be established. Thus, the GA4GH organization will interact and benefit from the hCNV community at various levels. The International Rare Disease Research Consortium (IRDiRC) will not only benefit from the Community but will also be able to promote its achievements through its members and the "IRDiRC Recognized Resources" labeling program. HGVS has also been approached to participate to their scientific meetings to disseminate the community's achievements.
Conclusions We believe that this white paper demonstrates the global need for ELIXIR to establish the human Copy Number Variation Community (hCNV) as it responds to a major challenge of NGS data interpretation in the era of whole genome sequencing both for research and in clinical settings. To do so, we have identified seven objectives ranging from CNV detection to data interpretation and sharing, for which various tasks have been described. The interactions with ELIXIR Platforms and Communities, and worldwide integration in the complex landscape of societies, initiatives and projects, has been addressed to avoid duplication of efforts and ensure fruitful collaborations. Finally, the growing interest for CNV detection and interpretation in human diseases will ensure the global recognition and expansion of the community and will trigger many interactions both for other ELIXIR Communities (such as Marine Metagenomics and Plant Sciences), and industry.
"The hCNV Community will develop innovative tools to annotate CNVs, facilitate their interpretation through a combinatorial approach, and help to pinpoint key genes in regions of interest. The following tasks have been identified and will most likely evolve as more data become available and as technologies evolve:" "Task #5. 1 will define CNV annotations including: type; genotype; genes and transcripts; expression level; exons; regulatory elements; breakpoints/ fusion fragments for WGS only"remove the space after "breakpoints/". "Task #5. 3 will develop specific bioinformatics tools to select candidate genes localized in the CNV region by combining genes' annotations and patients' phenotype. " -this reads a bit strangely. Candidate genes for what? I assume specific rare diseases? Objective #6: "This will respect databases' ownerships and national regulations' compliance" -there should be no trailing apostrophe after regulations; the compliance does not belong to the regulations.
2   Molecular genetics service,  AP-HP, Necker Hospital for Sick Children , F-75015, Paris, France In the white paper "The  ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research ", Salgado and co-authors present the working plan of the ELIXIR human CNV community. The manuscript summarises the strategy adopted in order to address current challenges in CNV detection and clinical interpretation. First, the introduction reviews the clinical relevance of structural variants in the human genome as well as the evolution of the technologies used for their identification. Second, a total of 7 main objectives are described, which are further detailed into specific tasks. Here, authors propose the development of enhanced CNV detection protocols, reference datasets, computational methods and analyses pipelines, standards for CNV reporting and data exchange and dissemination actions.
20 The Arab Orthodox struggle was directly linked to language. The clergy spoke Greek, a language allocated the virtue of being sacred, but which the congregation could not understand. Language, being the differential element, worked as a core criterion for the gradual construction of a distinct identity: that of the lay Orthodox, who spoke Arabic. Within the context of the developing Arab nation-building process, this state of affairs implied that the collective group could not be culturally self-sufficient, and had to accept its linguistic inferiority. In short, the Greek narrative was to a certain extent viewed as linguistic colonialism, and as such could not be accepted. In other words, language was the field on whose lines the self-determination process took place, producing the 'us v.
In children with active/post COVID-19 a 3D sequence for coronary artery imaging to detect eventual coronary dilation/ectasia in proximal or mean segments of the coronary artery tree is recommended. Data acquisition should be as short as possible by using undersampling methods and or reductions in spatial or temporal resolutions without loss of diagnostic image quality. Use of free-breathing and real-time acquisition methods is encouraged. If the patient's functional status allows a scan time of around 30 min, components indicated as "Desirable" in the table should be added to allow advanced tissue characterization and potential assessment of myocardial ischemia. Patients with acute COVID-19 infection often have respiratory compromisein which context risks of vasodilator (regadenoson/adenosine) stress increased: Utility of pharmacolologic stress should be considered on a patient specific basis, considering concomitant risks in the context of active COVID-19 infection.
sabina var. balkanensis population Examination of distributions of J. thurifera and J. sabina in the area (Fig. 6 ) reveals several J. thurifera populations Northeast of Sierra de Baza and a significant population of J. thurifera in the Alamedilla area, west-northwest (WNW) of Sierra de Baza. Although FAME database contained only 57 records from the Alamedilla area, there are likely many more trees around Alamedilla than 57. In the cases of Guadix (1) and Hoya de Baza (1), these sites each have only a single, isolated tree (personal observation, Carlos Salazar-Mendias (CSM)). The nearest large population of J. thurifera is Alamedilla that is approximately 26 km from J. sabina var. balkanensis, Sierra de Baza (Fig. 6 ). Wind direction and velocity are essential factors for LDT of pollen grains that are dispersed by wind which is the case in Juniperus.
In Sierra de Baza population, the unidirectional gene flow was shown between the hybrids and one of the parental species J. thurifera suggesting reproductive barriers developed in the hybrids towards the parental species J. sabina. Yet, further work is needed to discover the mechanisms of reproductive barriers involved in the studied taxa shaping their gene flow and evolution. Fig. 6  Distribution of J. thurifera and J. sabina in the region around Sierra de Baza (S. de Baza). Data from Anthos Spanish Plants Information System (http://www. anthos. es/index. php?lang=en) and FAME database  [81]. Numbers in parenthesis are the number of records in FAME database for that location (ex. Alamedilla  (57)  denotes 57 records at that location).
(San Francisco) for sequencing. 2. 31 (Technelysium Fig. 7  Frequencies of wind directions, Baza, Spain for January, February, March, and April. The most dominant directions were from WNW, 48. 4% (January) and SSW, 43% (April). Source: (Wind data from city of Baza, Spain  [63] ) Pty Ltd. ). Principle Coordinates (PCOR) and Minimum spanning networks software follows the formulations Veldman  [20]  Ordination and Adams  [93].
Flow cytometry analyses DNA contents (~3000 stained nuclei) were determined using CytoFLEX S flow cytometer (Beckman Coulter-Life Science United States). Each sample studied was repeated twice and fluorescence signals from stained nuclei were acquired with 561 nm laser line and 610/20 nm emission filter using CytExpert 2. 3 software. Analyses were performed using Kaluza Analysis 2. 1 software (Beckman Coulter). To calculate the 2C DNA value, we used the formula below that study the linear relationship between fluorescence signals from stained nuclei of the IS and juniper samples.
Acknowledgements We thank  Dr. Leonardo Gutiérrez  ( Andalusian Network of Botanical and Mycological Gardens in Natural Areas ), the  PhD student Juan Ortega-Vidal  and the forestry agents of  Natural Park Sierra de Baza  for their assistance at field work. We also thank the  General Directorate of Environment (Junta de Andalucía)  for allowing us access to FAME database. Authors want to thank the  National Council for Scientific Research in France (CNRS).
Availability of data and materials DNA sequences are available from GenBank repository accessions: GenBank MT136620-MT136701 for the region: trnS-trnG intergenic spacer, complete sequence; TrnG, partial sequence; chloroplast. GenBank MT137794-MT137875 for the region: 18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5. 8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 26S ribosomal RNA gene, partial sequence.
METHODS: This was an observational study using French National Health System claims data and including all adults with nonvalvular atrial fibrillation who initiated oral anticoagulant between 2014 and 2016. Outcomes of interest were major bleeding events leading to hospitalization (safety), stroke and systemic thromboembolic events (effectiveness), and all-cause mortality. Four approaches were used for comparative analyses: matching on propensity score (PS; 1:n); as a sensitivity analysis, matching on high-dimensional PS; adjustment on PS; and adjustment on known confounders. For each outcome, cumulative incidence rates accounting for competing risks of death were estimated.
This claims database currently covers >90% of the country's population. 5 he study population consisted of all patients aged ≥18 years covered by the SNDS, with ≥1 reimbursement for OAC treatments (VKAs, apixaban, rivaroxaban, or dabigatran) between January 2014 and December 2016, and newly initiating one of the study OAC treatments, that is, without the use of the same OAC in the 24 months before the index date (ie, date of the first dispensation). 6 Patients with atrial fibrillation diagnosed in the 24 months before inclusion were identified using a validated algorithm previously used by Bouillon et al  7  in the NACORA study. A second algorithm was developed to identify NVAF (based on the European Society of Cardiology definition). 8 ligible patients were allocated to 4 distinct subcohorts based on whether they received VKAs, apixaban, rivaroxaban, or dabigatran during the study period.
Patients with several OAC treatments, multiple doses or multiple prescribers at the index date, and patients possibly treated for indications other than stroke prevention in NVAF were excluded. Selected patients were followed up during their exposure to the studied anticoagulant treatment. Hence, each patient was studied from the index date until switch to another anticoagulant treatment, treatment discontinuation, patient's last health record (last care recorded in the database prior a 6-month period without any reimbursed care, which may include emigration and admissions to geriatric homes), death, or end of the study period (ie, December 31, 2016), whichever occurred earliest. Patients were censored at the first occurrence of one of these events. Details/definitions of switching treatment, discontinuation, and drug coverage can be found in the Supplemental Materials in the Data Supplement.
Outcomes The outcomes of interest were safety, defined as the risk of major bleeding events leading to hospitalization and identified through main hospital discharge diagnoses; effectiveness, defined as the risk of stroke and STE and identified through main hospital discharge diagnoses; and all-cause mortality, identified using the date of death recorded in the SNDS (Table  I  in the Data Supplement). Safety was also investigated considering 3 specific bleeding sites. For patients with >1 bleeding site at their date of first major bleeding event, the clinically most severe event was considered according to the following order of priority: intracranial bleeding, gastrointestinal bleeding, and other bleeding. The proxies of outcomes have been adapted from Friberg et al  9  and have been validated by Bouillon et al 7 on the SNDS.
Proportionality assumption was checked for exposure by including the interaction between a time function and exposure. If the proportionality assumption was violated, then 2 models were computed: the first without considering the nonproportionality that computed an average hazard ratio (HR) for each exposure over the period, and the second with the inclusion of the interaction between time function (log) and exposure to identify potential change of the HR over time. To support the robustness of the main analysis, 3 additional analyses were performed (see Supplemental Materials in the Data Supplement). All statistical analyses were performed using SAS (SAS Institute, NC), version 9. 4.
Ethics This study was approved by the French Institute for Health Data (Institut National des Données de Santé, approval No. 136 from September 8, 2015). It was conducted using anonymized data, approved by the National Informatics and Liberty Committee (Commission Nationale Informatique et Libertés, approval No. 1877931 from March 17, 2016), and registered at URL: https://www. clinicaltrials. gov; Unique identifier: NCT02640222.
Identification of the Study Population Among the 1 951 218 patients included in the French National Health System database who had been dispensed ≥1 course of VKA, apixaban, rivaroxaban, or dabigatran between 2014 and 2016, 1 040 864 patients (53. 3%) initiated one of the study OAC treatments. Almost all patients (99. 8%) were aged ≥18 years at OAC initiation, 438 280 patients had atrial fibrillation and 93. 9% (411 700 patients) had NVAF. After excluding patients without valid dosage or prescriber information, 411 077 patients were included in the study population. Of those included, 321 501 OAC-naive patients with NVAF were identified: 112 628 (35. 0%) initiated VKAs (69. 8% used fluindione, 27. 3% used warfarin, and 2. 9% used acenocoumarol), whereas 87 565 (27. 2%), 100 063 (31. 1%), and 21 245 patients (6.
To support the robustness of the main analysis and to include the full population (no attrition bias), we performed 2 additional analysis, using adjustment for confounding factors, and using adjustment for PS. Moreover, to try to improve the classical PS, we performed a third additional analysis, using matching on high-dimensional propensity score. In addition, to support the validity of the definitions used to identify outcomes, sensitivity analyses were conducted using modified definitions of these outcomes. Overall, these additional sensitivity analyses produced results consistent with the main analysis. Identification of patients with NVAF and associated risk scores from claims databases is complex. 12 The algorithm used in NAXOS relied on the criteria previously used in the ARISTOTLE trial  4  and in the NACORA study (Nouveaux Anticoagulants Oraux et Risques Associés).
CLINICAL AND POPULATION SCIENCES The relative risk of major bleeding events leading to hospitalization, the risk of stroke and STEs, and the risk of all-cause mortality with apixaban compared with VKAs were lower in NAXOS than in ARISTOTLE (HR, 0. 43 versus 0. 69, 0. 60 versus 0. 79, and 0. 44 versus 0. 89, respectively). These relative risks may reflect poorer international normalized ratio (INR) control among patients treated with VKAs in routine clinical practice, as opposed to the highly controlled environment of a randomized clinical trial and is consistent with data suggesting that the majority of patients treated with VKAs in France have inadequate INR control,  19, 20  compared with higher control rates in clinical trials that implement careful INR monitoring. 4  However, this assumption remains speculative, as INR results are not available in the French claims database.
Whatever the dose, the risk of major bleeding was lower with apixaban and dabigatran than with rivaroxaban, in agreement with the NAXOS findings. 23 he strengths of NAXOS are that it used a nationwide claims database (SNDS) covering both primary and secondary care, providing a broad range of data, including sociodemographic information, major medical history, and comprehensive healthcare reimbursement records, and comprises >90% of the French population. It is one of the largest nationwide observational cohorts of patients initiating OACs for the treatment of NVAF to date, providing high statistical power. Results were consistent across sensitivity analyses. Most importantly, it was population based and relied on a single payer (French National Health System) database, thereby minimizing the potential for selection bias.
The SNDS database does not collect diagnoses other than discharge diagnoses; therefore, some cardiovascular risk factors had to be identified from proxies based on treatments and hospital diagnoses (the drawbacks of using DRG and inability to fully ascertain the nature/cause of some outcome events are well known), and information was missing for major confounders (clearance of creatinine, hemoglobin, smoking status, weight, diet, and alcohol consumption), as is often the case for claims data, or even for medical records when data are not regularly updated. Thus, the CHADS 2 , CHA 2 DS 2 -VASc, modified HAS-BLED, and Charlson scores adjusted for age were assessed through algorithms based on proxies. It would have been of interest to separate the etiological subtypes of ischemic stroke and intracerebral hemorrhage, as we aware that the exact etiology is important for determining a causal relationship to anticoagulants' use.
However, in the database, we could not fully ascertain the nature/cause of these outcome events (for instance, in some elderly patients, no radiological investigation was performed, when the overall health status was poor). Although significant efforts were made to minimize confounding, residual confounding may be present, as in all observational analyses. Nonetheless, the consistency of our findings is reassuring, suggesting robust evidence. Large numbers of models were produced, opening a possibility of correction for multiple testing. However, the majority of our findings were highly statistically significant, and the application of corrections for multiple testing would not have affected the critical findings, even if a threshold of P=0. 001 and Bonferroni corrections have been used. Finally, edoxaban is not reimbursed in France for treatment of NVAF and therefore could not be included in the present analysis.
Acknowledgments All authors critically reviewed the manuscript. Drs Van Ganse  and  Steg  provided supervision, conceived and designed the study, interpreted the data, and drafted the manuscript. Drs Danchin ,  Mahé, Hanon , and Falissard were members of the  Scientific Committee. F. Jacoud  and  M. Nolin  performed the statistical analysis. F. Dalon ,  Dr Lefevre ,  Dr Cotte ,  Dr Gollety , and  Dr Belhassen  contributed to study design and interpretation of data. Dr Van Ganse is the guarantor of the study. We thank  Georgii Filatov  of  Springer Nature , who conducted an English language edit of this manuscript.
The letter also mentions the Voisin aeroplane and automobile company. A Voisin prefabricated house by Noël and Patout is illustrated in L'Art décoratif d'aujourd'hui, and Le Corbusier was writing the articles for this book in 1923. On folio 39v Le Corbusier notes, Le Corbusier sends Lafuma a cheque for 13,538 frs for the purchase of paper for the magazine, specifying that the cheque is predated 31 July  45  écrire Loos', and there is indeed a letter to Loos dated 21 July 1920 46 1920. It can be seen that this kind of research depends on a considerable backlog of data. In my own case, I have accumulated a database of around 20,000 documents, mostly concerning Le Corbusier but also some agendas that overlap with my own research interests. But my personal database only records documents relevant to research projects I have undertaken.
The Fondation Le Corbusier archive The Fondation archive includes around 400,000 documents of various sorts that have been digitised and can be accessed through a database. Unfortunately, this database has certain limitations. Most of the documents are held in A4 cardboard boxes, containing up to 200 sheets each. These were originally given alphanumeric numbers have been changed twice in the history of the Fondation but are now stable. The current database consists of an index of the label of each box rather than an index to each sheet. Over the years, the archivists have added considerable further information to each 'label', which has enriched the search engine. For example, the labels of boxes including the post war correspondence, which are ordered chronologically, have annotated in this way.
For example, there are several boxes of documents for each of Le Corbusier's built and unbuilt projects, containing tens of thousands of letters to clients and entrepreneurs. These names do not all appear in the general online index. To give one example, the painter and glazier used by Le Corbusier and Jeanneret in almost all their constructions of the 1920s, A. Célio, is referred to only once in the Fondation database under correspondence 47 for each project on which he worked. Similarly, there are over 1,700 documents connected with the Briqueterie d'Alfortville and the various agencies for which Jeanneret worked between 1918 and 1923, mostly consisting of letters to business associates. Hardly any of these names appear in the index under 'Correspondance'. Or again, Le Corbusier engaged in a massive propaganda campaign to reverse the judgement of the competition under Correspondance, but not all.
PCR products were sequenced commercially in Macrogen and GATC Biogen. All sequences have been deposited in GenBank (accession numbers MN413245-MN413327). Initially, we aimed to genotype partial cytochrome b gene, but none of the 7 tested primers (Additional file 1) amplified successfully. We used a set of 10 microsatellite loci in four multiplex PCR sets (for details see Additional file 1) to genotype a sample of the 251 individuals from 16 populations (Table  1 ). PCR products were separated on the ABI Prism® 3130 Genetic Analyzer (Applied Biosystems) and analysed using GeneMapper® v. 3. 7 (Applied Biosystems).
Analysis of mitochondrial DNA variation and historical demography Phylogenetic relationships within COI dataset were inferred by Bayesian (BI) approach. We used PartitionFinder v. 2. 1. 1  [22]  to select the most suitable substitution models for different parts of mtDNA using the corrected Akaike Information Criterion (HKY, GTR, and SYM + I for individual positions in codon). One sequence of Nothobranchius guentheri was used as an outgroup. Bayesian analysis was performed by Markov Chain Monte Carlo (MCMC) simulation using MrBayes 3. 2. 6  [23]. Two independent analyses were initiated from random trees. Three heated and one cold chain were run for 20 million generations per run, sampling every 1000 generations, and 25% of trees were discarded as burn-in. Bayesian posterior probabilities were used to evaluate branch support of the tree.
Phylogenetic analysis was performed on Cipres Science Gateway webserver  [24]  and the final tree was edited in FigTree v1. 3. 1 (http://tree. bio. ed. ac. uk/software/figtree). All sequences were geo-referenced and the geographical distribution of lineages was plotted onto map using QGIS 2. 18 (http://qgis. org). Diversity estimates, i. e. number of polymorphic sites (Np), number of haplotypes (Nh), haplotype diversity (Hd), nucleotide diversity (π, expressed as percentages, i. e. 0. 001 = 0. 1%), the average number of nucleotide differences (k) and Watterson's estimate of θ (θ = 4Ne*μ) were calculated using DnaSP v. 5. 10. 01  [25]. Within two most widespread lineages, historical demography was estimated using the neutrality tests, Tajima's D and Fu's FS, sensitive to population size changes  [26]  in DnaSP  [25] , with significantly negative values reflecting recent population expansion.