dataesr/scientific-paragraphs-categorization huggingface dataset:
Healthcare pathways for SP have been elucidated in a recent study by  Bobbio et al. in a large population of more than 40,000 patients. The hospitalization rate in medicine units was 73%, versus 27% in surgery  [10]. However, this report, based on data from the French national hospitalization database, did not inform about the effective first line treatment in the ED. Another multicenter study conducted in EDs in Australia did not provide any data concerning the type of equipment, the speciality of the physicians managing the patients, or the departments of hospitalization  [11]. Currently, there exists a gap in knowledge concerning real-life conditions of SP management in the ED, in particular the role of ambulatory management and the type of interventions performed. In this context, we report here the real-life management in the ED of SP including both primary and secondary spontaneous pneumothorax.
Measurements Patients were identified in the ED admissions databases of the participating centers from the medical informatics programs (software programmes: Resurgences® (Berger Levrault, Boulogne-Billancourt, France), Urqual® (Maincare Solutions, Cestas, France), TralcareClinicom® (Intersystems, Cambridge, USA), Cristalnet® (Alma,Grenoble, France). All patients with a primary diagnosis of pneumothorax (International Classification of Diseases (ICD) 10th revision code = J93) during the study period were retrospectively identified by medical informatics queries. Among these patients, a diagnosis of PSP (ICD code J93. 11) or SSP (ICD code J93. 12) was selected by research assistants in the medical files of the EDs. Furthermore, for the description of treatment in EDs, patients that were included a randomized trial that was ongoing at the time, were not retained for the analysis of the treatment to avoid bias.
Results Among 3088 cases of pneumothorax identified, 1098 (35. 6%) were traumatic and were thus excluded from further analysis. A total of 1990 SP were studied: 1632 (82%) PSP and 358 (18%) SSP. The details of the 1990 SP are presented in Table  1. Clinical data and vital parameters of SP are presented in Table  2. When considering hypoxemia, patients with SP had a good tolerance (SpO2 ≤ 90% in only 3. 5%). SpO2 was significantly higher for PSP than for SSP (p < 0. 0001). Furthermore, patients with PSP often declared dyspnea but had less chest pain than SSP (p < 0. 0001). For analysis of treatment, only 1868 patients were studied: 122 patients could not be analyzed because of their participation in a randomized trial over this period, concerning the therapeutic strategy (EXPRED study). Figures  1  and 2  present respectively the first line treatments for PSP and SSP (n = 1868), as well as the hospitalization and discharge rates.
Acknowledgements The authors thank all the physicians from the participating centers. We thank the members of the EXPPI study group:  B. Mazet ,  J. Schmidt ,  D. Honnart ,  G. Trebbes ,  J. Y. Lardeur ,  D. Lauque ,  J. B. Braun ,  A. E. Dubart , ED,  G. Duncan ,  N. Bronet ,  B. Goulesque ,  A. Delpechin  and  T. El Cadi. We thank the clinical research assistants in the participating centers who participated in the data collection. We also thank  Fiona Ecarnot  ( EA3920 ,  University Hospital Besancon, France ) for editorial assistance.
Recently, the N-CLASS criteria were proposed for the diagnosis of neurogenic claudication caused by LSS  [10]. This set includes: 1/ age > 60 years, 2/ positive 30-s extension test (typical leg symptoms reproduced during active spine extension performed in standing position for 30s), 3/ pain in both legs, 4/ leg pain relieved by sitting, 5/ leg pain decreased by leaning forward or flexing the spine, and 6/ negative SLR-60 test (Straight Leg Raise test: positive if leg pain is produced below 60°). In the present study, the clinical signs most frequently cited by French GPs differed from those included in these 2 published datasets. An explanation is that these datasets may lack applicability to primary care  [11]. In the ISSLS study, GPs represented only 1% of participants and were not included in Genevay's survey.
Acknowledgements The authors thank all the respondents to the survey. Assistance Publique-Hôpitaux de Paris, Rééducation et Réadaptation de l'Appareil Locomoteur et des Pathologies du Rachis, Hôpitaux Universitaires Paris Centre-Groupe Hospitalier Cochin ,  27 ,  Rue du Faubourg Saint-Jacques ,  75014  Paris, France. 2  Université de Paris, Faculté de Santé, UFR Médecine, Sorbonne Paris Cité, 75006 Paris, France. 3 INSERM UMR 1153 ,  Centre de Recherche Épidémiologie et Statistique Paris Sorbonne 75004 Cité, ECaMO Team, Paris, France. 4  Institut Fédératif de Recherche sur le Handicap, 75013 Paris, France. 5 INSERM UMR 1124 ,  Toxicité Environnementale ,  Cibles Thérapeutiques ,  Signalisation Cellulaire  ( T3S ),  Faculté des Sciences Fondamentales et Biomédicales ,  75006  Paris, France.
Design of the study and setting The medical records of patients who experienced S. maltophilia pneumonia from January 2012 to January 2017 were collected from 25 ICUs of the French Society of Anaesthesia & Intensive Care Medicine (SFAR) and AZUREA networks  [8]. Participating centers and casemixes are listed in Additional file 1. The collected data involved both ICU and hospital stays. Follow-up was stopped either after hospital discharge or death, whichever occurred first.
Source and method of selection The patient's files were extracted through French hospital discharge database containing individual records of all hospital stays using International Classification of Disease (ICD-10) for the terms "Stenotrophomonas maltophilia" and "pneumonia. " In addition, ICU medical charts were cross-checked with microbiology laboratoryspecific information systems to ensure exhaustivity. Each medical record was analyzed by local investigators to determine if clinical, biological, and/or radiological signs of S. maltophilia HAP were present, thus excluding respiratory tract colonizations (defined as a positive respiratory sample without clinical, biological, and/or radiological signs of S. maltophilia pneumonia). In case of uncertainty, consensus was obtained between local infectious disease specialists and study coordinators (PG, AB) to clarify S.
Data collection Usual demographic variables were collected, including previous hospital stays and previous exposure to antimicrobial therapies (agents and durations). Simplified Acute Physiology Score II (SAPSII) and the Sequential Organ Failure Assessment (SOFA) score were assessed. On the day of S. maltophilia HAP diagnosis, the SOFA score was collected, as well as the number and type of invasive devices inserted. The severity of hypoxemia was graded according to the Berlin acute respiratory distress syndrome (ARDS) criteria  [11]. Requirements for highflow nasal oxygen therapy, non-invasive or invasive mechanical ventilation, or extracorporeal membrane oxygenation (ECMO) were reported. Empirical antimicrobial therapy and secondary adaptations were recorded, as were durations.
Data management Data were collected and managed using Research Electronic Data Capture (REDCap) software  [14]. The database was approved by the institutional review board of the SFAR (IRB00010254-2015-010), which waived the need for signed informed consent of the participants, in accordance with the French legislation on noninterventional studies  [15]. The study was declared on clinicaltrials. gov (NCT03506191). This manuscript was written in accordance with the STROBE statement for the reporting of observational studies in epidemiology.
Acknowledgements The authors would like to thank  Geoffroy Cagninacci  and  Cédric Baumann  for their excellent implementation and support of  RedCap. Prof Jean-Michel Constantin MD. PhD :  Pôle de Médecine Péri-Opératoire (MPO) ,  Centre Hospitalier Universitaire de Clermont-Ferrand ,  Clermont-Ferrand , France ; mixed ICU. Dr Thomas Godet MD. :  Réanimation Adultes et Soins Continus, Pôle de Médecine Péri-opératoire, Hôpital Estaing ,  CHU de Clermont-Ferrand , France ; mixed ICU. Dr Philippe Guerci MD. :  Department of Anesthesiology and Critical Care Medicine, Institut Lorrain du Coeur et des Vaisseaux, University Hospital of Nancy, Vandoeuvre-Lès-Nancy , France; mixed surgical ICU. Dr Sebastien Perbet MD. PhD. :  Réanimation Médico-Chirurgicale ,  Pôle de Médecine Péri-opératoire ,  Hôpital Gabriel Montpied ,  CHU de Clermont-Ferrand , France ; mixed ICU.
K E Y W O R D S breast cancer screening, cost-effectiveness, costs, review We systematically searched PubMed via Medline, Scopus, Embase, and Cochrane databases in August 2016 and conducted updates and searches for gray literature in April 2018 and again in August 2018 (Appendix 1). As a deviation from the protocol, we included two systematic reviews that conducted the search in only one country-the USA, since they presented the most comprehensive data on the costs of breast cancer. The quality of the included reviews was assessed by using the Assessing the Methodological Quality of Systematic Reviews (AMSTAR) checklist  19  relevant for systematic reviews of cost and cost-effectiveness outcomes and an additional question on transferability of the findings. We considered that the conclusions of the reviews were transferable to comparable jurisdictions, if the reviews reported low variability and uncertainty of the results, and considered the quality of original evidence as high or sufficient (Appendix 2 presents the decision framework).
Countries' acceptability thresholds were expressed from one to three times the gross domestic product (GDP) per capita  21  in the year prior to the publication year of the original evidence. We identified 7768 abstracts through our database search, with 451 more gray literature sources reviewed (Figure  1 ). The interrater reliability between the two reviewers for decisions on full-text inclusion was 92% (Cohen's kappa = 0. 7; substantial agreement). The excluded reviews and reasons for the exclusion are outlined in Appendix 3. Out of 30 included reviews, 14 reported data on the costs of breast cancer and 16 on the costs of BCS (the characteristics of the included studies are indicated in Appendix 4). Most reviews did not limit their search to a particular setting; some, however, aimed to identify studies comparable to either the UK,  22, 23  North America,  [24] [25] [26] [27] [28] [29]  Sweden,  30  Iran,  31  Asia,  32  or high  33  -or low  34  -income countries.
| Other breast cancer screening modalities Besides mammography, limited (for BSE and CBE) to no (for ultrasonography) information was reported on other screening modalities. Even though CBE and BSE are generally perceived as low-investment approaches, they also require launch and maintenance costs related to the education and enrollment of women. Costs required for BSE education were reported in one review,  26  and the cost-effectiveness of CBE in another review, suggesting it to be a cost-effective method for some low-income settings (India, Ghana, and Egypt). 34 The secondary sources are consistent in presenting sufficient evidence of no benefits but harms of BSE and on insufficient evidence of a mortality decrease in breast cancer with regular CBE. 3  By this, models assessing the benefits of CBE would rely on intermediary outcomes-stage shifting of breast cancer-rather than real-life data on mortality decrease, which underpins assessments of the cost-effectiveness of this intervention.
Research on Cancer /  World Health Organization , the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the  International Agency for Research on Cancer / World Health Organization. The tenure of a postdoctoral fellowship of  Dr. Olena Mandrik  at the  International Agency for Research on Cancer  was partially supported by the  European Commission   FP7 Marie Curie Actions ,  People, Co -funding of regional, national, and international programmes (COFUND). European Commission  FP7 Marie Curie Actions ,  People, Co -funding of regional, national, and international programmes (COFUND).
F I G U R E 1 PRISMA 2009 Flow diagram n o i t a c i Records idenƟfied through database searching AddiƟonal grey literature screened (n = 451) f i t n e (n = 7768) d I Records aŌer duplicates removed Screening (n = 5681) Records screened Records excluded (n = 5681) (n = 5539) Eligibility Full-texts assessed for eligibility Full-text arƟcles excluded, with reasons (n = 113): (n = 143) Breast cancer -3 Country -2 SystemaƟc/reproducible search -50 Included Reviews included in qualitaƟve synthesis (n = 30) Individual evaluaƟon -5 Target outcomes -51 Duplicate -2.
Reads were aligned on the human genome (Human GRCh38. p7, from ENSEMBL) using STAR and a maximum mismatch rate of 5%. Reads aligned on each gene were counted using the module feature count. Statistical analysis of the read counts (quality checks, normalisation using scaling factors, fold change and p-values calculations) were performed using the R package SARTools (DESeq2)  [13]. Genes were differentially expressed for p < 0. 05. Heatmaps were generated with R (package heatmap2), using genes with differential expression for at least one pairwise comparison.
Thus, the control of VeroE6 infection observed in VeroE6-pDC cocultures could result from the production of IFN-I by pDCs. (d-g ) VeroE6 cells were infected with MOPV-Zflag or LASV-Zflag (MOI = 0. 3). After 24 h, pDCs were added to the cells, or infected with MOPV-Zflag or LASV-Zflag (MOI = 0. 1). 24 h later, cells were stained for phenotypic markers and the Z protein. Conditions were: infected VeroE6 ("veroE6"), VeroE6 cultured with pDCs ("coC"), and infected pDCs ("pDC"). Z-positive pDCs (d-f) and VeroE6 cells (e-g) were quantified by flow cytometry. All data are presented as the mean and standard error of mean (SEM) of three independent experiments. ANOVA In vivo, pDCs are not only in contact with viral particles, but also with infected cells. Infected cells could affect the properties of pDCs, including their permissivity.
Acknowledgments: We are grateful to members of the  Laboratoire INSERM-Jean Merieux   BSL4. We thank  Viroscan3D  for RNA sequencing. We thank  C. Clegg  and  G. Lloyd  ( Public Health England, Porton Down, Salisbury, United Kingdom ) for providing us with MOPV,  S. Becker  for the AV strain of LASV, and the  Etablissement Français du Sang  for providing healthy human blood. We thank  T. G. Ksiazek ,  P. E. Rollin , and  P. Jahrling  for LASV MAbs. We thank  M. Bouloy  and  R. Flick  for the tools used to develop the LASV and MOPV reverse genetics systems.
This results in a short terminal telomeric tract. (b,c) Upon telomerase removal and induction of flippase (encoded by FLP1), sequences between the FRT sites are excised in a circle that is diluted out upon successive cell divisions. Remaining telomeres are of wild-type length (b) or very short (c). (d) The wild type 6R chromosome end is modified to generate 6R-CTL (e) and 6R-VST (f) in a manner similar to 7L (a-c). Chromosome maps and annotations are from the Saccharomyces Genome Database and Centre for Genetic Architecture of Complex Traits website (https://www. le. ac. uk/colleges/medbiopsych/research/gact/resources/yeast-telomeres) using the sequence of strain S288C as reference. Red and orange colors correspond to genes encoding minimally characterized proteins or dubious/putative proteins, respectively.
The association of each protein to 7L, 6R or Y' telomeres or to the ARO1 locus was quantified by qPCR and the fold increase of telomere enrichment over ARO1 is represented. Two biologically independent experiments are shown. precisely, our results suggest that there is no single genetic element within the last 15 kb of the 7L that contributes to cell viability in a significant manner  30. In particular, the X-element, a conserved ~475 bp region, present in all chromosome ends  35  , and absent in the 7L-Δ8 kb strains, does not contribute to cell viability when telomeres become short. Also, our data suggest that homologous recombination involving the subtelomere of the shortest telomere is not required to maintain cell growth (Fig. 3 ). Rather, we speculate that the TG 1-3 repeats region of the shortest telomere might be directly involved in recombination or break-induced replication repair event, consistent with recombination mechanisms occurring in type II survivors  36, 37.
PCR products were electrophoresed and stained with Ethidium Bromide. Mean telomere length was estimated using the ImageLab software (Biorad). Chromatin immunoprecipitation. The protocol described previously  17  was slightly modified. Briefly, after germination in galactose-containing media, cells were plated on galactose-and nourseothricine-containing solid media and grown for two days at 30 °C. This allowed excision of the URA3-containing circle with more than 95% efficiency. Colonies were then pooled and grown to OD 600nm = 0. 8 and prepared for chromatin immunoprecipitation as reported  17  using oligonucleotides listed in Supplementary Table  2. RNA extraction and RT-qPCR. RNA extraction was adapted  43. 2. 10 8 exponentially growing cells were pelleted and resuspended in 400 µL of 50 mM CH 3 COONa, pH 5.
(d) The wild type 6R chromosome end is modified to generate 6R-CTL (e) and 6R-VST (f) in a manner similar to 7L (a-c). Chromosome maps and annotations are from the Saccharomyces Genome Database and Centre for Genetic Architecture of Complex Traits website (https://www. le. ac. uk/colleges/medbiopsych/research/gact/resources/yeast-telomeres) using the sequence of strain S288C as reference. Red and orange colors correspond to genes encoding minimally characterized proteins or dubious/putative proteins, respectively. Note that subtelomeric sequences of strains W303 -used in this work -and S288C -used as reference -7L diverge in a region spanning Ty5 to YGL262W.
Acknowledgements We wish to thank the  Teixeira and Luke lab members  for technical advice and fruitful discussions. We also thank all members of the  UMR8226  unit for technical support. We thank  R. Rothstein  and  A. Shinohara  for primary antibodies. Work in MTT lab was supported by the  European Research Council  ( ERC-2010-StG 260906-D-END ), the  Mairie de Paris (Programme Emergences) , the  "Fondation de la Recherche Medicale" ("équipe labellisée")  and by the  French National Research Agency (ANR)  as part of the  "Investissements d' Avenir" Program (LabEx Dynamo   ANR-11-LABX-0011-01 ) and  ANR-16-CE12-0026. In the Luke lab this work was supported by  CancerTelSys  ( 01ZX1302 ) in the E:med program of the  German Federal Ministry of Education and Research (BMBF). MG was supported through a  Hartmut Hoffmann-Berling International Graduate School PhD fellowship  and KS by the  Lebanese National Council for Scientific Research.
Solubility screening using ultracentrifugation identified n-dodecyl-β-D-maltoside (DDM) as a suitable detergent, which has previously been successfully used to solubilize lysenin and Etx pores  20, 34, 35  (Supplementary Fig. 2 ). Structural determination of the Etx pore. When observed using transmission EM, the isolated Etx material appeared heterogeneous. The extremely low yields (∼10 µg from 6 × 10 8 cells) meant that we could not pursue additional clean-up steps, such as size-exclusion chromatography. This heterogeneity hindered particle identification and selection using manual or automated picking procedures (Supplementary Figs. 3, 4 ). Despite this, an initial dataset of 613 micrographs resulted in ∼14,000 particles after 2D and 3D classification clean-up steps and produced a map that reached 4.
6 Å, at which resolution the β-strands just begin to separate (Supplementary Fig. 3, inset ). We reasoned that the use of a Volta phase plate (VPP) would be advantageous for two reasons. First, the contrast of the protein component would increase, aiding particle picking and alignment. Second, the number of particles required to achieve a high-resolution structure could decrease as compared to conventional defocused data  40. Therefore, we proceeded to image the exact same grid used before with the VPP. Although the samples still appeared heterogeneous (Fig. 2a ), approximately two times as many particles remained after clean-up steps as compared to the non-VPP dataset from a dataset that was only 25% larger. This resulted in a final map at an overall resolution of 3. 2 Å (Fig. 2c, d   Supplementary Fig.
5 ). Estimation of the B-factors for both datasets indicated that the phase plate data was indeed of higher quality when comparing the same number of particles used in a reconstruction (Supplementary Fig. 6 ). Architecture of the Etx pore. The atomic model of the Etx pore is shown in Fig. 3a, b. The overall architecture of the Etx pore resembles that of its structural homologues lysenin  20, 35  and aerolysin  36  , with a β-barrel that spans the height of the molecule, a motif that so far seems specific for the aβ-PFTs. The Etx pore also lacks a vestibule that is found in the α-hemolysin family of β-PFTs where the β-barrel begins close to the membrane-spanning region (Supplementary Fig. 7a, d , respectively). The Etx assembly measures ~120 Å across and ~98 Å in height. The lumen of the βbarrel measures ~24 Å (Cα-Cα) at its widest, although local restrictions are present (see below).
H162 (Nδ1) is within hydrogen bonding distance of D250 (Oδ2), which lies in the cap domain of the same chain (Fig. 3d  and Supplementary Fig. 8a ). The RBD. This region undergoes minimal conformational changes in the transition from the water-soluble form, as in lysenin  20. Unique to Etx, and unlike lysenin and aerolysin, the individual RBDs are well separated and do not interact with their neighbours (Fig. 3b  and Supplementary Fig. 7a-c ), and thus do not contribute to any oligomerization surfaces. The lack of physical constraints in the RBD could infer higher flexibility in receptor selection and binding, and in part explains why the resolution of this domain is lower than that of the other domains (Supplementary Fig. 5 ). Overall, the RBD in the oligomer overlaps well with the corresponding region of the crystal structure of Etx in its monomeric form (PDB ID: 1UYJ) (Supplementary Fig.
Use of the VPP proved essential in our studies to achieve high resolution, owing to the challenging sample rather than its molecular mass (∼225 kDa). First, particles could be identified by the automatic and manual picking procedures more efficiently, resulting in more particles (Supplementary Fig. 4 ). Second, the overall quality of the data, as judged by Bfactor estimation from both datasets, was higher for the VPP data, meaning we could achieve higher resolution than with the non-VPP data, given the number of particles (Supplementary Fig. 6 ). While this manuscript was under review, another cryo-EM study of a relatively large complex (~500 kDa) also benefited by the use of the VPP  47  , suggesting that VPP use could be advantageous for certain specimens that are not size limited. The resulting map at 3.
Methods Materials. Chemicals were purchased from Sigma, UK, unless otherwise stated. The polyclonal antibody against Etx mutant Y30A-Y196A was raised in rabbits as described in ref. 51. After electrophoretic separation purified Etx pore was detected by SimplyBlue staining (Invitrogen Ltd, Paisley, UK). Protein concentrations were determined using the Pierce™ BCA Protein Assay Kit (Fisher Scientific Ltd, Loughborough, UK). Synthetic oligonucleotides were sourced from Eurofins Genomics, Germany. Recombinant protein production and purification. The gene, etxB, encoding epsilon protoxin (P-Etx) was PCR amplified using synthetic oligonucleotides Etx-NcoI-F and Etx-XhoI-R (Supplementary Table  1 ) designed to bear restriction enzyme sites NcoI and XhoI, respectively, to facilitate directional cloning into the expression vector pHis-Parallel1 (GenBank: AF097413.