dataesr/scientific-paragraphs-categorization huggingface dataset:
Some final interesting observations come from the methodology of this work. First, the results of the survey were integrated by additional research of rCTDs registries performed in the existing databases online, thus capturing registries that would have likely been missed otherwise. Secondly, it should be underlined that the quality of the identified registries was not addressed by this mapping activity. In fact, all the registries identified by the survey and the web-searching were included, regardless of the data setting, sample size, geographical coverage and current state (still ongoing/not ongoing). This overview aims to give a starting point to identify the gaps and the strengths of registries covering rCTDs, which TogethERN ReCONNET is expected to fill and enhance, respectively. The biggest challenge is the current lack of registries for some rare clinical conditions.
However, existing registries offer the basis to develop a common data set for TogethERN. ReCONNET, in order to promote a homogeneous approach for data collection on rCTDs, by avoiding fragmentation and duplication of data. In addition, the future work of TogethERN ReCONNET will also include the alignment to the to the quality and Fairification requirements and to the European Platform on Rare Disease Registration, such as the adoption of the set of common data elements for Rare Diseases Registration.
Acknowledgments A special thank goes to the following persons for providing their important support in collecting the data:  Micaela Fredi  and  Cecilia Nalli  ( Rheumatology and Clinical Immunology Unit, ASST-Spedali Civili and University of Brescia, Brescia );  Laura Damian  and  Cristina Pamfil  ( Department of Rheumatology, Emergency County Teaching Hospital, University of Medicine and Pharmacy Iuliu Hatieganu Cluj-Napoca, Romania );  Sabrina Paolino (Laboratory of Experimental Rheumatology and Division of Clinical Rheumatology, Department of Internal Medicine DIMI-University of Genoa , Genoa, Italy;  IRCCS Polyclinic Hospital San Martino, Genoa, Italy) ;  Chiara Cioni  ( Rheumatology Unit, Azienda Ospedaliero Universitaria Pisana, University of Pisa, Pisa, Italy ).
Acknowledgements None. Author contributions All the authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by  Frederik G. Dikkers ,  Marc Remacle ,  Antoine Giovanni ,  Riaz Y. Seedat ,  Guillermo Campos  and  Guri Sandhu. The first draft of the manuscript was written by  Frederik Dikkers , and all the authors commented on previous versions of the manuscript. All the authors read and approved the final manuscript.
Materials and Methods Data from COVID-19 autopsies were collected through a questionnaire survey. The electronic template was submitted via email to nine pathologists, members of the European Society of Pathology-Pulmonary Pathology Working Group, experts in thoracic pathology and involved in autoptic activities during the COVID-19 pandemic. The involved centers included: University Hospital of Padova (Italy); University Côte d'Azur (France); University Clinic of Respiratory and Allergic Diseases (Slovenia); Hospital of Navarra (Spain); Erasmus MC (The Netherlands); Moscow City Hospital #40 (Russia); Medical University of Graz (Austria); Lausanne University Hospital (Switzerland); Karolinska University Hospital (Sweden) (Figure  1a ). For all centers, no specific inclusion criteria were used for patient enrollment in this study.
Autopsies are usually performed to confirm dubious diagnoses and specific clinical-scientific questions. Particularly, the autopsies were performed for the patients who had shown an unusual clinical course. Participants were asked to provide data regarding their COVID-19 autoptic practice during the first (from March to August 2020) and the second wave (from September 2020 to February 2021) of the pandemic. Specifically, participants were asked to report the number of autopsies performed in these two different periods and provide: demographic data; technical procedures of autopsy and lung sampling; and the frequency of occurrence of several pathological signs related to COVID-19 lung-related pathological lesions (e. g. , diffuse alveolar damage [DAD] with vascular impairment, airway inflammation, emphysematous changes with large bullae, bacillary and fungal pneumonia, concomitant lung lesions such as cancer or interstitial lung disease, and pleural involvement).
Results All centers responded to the survey in a period between two weeks and three months. All responses are reported in Supplementary Material (S1). Comparative data came from a total of 313 autopsies. Full autopsies were performed in five centers, limited autopsies (although always inclusive of the complete examination of both lungs) in the remaining centers. The lungs were extensively studied from a histological point of view: in seven centers more than ten lung parenchyma samples were analyzed (between four and ten in two centers), and the large airways were sampled from almost all the participants (8/9). Table  1  summarizes some demographic and clinical-pathological data, which are extensively listed in Supplementary Material (S1). Figure  1a  shows the European.
Results All centers responded to the survey in a period between two weeks and three months. All responses are reported in Supplementary Material (S1). Comparative data came from a total of 313 autopsies. Full autopsies were performed in five centers, limited autopsies (although always inclusive of the complete examination of both lungs) in the remaining centers. The lungs were extensively studied from a histological point of view: in seven centers more than ten lung parenchyma samples were analyzed (between four and ten in two centers), and the large airways were sampled from almost all the participants (8/9). Table  1  summarizes some demographic and clinical-pathological data, which are extensively listed in Supplementary Material (S1). Figure  1a  shows the European country countries involved in the survey.
Here we investigate the behavior of stochastic-threshold incision models across the south-eastern margin of the Massif Central in France which is characterized by significant relief and the regular occurrence of high-discharge events. Our study is based on a new dedicated dataset combining measurements of discharge variability from gauging stations, denudation rates on 34 basins from 10 Be cosmogenic radionuclide (CRN) concentration measurements in river sediments, morphometric analysis of river long-profiles analysis and field observations. This new dataset is used for a systematic investigation of various formulations of the SPM and discuss the importance of incision thresholds. Denudation rates across the SE margin of the Massif Central are in the 20-120 mm/ka range and they positively correlate with slope and precipitation.
DiBiase and  Whipple (2011)  provided the first of such investigations in the San Gabriel mountains in California, and demonstrated the suitability of river incision models combining an incision threshold and a power law distribution of extreme discharge events to account for observations on river profile steepness and erosion rates. More generally, they explored the behavior of this relationship across a wide range of climatic configurations to highlight limits in the response of channel incision to increase in runoff. Based on a denudation dataset spanning very contrasted climates along the central Chilean Andes,  Carretier et al. (2013)  demonstrated the role of extreme discharge event in driving most of the erosion for arid settings. Scherler et al. (2017)  developed an analysis at the scale of the whole Himalayan arc and Eastern Tibet in order to explore the underlying reasons for long-wavelength variations in the relationship between channel steepness and erosion rates.
They notably explored the influence of a spatially variable incision threshold and assessed the importance of climatic controls such as characteristics of monsoon precipitation. More recently,  Campforts et al. (2020)  highlighted the importance of taking into account lithological and climatic spatial differences when using this type of model to analyze the variance in CRN-derived denudation rates datasets. These studies were critical tests of our ability to reconcile topographic and geochronological observations using physicallybased framework for river incision. However, many of these earlier investigations relied on pre-existing CRN datasets that were acquired with sometimes independent sampling strategies. It implies datasets combining catchment areas varying over two order of magnitudes, and with notably large basins (>100 km 2 ) which cover surfaces displaying important variations in bedrock geology and climate.
In contrast with most previous studies which have addressed such questions, we design a dedicated sampling strategy focusing on a the Southeastern margin of the Massif Central (France), a region with well defined short-wavelength climatic and hydrological gradients and limited recent tectonic activity. For that purpose, we acquired a new consistent CRN dataset for catchment-wide denudation to compare measured landscape evolution rates with predictions of various river incision models. We analyzed river profiles and basins morphometric parameters to evaluate their relationships with denudation rates, we compiled hydrological data from gauging stations in order to characterize discharge variability, and we combined new and existing bedload size data to constrain the incision threshold. Based on the premise that river networks are the main drivers of landscape evolution, the relationship between channel steepness and erosion rates have been intensively scrutinized, in particular to assess the implications of its degree of nonlinearity.
At first-order, our new dataset displays a complex structure between these two observations, which can not be adequately fitted by a simple scaling relationship and highlight the need for a careful consideration of spatial variations in the lithological, climatic and hydrological parameters. We develop this argument by first recalling the theoretical background behind stochastic incision models and outlining the main characteristics of our study area, with an emphasis of the specific characteristics which make it a particularly appropriate setting for our investigation of such models. Then, we describe the methods used and the dedicated sampling strategy we designed, as well as the results obtained. On the basis of these results, we explore the consistency of model predictions with the observed denudation rates.
, 2020). Bedrock lithology is dominated by crystalline Hercynian basement (granites, gneisses and micashists), Mesozoic-Cenozoic sedimentary series and Late Cenozoic volcanic rocks (Fig. S1 ). In the following we focus on the quartz-bearing lithologies when collecting samples for 10 Be analysis. In summary, the SE Massif Central presents a clear topographic margin with contrasting domains on both side of the drainage 165 divide, associated with strong climatic and hydrological gradients. In our study we take advantage of this particular configuration as well as low tectonic activity and strong climatic variability, to explore stochastic-threshold incision models. We present the various datasets which were acquired or used for our study. For the sake of clarity, for each type of data we successively present the methodology and corresponding results.
Results We observe a positive correlation between basin-averaged MAP and runoff measured at gauging stations (Fig. 4 ). Runoff (mm) There is no clear distinction in behavior between the interior of the massif and its Southeastern margin, and catchments draining over carbonate lithologies do no display a different trend than the rest of the dataset. We use the fitted linear relationship between M AP and R in order to compute an estimate for runoff R for the catchments where we obtained 10 Be denudation rates (table  S3 ). • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • • R= 1. 087 MAP -635 R = 0.
Methods We calibrate the scaling relationship between discharge and channel width (equation 5), with measurements at various locations in our region of interest. We use IGN orthophotos (BD ORTHO IGN -50 cm resolution) in low-vegetation areas or field measurement with a laser range finder. We combine our data with measurements from the Carhyce database  (Gob et al. , 2014)  (http://194. 57. 254. 11/IED/, accessed 01/05/21). Discharge values at the measurement site were calculated from the runoffprecipitation calibration relationship (Fig. 4 ). We restricted our analysis to drainage areas < 400 km 2 and discharge >0. 1 m 3. s -.
Results We observe a positive correlation between channel width and discharge (Fig. 5A ) and, for a given discharge, channel widths are larger along the margin (Cévennes and Ardèche) than west of the divide (red symbols). We fit power laws to the whole dataset and to subsets corresponding to both sides of the divide in order to calibrate the relationship described by equation 5. When considering the whole dataset we obtain a value for the exponent ω b = 0. 44 which is within the range of reported previous observations  (Campforts et al. , 2020) , and close to the ω b = 0. 55 we impose in order to keep equation 8 dimensionally consistent when using m/n = 0. 45. In this case we obtain a value of k w = 5. 56 ± 0. 37 m -0. 65 s 0. 55. If we distinguish the regions East and West of the divide, the values of k w are 4.
Methods We use bedload median size D 50 to estimate the critical shear stress τ c using equation 3. We performed bedload counts at some sites in the Cévennes and Ardèche areas and combined these results with D 50 measurements from the Carhyce database  (Gob et al. , 2014)  (http://194. 57. 254. 11/IED/, accessed 01/05/21). In addition to the determination of a single τ c value derived from the average D 50 over our study area (DiBiase and  Whipple, 2011) , we also consider the possibility of spatial variations in τ c. Such variability can be parametrized using equation 3 and a power law relationship between k sn for the upstream basin and the median bedload grain size D 50  (Attal et al. , 2014; Scherler et al. , 2017) , such as, D 50 = k 50 k q sn (13).
Results Median bedload size is ranging from 10 to 200 mm over our study area. The average D 50 is 80 mm (Fig. 5B ), corresponding to τ c = 40 Pa which is similar to the value used by DiBiase and  Whipple (2011)  in the San Gabriel Mountains. Coarse bedload was dominant in the river we surveyed along the margin, whereas we observed occurrences of gravel or sand-dominated reaches for the low relief parts of the landscape, west of the divide. Fitting equation 13 to the dataset support the existence of a power-law relationship between D 50 and k sn , with exponent ∼0. 8. We do not observe a difference in scaling between the two sides of the divide. For the low-k sn regions, corresponding mostly to areas west of the divide, measured D 50 values are dominantly in the 30-60 mm range, whereas they are mostly >50 mm for the eastern catchments draining toward the Rhône.
Results Measured 10 Be concentrations in the 34 sampled catchments range from 51 to 345×10 3 at/g (table  S1 ). The corresponding calculated denudation rates range from 24 to 126 mm/ka (Fig. 1A ), which correspond to integration time of 25 and 5 ka, respectively. We observe clear regional differences in denudation rates between the main sampling areas. The upper Loire and Garonne catchments, in the interior of the Massif Central, display the lowest denudation rates with averages of 33±4 mm/ka and 37±4. 5 mm/ka, respectively. Significantly faster denudation is observed along the margin of the Massif, in the Ardèche mountains (58±7 mm/ka) and especially in the Cévennes area (95±11 mm/ka). We note that Basin CDX-14, with the highest denudation rate of the dataset, is located next to the main divide between Garonne and Rhône watersheds, very close to the Cévennes area and is draining over schist bedrock.
This range of denudation rates is consistent with previous observations in the Massif Central  (Schaller et al. , 2001 (Schaller et al. , , 2002;; Molliex et al. , 2016; Olivetti et al. , 2016). Denudation rates are positively correlated with basins average slope and relief (Fig. 6A  and S4 ) but the dataset as a whole does not display any clear relationship with steepness index (Fig. 6B ). With the exception of CDX-CRN-30, all the sampled basins have areas between 20 and 100 km 2 and we do not observe any dependence of denudation rates with catchment area over this range (Fig. S2 ), suggesting that there is no 1 st order scaledependent bias in terms of the processes contributing to denudation in our dataset  (Niemi et al. , 2005; Yanites et al. , 2009). 5 Denudation rates modelling.
After the presentation of the data and main results of our study, we now discuss our denudation rates dataset in the context of the SE margin of the Massif Central, the relative efficiency of the various SPM formulations which can be used to explain the distribution of these denudation rates, and the comparison of our observations with other similar studies in other regions. We note that the time scale of our study is relatively short and set by the integration times of denudation rates ranging from 5 to 25 ka (table  S1 ).
Distribution of denudation rates Here we discuss the spatial distribution of denudation rates across the SE margin of the Massif Central and their relationship with morphological parameters. As we described earlier, the range of denudation rates from our sampled catchments is consistent with previous observations in the Massif Central. Olivetti et al. (2016)  report denudation rates ranging from 34 to 79 mm/ka on 27 watersheds located directly north of our studied catchments in the Ardèche mountains, with similar lithologies and areas. As many of the catchments from  Olivetti et al. (2016)  contain knickpoints, the relationships between denudation rates and morphology is not directly comparable with the one observed with our dataset, for which we specifically selected basins according to the regularity of river long profiles.
A larger scale analysis of denudation in the Gulf of Lion drainage system was performed by  Molliex et al. (2016) , with 4 sampled watersheds along the south-eastern margin of Massif Central, corresponding to the Eyrieux, Ardèche, Cèze and Gard rivers near the Cévennes mountains, with average denudation rates of 79. 6±15, 67. 4±11. 5, 78. 0±16. 2 and 70. 0±11. 9 mm/ka, respectively. The sampled basins are one order of magnitude larger than the ones in our dataset, and drain over heterogeneous lithologies with a significant contribution of the sedimentary cover in the low relief area between the Massif central Margin and the Rhône river, which might explain the slightly lower denudation rates when compared to our samples from the Cévennes area. Denudation rates of 33±7 and 68±16 mm/ka were obtained by  Schaller et al.
(2001)  on the other side of the divide for the Allier and Loire catchments, respectively. Both catchments are larger (>250 km 2 ) than the ones we sampled and include Cenozoic volcanics, but the denudation rate reported for the Allier headwaters from Schaller et al. (  2001 ) is consistent with our observations from smaller catchments 11 and 12, while we have no equivalent in our dataset for the Loire headwaters catchment where higher denudation rates are reported. Denudation rates are positively correlated with basin-average slope (Fig. 6A ), with a progressive linear increase in low-relief basins of the interior of the Massif with slope ranging from 5 o to 15 o and then a much more rapid increase beyond 20 o for the Cévennes and Ardèche basins along the margin. Such relationship between denudation rates and slope is consistent with nonlinear models of hillslope evolution, where denudation rate increase very rapidly when hillslope angles become close to their stability threshold  (Ouimet et al.
Equations 8 and 10 predict a non-linear relationship between denudation rate and steepness index k sn with a strong influence of the discharge variability parameter k (DiBiase and  Whipple, 2011). Due to the absence of a clear unique trend in our dataset, no single theoretical relationship can explain the distribution of denudation rates and k sn when using regionally averaged values for model parameters (Fig. 6B ). Even if Cévennes basins data appear to be consistent with model predictions for low discharge variability k values, in other areas the k values which would yield the better correspondence between data and model do not agree with observations. For example, basins from the Ardèche mountains and the Loire headwaters display low and high k values, respectively, whereas the theoretical relationship between denudation rate and k sn on figure 6B would imply the opposite.
Such discrepancy highlights the limitations of using regionally averaged values for model parameters such as erodibility or runoff, and notably the necessity of taking into account the strong climatic spatial gradients observed over our study area (Fig. 1B ). Although our dataset does not display a single clear trend between k sn and denudation it is consistent with the global trend delineated by other similar studies using catchment-wide denudation rates (Fig. 8 ). Our dataset lies at the lower end of the global distribution and overlap with data from other areas such as the Ecuadoran Andes  (Vanacker et al. , 2015)  or Eastern Tibet  (Ouimet et al. , 2009). We note that the dispersion of our data around the trend, both in terms of denudation rate or k sn , is similar to that of other regional datasets.
Performance and limitations of modelling formulations We now discuss the relative behavior of various model formulations of increasing complexity and their ability to explain the variation in denudation rates observed in our dataset. Similarly to results by  Campforts et al. (2020)  we observe an improvement of the predictive power between the A-SPM and R-SPM types of models (Figs. 7A  and 7B ), highlighting the importance of the spatial distribution of precipitation in controlling that of denudation, at least in this type of context (e. g. Moon et al. , 2011). In contrast with many observations in tectonically active settings (e. g. Godard et al. , 2014; Scherler et al. , 2014)  In our case, using a ST-SPM setting the critical shear stress according to observations to τ c = 40 Pa induces a clear failure of the model ability to reproduce the observed denudation rates (Fig.
Field measurements, in the area we investigate, are consistent with such dependency (Fig. 5B ), and following  Scherler et al. (2017) , we have tested the impact of introducing a variable incision threshold dependent on k sn (equations 13 and 3). Such parametrization yields a significantly better fit than the constant threshold case (Fig. 7D ), in particular for some of the low-denudation catchments of the dataset, and allows to take into account differences in bedload size across the divide. However, this model formulation still largely underpredicts erosion rates for many of the low-denudation interior catchments, and as a consequence yields a fit to the observations which is still inferior to R-SPM predictions. We note that the Stochastic-Threshold Stream Power Model is built on the assumption that river incision is detachment limited and a function of bed shear stress τ.