dataesr/scientific-paragraphs-categorization huggingface dataset:
Data sets The 15 participants in this study are listed as authors and all are studying or have 1 or more university degrees in biology. Each observer has up to 50 years of field experience in bird surveys. The 15 participants in this project were mainly chosen as part of a 1-week workshop in scientific communication organized by A. P. M. in Guangdong Institute of Applied Biological Resources, Guangzhou, China during November 2017. All study sites were located where the participants were living and hence had a good knowledge of the local avifauna. We collected field data on the number of birds per tree in forests, parks and other habitats with trees. Where possible a pair of forested sites with rural and urban habitats was investigated. We used the definition by  Crowther et al. (2015)  for a tree as a plant with a woody stem larger than 10 cm diameter at breast height.
Three sites had less than 1000 trees surveyed for logistic reasons, but the conclusions of the analyses were qualitatively similar if these three sites were deleted from the analyses. The same observers were generally responsible for surveys of nearby urban and rural habitats. Sociality was defined as the occurrence of individuals that moved together as defined in del  Hoyo et al. (1992 Hoyo et al. ( -2010)). We were able to identify almost all species due to the extensive field experience of the participants. We recorded a few unknown calls using mobile phones and took photographs with mobile phones to identify a few additional species. We provide the data in Electronic Supplementary Material Table  ESM 1.
Septal thickening is a non-specific sign and can be the result of numerous causes: lung fibrosis due to ARDS, or any venous, lymphatic or infiltrative diseases. Despite the rigorous selection of patients in our study, this bias was possible. Others CT scan fibrosis scores are described in the literature  [22, 23] , but, unlike the score used  [24] , none were validated by histological data. To date, the alveolar level of NT-PCP-III can be considered as the best surrogate marker to an OLB for the diagnosis of lung fibroproliferation  [15]. However, the treatment by corticosteroids of lung fibroproliferation remains discussed  [10, 13]. Steinberg et al. showed a trend in mortality reduction in the ARDS patients with high alveolar levels of NT-PCP-III and treated by methylprednisolone. We started a confirmation study (PROCOCO, NCT03371498).
Context. Ruprecht 147 is the oldest (2. 5 Gyr) open cluster in the solar vicinity (< 300 pc), making it an important target for stellar evolution studies and exoplanet searches. Aims. Derive a census of members and the luminosity, mass, and spatial distributions of the cluster. Methods. We use an astro-photometric data set including all available information from the literature together with our own observations. We process the data with an updated version of an existent membership selection methodology. Results. We identify 259 high-probability candidate members, including 58 previously unreported. All these candidates cover the luminosity interval between G 6 mag to i 21 mag. The cluster luminosity and mass distributions are derived with an unprecedented level of details allowing us to recognize, among other features, the Wielen dip.
The mass distribution in the low-mass regime drops sharply at 0. 4 M even though our data are sensitive to stellar masses down to 0. 1 M , suggesting that most very-low-mass members left the cluster as the result of its dynamical evolution. In addition, the cluster is highly elongated (ellipticity ∼ 0. 5) towards the galactic plane, and mass segregated. Conclusions. Our combined Gaia+DANCe data set allows us to obtain an extended list of cluster candidate members, and to derive luminosity, mass and projected spatial distributions in the oldest open cluster of the solar vicinity.
Given its proximity and advanced age, it provides a unique opportunity to benchmark our current understanding of open cluster evolution. Comparing its mass, spatial and kinematic distributions with those of younger and intermediate age clusters can shed light on the processes that shape the clusters life and ultimate dissolution in the galaxy. The mean proper motion of the cluster reported by  Curtis et al. (2013)  is relatively large (µ α cos(δ), µ δ )=(-1. 1,-27. 3) mas yr - 1  , making it a propitious target for the COSMIC-DANCe survey (see for example  Bouy et al. 2013 Bouy et al. , 2015b)). The availability of a significant number of archival images obtained as early as 2008 incited us to include the cluster in our target list and observations. In this work we use Gaia DR2 data at the bright end, complemented with the DANCe one at the faint end to identify Ruprecht 147 members, derive empirical isochrones in standard filters, and obtain its luminosity and mass distributions 1.
Assumptions This section intends to explicitly state the assumptions and simplifications made to accomplish our objectives. They are sorted in order of appearance. 2. 1. In the data set Assumption 1. We limit the study to a circular area of 6 • radius around the cluster centre set at R. A. =289. 10 • , Dec. =-16. 38 •. The latter correspond to the mean positions of the candidate members of Gaia  Collaboration et al. (2018a). The 6 • limit (∼ 33pc) is chosen to provide a sample size that can be computationally tractable. We note that the corresponding area is four times larger than that covered by the previous studies of Gaia  Collaboration et al. (2018a)  and  Cantat-Gaudin et al. (2018a) , who analyzed the central 3 • (∼15pc) radius area. Assumption 2. Measurements (e. g. photometric magnitudes, parallaxes, proper motions) are normally distributed, with mean at the observed value, and standard deviation as the uncertainty.
The entries in the data set provide all necessary information (i. e. mean, variance and correlations) to reconstruct the distribution of measurements of the given observable. Assumption 3. The missing-value mechanism, the cause behind the unobserved values in partially observed sources, is completely at random. This assumption is not entirely correct (e. g. the missing values can be more frequent at the bright and faint limits of sensitivity). However, the correct treatment of the missing value mechanism requires knowledge of the selection function, which is currently unavailable for any of our data sets.
This assumption implies that the true distribution can be recovered by deconvolving the uncertainty distribution. Assumption 8. The observed values and uncertainties of a source are independent of the rest of the sources. Lindegren et al. (2018)  show that the astrometric uncertainties of the Gaia DR2 are correlated, and this correlation can be expressed as function of the angular separation (see their Fig. 14  and 15 ), which implies that this assumption is incorrect. Nevertheless, given the large coverage of our data sets (see Assumption 1), we consider the error introduced by this assumption to be negligible (0. 0008 [mas • yr -1 ] 2 in the variance of proper motions and 200 µas 2 in the variance of parallax). Assumption 9. The cluster true properties are either normally distributed or can be reconstructed by a finite linear combination of normal distributions (i.
DANCe data DANCe (Dynamical Analysis of Nearby Clusters) is a multiinstrument survey that combines public archival data (i. e. catalogues and images) with our own observations, and derives comprehensive astrometric and photometric (visible and nearinfrared) catalogues of sources in nearby (<500pc) clusters (see for example  Bouy et al. 2013 Bouy et al. , 2015a,b),b). In this article, we present our astrometric and photometric analysis of a 8 • × 6 • region centered on Ruprecht 147, which is based on the combination of archival and new wide field images obtained between 2008 and 2017. We searched: the European Southern Observatory (ESO) archive the National Optical Astronomy Observatory (NOAO) archive the PTF archive hosted at the NASA/IPAC Infrared Science Archive (IRSA) the Canadian Astronomy Data Centre (CADC) archive the Isaac Newton Group (ING) archive the WFCAM Science (WSA) archive for wide field images within a 8 • × 6 • region centered on Ruprecht 147.
Astrometric analysis After a visual rejection of problematic images (mostly due to loss of guiding, tracking or read-out problems), the dataset included 2 068 individual images originating from 8 cameras. A total of 303 195 115 individual sources were detected in these images and the final catalogue includes 10 201 564 unique sources. The astrometric calibration was performed as described in  Bouy et al. (2013) , with the following updates: -Support for differential geometry maps to correct for the "tree rings" and the edge distortions in thick, backilluminated, fully-depleted CCD (e. g. DECam,  Derylo et al. 2006 ) improved cross-matching algorithm with HEALPix tessellation  (Górski et al. 2005)  A&A proofs: manuscript no. Rup147  (a) Large gaps between detectors, partial coverage of the focal plane (b) One of the 12 detectors is dead   2014 ), (  6 ) Kuijken (  2011 ), (  7 )  Rahmer et al.
(2018, see their Fig. 7 ) for a density of 10 5 (as that of our data set). On the other hand, a total of 2 820 764 sources from the Gaia DR2 catalogue have no counterpart in our catalogue, either because they are saturated in our images or because they fall in areas of the region defined above not covered by any image in our data set. Because Gaia's proper motion measurements are much more accurate and reliable than our ground-based measurements, we always prefer them over our own measurements, and keep our proper motion measurements only for sources without counterparts in the Gaia DR2 catalogue. Given the heterogeneous spatial coverage of the various datasets, we complement the combined DANCe+Gaia DR2 catalogue obtained above (and including u,g,r,i,z,y,J,H,Ks,G,BP,RP) with Pan-STARRS (g,r,i,z,y), 2MASS (J,H,Ks) and ALLWISE (all 4 bands, Wright 2008) photometry.
In the field model, we include the parallax as any other feature (i. e. allowing for correlations in the multidimensional GMM). The uncertainties and their correlations are incorporated by means of full covariance matrices and deconvolved from the the cluster intrinsic dispersion using the ExtremeDeconvolution package  (Bovy et al. 2011). The latter uses the Expectation-Maximization algorithm to obtain the parameters of a GMM in which the individual uncertainties (in the form of a full co-variance matrix if available) are deconvolved to obtain the intrinsic covariance matrices of the GMM. In a similar way, the photometric uncertainties are deconvolved from the cluster intrinsic photometric dispersion. In both photometric and astrometric models, the value of the w parameter 3  , required by the ExtremeDeconvolution package, is set to the square of the minimum uncertainty present in the data set.
Representation space The representation space is chosen using the method described in  Sarro et al. (2014). However, we always include proper motions and parallaxes (if present) in the representation space because in our experience these are discriminant features. To select the photometric features of our representation spaces we use the members and non-members in each of the completely-observed data sets to run random-forest classifiers (R package RandomForest, Breiman 2001). The latter were trained ten times with a maximum number of 3 features and 1000 trees. We select features based on both their importance (given by the mean decrease in the Gini impurity 4  ) and its percentage of observed sources, preferring those with less missing values. The only condition to choose features is that they must be linearly independent, otherwise it results in redundant information.
| Patient population This multicentric study was conducted in 6 French KT centers (teaching hospitals of Angers, Clermont-Ferrand, Paris-Necker, Poitiers, Rouen, and Tours). The inclusion criteria were as follows: (1) patient aged >18 years and (2) donation after brain death (DBD) (with DIC (DIC+), information available at the biomedicine agency since January 1, 1996. The exclusion criteria were as follows: (1) organ donation after cardiac death and (2) multi-organ transplantation. In France, once the diagnosis of brain death is confirmed, an intensive care unit (ICU) physician and a transplant coordinator collect a clinical history, morphologic evaluation, and laboratory data, including the presence or absence of DIC in the donor. The medical data are then vetted by decentralized departments of the French Biomedicine Agency, the services de régulation et d'appui responsible for controlling and coordinating organ procurement and allocation activities between regions of France.
Thus, between January 1, 1996, and December 31, 2012, 169 (3%) patients with transplants from a DIC+ donor were identified from the Biomedicine Agency's prospective database CRISTAL of 5629 transplantations with a kidney from a DBD in these 6 centers. The presence of DIC criteria defined according to the International Society of Thrombosis and Haemostasis (ISTH)  11  could not be verified in the donors of 24 patients due to a lack of data. Each recipient of a transplant from a DIC+ donor was compared with 2 KT patients who received kidneys from donors without DIC (DIC-). The matching criteria were as follows: (1) the transplantation center, (2) the graft year, (3) the donor's age (± 5 years), (4) the donor's sex, and (5) whether or not the graft was from an expanded criteria donor. 1  This study was approved on April 10, 2013, by the ethical research committee ("Comité de Protection des Personnes Sud-Est 6") (IRB 00008526) and by the consultative committee on the use of health research information on September 4, 2014 (14.
| Patient data The patients' medical and demographic data were retrieved from hospital records and from outpatient and hospitalization files. The following data were collected: (1) for the donor-age, sex, BMI, causes of death, cardiovascular risk factors, and intensive care data (cardiorespiratory arrest, transfusion of labile blood products, use of vasopressor amines, last hourly diuresis and/or any oliguria, first and last blood creatinine and any proteinuria); and (2) for the recipient-age, sex, cause of end-stage renal disease, duration of dialysis, cardiovascular disease, HLA compatibility, cold ischemia time, and postoperative immunosuppressive regimen. We evaluated the outcome of KT patients, including delayed graft function (defined as the need for at least one dialysis session during the first 7 days after KT  12  ), initial stay duration, graft survival, and cause of graft loss.
| Statistics All statistical analyses were performed using Stata statistical software (version 13, StataCorp, College Station, TX). The tests were 2-sided, with a type I error set at α = 0. 05. Categorical data were expressed as number of patients and associated percentages. Quantitative parameters were expressed as the mean ± standard deviation or median [interquartile range], according to statistical distribution (assumption of normality was checked using the Shapiro-Wilks test). Comparisons between independent groups (DIC+ and DIC-) were performed using a chi-square or Fisher exact test for categorical parameters and Student's t test or Mann-Whitney test when t-test conditions were not met (normality and homoscedasticity by the Fisher-Snedecor test) for quantitative variables. Correlated repeated data were analyzed using a random-effects model (generalized linear mixed model [GLMM] with logit link function) to consider between-and within-patient variability because the data could not be assumed to be independent.
Consistent with current literature data, in our study, the type of induction  23, 29, 30  or delayed introduction of a calcineurin inhibitor  23, 29  (≥72 hour or >120 hour) had no impact on the DGF rate or on the renal function of patients, whether or not their graft was from a DIC+ donor. 31 r work has several limitations. First, because of the retrospective nature of this study, some patients may have received a DIC+ kidney unknowingly, and so they were not included as such in the study; only 2. 6% of brain-dead donors who gave kidneys were DIC+, according to the data recorded by the Biomedicine Agency in 2013 (unpublished data), whereas the prevalence of DIC defined according to the criteria 11 in ICUs is estimated at between 17% and 30%. 3 Thus, several brain-dead patients presenting with severe DIC+ were probably ruled out for kidney donation before proposal to the transplant team.
The planning and operation of Hydrogen Supply Chains (HSC) often require easily extensible, generic dynamic simulation tools. In this paper, the non-conventional modeling and simulation methodology of Programmable Process Structures is applied for the description of these process systems. Programmable Process Structures of HSC models are generated from the two general functional meta-prototypes of the method and from the description of the studied HSC network. The actual program prototypes of production, transformation, transportation, utilization and intermediate storage are copied from the meta-prototypes and filled with the locally executable declarative program code for the various classes of elements. The actual state and transition elements are parameterized and initialized according to their case-specific prototypes.
The freely editable, actual program of the prototypes contain symbolic input, parameter and output variables, as well as a locally executable GNU Prolog [21] code. In the various cases, the actual state and transition elements can be modeled with the same or a similar reusable local program, while the number of program prototypes is considerably less than the number of actual elements. The state and transition elements of the Programmable HSC Structures can be parameterized and initialized concerning their case-specific prototypes. During the simulation, the actual elements are executed by the prototypes associated with them. This execution results in cyclically stepwise, connection-based communication of the state and transition elements of the programmed structure with the general-purpose kernel that works like an operational system.
The structure also contains the two empty meta-prototypes. The generated Programmable Process Structure describes all of the state (storage of resources, intermediates and products) and transition elements that represent the transformation and transportation in the various compartments (spatial scales) individually, because they may have different parameters and connections. By default, the transportations belong to the sending compartment. This representation does not result in the multiplication of the program code because many elements are executed by the same meta-prototypes that contain the local programs (see the next Section). The connections from the state to transition elements represent the causally right transfer of quantitative and qualitative amounts and signals necessary for the calculation of the transitions.
Generation and simulation of the example HSC system Programming of the process structure is followed by its automatic interpretation into the executable dynamic databases of the given model. Now the general model generator of the kernel reads the GraphML file and generates: • the facts that describe the actual state & transition elements and those that determine state → transition and transition → state connections in the "user" file; • the clauses that declare the program prototypes in the "expert" file. The resultant user and expert files contain a detailed description of the process model, including the locally executable program prototypes as well as the actual elements and connections that contain the initial data and parameters. Having generated the model, the executable code has to be supplemented by the (optionally scale-specific) global data, e.
g. g(dt, DT ), that also declares the main time step in the previous example code. Dynamic simulation is executed by the general kernel program that comprises the cyclically repeated processing of state elements, state → transition connections, transition elements and transition → state connections. For example, the execution of all transitions associated with the prototype of prot_photovolt are executed by the the unification of them, e. g. is unified with the prototype where Program_prot_photovolt refers to the example code above. The variables in prototypes are described by alphanumeric symbols that start with a capital letter. The variables and constants in the functors i(), c() and o() are described by lists of the triplets d(Identifier, Variable_list, Instructions).
• the extensibility of Programmable Process Structures favours stepwise structural and functional changes in supply and demand without reformulation of the model. • optional multiscale compartmentalization helps to represent multiple districts and sites via the optional connection between spatial coordinates of the elements with an external GIS tool. • individual elements and connections can be associated with a time-driven execution at given points in time and/or over prescribed time intervals. • material and energy balances can be combined with signal and rule-based, event-driven processes. • a Programmable Process Structure has built-in capabilities for robust communication with external (e. g. meteorological) databases and collaborating (e. g. metaheuristic optimization) programs. • the method supports the handling of the extraordinary uncertainty of coefficients of cost and some other parameters over a longer time horizon.
Neutrophils, basophils and eosinophils are not detected, consistent with reports of granulocytes emerging during fetal BM haematopoiesis  7. Early stage samples show erythroid lineage bias, with later lymphoid and myeloid lineages representation, as previously shown  5  (Figure  1c  and Extended Data 1g). Our fetal liver dataset can be explored using an interactive web portal through the following weblink: https://developmentcellatlas. ncl. ac. uk//datasets/hca_liver/. We provide comprehensive expression profiles of genes known to cause primary immunodeficiencies  8  to aid future molecular phenotyping of these disorders (Extended Data 8).
We hypothesized that the cellular composition of the developing fetal liver resulted from local modulation of HSC/MPP potential. To test this, we FACS-isolated single cells from the CD34 + CD38 + , CD34 + CD38 -CD45RA -and CD34 + CD38 -CD45RA + FACS gates and profiled them by both plate-based single cell transcriptomics (Smart-seq2) and single cell clonal differentiation assays  44, 47  (Extended Data 7a). A support vector machine trained on the fetal liver dataset identified enrichment of HSC/MPPs (~85%) in the CD34 + CD38 -gate, with the majority of cells in the CD34 + CD38 -CD45RA + MLP gate also classified as HSC/MPP (Extended Data 7b). This is in agreement with reported transcriptional similarity between HSC/MPP and MLP 78 and our identification of lymphoid priming in the HSC/MPP compartment.
Cytospins and mini bulk RNA-seq validation Fetal liver cells were immunostained with two separate panels (see Supplementary Table  15  for antibody details). Cells were stained for 30 minutes on ice followed by DAPI staining. FACS was performed on a BD FACSAria™ Fusion instrument, and data analysed using FlowJo (v10. 4. 1). Cells were isolated into chilled FACS tubes coated with FBS and prefilled with 500μL sterile PBS for cytospin (500 -2000 cells), or into 1. 5mL microfuge tubes containing 20μL lysis buffer (100 cells). Giemsa staining (Sigma-Aldrich) was used to determine the morphology of sorted cells on cytospins. Slides were viewed using a Zeiss AxioImager microscope, images taken of 4 fields from n = 3 samples using the 100x objective, and viewed using Zen (v2. 3). Raw images supplied in Supplementary Images.