dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We are very grateful to (in alphabetical order) Bilal Barakat,  Anna Baranowska-Rataj ,  Andrew Clark ,  Hippolyte d'Albis ,  Alexia Fürnkranz-Prskawetz ,  Roman Hoffmann ,  Wolfgang Lutz ,  Anna Matysiak ,  Bernhard Riederer ,  Erich Striessnig ,  Jonas Vossemer  and the participants of various conferences and seminars for their helpful comments.
Funding Open access funding provided by  University of Vienna. This project has received funding from the  Austrian Federal Ministry of Science, Research, and Economy (BMWFW)  and the  French Agence nationale de la recherche  ( Award  no. ANR-16-MYBL-0001-02 ) in the framework of the  Joint Programming Initiative (JPI) "More Years, Better Lives -The Challenges and Opportunities of Demographic Change ".
ADCC enables the targeted killing of cells that display SARS-CoV-2 Spike protein at the membrane surface and our in vitro assay uses CEM-NKR cells stably expressing 2019-nCoV Spike cultured with primary effector cells from healthy donors in the presence and absence of anti-Spike mAbs. P2G3 mAb exhibited a robust ADCC activity that was superior in killing Spike positive cells compared to all other anti-Spike mAbs tested (Extended data Fig. 3a ). Although these studies were not performed with an Omicron Spike stable cell line, it is generally accepted that ADCC functional activity is maintained against the different SARS-CoV-2 VOCs for mAbs that conserve Spike variant binding  26. We next evaluated ADCP activity using 2019-nCoV or Omicron BA. 1 Spike trimer coated fluorescent beads mixed with different concentrations of P2G3 and/or P5C3 then incubated with U937 effector cells.
We thus tested the impact of these mutations on viral infectivity using lentivector pseudotypes. P5C3-escaping Spike proteins were significantly less infectious than the wild-type control in both the ancestral D614G and Delta backgrounds, correlating with a drop in affinity for the viral ACE2 receptor in an in vitro binding assay, whereas the P2G3-escaping K444T substitution had a milder effect in both assays (Fig. 4b-c ). Yet, an examination of the GISAID EpiCoV database revealed that mutations G476D, F486S or N487K/D/S found in P5C3 escapees are only exceptionally encountered in SARS-Cov2 isolates, representing together only 0. 0087% of the 8'568'006 available sequences as of March 2022, and that the K444T mutation is equally rare (0. 0024% of compiled sequences), strongly suggesting that the corresponding viruses have a markedly reduced fitness in the wild.
Cryo-electron microscopy Cryo-EM grids were prepared with a Vitrobot Mark IV (Thermofisher Scientific (TFS)). Quantifoil R1. 2/1. 3 Au 400 holey carbon grids were glow-discharged for 120 s at 15mA using a PELCO easiGlow device (Ted Pella, Inc. ). 3. 0 µL of a 0. 7 mg/ml Omicron Spike mixed with 0. 16 mg/mL each of P5C3 and P2G3 Fab fragments (Final 3. 2 uM Omicron Spike:1. 5 uM P5C3:1. 5 uM P2G3) was applied to the glow-discharged grids, and blotted for 6 s under blot force 10 at 100% humidity and 4 °C in the sample chamber, and the blotted grid was plungefrozen in liquid nitrogen-cooled liquid ethane. Grids were screened for particle presence and ice quality on a TFS Glacios microscope (200kV), and the best grids were transferred to TFS Titan Krios G4. Cryo-EM data was collected using TFS Titan Krios G4 transmission electron microscope (TEM), equipped with a Cold-FEG on a Falcon IV detector in electron counting mode.
Falcon IV gain references were collected just before data collection. Data was collected using TFS EPU v2. 12. 1 using aberration-free image shift protocol (AFIS), recording 4 micrographs per ice hole. Movies were recorded at magnification of 165kx, corresponding to the 0. 83A pixel size at the specimen level, with defocus values ranging from -0. 8 to -2. 5 µm. Exposures were adjusted automatically to 60 e -/Å 2 total dose, resulting in an exposure time of approximately 3 seconds per movie. In total, 22 758 micrographs in EER format were collected.
Cryo-electron microscopy model building A model of a Spike trimer (PDB ID 7QO7) or AlphaFold2 (ColabFold implementation) models of the P5C3 and P2G3 Fabs were fit into the cryo-EM maps with UCSF Chimera These docked models were extended and rebuilt manually with refinement, using Coot and Phenix  41, 42.
Acknowledgements We thank the  Service of Immunology and Allergy at the Lausanne University Hospital  for analysis of serum samples for levels of anti-Spike protein IgG antibodies. We thank  Isabella Eckerle ,  Meriem Bekliz  and the  Virology laboratory of Geneva University Hospital  for the Omicron RNA sample and variant isolates collection, the  Geneva Genome Center  for sequencing and  Julien Duc  for the development of in house scripts for analyses. We thank  Laurence Durrer ,  Rosa Schier ,  Michaël François  and  Soraya Quinche  from the  EPFL Protein Production and Structure Core Facility  for mammalian cell production and purification of proteins,  Alexander Myasnikov ,  Bertrand Beckert  and  Sergey Nazarov  from the  Dubochet Center for Imaging  (an  EPFL, UNIGE, UNIL initiative ) for cryoEM grids preparation and data collection and  Davide Demurtas  for set up of cryo-EM condition for automated acquisition in related studies not included in this manuscript.
We would also like to thank  David Wyatt  and members of the  CARE-IMI  work package 4 team for helpful discussions. G. P. received a grant from the  Corona Accelerated R&D in Europe (CARE)  project funded by the  Innovative Medicines Initiative 2 Joint Undertaking (JU)  under grant agreement No  101005077. The JU receives support from the  European Union 's  Horizon 2020 research and innovation program , the  European Federation of Pharmaceutical Industries Associations (EFPIA) , the  Bill & Melinda Gates Foundation ,  Global Health Drug Discovery Institute  and the  University  of Dundee. The content of this publication only reflects the author's view and the JU is not responsible for any use that may be made of the information it contains. Additional funding was provided through the  Lausanne University Hospital  (to G.
The systematic examination of the surviving copies of incunabula editions considerably diminishes the information available but also limits the risks of over interpreting the results. Cristina Dondi and her ERC Project 15c Booktrade aimed to make a systematic catalog of all remaining incunabula by examining all the marks that could reveal information on their circulation until today  (Dondi 2013). This project gave birth to Material Evidence in Incunabula (MEI), a database "which provides copy-specific information on some of the copies listed in ISTC," according to the presentation. For the 1482 and 1485 Ratdolt editions cataloged in the ISTC, only sixteen and eight copies out of 113 and 110, respectively, are present in the MEI database. This is a drastic reduction of data, but one which can nevertheless yield interesting results.
The MEI visualization tool (https://15cbooktrade. ox. ac. uk/visual ization/) shows that Ratdolt's 1482 edition was probably well distributed in Italy, with five exemplars that can be traced in the peninsula before 1500. However, some copies arrived in Switzerland, Austria, and England not long after the publishing date. The information concerning the 1485 edition is scarcer, but one can still observe that one copy was in Spain around 1500. These observations are confirmed by the examination of copies in other libraries that are not yet included in the MEI database. For example, the copies currently at the Bayerische Staatsbibliothek were bought by German institutions at the end of the fifteenth or the beginning of the sixteenth century. One copy of  (Sacrobosco et al. 1482 ), 17  has an ex libris from the Benedictine convent of the Holy Virgin in Scheyern, in Bayern.
OBJECTIVES This study sought to assess the association between postprocedural anticoagulation (PPAC) use and several clinical outcomes. BACKGROUND PPAC after primary percutaneous coronary intervention (pPCI) in patients with ST-segment elevation myocardial infarction (STEMI) may prevent recurrent ischemic events but may increase the risk of bleeding. No consensus has been reached on PPAC use. METHODS Using data from the Improving Care for Cardiovascular Disease in China-Acute Coronary Syndrome registry, conducted between 2014 and 2019, we stratified all STEMI patients who underwent pPCI according to the use of PPAC or not. Inverse probability of treatment weighting and a Cox proportional hazards model with hospital as random effect were used to analyze differences in in-hospital clinical outcomes: the primary efficacy endpoint was mortality and the primary safety endpoint was major bleeding.
30 In this study of data from the CCC-ACS registry, patients experiencing out-ofhospital cardiac arrest or receiving mechanical circulatory support, indicating a group of patients with severe degree of shock, were excluded from the analysis. We included variables such as age, sex, CS, timely revascularization, and multivessel disease in the adjusted analyses. As previous studies have reported differences in revascularization strategy for CS and non-CS patients with STEMI undergoing pPCI,  28  PPAC may also differ in this special population. Our findings should be considered as the basis of a hypothesis for further investigation. STUDY LIMITATIONS. As an observational study, selection bias and residual confounding exist, and the results must be interpreted as hypothesis-generating. Nevertheless, the study provides real-world data from the CCC-ACS registry, a nationwide cohort with over 110,000 patients, including complete coverage of STEMI patients who underwent pPCI in China.
STUDY DESIGN AND PATIENT SELECTION. Data from the prospective CCC-ACS (Improving Care for Cardiovascular Disease in China-Acute Coronary Syndrome) database were used in the study. Launched in 2014, the CCC-ACS project (NCT02306616) is a nationwide registry involving 159 tertiary and 82 secondary hospitals across China, and completed in December 2020 with 124,363 participants. The registry is a collaborative program of the American Heart Association and the Chinese Society of Cardiology, focusing on quality improvement efforts for ACS care and modeled in part on the American Heart Association Get With The Guidelines program. 8 Details of the rationale and design of the CCC-ACS project have been reported previously. 9 Briefly, in every month, the first 20 to 30 consecutive ACS patients were recruited in tertiary and 10 to 20 in secondary hospital.
DEFINITIONS OF VARIABLES. Medical history and periprocedural details were obtained from patients' medical charts and entered into the database by trained data abstractors. Standardized definitions were utilized across all hospitals for variable collection. STEMI was defined in accordance with the guidelines published by the Chinese Society of Cardiology and extracted from the patient's original medical records. 10 Patients were considered to have comorbidities, such as diabetes, hypertension, or hyperlipidemia, if those had been documented in admission. Renal insufficiency was defined as an estimated glomerular filtration rate of lower than 60 mL/min/1. 73 m 2. 11 Patients were classified as having PPAC if they had received anticoagulation therapy with UFH, low-molecular-weight heparin (LMWH), fondaparinux, or other anticoagulants after the procedure.
uttamchandani@strath. ac. uk; ralf. bauer@strath. ac. uk). All research data and materials supporting this publication can be accessed at DOI: https://doi. org/10. 15129/c589d644-e614-4c0c-80b6-5af7fe786492 frequency tuning mechanism is presented. The mirror, fabricated with a multi-user process, allows tuning of the orthogonal angular movement frequencies by up to 5. 5 kHz and 0. 55 kHz, or 4% and 0. 3% of the respective resonance frequency. The tuning is achieved through on-chip electrothermal actuators with tuning tips which are in close proximity to the scanner main torsion beams. It is shown that while all resonance mode frequencies are tuned at the same time using the electrothermal tuning, an order of magnitude difference in the rate of change allows for adjustment of the ratio between orthogonal movement mode frequencies.
The actors easily recognize each other and can very quickly place one another in their respective worlds. iv  In my fieldwork, I have observed the lives of ninety violinists and I have had contact with about thirty parents of young virtuosos. I have collected data on the activity of more than twenty violin teachers. In addition, I have done interviews with the violinmakers and concert organisers. I have also established good relationships with twenty researchers working in bio-chemical physics laboratories. I have done interviews with scientific conference organizers and merchandisers of scientific equipment. I have supplemented the data with biographical books about celebrities from the world of violin and worlds of physics, chemistry and biology. For eight years, I have used the method of participant observation and played different roles: a young virtuoso's relative, a translator, a concert organizer, a member of the association for young talents, host family druing the time of violin competitions, a guide for people taking part in a scientific conference, and a sociologist.
Model building strategies included univariate screening in a large number of models ( n = 13, 45% kidney transplant models, n = 19, 95% liver transplant models), and details on accounting for complexities in the data (e. g. , censoring, competing risk), handling of predictors or correcting for optimism as recommended by PROBAST were infrequently provided. Many models were neither internally nor externally validated ( n = 11, 38% kidney transplant, n = 10, 50% liver transplant), and four (14%) kidney and four (20%) liver transplant models even lacked reporting of apparent performance measures. In validation studies, two (33%) kidney transplant models had an unclear risk of bias for the analysis domain. Four out of six (67%) kidney and all liver transplant models were at high risk of bias, because the datasets contained less than the recommended minimum of 100 events for external validations  [23].
In contrast to prediction models in other medical areas, selection of participants and study designs used were appropriate in most models, likely because organ transplantations are performed in transplant centres only and often recorded in a single centre database or national registry  [30]. On the downside however, more than half of the models violated basic principles by including predictors that are unknown at the time of risk estimation (i. e. , before transplantation) but partly measured as late as 6 months after transplantation. Interestingly, all models with time to event endpoints reported hazard ratios rather than directly predicting expected (restricted) survival time  [31]. Living donor transplants are medical interventions of rather low frequency, limiting the number of participants and events available for modeling.
Calibration-in-the-large or the calibration slope were not reported  [39]. Furthermore, there is dearth of externally validated models, despite performance evaluation in independent datasets being a requirement to confirm a model's generalizability for clinical use  [ 40 , 41 ]. Transparent reporting is a prerequisite for reproducibility and critical assessment of research in general, and for external validation of proposed models and their bedside use specifically for prediction models. Most severely, only half of included models were presented in full with intercept or baseline risk or with a calculator. Consequently, many models are not even available in a format allowing their use for a single individual or external validation. From a methodological perspective prediction models in transplantation of organs from living donors are unique in the sense that they should include variables characterizing donors and recipients.
Future research Future research should primarily focus on external validation and recalibration of existing models at low risk of bias. Second, if new models are needed prospectively planned collaborations to develop and validate models using individual patient data meta-analysis, and prospectively calculating the required sample size are recent initiatives to improve generalizability of proposed models and to reduce methodological challenges when facing limited sample size  [ 43 -45 ]. Future prediction model developers should pay special attention to transparent reporting to allow use of developed models for updating or external validation in other datasets as well as synthesis with other models  [ 13 , 46 ]. Herein, journals play a pivotal role in demanding adequate reporting of risk prediction models to reduce the volume of misleading research published.
In a Dutch survey, NITs were never (73%) or rarely (22%) used by GPs to evaluate disease severity  [102, 107]. Therefore, most patients diagnosed with a risk factor for chronic liver disease are referred to a liver specialist because of nonspecific liver enzyme abnormalities rather than abnormal NITs suggesting advanced liver fibrosis  [102, 107]. Interestingly, however, after a brief explanation of the simple NITs, almost all physicians expressed a willingness to use them in practice  [105]. Low awareness is not limited to GPs. A retrospective analysis of the French hospitalizations database found a very low 0. 4% prevalence of the NAFLD/NASH diagnosis code among 50 million adult patients  [108]. A questionnaire sent to non-liver specialists in two tertiary hospitals in Brisbane (Australia) showed that the respondents were aware of the association of NAFLD with cardiovascular risk factors (90%) and that of NASH with increased overall mortality, but 71% of them did not refer patients to hepatology if NAFLD was suspected  [109].
In countries with high cycling levels, it has been assessed that physical activity through cycling generates substantial population-level health benefits  [4]. Due to the scarcity of country-level representative mobility data, the contribution of current levels of cycling is still unknown for France. Until recently, the latest nationally-representative mobility survey was conducted in 2008. In early 2022, the data was released from the most recent round of this mobility survey, the Enquête mobilité des personnes (People's mobility survey) conducted in 2018-2019  [5]. We used this updated data to assess the health and related economic benefits of cycling in 2018-2019 in metropolitan France.
Bioinformatics Analysis Clinically relevant genomic alterations (CRGA) were defined as alterations that are targetable by anti-cancer drugs available on the market or in registered clinical trials. Germline variants documented in the dbSNP database (dbSNP142; https:// www. ncbi. nlm. nih. gov/snp/), with 2 or more counts in the ExAC database (https://gnomad. broadinstitute. org), or recurrent variants of unknown significance that were predicted by an internally developed algorithm 10 to be germline were removed, with the exception of known driver germline events (eg, documented hereditary BRCA1/2 and deleterious TP53 mutations). Known confirmed somatic alterations deposited in the Catalog of Somatic Mutations in Cancer (COSMIC v62) were highlighted as biologically significant. 13 All inactivating events (ie, truncations and deletions) in known tumor suppressor genes were also called as significant.
Clinical and Pathological Characteristics A total of 90 thymomas and 174 thymic carcinomas were analyzed; as per Foundation Medicine prerequisite for conducting CGP, all cases had to be clinically advanced and refractory to standard of care for recurrent disease. Patient's characteristics are summarized in Table  1. For CGP, given the low incidence of GA, the 90 thymomas were organized into 2 groups based on previously reported studies. 2, 15, 16 ] [17]  Thymic carcinomas, given the limited amount of data in the literature regarding grading,  1  were analyzed based on Figure  1. Continued histologic subtypes: squamous cell carcinomas (n = 69, 40%), non-neuroendocrine undifferentiated carcinomas (n = 54, 31%), neuroendocrine carcinomas (n = 30, 17%), adenocarcinomas (n = 7, 4%), basaloid carcinomas (n = 5, 3%), lymphoepithelioma-like carcinomas (n = 5, 3%), and sarcomatoid carcinomas (n = 4, 2%).
25 PI3K targeting may then be an effective strategy in the treatment of thymic malignancies; a phase II study with buparlisib is currently ongoing (clinicaltrials. gov ID NCT02220855) (Fig. 3 ). Several phase I/II studies of mTOR inhibitors were reported in advanced thymic epithelial tumors, reporting on high disease control rates. 26, 27 th regards to other CRGA, one new finding of our study is the identification of potentially targetable amplification in the NTRK1 gene in an unresectable, stage III, type B3 thymoma. 28 Taken together, our findings support the development of trials or prospective cohorts combining routine use of comprehensive genomic profiling of refractory thymic epithelial tumors to identify CRGA, which are actually diverse and rare at the individual level, together with treatment with targeted agents; such umbrella strategies are needed to actually assess the value of such precision medicine approach, that demonstrated a survival benefit in other solid cancers, such as lung cancers.
Study population Participants were selected from an on-going randomized controlled trial on smoking cessation: "Efficacy, Safety and Toxicology of Electronic Nicotine Delivery Systems as an aid for smoking cessation: the ESTxENDS multicenter randomized controlled trial" (ClinicalTrials. gov Identifiers: NCT03589989) approved by the ethics committees of Bern, Geneva, and Lausanne (Project-ID: 2017-02332), Switzerland. The study was conducted in accordance with the Swiss law and the ethical principles of the World Medical Association Declaration of Helsinki and the International Committee on Harmonization for Good Clinical Practice. All participants provided written informed consent. Inclusion criteria for the ESTxENDS study were: aged 18 or older, current smoker who had consumed five or more cigarettes per day for at least 12 months, and were willing to try to quit smoking within the next three months (exclusion criteria can be found in supplementary information).
Study strengths and limitations Our study has several strengths. We measured a large number of exposure biomarkers (20 biomarkers of tobacco smoke exposure) and two oxidative stress biomarkers. We also had data on factors that influence relationships between the exposure biomarkers and effect biomarkers, such as health status and lifestyle habits. This was particularly important as the oxidative stress biomarkers are not just related to chemical exposures but also lifestyle factors, and can vary greatly between individuals. We were able to characterize exposure biomarkers and their variability from a single exposure source due to our cohort of smokers, and allowed us to assess the relative importance of factors influencing oxidative stress levels. This study had a convenience sampling design.
Acknowledgments The authors are very grateful to all health care workers and researchers working in the " ESTxENDS " project, especially research nurses; to employees of the  Unit of Forensic Toxicology and Chemistry of CURML (Lausanne-Geneva, Switzerland)  for their collaboration; and to employees of the Department of occupational and environmental health of  Unisanté (Lausanne, Switzerland)  who helped with the logistics of urine samples.