dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This work resulted from the collaborative project  CAPTURE  led by INRAE REVERSAAL. We thank the  Agence de l'Eau Rhône Méditerranée Corse  for their funding under the grant number  2018 0685. This work was performed within the framework of the  EUR H2O ' Lyon  ( ANR-17-EURE-0018 ) of  Université de Lyon (UdL) , within the program " Investissements d'Avenir " operated by the  French National Research Agency (ANR).
Based on a pblast (https://www. genome. jp/tools/blast/, accessed on 20 December 2021) of S. aureus SrtA against all mycobacterial genomes in the KEGG database, these genera do not seem to possess any sortase genes. To our knowledge, no sortase activity has ever been reported for any mycobacterial species. Peptidoglycan-anchored adhesin-host factor complexes can withstand considerable shear forces, with extreme examples uncovered recently in staphylococci that resist tensile forces under which covalent bonds can rupture (in excess of 2000 pN for a single molecular complex under physiologically relevant rates of force application)  [197] [198] [199] [200]. The small number of force spectroscopy studies that have been done on mycobacterial adhesins interacting with their ligands revealed much weaker mechanical stabilities.
Information and Data Management Systems Information plays a central role in the operationalization of organized screening programs. Sophisticated data management systems are needed to bring together all data elements, including regularly-updated recruitment databases, screening results, image banks, and follow-up data, to allow ongoing evaluation and monitoring of the program and its impact. Programs also need to have a proper data infrastructure to ensure the recruitment of eligible populations at successive screening rounds. Identifying the eligible population for targeted LDCT screening is infinitely more complex than for breast, cervical, or colorectal screening, in which eligibility is solely on the basis of age and sex. Detailed individual data on smoking history are needed, yet most countries lack a populationwide database that contains this information.
19 One exception is the United Kingdom, where smoking status is recorded in electronic medical records by GPs. However, these data are not always entirely reliable. 19 Most often, a multistep approach is needed to identify those eligible for LDCT screening, involving a combination of centralized recruitment, individual outreach by GPs, and online questionnaires that capture other data to refine candidate selection. 16, 52 In Germany, the German Radiological Society and the German Respiratory Society recommend that initial invitations to screening should be issued by pulmonologists rather than GPs. 34 ll countries are also exploring the use of existing personalized risk models to expand recruitment to people who are at high-risk for lung cancer owing to other factors, such as race and ethnicity, socioeconomic status, family history, and the presence of comorbidities.
Key Considerations for Successful Implementation of Lung Cancer Screening ProgramsOptimal selection criteria for screening are defined, to ensure broad outreach to the population at the highest risk of lung cancer, and built into the invitation database The selection of organization model (centralized vs. decentralized) balances the need for consistent quality with ease of access to the population Shared decision-making is built into screening protocol to ensure participants are fully informed of the risks and benefits of screening Targeted outreach and careful messaging to address known barriers to attendance in vulnerable groups, including fears of diagnosis, and stigma surrounding smoking.
Acknowledgments We wish to thank  Martijn Hidding ,  Costas Papadopoulos ,  Michael Ruf  and  Nikolaos Syrrakos  for discussions. The work of B. P. has been supported by the  French Agence Nationale pour la Recherche , under grant  ANR-17-CE31-0001-01. This project has received funding from the  European's Union Horizon 2020 Research and Innovation Programme  under grant agreement number  896690 , project ' LoopAnsatz '. W. T. 's work is funded by the  German Research Foundation (DFG)  within the  Research Training Group GRK 2044. The authors acknowledge support by the state of  Baden-Württemberg  through bwHPC.
Introduction This survey summarizes a series of papers  [1, 2, 3, 4]  by the author inferring protein function and mutation from protein geometry, together with the applications to date. Continuing to learn basic biology, the author increasingly finds geometry often at the heart of the matter, from enzymes to viruses to immunology to cell signaling to morphogenesis and beyond. For reasons to be explained, viral glycoproteins provided the first proving ground for the new geometric techniques, coincidentally predating the pandemic, with attention naturally subsequently focused on the SARS-CoV-2 spike glycoprotein in particular, to be called here simply the spike. The method to be explained depends upon a database of protein geometry computed in the joint work  [5] , whose application described here provides a novel tool in structural biology.
An essential database 2 in protein theory is the Protein Data Bank  [11]  or PDB, which contains the 3-dimensional structures of nearly 200,000 proteins as of this writing. The PDB provides the relative spatial coordinates in Angström of the centers of mass of each of the constituent atoms in the proteins catalogued in this database. These 3-dimensional data comprise the protein tertiary structure 3. 1 To interpret the standard cartoon representation of protein introduced by Jane Richardson, let us mention the two pervasive protein secondary structure motifs: the α helix and the β strand. An α helix is comprised of a consecutive sequence of N i -H i forming BHBs C i+4 =O i+4 ::N i -H i ; α helices are nearly always right-handed and are represented in cartoons as helical ribbons. In contrast, β strands can be long-range along the backbone, where BHBs are formed between one sequence of consecutive backbone C and N atoms with another such sequence, either preserving orientation (parallel) of the two backbone segments or reversing it (anti-parallel).
These strands, represented as oriented ribbons, can combine into β sheets. 2 You can access this database by typing "RCSB" into your browser, query in English your desired protein such as "hemoglobin" or "SARS spike" at the top, click on a resulting PDB entry and then on "1d-3d View" on the left for cartoon images. Please do give it a try and start exploring this vast and marvelous resource. 3 Some biologists deprecate the PDB as artificial since the proteins require chemical or other manipulation; moreover, the refinement of experimental data to 3-dimensional structure is also arguably ad hoc. The former objection has been attenuated somewhat since recent years have witnessed a resolution revolution for Cryo Electron Microscopy methods, which can be less invasive.
This method determines a collection of PDB files for proteins whose primary structures are sufficiently dissimilar, yet are representative of the entire collection of primary structures in the PDB. The degree of similarity of primary structure is described by a percentage of homology identity, which we took to be 60%, while not allowing monomer repeats. There are also constraints of PDB file quality, and for completeness, we mention that we furthermore stipulated: the atomic resolution was ≤2Å and the R factor ≤0. 2, the latter of which describes the correlation between the measured data and the final tertiary structure of the PDB file. Running PISCES on 12Mar2012 with these parameters produced a subset of the PDB; running DSSP using the parameters described on this set of PDB files yielded a collection of 1166165 BHBs, and hence an equi-numerous collection H ⊂ SO(3) of corresponding rotations.
1, as opposed to a just a few, namely, three to eight in each of the other strains, often shared by one or more of the selected variants. Furthermore, most of these thirty or so residues which mutated in Omicron BA. 1 do in fact participate in BHBs in Wuhan-Hu-1. It is interesting to note that virtually all of these thirty or so residues are free from BHBs in the Delta variant, which was the predominant global strain pre-Omicron. Furthermore from the ancestral Omicron strain BA. 1 to the currently predominant BA. 2/BA. 4/BA. 5 strains of Omicron, all the nearly 30 further mutated spike residues 7 save one (residue number 547) do not participate in BHBs in the highest quality PDB file for BA. 1 (the PDB file with accession number 7WP9). This strongly confirms the earlier finding. There are two related explanations  [18]  for these anomalies of Omicron: the virus may have mutated in an immunocompromised individual, or it may have been sequestered in a small isolated group of hosts before exiting to the general population only when it was a fit competitor to other variants.
In any case, the degraded mRNA has inferior productive longevity, and consequently Moderna untranslates the spike to mRNA cargo to maximize secondary structure. 12 Though the arguments linking secondary structure to polymerase fidelity and degradation avoidance may apply more generally, this biophysical mirror symmetry principle pertains only to mRNA and not to other RNAs, and only for RNA viruses. We do not discount the possibility that the principle may hold more generally, though it does not take account of mutational errors during DNA replication. 13 The principal repository for nucleic acid structures is the Nucleic Acids Database (NDB). The NDB is derived from the PDB with additional search capabilities specialized to nucleic acids. The NDB catalogues about 1,650 RNA structures as of this writing.
Ethics approval The TUDCA-ALS consortium implements this study in full respect of the legal and ethical European requirements and codes of practices on the conduct of clinical trials. All procedures involving human beings conform to the Declaration of Helsinki and to Good Clinical Practices (GCPs) (22). Written informed consent is obtained from the enrolled study subjects at the initial screening visit. A contract research organization (CRO) controls the ethical standards of the planned work and guarantees that all the personnel involved in the study is adequately trained on ethical and safety requirements. The trial protocol received EudraCT number 2018-002722-22 and was registered on ClinicalTrials. gov as NCT03800524. The full protocol, the informed consent forms (ICFs), and all supporting documents are approved by all the involved ethics committees and by national regulatory authorities.
The IEB-DSMB Clinical Expert has the role to alert the Steering Committee whenever in his view serious safety concerns need to be addressed by the consortium. The Clinical Expert may request unblinding from treatment allocation, should serious safety concerns be suspected. In this case, the Clinical Expert alone is unblinded, whereas all the other personnel remains blinded. The IEB-DSMB charter defines the board composition, its duties and responsibilities, as well as its relationship with other consortium bodies. Personal data are processed only for the purpose of the clinical research project. All records identifying the patients are kept confidential and, to the extent permitted by the applicable laws, not made publicly available. Electronic data are stored in the eCRF for the entire duration of the study, until transferred to IIH for statistical analysis.
Dissemination policy Sharing TUDCA-ALS data is an objective of the consortium. The MNDA aids in promotion and diffusion of trial outcomes to the general public and to key stakeholders, including the patients. Each partner guarantees open access to all peerreviewed scientific publications relating to TUDCA-ALS results. Once the dataset has been analyzed, a complete, cleaned, anonymized copy of data used in conducting the final analyses can be made available to qualified, designated persons from other academic institutions or private companies on request, via a data repository accessible through Internet by registered users. Patient anonymity and legal compliance are assured throughout all the steps of data transfer. After the trial, biological samples collected during the trial are kept in the Ulm NeuroBioBank and used for further exploratory analysis or shared with other organizations.
PM findings The camels, sheep and goats were euthanized on the day 21 pi. The postmortem findings for euthanized and dead animals were congestion in liver and intestine, pneumonia in lung and enlargement of mesenteric lymph nodes. Detection of PPR antigen in tissue samples using Ic-ELISA Four out of five infected camels (IV D 1, 2, 4, 5), 3 out of 5 in-contact sheep (IV S 1, 4, 5) and 3 out of the 5 in-contact goats (IV G 1, 2, 3) were found positive for PPR antigen using Ic-ELISA (Table  2 ). Detection of PPR genome using RT-PCR Some of PPR Ic-ELISA positive samples (n = 12 lung samples; 7 camels, 3 sheep and 2 goats) were selected for PPRV genome detection using QIAGEN One step RT/PCR Kit and PPRV-specific primers. All the samples tested positive for PPR genome (data not shown). Detection of PPR antibodies using c-ELISA Sera were collected from all camels, sheep and goats 21 days after the experiments and tested for PPR antibodies.
Notes: Data are reported as median frequency on the total sample (grey dot) and as median frequency on the sample of women giving birth in each country (coloured dots); horizontal grey line represents the range of the median frequencies. All the indicators in the domain of provision of care are directly based on WHO standards. Indicators identified with letters (eg, 3a, 3b) were tailored to take into account different mode of birth (ie, spontaneous vaginal, instrumental vaginal, and caesarean section). These were calculated on subsamples (eg, 3a was calculated on spontaneous vaginal births; 3b was calculated on instrumental vaginal births). The changes to Figure  2  do not impact eighter the text or conclusions of the manuscript. Abbreviations: CS = caesarean section; HCP = health care provider; IVB= instrumental vaginal birth; SVB = spontaneous vaginal birth.
Notes: Data are reported as median frequency on the total sample (grey dot) and as median frequency on the sample of women giving birth in each country (coloured dots); horizontal grey line represents the range of the median frequencies. All the indicators in the domain of experience of care are directly based on WHO standards. Indicators identified with letters (eg, 2a, 2b) were tailored to take into account different mode of birth (ie, spontaneous vaginal, instrumental vaginal, and caesarean section). These were calculated on subsamples (eg, 2a was calculated on spontaneous vaginal births; 2b was calculated on instrumental vaginal births). The changes to Figure  2  do not impact eighter the text or conclusions of the manuscript. Abbreviations: ECS = emergency caesarean section; HCP = health care provider; IVB= instrumental vaginal birth; SVB = spontaneous vaginal birth.
Context of the M2PRUSSE Study The study enrolled patients who met the inclusion criteria (admitted in one of the four participating EDs, one visit to the same ED in the 90 days prior to inclusion, or twice in the last 6 months, or 3 or more times in the last 12 months; to have an EPICES social precariousness score higher than 30  [7] , to volunteer) and who did not meet the exclusion criteria (aged less than 18 years; under guardianship or deprived of their rights; in a life-threatening emergency situation; accommodated with a social health-care institution; unable to answer a face-to-face questionnaire) (Study NCT03660215). Two EDs were in densely populated urban areas with high levels of precariousness (Hôpital Nord and Hôpital Européen, in northern districts of Marseille); the two other EDs were in less urbanized areas characterized by pockets of neorural precariousness (Arles and Manosque).
Data Analysis All interviews were recorded and fully transcribed. We performed a thematic content analysis, which explores the semantic discourse of all interviewees and implements systematic and objective procedures for describing the content of the interviews, aiming at inferring knowledge on production conditions  [28]. For each interview, a rst reading of the transcript identi ed the themes evoked through a oating reading  [29]. The content was then broken down into units of meaning, themselves classi ed into different categories according to analogical groupings. The aim was to identify the units corresponding to a theme in the discourse, which could be a word or a paragraph. Within each theme, the units were discriminated into sub-themes to specify the characteristics of the theme evoked by the persons, re ecting their social experience.
Acknowledgements We thank all the patients and professionals in the emergency departments of  Hopital Nord, Marseille (Pr Antoine Roch );  Hôpital Européen, Marseille  ( Dr Aymeric Vasseur) ,  Centre Hospitalier Louis Raffalli ,  Manosque  ( Dr Anne-Sophie Peron ),  Centre Hospitalier Joseph Imbert ,  Arles  ( Dr Richard Daltroff ). We also thank the health mediators:  Ana Rojas ,  Ella Ragot ,  Fatima Hassani ,  Jean Michel Amata ,  Dalila Soudjay ; all the APHM staff who supported the project:  Dr Anne Galinier ,  Margaux Vieille ,  Claire Morando ,  Olivier Gauche ,  Mariola Klimokowska. We are grateful to the two territorial support platforms  APPORT-Santé and PRATIC-Santé  for their backing.
Cointegration implies that a linear combination of the non-stationary variables (defined by the cointegrating vector) is stationary. The second step uses the lagged residuals to test for cointegration using the error correction model (that cash reserves revert towards the long-run equilibrium defined by these variables) (Engle and Granger 1991). If a levels relationship exists, the demand for banking system reserves should be cointegrated with the evolution of the notional value derivatives (mostly with shadow banks), the cost of Fed Funds, and a measure of risk. This allows for a levels demand for central bank money related to these variables. 15 The cointegration equation is shown in Equation (1). logR(t) = Intercept + αlog(DERIV(t)) + β(FFunds(t)) + λ(MOVE(t)) + δ(DERIV CCP(t) + (t)) (1) where: (R) is the size of liabilities of the Federal Reserve system; (DERIV) is interpolated BIS data on the notional value of global derivatives; FFunds is the Fed funds rate; MOVE is an index measure of the volatility of movements in US Treasuries 16 (yield volatility implied by current prices of one-month over-the-counter options on 2-year, 5-year, 10-year and 30-year Treasuries); and DERIV CCP is the notional value of derivatives cleared with central counterparties used as a dummy variable for this structural shift.
Enveloped Virus Homotrimer Monomer PDB Entry * Reference Ebola virus (EBOV) Homotrimer 7JPH  [7]  Influenza virus (IV) Hemagglutinin A Homotrimer hemagglutinin A 6Y5G  [8]  Human cytomegalovirus (HCMV) Homotrimer B glycoprotein 5CXF  [9]  Herpes simplex virus (HSV) Homotrimer B glycoprotein 2GUM  [3]  Human immunodeficiency virus (HIV) Homotrimer gp140 4TVP  [10]  Lassa virus (LASV) Homotrimer GPC glycoprotein 5VK2  [11]  Middle east respiratory syndrome coronavirus (MERS-CoV) Spike S protein 5W9H  [12]  Severe acute respiratory syndrome coronavirus-1 (SAR-CoV) Spike S protein 6ACD  [13]  Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) Spike S protein 6VXX  [14]  Chikungunya virus (CHIV) Homodimer E protein 3N40  [4]  Dengue virus (DENV) Homodimer E protein 1UZG  [5]  Zika virus (ZIV) Homodimer E protein 57BUB  [6]  * A single PDB code is indicated but several PDB entries are available at the PDB.
They are built from the non-covalent association of two identical monomers built up from a heavy (β-chain) and a light (α-chain) subunit and possess an overall jelly roll structure similar to that of Con A, the single-chain Manbinding lectin from Jackbean (Canavalia ensiformis)  [38]. A detailed crystallographic study of the Lathyrus ochrus isolectin-II (LoL-II) in complex with an octasaccharide derived from the human lactotransferrin (PDB code 1LGC)  [39]  revealed that the enhanced affinity of Vicieae lectins towards the α1,6-fucosylated Man3GlcNAc2 core depends on the direct interaction of the α1,6-linked Fuc residue with some of the amino acid residues forming the carbohydrate-binding site (CBS) of the lectin via a few hydrogen bonds (Figure  4 ). In addition, complexes of pea lectin and Lathyrus ochrus lectin with non-fucosylated trisaccharides, indicated that Vicieae lectins also interact with one of the terminal Man of the trimannosyl core from the non-fucosylated N-glycans  [40].
Bioinformatics Atomic coordinates of fusion proteins, B glycoproteins, and E glycoproteins were taken from the Protein Data Bank (PDB): 7JPH (EBOV)  [5] , 6Y5G (IV)  [6] , 5CXF (HCMV)  [7] , 2GUM (HSV)  [8] , 4TVP (HIV)  [9] , 5VK2 (LASV)  [10] , 5W9H (MERS-CoV)  [11] , 6ACD (SARS-CoV)  [12] , 6VXX (SARS-CoV-2)  [13] , 3N40 (CHIV)  [14] , 1UZG (DENV)  [15] , and 7BUB (ZIV)  [16]. The molecular surface of the lectins and envelope glycoproteins from pathogenic enveloped viruses were calculated and displayed with Chimera  [149]  and Chimera-X  [150]. Assuming that putative N-glycosylation sites, NXT/S, of envelope glycoproteins are actually glycosylated, a classic N-glycan chain corresponding to the trimannoside core Man 3 GlcNAc 2 , was modeled using the GlyProt server (http://www. glycosciences.
simplex virus (HSV) (PDB code 2GUM), human immunodeficiency virus HIV (PDB code 4TVP), Lassa virus (LASV) (PDB code 5VK2), Middle East respiratory syndrome virus (MERS-CoV) (PDB code 5W9H), severe acute respiratory syndrome (SARS-CoV) (PDB code 6ACD), and severe acute respiratory syndrome-2 (SARS-CoV-2) (PDB code 6VXX). Lateral face of the molecular surface of the dimeric organization of the E glycoprotein of chikungunya virus CHIV (PDB code 3N40), dengue virus DENV (PDB code 1UZG), and Zika virus ZIV (PDB code 7BUB). Monomers forming the homotrimeric and homodimeric associations of envelope glycoproteins are colored differently, and N-glycan chains forming the glycan shield are represented by cyan colored balls.
Public engagement Major public event are a well established tradition in our field, and this conference was no exception. However, public engagement can be more active, through detector construction, data collection and even analysis: the Italian Extreme Energy Events project  [3]  allowed to build a network of 60 muon tracking telescopes installed inside high schools over the full country. Hundreds of students take, analyze and discuss data each year. Local communication and events are encouraged, hopefully spreading the students knowledge and curiosity in the rest of society. The Auger collaboration went one step further, by enrolling the Observatory neighbors into the building and commissioning of upgrade modules, which are then named and "looked after" with the team. The presentation of the REINFORCE citizen science project  [4]  was one of the highlight of the session, as it offered four demonstrators to the public: gravitational waves noise hunting, KM3NeT neutrino telescope deep sea environmental data classification, search for new particles with the ATLAS detector at the LHC, geoscience and archeology studies with Muography.