dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments We thank the  Animal Facility (UMS006, Toulouse, France)  and the  I2MC Toulouse  platforms (Cytometry ( Elodie   Riant), Histology and Imaging ) for technical support. We also acknowledge  Dr. Thomas Farge  ( I2MC, Toulouse, France ) for providing the cancer cell lines and  Dr. Véronique Gigoux  ( CRCT, Toulouse, France ) for providing LAMP1-RFP plasmid.
Funding This work was supported by grants from the  Institut National de la Santé et de la Recherche Médicale (INSERM) ,  Agence Nationale de la Recherche  ( ANR-19-CE14-0038-01 ),  Région Occitanie ,  Fédération Française de Cardiologie ,  Fondation pour la Recherche Médicale  (" Equipes FRM 2021 ,  EQU202103012601 "). This study was also supported by the  NIH/NHLBI   1K01HL159038-01A1  and  5R25HL146166  (to MB).
An infrared sensor is mounted on the moving electronic module to measure the temperature of the soil surface. Two thermocouples are placed within the soil. Details on the design and instrumentation of the climatic chamber may be found in previous publications  (Lozada et al. 2016)   [7]. After soil moisture conditioning and compaction, the samples were directly placed in the climatic chamber for the thermo-hydric solicitations. Average values of air temperature, relative humidity and wind velocity of 22. 5°C, 46%, and 1. 0 m•s -1 , respectively, were selected for the tests presented in this study. An electronic scale recorded the water mass loss during soil desiccation. All electronic devices and sensors are connected to a data acquisition system that records during the tests at set intervals (10 seconds).
Finally, a digital camera was used to evaluate soil volumetric changes and cracking through image analysis. The images acquired throughout the tests were processed using the Image J software. The images, whose brightnesses have been adjusted, are binarised and then thresholded (Max Entropy). In this method, the area of the black pixels identified as background noise in the first image is subtracted from each image in the series. Each image was trimmed for shrinkage, and the number of black and white pixels was used to calculate the cracked area.
, J. -D. R. , L. D. , M. W. and G. N. ; project administration, C. W. , S. -M. W. , J. -D. R. , L. D. , M. W. and G. N. ; funding acquisition, S. -M. W. , J. -D. R. , L. D. , M. W. and G. N. All authors have revised the work critically for important intellectual content, approved the final version to be published, and agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. All authors have read and agreed to the published version of the manuscript. Funding: This research was funded by a German Federal Ministry of Education and Research (BMBF) grant to G. N. and M. W. in the framework of project MAPVAP (01KI2124), and to L. D. and J. -D. R. by the Agence Nationale de la Recherche (ANR) in the framework of the project MAPVAP (ANR-19-AMRB-0002).
Acknowledgments: We thank  S. Häußler  ( TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover, Germany and Department of Clinical Microbiology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark ) for providing P. aeruginosa clinical strains. We thank the  Core Facility for Electron Microscopy of the Charité Berlin  for support in acquisition (and analysis) of the data. presentation. Unrelated to this project, G. N. received funding for research from  Biotest AG  and M. W. received funding for research from  Bayer Health Care, Biotest AG, Pantherna , and for lectures and advisory from  Actelion, Aptarion ,  Astra Zeneca ,  Bayer Health Care, Biotest AG, Boehringer Ingelheim, Chiesi, Glaxo Smith Kline, Inflarx, Insmed, Novartis, Pantherna, Pherecydes, Sinoxa  and  Teva.
EPMA Element concentrations in sphalerite and pyrite were measured at GFZ Potsdam, Germany, using a field-emission JEOL Hyperprobe JXA 8500F. The conditions for the electron probe-microanalysis conducted in the wavelength-dispersive mode are 20 keV, 20 nA at a beam size of ca. 0. 5 μm. Quantitative analyses were determined by calibrating with natural pentlandite (Fe, Ni, S), sphalerite (Zn), galena (Pb), rhodonite (Mn) and pure metals for Cd, Cu, Ga, Ge, and Te. Counting times on the peak varied between 10s, 20s, and 40s with corresponding backgrounds collected in half of the peak acquisition time. Data reduction was done using a ZAF correction, both taking into account the interactions between incident electrons and the target (Z), between the generated photons and the matrix (A) as well as the fluorescence (F).
13 ). This implies that K enrichment in these fluids is not controlled by the fluid type or its origin, instead WRI played a major role in scavenging K from rocks. Group B fluid inclusions from sample D3-73 are not only enriched in K but also are most intensely depleted in Mg compared to all other FIA's (Figs. 13a, 14c ). In contrast, group C inclusions are the least depleted in Mg and the most enriched in Ca (Fig. 14c ). This implies that these Ca-Mg-rich brines were not affected by dolomitization, instead they experienced Ca gain with simultaneous Na loss through Na-Ca exchange reactions during albitization of feldspars, as they plot significantly to the left of the SW value (Fig. 12a ). The dataset from the Perm Mine as well as sphalerite-hosted FIA's always show general depletion in Mg, with minor exceptions (well B1), and enrichment in Ca relative to the seawater evaporation trajectory (Fig.
14c-d ). Sphalerite-hosted FIA's have elevated concentrations of Sr compared to Zechstein Ca2 and Upper Carboniferous formation waters, in contrast, quartz-hosted FIA's show Sr concentrations that are similar to data of formation waters (Fig. 14d ). These inclusions preserve geochemical characteristics of mixed end-member fluids (metalliferous and Zechstein Ca2-derived H 2 S-rich) and thus their Sr signatures are determined by marine Zechstein carbonate and deeper sources. Significant Sr enrichment in sphalerite-hosted  FIA's (Figs. 7a, 8, 14d)  relative to formation waters indicates that neither Upper Carboniferous nor Zechstein Ca2 formation waters, nor their mixing could have accounted for the bulk Sr budget of the sphalerite-precipitating fluid (Fig. 14d ). Therefore, interactions of metalliferous end-member fluids with deeper Sr-rich sources, e.
In order to assess the Anghiari fault capability to break the surface during strong earthquakes and be the source of historical earthquakes, we acquired high resolution topographic data, performed field survey and geophysical investigations (Seismic reflection, Ground Penetrating Radar, Electrical Resistivity Tomography) and dug three paleoseismological trenches across different fault sections of the Anghiari fault. The acquired data reveal for the first time the Late Pleistocene to historical activity of the Anghiari fault, constraining the age of seven paleo-earthquakes over the last 25 ka, the youngest of which is comparable with one of the poorly constrained historical earthquakes of the Sansepolcro basin. The yielded slip rate is >0. 2 mm/yr averaged over the last 25 ka and the recurrence interval is about 2,500-3,200 years.
We performed detailed geological and geomorphological mapping of the Anghiari fault by means of traditional field work and digital topographic data, including high-resolution digital surface model (DSM) from satellite imagery and local very high-resolution LIDAR digital terrain model (DTM). Near-surface geophysical techniques including Seismic Reflection (SR), Ground Penetrating Radar (GPR) and Electrical Resistivity Tomography (ERT) were used to plan and accurately locate the sites for paleoseismological trenching and analysis. In this paper we will present data and evidence of recent activity on the Anghiari fault in the form of discrete, recurrent surface faulting events, that are likely associated with large earthquakes. The implications for the activity and seismogenic behavior of the Altotiberina LANF are also discussed.
Field and Remote Sensing Surveys Field investigations and geological and geomorphological mapping were carried out along the eastern side of the Anghiari ridge in order to map the surface trace of the Anghiari fault as well as to identify faulted stratigraphic and topographic markers constraining the fault slip history and slip rate. Most of the geologic and geomorphic features such as fault traces and the contacts of Quaternary geological bodies were identified integrating both conventional field mapping and remote sensing techniques: the former was performed using a field tablet integrating a commercial GPS device and a dedicated digital mapping suite (Field Move Software Suite, Petroleum Experts); the latter included the acquisition and analysis of LiDAR data, airborne-acquired through a Riegl miniVUX Sys DL laser scanner mounted on a DJI Matrice 600 pro drone.
Despite the clear high conductivity of the soil at the study site, limiting the probing depth to ∼2 m, the processed GPR profile shows an improved image of the shallow geometries. The processed SEG-Y files were finally imported in the seismic interpretation software OpendTect Pro v. 6. 4 (academic license courtesy of dGB Earth Science, https:// www. dgbes. com, last access: 3 January 2023) for an enhanced display obtained by the calculation of selected seismic attributes  (Taner et al. , 1979)  computed on the GPR signal amplitude and phase, already proven to be effective for detecting fractures and faults  (Ercoli et al. , 2015; Forte et al. , 2012). In particular, the instantaneous phase  (Cinti et al. , 2015)  enhances the interpretability of the reflections geometry and the enhancement of lateral discontinuities.
Paleoseismological Trenching The paleoseismological investigations were conducted between winter 2021 and summer 2022 in two sites across the Micciano fault section (Villa Sterpeto, Podere Todari sites) and two sites across the supposed trace of the Anghiari-Motina fault section (Anghiari sites A and B) (Figure  4 ). First we dug by backhoe a semi-benched trench, 60°-trending, 50 m-long and 3 m-deep at the Villa Sterpeto site, across the fault trace highlighted by the high-resolution SR and GPR data interpretation. In all the four sites, the trench walls were accurately smoothed and cleaned. The faults and the main stratigraphic contacts were identified, flagged with colored pins, and logged. Wall logs were drawn at 1:50 scale for Villa Sterpeto and Anghiari sites and 1:20 scale for Podere Todari site.
Recurrence Intervals and Coefficient of Variation The mean recurrence time interval has been estimated from our paleoseimological earthquake time series and its uncertainties in dating, with a Monte Carlo simulation approach through the tool RP included in the FISH tools package for seismic hazard assessment  (Pace et al. , 2016 , code available at http://fault2sha. net/wp-content/uploads/2020/07/FiSHvers1. 02. zip). Given the time windows of a series of paleo-events the RP tool produces a number of earthquake catalog simulations and computes the average recurrence time and its coefficient of variation (CV), namely the standard deviation of the recurrence times over their mean. CV is a critical parameter for time-dependent seismic hazard estimates, it is often poorly constrained (e. g. ,  Ellsworth et al.
METHODS Simulations. Three-dimensional (3D) mode shapes presented in Fig. 2  are computed via finite element methods using COMSOL Multiphysics software. The following mechanical parameters are used for the material adopting a linear elastic constitutive law: density ρ = 1180 kg/m 3 , Young's modulus E = 2. 96 GPa, and Poisson ratio ν = 0. 38. Domains are meshed by means of three-dimensional 8-node hexahedral quadratic elements of maximum size LF E = 0. 5 mm, which is found to provide accurate eigensolutions up to the frequency of interest. The color-map of the mode shapes reported in Fig. 2  describes the axial displacement of each mass from its equilibrium configuration. It varies from negative (blue) to positive (red) and it is normalized with respect to the displacement maximum value. Sample manufacturing and experimental measurements.
1, 1]. The experimental frequency response function presented in Fig. 1C  is calculated as the ratio of the detected (averaged over 100 times) and the imparted velocity at the acquisition and excitation point, respectively. Elastic waves are excited impacting manually the left edge of the specimen and longitudinal wave velocity is acquired at the opposite edge through a scanning Laser Doppler Vibrometer (SLDV). The laser sensitivity was set to 20 mm/s/V for all the measurements. The data at each λ has been individually normalized with respect to its maximum value. A similar procedure is adopted for the experimental mode shape reconstruction reported in Fig. 2 , and mass #7 was selected as the excitation point (see Supplementary Note 3 39 for further details). A.
Acknowledgements. M. M. is funded by the  European Union 's  Horizon 2020   FET Open (Boheme)  under grant agreement No. 863179. R. K. P. is supported by startup funds from  Kansas State University  and by  U. S National Science Foundation  Award No. 2027455. F. A. acknowledges  N. Herard ,  B. Skoropys ,  M. Coimbra ,  T. Lata ,  N. Compton ,  I. Frankel  and  N. Boechler  for earlier investigation on the experimental realization of a mass-spring system via additive manufacturing.
coli  [33]. The main advantages of this medium compared to the pooled human urine are its reproducibility and its stability  [32, 34]. The higher mean doubling time observed for our clinical isolates in AUM (G = 45. 8 min) than that described for UPEC in pooled human urine (between 36. 3 and 40. 5min)  [34, 35]  can be explained by the greater complexity of human urine, which contains more usable substrates (carbohydrates, amino acids…) than the AUM that only contains small amounts of peptone and yeast extract  [31, 32]. Although no difference in mean doubling time was observed between RCIs and SCIs, we found a notable within-group diversity, that cannot be explained by the genomic profiles of the isolates. However, as genomic data did not highlight any common pattern but suggested that isolates might adapt specifically to conditions encountered in their host, the use of AUM might not be able to reveal the physiological changes following such specific adaptations.
A control group (n = 35) was formed with UPEC "sporadic isolates" (SCIs) collected from patients experiencing only one cystitis episode over the 17-month period of the VITALE study. The SCIs were selected based on their genetic proximity with the RCIs, according to a phylogeny constructed with CH typing data  [11]. Briefly, each iRCI was paired with a SCI from the same CH type when possible. If not, a SCI from the genetically closest CH type was used. Proximity between CH types was determined using a phylogeny based on concatenated sequences of fumC and fimH  [11]. A minimum spanning tree was constructed with BioNumerics software (Applied Maths NV, Sint-Martens-Latem, Belgium) using the unweighted pair group method with arithmetic mean (UPGMA). Comparative genomic studies were performed on 48 isolates: the 24 iRCIs and 24 phylogenetically paired SCIs from the 35 SCIs control group.
Whole genome sequencing and assembly Short read whole genome sequencing (WGS) and assembly were performed on SCIs and RCIs as previously described  [11]. Briefly, sequencing was performed on an Illumina NextSeq500 using the Nextera XT library kit (Illumina Inc. , San Diego, CA, USA) and assemblies were producted using fq2dna v21. 06 (gitlab. pasteur. fr/GIPhy/fq2dna) (Table  S1 ). Long read WGS was also performed for the initial occurrence of each RCI (iRCI). These were amplified by overnight incubation in 10mL of lysogenic broth (LB, MP biomedicals, Santa-Ana, USA), at 37°C and under agitation. Up to 2. 10 9 cells were used for genomic DNA extraction using the Dneasy Blood and Tissue minikit (Qiagen, Hilden, Germany) according to the manufacturer recommendations for isolating Gram-negative bacteria DNA.
SCI and RCI comparative genomic study Short read assemblies of phylogenetically 24 paired iRCIs and SCIs were annotated using Prokka 1. 14. 5  [49]  with defaults parameters. The protein sequences of VFDs used in the study of Ejrnaes et al. [17]  were retrieved from the annotated genomes and compared using MEGA X  [50]. A virulence score corresponding to the total number of VFD for a given isolate. RCI and SCI short reads were also mapped to the sequence of pUTI89 (NC_007941. 1) using Snippy v4. 3. 6 (github. com/tseemann/snippy). More than 75% coverage of the plasmid sequence was interpreted as positive match. Pan-genome analysis of the 48 RCIs and SCIs was performed using Roary 3. 12. 0  [51]. Neighbor joining tree inference was performed using MEGA X  [50]  based on the translated core gene alignment produced by Roary.
The genes in which SNPs were identified between an iRCI and its rRCIs were listed and their sequences were submitted to BlastKOALA  [56]  and Kegg Mapper Reconstruct  [57]  for functional classification. For evolution rate analysis, SNP/day rates were calculated based onthe number of SNPs obtained above for each iRCI/rRCI pairdivided by the time (days) elapsed between rRCI and iRCI sampling. Evolution rate plot was constructed using Microsoft Excel (Microsoft corporation Available from: https://office. microsoft. com/excel). Correlation between time and evolution rate was tested with Spearman's rank correlation test, using R software (V 4. 1. 3, R Foundation, Vienna, Austria).
Biofilm assays Isolates were grown to late stationary phase in LB or AUM; overnight cultures were adjusted as described above and incubated in a microplate in static conditions at 37°C for 24h. Nonadherent bacteria were removed by washing with H2O before adding crystal violet 0. 5%. After 10 min of incubation under gentle shaking at room temperature, the excess of dye was discarded, and each well was washed 3 times with H2O. Ethanol 95% was then added, and the plate was incubated under gentle shaking at room temperature for 10 min. Absorbance at 590nm (A590nm) was measured using a microplate reader. All experiments were performed at least three times. The E. coli str. K12 strain was used as a positive control and fresh medium as a negative control for each experiment. Data were expressed as percent of biofilm formation relative to the positive control.
Fisher's exact test for count data. Global means comparison were performed using Kruskal-Wallis rank sum test and pairwise comparison were performed using Wilcoxon, Mann-Whitney test. Figures Fig 1. Isolate and workflow description. RC patients = patients with recurrent cystitis, iRCI = initial Aknowledgements recurrent cystitis isolate, rRCI = recurrent cystitis isolate associated with relapse(s), SCI = sporadic The VITALE study (NCT02292160) was funded by the French Ministry of Health (Programme cystitis isolate. Hospitalier de Recherche Clinique) We are grateful to Normandy Region and Rouen University for funding in part the cursus of Nicolas Vautrin. 3, R Foundation, Vienna, Austria). Comparison of proportions were performed using Pearson's chi-squared test when applicable. Otherwise, we used.
This study used a real-world population as a synthetic comparator for the single-arm TRANSCEND NHL 001 study (TRANSCEND; NCT02631044) to evaluate the efficacy of lisocabtagene maraleucel (liso-cel) compared with conventional (noncellular) therapies in patients with relapsed/refractory (R/R) large B-cell lymphoma (LBCL). Inclusion and exclusion criteria for the real-world study closely matched the enrollment criteria in TRANSCEND. The analytic comparator cohort was created by matching and balancing observed baseline characteristics of real-world patients with those in TRANSCEND using propensity score methodology. Efficacy outcomes comparing liso-cel-(n ¼ 257) and conventional therapy-treated (n ¼ 257) patients, respectively, significantly favored liso-cel: overall response rate (74% vs 39%; p < 0.
A recent study using a matching-adjusted indirect comparison (MAIC) approach evaluated the comparative efficacy of liso-cel versus salvage chemotherapy based on individual patient-level data from TRANSCEND and summary-level data from SCHOLAR-1. In this comparison, liso-cel had favorable efficacy compared with salvage chemotherapy in patients with R/R LBCL  [9]. However, the MAIC analysis was limited to summary-level data available from SCHOLAR-1 and was unable to adjust for many unreported patientlevel baseline characteristics. The current analysis overcomes these 2 limitations by selecting an external control cohort from a large, pooled, real-world data set (NDS-NHL-001) matched at the individual level to patients from TRANSCEND, thus placing TRANSCEND study results into the context of conventional therapies for patients with R/R LBCL.
Data sources The primary data source for liso-cel was individual patient data from TRANSCEND, which is an open-label, multicenter, multicohort, seamless design clinical trial evaluating the efficacy and safety of liso-cel in adults with R/R DLBCL (de novo or transformed from any indolent lymphoma), high-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (doublehit or triple-hit lymphoma), primary mediastinal B-cell lymphoma, or follicular lymphoma grade 3B  [6]. The data cutoff date for TRANSCEND was June 19, 2020, with a median (range) on study follow-up of 17. 4 (0. 2-24. 0) months. The primary data source for conventional therapy was patient-level data from the NDS-NHL-001 study. NDS-NHL-001 was a global, multicenter, retrospective, observational study that described treatment patterns and evaluated clinical outcomes of adults with R/R LBCL treated in the real-world setting.
All real-world patient-level data collection was retrospective and did not influence clinical practice or patient visit schedules. The cutoff date for the real-world data was December 20, 2019, with a median (range) follow-up of 6. 3 (0. 4-24. 0) months. Each data source for NDS-NHL-001 was responsible for ensuring that data collection complied with applicable national and local ethical, legal, and privacy regulations. Data were acquired from multiple sources to achieve a patient population representative of different clinical care settings and geographic regions.
Statistical methods Statistical methods for the comparison of TRANSCEND to the real-world cohorts were prespecified, including all details for evaluating and handling of missing data and creating the PS and the matches between cohorts, with the exception of the sACC that was conducted post hoc. To ensure balance across baseline characteristics, the PS-stabilized IPTW was used to weight the realworld and respective cohorts from TRANSCEND. Potential prognostic factors for effectiveness and allcause mortality were identified based on available demographic and baseline disease characteristics in TRANSCEND, with additional factors included based on literature review and medical review. Prognostic factors with 15% overall missing data were included in the full multivariable logistic regression after multiple imputations for missing values.
All possible models were evaluated with the best model fit being selected to obtain PS  [10]. PS were obtained for each of the imputed data sets. The final PS model included age, sex, months since diagnosis, number of prior LOTs per year since initial diagnosis to the index date, best response to any prior therapy, R/R to last therapy, prior HSCT, chemotherapy refractory or chemotherapy sensitive to last therapy, bulky disease, extranodal disease, and disease stage. The final PS obtained for each imputed data set and the PS-stabilized IPTW were then used to perform the balancing. Assessment of balance for important baseline covariates between cohorts was conducted through a sideby-side comparison of baseline data for the TRANSCEND and real-world cohorts. For these comparisons, pooled standardized mean differences were computed using Rubin's rules before and after balancing.