dataesr/scientific-paragraphs-categorization huggingface dataset:
The statistical significance of excess deaths was determined using the 95% CIs estimated by the model. It is important to note that only countries providing weekly data (n ¼ 19) were included in the second methodological approach. In addition, 2019 weekly mortality data were not available for Scotland and therefore the estimation of 'baseline' was based on 2015-2018 data in both methods. For Northern Ireland and Spain, sex-specific all-cause mortality data were not available at the time of data analysis, so sex-specific all-cause mortality was calculated for 17 countries. England and Wales were considered as one country for the purposes of analysis and reporting of results, as combined data are routinely provided this way. For each country, the reported type of COVID-19 death was used in both methods and no between-country comparisons were attempted.
Selection of methods The review process followed the main steps of the framework for systematic reviews in agricultural science  (Koutsos et al. , 2019)  derived from the most widely used and more formal PRISMA framework developed by  Moher et al. (2010). Our inventory covered the period between 1993 and 2019 and included scientific literature and grey literature. We ran the equation of  Rasmussen et al. (2017)  on Web of Science and the equations of  Lampridi et al. (2019)  on Scopus, applied to the study period (see equations in Fig. B. 1 in the supplementary materials). This database query was completed with ESAM from the inventories of  Buckwell et al. (2014 ), De Olde et al. (2016) , and  Wustenberghs et al. (2015b)  and our research group, who built the INDIC® database (GIS GC HP2E, 2018).
These four reviews were carried out using a snowballing approach, where the reference list and citations of relevant papers were reviewed to identify new papers. Two authors reviewed the papers; one examined the entire set of papers and the second author reviewed at least half of them to reach a consensus. As noted by  Levitan (2000)  with regard to the pesticide risk indicator, several ESAM were published only in grey literature in reports, or more recently on websites. The whole inventory resulted in a dataset of 4523 dedicated methods and case studies. We applied a set of elimination criteria (see Table  1 ) to eliminate any methods which did not have an environmental dimension or pertain to the agricultural sector, such as those focusing only on landscape or forestry management. The last criterion for articles published about a simple application of a dedicated method or methodological framework such as LCA helped eliminate the voluminous literature on LCA implementation.
Statistical analysis Following a descriptive analysis, we performed a multivariate analysis to look for trends and clusters. We performed a first multiple correspondence analysis (MCA) for the 262 ESAM on 12 descriptors that we felt were most relevant and a second MCA on 17 themes (see Table  2 ) using RStudio version 1. 3. 959 and the FactoShiny package  (Husson et al. , 2010). Next, we performed a hierarchical ascendant classification (HAC) to obtain several clusters using the FactoMineR package. Finally, we ran a Chi-Square test to cross-check the HACs to determine whether the ESAM and theme clusters were independent or dependent.
General information on methods The research equations described in Lampridi and Rasmussen logically resulted in the most ESAM, followed by the INDIC® database (Fig. B. 3a). With regard to the chronological distribution between ESAM sources (Fig. B. 3b), we observed that the INDIC® database provided the most methods for the first half of the review period; the equation research resulted in more methods for the second half. Most of the methods in our inventory came from scientific literature (81%). A total of 60% of studies dealt with a "dedicated method" while "case studies" represented only 37%; the remainder (3%) were "methodological frameworks". Our ESAM sample covered 60 different countries in all. The major contributing countries were France (12%), Italy (8%), Spain (5%), China (5%) and Brazil (4%)  (Figs.
To make our inventory more comprehensive, we completed the inventory with two databases containing more than 100 methods, built by the snowball approach (Wohlin, 2014). In both the PRISMA framework  (Moher et al. , 2010)  and the framework for systematic review for agricultural science developed by  Koutsos et al. (2019) , additional reviews may be added manually to fill gaps  (Babí Almenar et al. , 2021). For our review, 27% of the ESAM come from manual additions. Moreover, unlike De Olde et al. (  2016 ), we analysed the whole inventory to obtain much more solid and representative results than with those previously obtained. De Olde and Wustenberghs carried out four  (De Olde et al. , 2016)  to 53 samples  (Wustenberghs et al. , 2015). A second novel aspect of this review lies in our aim to clearly identify and characterize conceptual and methodological trends across this broad inventory and to identity gaps in those domains.
Unlike De Olde et al. (  2016 ) and  Marchand et al. (2014) , we were not attempting to compare methods in order to help end-users select an operational method. Thus, we did not include descriptors on the type of data, the time needed for implementation etc. to evaluate feasibility. In all the cited reviews, we noticed a mix of real descriptors (e. g. assessment purpose, scales etc. ) and evaluation criteria (user-friendliness, validation of results, transparency etc. ; see  Dale and Beyeler (2001) ;  Binder et al. (2010) ;  Bockstaller et al. (2009) ;  Bonisoli et al. (2018) ;  Marchand et al. (2014) ). However, in our study, some descriptors or themes could also be used to evaluate and help users select a method (as we discuss in section 4. 3. ). The Excel files provided in Tables D and F in the supplementary materials may be used as a database to select methods meeting a research query, based on a set of descriptors (e.
, 2020). With regard to antibiotics,  Lynch et al. (2019)  stated in their research of sustainability indicators for Ireland that the only indicators that could be proposed would be based on national statistics of antibiotic use. This would be a causal indicator which provides no information on the risk of antibiotic resistance. Agricultural soils are not only major receptors of microplastics through sewage sludge but also a source of microplastics through plastic mulches and polytunnels. Data exist for sewage sludge but not for mulches and polytunnels  (Horton et al. , 2017). The impacts of microplastics could be again assessed by causal indicators such as the amount of plastic used or amount of waste. In our review, 12% of the methods covered waste management and some addressed plastic use (e.
However, all of those papers only dealt with one or two sustainability themes (in many cases profitability or productivity). There is a need to continue such studies, but they need to take a multi-criteria approach to a set of sustainability indicators. Starting with the study by  Sands and Podmore (2000) , one possibility would be to integrate one or several years with a strong perturbation (e. g. severe drought or water excess) in climatic series and model the system behaviour to calculate the time of system recovery, which could be an indicator of resilience. Such a study would require a modelling effort and adapted datasets.
Conclusion In this study, we performed a review of unprecedented size of environmental sustainability assessment methods from all over the world. The main aim was not to look at comparison criteria, even if the databases describing the methods may make it possible. Rather, we sought to thoroughly analyse the conceptual and methodological framework behind these methods as well as the environmental themes they covered. We identified four clusters of method descriptors and four clusters of environmental themes. Two of the method clustersone characterized by ex ante methods to select, classify or rank at field level and one characterized by LCAmainly deal with limited themes covering the main environmental issues (climate change, water quality, soil erosion etc. ). ESAM developers can take away several general recommendations from our review.
Acknowledgements This study is part of a PhD research project supported by a grant (n •  2019/0020 ) overseen by the  French National Research Technology Agency (ANRT). The authors would like to thank  Philippe Girardin  for having initiated this research 15 years ago;  Jerôme Rosnoblet  and  Chloé Schneller  for their early contributions to the INDIC® database;  Pauline Feschet  and  Emilie Thomas-Delille  for the INDIC® database;  Maria Lampridi  ( IBO, University of Thessaloniki ) for the literature database;  Allan Buckwell  for the file of methods supporting his report; the members of the PhD steering committee,  Frédérique Angevin ,  Philippe Jeanneret ,  Nicolas Munier-Jolain ,  Olivier Therond  and  Clotilde Toqué  for their advice, and  Jean Villerd  for statistical support.
Methods We numerically simulated impact craters made by the Apollo S-IVB impacts on the Moon and quantified the seismic efficiency and seismic moment using the iSALE-2D shock physics code  (Amsden et al. , 1980; Collins et al. , 2004; Wünnemann et al. , 2006). As the orientation of the S-IVB boosters at impact is not known, we explored the sensitivity of impact outcomes to booster (impactor) geometry by considering six idealized scenarios. The enforced axial symmetry of our impact geometry limited the scenarios that could be considered for vertical impact of right cylinders and spheroids. It is expected that penetration modes produced by more disk-like projectiles will be different from those caused by spherical projectiles  (Walker, 1999). In order to explore the sensitivity of crater radius to projectile footprint area, which might give some insight into the possible range of crater ellipticity, our scenarios vary in radius and length depending on the projectile geometry presented.
Acknowledgments A. Rajšić  and  K. Miljković  are fully funded by the  Australian Government  through the  ARC  ( DE180100584 ,  DP180100661 ). N. Wójcicka  and  G. S. Collins  research is funded by the  UK Space Agency  (Grants  ST/S001514/1  and  ST/T002026/1 ). I. J. Daubar  was supported by  NASA   InSight Participating Scientist grant   80NSSC20K0971. The authors gratefully acknowledge the developers of iSALE (https://isale-code. github. io).
Study design We performed a prospective non-interventional study over a threeyear period (between June 2016 and February 2019) under the approval of a regional ethics review board (ID-RCB: 2016-A00036-45), which was granted on March 22, 2016. Every patient was informed and had given their signed written consent to participate in the study prior to surgery. Patient characteristics, including anatomical and clinical data, were collected perioperatively and registered in a dedicated institutional database.
Statistical analysis Dichotomous/categorical patient characteristics are expressed as the frequency (percentage) and continuous patient characteristics as the mean and standard deviation. Intergroup differences were evaluated by logistic regression with univariate (threshold p < 0. 20) and multivariate analysis. As a descriptive study, the protocol estimated the number of cases to include to be at least 20 patients to match the preliminary study, which was raised in order to perform a multivariate analysis. Statistical analysis was performed by a dedicated biostatistician using SAS software (version 9. 4, SAS Institute Inc. , Cary, NC, USA).
Patients In this prospective study, 62 patients matched the inclusion criteria and 53 were enrolled after the exclusion of nine patients. Among the nine excluded patients, seven were excluded because of intraoperative adhesiolysis, compromising the assessment of lymphatic drainage of the visceral pleura, and two because of an unplanned intraoperative wedge resection required for frozen section examination. The population of the study consisted mostly on early stage lung cancer (n = 34/53, 64. 2 %, stage cI), with a predominance of adenocarcinoma (n = 32/53, 64. 2 %). The characteristics of the included patients, including preoperative and intraoperative data and postoperative outcomes, are summarized in Table  1.
Article We then tested the role of these adhesion molecules in parasite extravasation and reservoir establishment. At day 6 postinfection (day 8 post-treatment), animals were subjected to intravital microscopy. Extravascular parasite density was measured by IVM, and data are presented in a heatmap as a fold change relative to (day 0) control (left panel) and as the percentage of values of WT untreated mice (whose value for each organ is taken as baseline, 100%) (Figure  6D ; Figure  S10 ). Interestingly, blocking ICAM1 and VCAM1 resulted in either no change or an increase in parasite density in most organs (except the spleen, where parasite density decreased significantly), while not affecting significantly overall blood parasitemia or mouse survival. Conversely, blocking PECAM1 had no effect on the presence of extravascular parasites in most organs (Figure  6D ).
On the bottom compartment, we added HMI-11 media. We then added T. brucei parasites to the top chamber, and after 1-h incubation, we counted how many parasites crossed from the top to the (H) Heatmap of parasite enrichment in multiple organs on day 6 post-infection, calculated from the ratio of detected parasites per area in the extravascular space, in mice homozygous or heterozygous for CD36 depletion versus wild-type littermates. Zero was set as the baseline control, and data are plotted in a log10 scale. Graphs in the middle and right panels show the extravascular parasite density in g-WAT and pancreas on day 6 post-infection. For all experiments, measurements correspond to triplicate experiments obtained from 9-12 mice. Heatmaps correspond to the score of at least 100 measurements from at least 12 individual mice.
For ex vivo imaging of perfused organs, mice were injected with RediJect as described above, and sacrificed using CO 2 within 3 minutes following this injection. The chest was then exposed, the inferior vena cava was cut, and the heart was injected with 40 mL of warm 1x PBS. Organs were then imaged as described above. Image acquisition was obtained, and image analysis performed using the Living Image â software version 3. 0. 4. 6. For all bioluminescence measures, the results of 9 animals (3 biological replicates in triplicate) are expressed.
QUANTIFICATION AND STATISTICAL ANALYSIS Data were displayed in graphs and heatmaps generated using Prism 9 software (GraphPad). Means, medians, survival, correlation tests, comparison tests, and error measures were calculated from triplicate experiments with 3 biological replicates each, and/or at least 100 images per condition. For comparisons of bioluminescence measures between organs of different groups we performed multiple t tests in addition to a one-way ANOVA (differences were considered significant when p < 0. 05). Pearson correlations measures (R), and R 2 values were calculated to determine the strength of linear association between parasite density and either vascular permeability or vascular density. For comparison of proportions between parasites in vessels of different diameters and proportions in vessels of equal diameter across vascular groups, a linear model was performed, and p values < 0.
ACKNOWLEDGMENTS The authors thank  Brice Rotureau  ( Institut Pasteur ) for providing the triple reporter (TY1-TdTomato-FLuc) AnTat1. 1 E T. brucei parasite line. We thank  Ruy M. Ribeiro  for helpful advice for statistical analysis and  Leonor Pinho  for logistical help regarding experimental setups. We acknowledge the  Rodent and Bioimaging Facilities of the Instituto de Medicina Molecular. We thank  Maria Angeles Dominguez Cejudo  from  Claudio Franco's lab (IMM)  for technical support. We also thank  Francisca Vasconcelos ,  Sara Silva Pereira ,  Fabien Guegan , and  Idalio Viegas  for carefully reading this manuscript and providing helpful and critical feedback. This work was supported by  HFSP  ( LT000047/2019-L ) and  EMBO  ( ALTF 1048 ( ALTF -2016 ) ) to M. D. N. L. M. F. is an Investigator CEEC of the Fundacão para a Ciência e a Tecnologia ( CEECIND/03322/2108 ), and the laboratory is funded by  ERC (FatTryp , ref.
As such, we can easily see that approaches such as LDA-1/2 are bound to fail in this case. As a first strategy to solve this problem, we decided to include samples calculated within ensemble-DFT at fractional densities in our training. To obtain this data we created a set of total energies and electronic densities for a series of 1-dimensional exact calculations. We then constructed ensemble densities and inverted the ensemble Kohn-Sham equations, in order to compute the exact xc energy and potential for these systems. We used an inversion algorithm based on Ref. [44]  that we extended for both spin-DFT  [45]  and to ensemble systems. As a result, we created exact training and testing data with particle numbers between 1 and 3 electrons, that we used to train our models. In Fig. 2  we compare the mean absolute error (MAE) of the total energy for a functional trained with fractional densities (blue) and a functional trained only for systems with integer densities (red) (averaged over a test set of 100 external potentials).
Instrumentation 1 H NMR and 13 C NMR spectra were obtained of the solutions in deuterated chloroform (CDCl 3 -d 6 ) with a Bruker Avance III spectrometer. The data are given as chemical shifts in δ (ppm) and tetramethylsilane was used as Elemental analysis was performed with an Exeter Analytical CE-440 elemental analyser, Model 440C/H/N/. an internal standart. Mass spectra were obtained on a Waters ZQ 2000 mass spectrometer. IR spectra were recorded with a Vertex 70 Bruker spectrometer. Elemental analysis was performed with an Exeter Analytical CE-440 elemental analyser, Model 440C/H/N. Thermogravimetric analysis (TGA) was performed on a TA Instruments Q50 apparatus at a heating rate of 20 • C/min under nitrogen atmosphere. Differential scanning calorimetry (DSC) measurements were performed on a 100 TA Instruments Q2000 thermal analyser at a heating/cooling rate of 10 • C/ min under nitrogen atmosphere.
Mass spectrometry analysis -µHPLC-Q-exactive plus The sample was analyzed by liquid chromatography coupled to a mass spectrometer equipped with a heated electrospray ionization (HESI) probe. HPLC was performed using a Dionex U3000 RSCL Instrument. The injection volume was fixed at 5 µl (Ultimate 3000, Thermo Fisher Scientific). Protein analysis was performed on a 2. 1mm i. d. x 150mm , 5µm, Syncronis C18 column at a flow rate of 250 µl/min. The elution program was based on water (solvent A) and acetonitrile (solvent B) both containing 0. 1% formic acid (v/v): 0 min 5% B, 18 min 80% B, 19 min 90% B. The Q-exactive plus spectrometer completely controlled by the Xcalibur software was operating in electrospray positive mode. Typical ESI conditions were as follows: electrospray voltage 4 kV; capillary temperature 320°C, probe temperature 325°C, sheath gas flow 40U and auxiliary gas 10U.
Cells were seeded on µDish or µSlide (Ibidi). Plasmids were transfected using Lipofectamine 3000 reagent according to the instruction's guidelines (ThermoFisher Scientific). After 6 hours, the cells were fixed with PFA 4% for 20 min at room temperature. Golgi staining was performed using sheep polyclonal antibody against TGN46 (AHP500G, Bio-Rad). Live cell observations for FRAP experiments were done using a confocal microscope (Zeiss LSM-780). Images were analyzed using Fiji J software. To determine the fraction of GFP-TPD54 and mutants at the Golgi, we outlined the Golgi area from the TGN46 signal carried out in the red channel. Then, we applied the corresponding mask to the green channel to define a region of interest (ROI) at the Golgi and a ROI of the same area in the cytosol. Once the background was subtracted, we determined the average fluorescence in each ROI and calculated the Golgi/cytosol ratio.
All images were acquired with a confocal microscope and were analyzed using Volocity software. For STED experiments, TPD-54 and ALPS(GMAP-210)-ACC1 were cloned in the halo-tag vectors HTN and HTC, respectively. After transfection, these constructs were revealed using a Janelia Fluor 549 ligand (promega). Endogeneous proteins were labeled with Rb polyclonal antibody anti-TPD52L2 (proteintech), Rb polyclonal antibody anti-GMAP-210 (proteintech) or Ms monoclonal anti-Trip230 human (Invitrogen). Images were acquired on a Leica confocal TCS SP8 STED microscope. Deconvolution was performed using Huygens Professional software. 54. Larocque, G. , Moore, D. J. , Sittewelle, M. , Kuey, C. , Hetmanski, J. H. R. , La-Borde, P. J.
Versions 6. 1. 0 to 6. 1. 11 are therefore bit-reproducible for a given domain decomposition, compiling options and supercomputer. LMDZ, XIOS, NEMO and ORCHIDEE are released under the terms of the CeCILL licence. OASIS-MCT is released under the terms of the Lesser GNU General Public License (LGPL). IPSL-CM6A-LR code (version 6. 1. 0) is publicly available through Apache Subversion (svn) control system, with the following command lines under Linux: svn co http://forge. ipsl. jussieu. fr/igcmg/svn/modipsl/trunk modipsl; cd modipsl/util;. /model IPSLCM6. 1. 11-LR (IPSL-CM model development team, 2021). The mod. def file provides information regarding the different revisions used, namely (1) NEMOGCM branch nemov36STABLE revision 9455; (2) XIOS2 branchs/xios-2. 5 revision 1873; (3) IOIPSL/src svn tags/v224; (4) LMDZ6 branches/IPSLCM6.
0. 15 rev 3643; (5) tags/ORCHIDEE20/ORCHIDEE revision 6592; (6) OASIS3-MCT 2. 0branch (rev 4775 IPSL server). The login and password combination requested at first use to download the ORCHIDEE component is "anonymous" and "anonymous". We recommend referring to the project website, http://forge. ipsl. jussieu. fr/igcmg_doc/wiki/Doc/Config/IPSLCM6 (IGCMG, 2022), for a proper installation and compilation of the environment (version 6. 1. 10). The UK Earth System Model is documented in  Sellar et al. (2019a). Due to intellectual property rights restrictions, we cannot provide the source code or documentation papers for the Unified Model (UM). The Met Office UM is available for use under licence. A number of research organizations and national meteorological services use the UM in collaboration with the Met Office to undertake basic atmospheric process research, produce forecasts, develop the UM code, and build and evaluate Earth system models.
The effects of SAR340835 on the autonomic nervous system (ANS) were explored. Spectral analysis of heart rate variability was performed for the evaluation of autonomic tone in all telemetered dogs before and at the end of the 3 hours of dosing. This spectral analysis using a fast-Fourier transform algorithm on sequences of 512 points (5 minutes) was performed with the HEM CsA10 software (Notocord Systems, Croissy, France). Specific frequency bands of heart rate variability permitted the simultaneous assessment of sympathetic [Low Frequency] and parasympathetic [High Frequency] modulation, with the Low Frequency/High Frequency ratio illustrating the sympathovagal balance. Spectral powers were determined as the area under the curve calculated for the very low frequency (0. 04-0. 05 Hz), low frequency (0.