dataesr/scientific-paragraphs-categorization huggingface dataset:
Ensemble star formation relations in VERTICO Figure  2  shows the relation between the star formation rate surface density, Σ SFR , and the molecular gas surface density, Σ mol , for the ensemble sample of galaxies selected from VERTICO. The left panel shows the VERTICO data at 9 (720 pc) resolution, while the right panel shows the same dataset convolved to A3, page 5 of 25  Resolved KS relation for the ensemble of VERTICO galaxies at a resolution of 720 pc (left) and for the data convolved to a linear resolution of 1. 2 kpc (right). Only galaxies with i < 80 • have been selected, excluding edge-on targets, in order to avoid absorption and strong projection effects. Color code shows increasing point density. Contours show the corresponding KS relation using the sub-sample of field galaxies extracted from the HERACLES survey.
We note that values for Σ SFR and Σ mol have been corrected to face-on via cos i. 15 , corresponding to physical scales of 1. 2 kpc. In both panels, the individual bins are color-coded by point density, where brighter colors show higher density of data points. The panels also include levels of constant depletion times of 0. 1, 1. 0, and 10 Gyr, respectively, as dashed gray lines. These diagonal lines represent an estimation of the time that the rate of star formation would need in order to deplete the molecular gas reservoir to produce stars. The blue contours shown on top of the VERTICO data correspond to sub-samples of HERACLES field galaxies, chosen to match the fixed-physical scales samples in each panel. Therefore, these data are also plotted at 720 pc and 1. 2 kpc resolution in order to compare two datasets that are intrinsically very different, between cluster and field galaxies.
The plot shows that the KS relation between SFR surface density and the molecular gas surface density for the high-density points of VERTICO galaxies is very similar to that found for the HERACLES field galaxies. The scatter in the data shown in Fig. 2  is approximately symmetric around depletion times of 1-3 Gyr. Figure  2  therefore demonstrates visually the first main conclusion of this paper: when considered as an ensemble, the A3, page 6 of 25 Notes. Best-fit slope (N), intercept (referenced to Σ mol units of 1 M pc -2 ), and scatter (σ) results for the resolved KS relation in the VERTICO sample, comparing the ensembles at 720 pc and 1. 2 kpc resolution, as well as the HI-normal and HI-deficient samples of galaxies. KS relation for Virgo cluster disk galaxies is consistent with field galaxies.
a log 10 Σ SFR /Σ mol = -9. 10 ± 0. 06 and a 1-σ scatter of 0. 41 dex. These two statistically different KS relations indicate that HI-deficient galaxies are offset toward more quiescent SFR surface densities by 0. 23 dex. These differences clearly show that the resolved KS slope and star formation efficiency are moderately affected by the galaxy environment, in the sense that more HI-deficient galaxies tend to have steeper slopes and show lower molecular gas efficiency than HI-rich galaxies. We compare these two samples of galaxies in the right panel of Fig. 3. This plot represents the SFR -M relation in VERTICO, limiting our sample to those HI-deficient and HInormal galaxies covering the same range in stellar mass. This approach allows us to compare their properties more homogeneously. The blue data points indicate HI-normal (nondeficient) galaxies, whereas the red data markers represent the HI-deficient subsample of galaxies.
Star Formation Efficiencies in VERTICO Our results can additionally be analyzed in terms of the star formation efficiency of the molecular gas, SFE mol or, conversely, in terms of the depletion time τ dep as defined in Sect. 5. 1. VERTICO allows us to resolve different regions within galaxy disks, so that we can explore dependencies of the depletion times as a function of the local environment. While combining our measurements into a single dataset is helpful to understand the ensemble tendencies of our galaxies, it can obscure real trends and differences among them. Figure  5 , together with our measurements in Table  A. 1 show systematic variations in the power-law index among galaxies, as well as in their median τ dep values from galaxy-to-galaxy. In addition, we also encounter large internal variations in the depletion times for the majority of the sources, as reflected by the individual mean scatter of ±0.
Summary and conclusions In this work we employ new data for 37 spiral galaxies included in the ALMA large program VERTICO. These observations were used to investigate the resolved properties of the molecular gas and, combined with tracers of star formation activity, they allowed us to explore the resolved scaling relation between Σ SFR and Σ mol , known as the resolved KS relation, for the first time in a sample of star-forming galaxies within a cluster. In order to assess the universality of the KS relation, we explored the ensemble and individual scaling relations, and compared our results to a controlled sample of field, isolated galaxies from the HERACLES survey. Our main results are the following: 1. We confirm a strong correlation between Σ SFR and Σ mol at a linear resolution of 720 pc for the ensemble of galaxies, with a mean slope of N = 0.
Acknowledgements. MJJD thanks  Miguel Querejeta ,  Eric Pellegrini  and  Ivana Bešlić  for helpful discussions during the development of this work. CDW acknowledges support from the  Natural Sciences and Engineering Research Council of Canada  and the  Canada Research Chairs program. IDR acknowledges support from the  ERC Starting  Grant Cluster Web  804208. AC acknowledges support by the  National Research Foundation of Korea (NRF) , grant No. 2018R1D1A1B07048314. Parts of this research were supported by the  Australian Research Council Centre of Excellence for All Sky Astrophysics in 3 Dimensions  ( ASTRO 3D ), through project number  CE170100013. LCP acknowledges support from the  Natural Science and Engineering Council of Canada. The work of JS is partially supported by the  Natural Sciences and Engineering Research Council of Canada (NSERC)  through the  CITA National  Fellowship.
We selected one crop farm and one livestock farm that are representative of the study area according to regional statistics and local experts. These farms could exchange straw and manure: the livestock farmer buys straw and produces more manure than the quantity required to maintain soil organic matter, while the crop farm purchases mineral fertilizers and its soil organic matter is below 2%. The crop farm has 250 ha of UAA with two worker units (two full-time equivalents). We chose to model a rapeseed-wheat-barley crop rotation, which is typical of the region. Straw is systematically ploughed back into the land. The data used to describe the cash crop farm are taken from the published average data for local cash crop farms in the Saône-et-Loire  (DRAAF, 2016). The specialized livestock farm is a Charolais cow-calf operation (male calves are sold to feedlot finishers) producing fattened heifers and cull cows (Institut de L'Elevage, 2016).
L is the amount of N lost by leaching, which has been neglected here as we assume that R i is measured at the beginning of the growth season. The values of these parameters were defined according to the data of GREN Bourgogne 2012 (Appendix IV). Two levels for net humus mineralization (Mh) are considered: the first level corresponds to irregular inputs of organic matter through application with regular straw plough-in (33 kg N ha -1 yr -1 ), while the second level corresponds to regular long-term manure inputs and partial straw export (50 kg N ha -1 yr -1 ). According to local experts, 24 tons of manure for every 2 yr would be sufficient to reach this level of mineralization of 50 kg N ha -1 yr -1 on field crops and 10 tons on grasslands. The fact that grasslands are not very sensitive to variations in amount of manure applied is explained by the turn-out of livestock to pasture and by microbial life under grasslands  (Chabbi and Lemaire, 2007; Curien et al.
, 2017). Consequently, if the machine is used more intensively, its depreciation and maintenance costs per hour of use decrease. The time and machinery needed for manure application depend on the quantity of manure and the capacity of the manure spreader. The time and machinery needed to spread mineral fertilizer depend on the number of applications per hectare and type of spreader. The time and machinery needed to harvest the straw and transport it to the farm depend on quantity of straw and size of the trailer. The duration of the work performed, fuel consumption and maintenance and depreciation costs are all taken from the Chambre d'Agriculture des Hauts de France (2016) database, and are listed in Appendix V. Input and output costs and net income: Net income corresponds to the total output from crop and livestock production, plus added government subsidies and minus operating costs, farm overheads, employee salaries, depreciation, rent and interest paid.
Straw is sold at €60 ton -1. 1 The price of the straw purchased is made up of 80% of the price of the straw sold and 20% of the price of transport. The prices of the synthetic fertilizers used in the model are taken from French agricultural statistics based on the purchase price of agricultural inputs in France (IPAP), and from data provided by Arvalis (technical institute for crop production). The average price of these items over the 2010-2015 period was €1. 045 per kg N for ammonium nitrate with 33. 5% nitrogen, €0. 834 per kg P for phosphorus chloride with 45% phosphorus and €1. 017 per kg K for potassium chloride with 60% potassium. Comparative data between the optimized farming system and the reference system are provided in Appendix III.
Acknowledgments. The authors thank the development-project agents:  Denis Chapuis ,  Antoine Villard ,  Christine Boully  and  Joris Deville  who participated in the collective workshop and proposed their expertise to help validate certain data from the study. We also thank  Sylvie Recous ,  Gwenaelle Lashermes ,  Sabine Houot  and  Bernard Nicolardot  for their valuable expertise on nitrogen dynamics data and manuring recommendations. We finally thank  Geoffrey Phillips  for his revision of the English version of this paper. Financial support. This study was funded by  PSDR program  (supported by  INRA , the  European Union  and the  regions Bourgogne-Franche-Comté and Rhône-Alpes ).
| Root system and grain yield analyses Root samples were collected between the 25 of May and the 3 of June, 2021 by using one soil core of 0. 08 m diameter and 0. 15 m length per plot, in the central row of each plot. Total sampled depth varies among sites, while cores of a 0. 15 m depth were collected from soil surface until bedrock layer (Supporting Information: Table  S1 ). Since the volume of the last core was not always the same, data were normalized per gram of soil. After sampling session, elutriation  (Smucker et al. , 1982) , a method based on differential sedimentation  (Fenwick, 1940)  and adapted by  Blouin et al. (2007) , was used to separate the roots from soil mineral particles and dead OM: Afterward, root pieces were recovered and stored in water at 4°C for a week for further image analysis and incubations.
| Statistical analysis Analyses of root traits, incubations and grain yield data were performed with the Rstudio software (RStudio Team, 2020). Normality and homoscedasticity of the data were assessed using Shapiro and Bartlett test, respectively, using R default functions. Non-normally distributed data (Root Biomass, Average Diameter, Projected Area for all sites and Root Length for Dijon) were log-transformed. Data were analyzed site by site in one-way analysis of variance (ANOVA), with the breeding type as a factor for estimated CO 2 emissions per square metre and grain yield (no relevance of depth), or in two-way ANOVA, with the breeding type and depth as factors, for root traits and measured CO 2 emissions. Data were also analyzed for all sites taken together in two-way ANOVA with the breeding type and site as factors, for estimated CO 2 emissions and grain yield.
We also performed three-way ANOVA, with the breeding type, the depth and the site as factors. The data of root traits for all sites taken together were analyzed with the Scheirer-Ray-Hare test. These analyses were followed by a post-hoc Tukey'Honest Significant Difference test (p < 0. 05, package 'agricolae', (De Mendiburu, 2017)). To get an overview of the links between measured CO 2 emissions, plant traits and soil parameters (SOC, TN, C/N, Clay, Silt, Sand, pH and CEC), we performed a multivariate analysis (principal component analysis [PCA]) across sites. We also performed a second PCA for each site independently to get an overview of the covariation between some root tissues' elementary composition (percentage of C and N) with the other variables (root biomass, estimated CO 2 emissions and grain yield).
Whatever the study site, the observed trend is a decrease in root biomass with depth (Figure  1 ). The sites of Breteniere and Morvan presented a higher biomass within the first 0. 15 m of soil (0. 72 and 0. 71 mg g -1 of soil, respectively) than those of Saint Romain and Dijon (0. 53 and 0. 39 mg g -1 of soil, respectively) (Figure  1 ). We also tested the specific root length (length of root per gram of dry root), on which the breeding type had no impact (p = 0. 27, data not shown).
ACKNOWLEDGEMENTS The authors thank  Institut Agro Dijon  for its experimental facilities. The authors are grateful to  Jean-Philippe Guillemin ,  Wilfried Queyrel  and  Etienne Gaujour  for their advices in wheat culture and the management of the experimental site. The authors thank  Graines de Noé , especially  Hélène Montaz , for providing the seeds of ancient varieties, as well as  RAGT Semences , Secobra,  Saaten Union  and  Limagrain  for providing the modern varieties. The authors would also like to express our gratitude to  Jean Lévêque  and the  GISMO platform (Biogéosciences ,  University Bourgogne Franche-Comté ,  UMR CNRS 6282, France)  for their help in the incubations process. The authors also thank  Léa Luttenbacher ,  Juliette Bouteille  and  Solenn Salaun  for the help they provided during their internships.
Introduction Both non-contrast Computed Tomography (CT) and ultrasound (US) are used for the diagnosis of renal colic in the emergency department (ED). Although US reduces radiation exposure, its diagnostic accuracy is inferior to that of CT. In this context, data regarding the cost and organizational impact of these strategies represent essential elements in the choice of imaging; however, they remain poorly documented. Aim of the study The aim of this study was to compare the costs and effectiveness of diagnostic workup by US and CT for patients consulting with renal colic in the ED. Methods We conducted a monocentric real-life retrospective study of patients consulting for a renal colic in an ED between 1 July 2018 and 31 December 2018. We estimated length of stay (LOS), total hospital costs at 60 days including ED, and initial and repeat admissions.
Currency, Price Date, and Conversion Hospitalization and monitoring data were obtained from local hospitals claims databases. Hospitalizations were valued using the corresponding French disease-related group (DRG) cost, adjusted by LOS and number of days in intensive care  [13] [14] [15]. For patients who were not hospitalized, we imputed the average cost of outpatient ED visits plus the cost of ED imaging, assessed using the statutory health insurance tariffs (Table  S1 ).
Selection, Measurement and Valuation of Effectiveness Primary Endpoint The incremental cost-effectiveness ratio (ICER) was calculated as the difference in costs divided by the difference in ED LOS. As the secondary endpoints, we measured: 1. Time to imaging, measured as the time from admission to the time of first imaging, as recorded in the ED electronic health record; 2. Proportion of patients who underwent a second imaging in the ED; 3. Care pathway after ED workup as a proportion of admissions (by medical service type, including intensive care unit [ICU] and short-stay unit); 4. Proportion of rehospitalizations during follow-up from local hospital claims databases; 5. Proportion of patients with imaging during 60-day follow-up recorded in medical file.
Rationale and Description of Model In order to compare the outcomes between US and CT in the EDs in this nonrandomized study, we used a regression model weighted by inverse probability of the propensity score using demographic variables (age and sex), laboratory tests (C Reactive Protein-CRP-, leucocyte numbers, and Cockcroft estimated glomerular filtration rate-eGFR-), and presence of hydronephrosis. For missing data, we used multiple imputation with chained equations to create and analyze 10 multiply imputed datasets. Incomplete variables were imputed according to a fully conditional specification, using the default settings of the mice 3. 0 package  [16]. For each data set, we used a generalized linear model to model ED LOS and employed a Gaussian family with a log link because the distribution of ED LOS was skewed and lower bounded to 0.
Analytics and Assumptions We computed the groups' marginal effectiveness and costs with US as a reference. For the main effectiveness measure, we used the negative value of LOS in the ED (2 h became -2 h) in order to reflect the incremental cost saved for 1 h saved in the ED. Quantitative variables were described as mean ± standard deviation, while categorical variables were described as numbers and percentages. Chi-square or Fisher's exact tests, analysis of variance (ANOVA), and the Kruskal-Wallis test were used as appropriate. There were no missing data concerning cost and effectiveness since we extracted the data from the electronic health records and the health insurance national database. A p-value < 0. 05 was considered significant.
After ED management, the consumption of care is another criterion to be considered for the effectiveness of the imaging strategy. However, there are few data on ED revisits as a function of imaging strategy and results concerning ED revisits differ according to the studies. In the study of Blecher et al. , revisits to the ED were less frequent for US than CT, with rates of 12% and 19%, respectively; however, a second CT was performed in the ED for more than 50% of patients with initial US  [29]. Although other studies have not found a difference in revisits according to initial imaging  [28, 35] , our study revealed that the strategy involving US was more costly than CT, particularly because of the cost of rehospitalization and the need to perform a second imaging in the ED for some patients.
Finally, our measure of effectiveness did not take into account diagnostic accuracy and patients' health states, which could be debated. However, the superiority of CT diagnostic accuracy over US was already known, and the goal of changing the imaging strategy in the ED was correlated with the need for efficient triage to optimize patient flow. Indeed, the LOS in the ED is notably influenced by the imaging strategy and represents a major outcome in evaluating the effectiveness of imaging on the management of patients in these units, with the need for quick and accurate decisions to initiate treatment if necessary and control overcrowding. Thus, the time spent in the ED seemed to be the better performance outcome. To our best knowledge, this is the first study to provide real-world data on the costeffectiveness of imaging strategies performed in the ED for the diagnostic workup of patients with renal colic.
The availability of CT, especially low-dose CT, is a relevant method to improve patient flow in the ED with a rapid care pathway dedicated to suspected ureteral calculi. In our center, for example, multidisciplinary collaboration between radiologists and emergency physicians has made it possible to set up a care network with rapid access to the ulta-low-dose CT for patients consulting with a strong clinical suspicion of renal colic, as soon as they arrive in the ED (excluding women of childbearing age). This may be a solution to allow for more efficient management of these patients in the ED. Finally, it would be very informative to compare these data with a more recent dataset, as the trend and difference between the two modalities (US and CT) would be even more significant with the increasing availability of low-dose CT scanners allowing reduced radiation with better diagnostic relevance compared to US.
All other patients in the study were unrelated. In our cohort, nine patients had frameshift variants, two had partial deletions, one had a deletion of a single amino acid, 11 had nonsense variants, three had splice site variants, and 16 had missense variants (Fig. 2A ). Most of the missense variants were in the SET domain. Human population-level genetic data [gnomAD (Genome Aggregation Database)] show that pLOF variation in KMT5B is highly constrained (i. e. , extremely rare; LOF pLI = 1. 00) but that some level of missense variation may be tolerated (Z = 2. 79). This is likely domain specific with less variation tolerated within the SET domain. The missense variants in our study were in regions that are highly conserved (Fig. 4A  We performed in silico modeling using mCSM (mutation Cutoff Scanning Matrix)  (30)  and RING (Residue Interaction Network Generator)  (31)  to evaluate the functional impact of our 14 unique missense variants.
RNA-seq of KMT5B haploinsufficiency in human and mouse Given the chromatin modifying functions of KMT5 enzymes, we subjected our patient-derived lymphoblast cell lines and mouse resources to further gene expression experiments to identify genes and pathways whose expression patterns are regulated by KMT5B. We subjected transformed lymphoblast cell lines  (35)  from seven patients in the study to RNA-seq in tandem with seven age-and sex-matched controls. KMT5B is expressed in human Epstein-Barr virus-transformed lymphocytes according to GTEx with expression levels similar to most adult brain regions. Quality control metrics for this dataset are shown in fig. S5. Human differentially expressed genes (hDEGs) were defined as those that met a raw P value of P < 0. 05. By this metric, 654 genes were up-regulated and 648 genes were down-regulated in cases compared to the controls.
Twenty-one genes survived false discovery rate (FDR) correction (q < 0. 05; Fig. 6A ). See table S5 for a full list of hDEGs. Ingenuity Pathway Analysis (IPA) of all hDEGs with P < 0. 05 provided an unbiased evaluation of pathway enrichment and revealed significant enrichments for axon guidance signaling (P = 1. 85 × 10 -9 ), glycoprotein 6 signaling (P = 9. 63 × 10 -9 ), and CXCR4 signaling (P = 1. 61 × 10 -6 ) pathways (Table  1 ). While the top disease pathway enrichment in the hDEG dataset was cancer (P = 2. 06 × 10 -4 to 6. 78 × 10 -21 ), there was also a strong signal for nervous system development and function pathways (P = 2. 13 × 10 -4 to 2. 46 × 10 -9 ; table  S6 ), predicting significantly increased growth of neurites (P = 4. 95 × 10 -6 ), outgrowth of axons (P = 1. 15 × 10 -5 ), outgrowth of neurites (P = 1.
43 × 10 -5 ), and growth of axons (P = 2. 10 × 10 -4 ). Significant predicted upstream regulators included Paired box gene 3 (PAX3; P = 1. 82 × 10 -8 ), Proline-, glutamic acid-, and leucine-rich protein 1 (PELP1; P = 3. 76 × 10 -7 ), β-estradiol (P = 5. 48 × 10 -7 ), and transforming growth factor-β receptor 2 (TGFBR2; P = 1. 37 × 10 -6 ; table  S7 ). A summary of all IPA findings highlighted brain-relevant phenotypes focused on changes in fibroblast growth factor 2 (FGF2) signaling (Fig. 6B ) and further that cell growth and migration may be affected by KMT5B expression. Notably, several genes linked to the phenotypes in our cohort were differentially regulated in the hDEG dataset including MRAS, GNAQ, WDFY3, PLCB1, and NR2F2. We have previously shown that the embryonic mouse brains of Kmt5b haploinsufficient mice show a robust down-regulation of Kmt5b expression and an increase of H4K20me1  (33).