dataesr/scientific-paragraphs-categorization huggingface dataset:
However, as shown by the scatter plots and the NSE SCD criterion, considering a variable melt factor in SIAR improves spatial simulations. The general results for the entire dataset (Fig. 10 ) confirmed that SIAR (S1) was better able to reproduce the duration of snow cover than the version (S3e) based only on a constant degree-day-factor. Interestingly, SIAR also performed better in SWE (NSE SWE ) and runoff (NSE Q and NSE 1/Q ) simulations. The reproduction of runoff is similar to that in the semi-distributed application in elevation bands (see boxplots of S1 in Fig. 3  for comparison). On the other hand, the local snow simulations (NSE SWE ) were not as good. However, the calibration parameters used here were those optimized based on an adaptable number of elevation bands (i. e. not optimized in full distribution mode).
Q8: How does SIAR perform compared with the Cemaneige snow model in the catchments tested? To finalize the comparative assessment, the proposed S1 version of SIAR was compared to the Cemaneige snow-accounting model. Given the preceding results, the models were applied using an adaptable number of equal-area elevation bands. The original version of Cemaneige (C2,  Valéry et al. , 2014b)  and its version with hysteresis (C4,  Riboust et al. , 2019)  can be found in the R airGR package  (Coron et al. , 2017). In these versions, forcing data (precipitation and air temperature) are modified using the elevation gradients proposed by  Valéry et al. (2010) , i. e. , for France, an exponential modulation for precipitation and a seasonal variation in the temperature lapse rate (see Table  6  caption for details).
For further comparison with SIAR, the Cemaneige version with hysteresis was also modified to include some methods proposed in the current paper to adjust temperature inputs for elevation-dependency (Eq. (  2 )), and snowfall for both gauge under-catch and orographic enhancement (Eq. (  5 )). The parametrization of the models is detailed in Table  6  while their performance is shown in Fig. 12  for four criteria. Note that the models were run under exactly the same conditions (i. e. using the same data, the same calibration procedure and the same testing scheme). The performance values for the entire catchment dataset (Fig. 12 ) indicate that SIAR (S1) is more suitable for simulating high and low flows as well as snow dynamics, since it outperforms all versions of Cemaneige. These results also show that the precipitation and temperature lapse rates included in the original C2 and C4 Cemaneige versions are not suitable for the catchments studied here.
Indeed, the SFA parameter makes it possible to correct for snowfall gauge under-catch as well as to increase snowfall with elevation (and then total precipitation), which seems both essential and sufficient to ensure the water balance at catchment scale (streamflow simulations) in addition to satisfactory SWE and snow cover simulations. This proves that control data bear the signature of orographic enhancement and snowfall under-catch, which can be successfully exploited to improve hydrological models. We thus found that the estimated total precipitation was 1. 25 times higher on average in the catchments (values ranging from 1 to 1. 6 depending on the catchments) than that recorded by nearby precipitation gauges. Whether such an inverse approach reconstructed the true orographic precipitation and/or snowfall under-catch is worth discussing.
Recommendations Although the results obtained may be applicable to catchments with similar characteristics, they are only valid for near-natural catchments across the French Alps and Pyrenees at the space and time scales considered. In particular, a daily time step was retained in relation to the input and control data available, and no sub-daily process was considered. On the other hand, simulations were evaluated using different sources of daily measurements (local SWE, satellite data and runoff) and different catchments, which gives us confidence in our findings. Of course, this does not mean that SIAR is the best possible snow module, and a more appropriate solution may be identified to jointly simulate snow and runoff. However, SIAR is sufficiently simple and general to be easily applied to a wide range of mountain catchments influenced by snow and ice.
Prospects It should be noted that this work did not cover all possible approaches to snow models. Only degree-day approaches were tested, due to limited availability of the input data implied by a large catchment dataset and by the spatial (catchment areas ranging from 45 to 3 580 km 2 ) and time (18-year simulation period at the daily time step) scales considered. A more physics-based model would indeed lead to a more complex numerical scheme and increase the amount of input data required, especially if the parameters vary spatially. Moreover, it is known that upscaling physical laws within imposed morphologies does not necessarily result in a reliable description of reality  (Savenije, 2009)  and, as such, energy balance models may also require calibration parameters, at least to adjust the meteorological inputs, if they are to be applied at the space and time scales considered in the present paper.
Data availability The hydro-meteorological data and MODIS snow products used in this study are available via the respective websites of the dataset producers: Météo-France (https://publitheque. meteo. fr), Banque Hydro (https://www. hydro. eaufrance. fr), and NASA's National Snow and Ice Data Center (NSIDC, https://nsidc. org) Distributed Active Archive Center (DAAC). The in-situ SWE measurements were provided by Eléctricité de France through the CNRS contract ID415-228735.
Acknowledgements The author is very grateful to  Eléctricité de France (EDF) ,  Météo-France  and  Banque Hydro  for respectively providing the necessary in-situ SWE measurements, meteorological data and runoff for the study. NASA 's National Snow and  Ice Data Center (NSIDC) Distributed Active Archive Center (DAAC)  is also acknowledged for providing MODIS snow products. Finally, the author is sincerely grateful to the associate Editor ( Saman Razavi ) and to the two anonymous reviewers for their careful reading of the original manuscript and their insightful comments and constructive suggestions for improvements.
Patients All study groups affiliated with the I-BFM-AML SG were invited to participate in this retrospective cohort analysis. In addition to data regarding patient characteristics, laboratory results (cytogenetic and molecular tests including karyotype and fluorescence in situ hybridization [FISH]), and outcome, the study groups were requested to provide the number of patients with AML with full karyotyping within the study period to assess the frequency of hypodiploidy. Patients from study groups with no information on full number of karyotyped patients were excluded from calculation of hypodiploidy frequency (n = 7). Children below the age of 18 years diagnosed with de novo AML between January 2000 and December 2015 and a hypodiploid karyotype were considered eligible for the study. Children with either acute promyelocytic leukemia, Down syndrome, juvenile myelomonocytic leukemia, AML secondary to bone marrow failure syndromes or therapy-related AML were excluded.
Consolidation with SCT in CR1 did not improve the outcome. However, because we did not have detailed information on SCT indication, there might be a selection of poor responders or poor genetics among patients treated with SCT, and the study is small. Reduced EFS and OS were also observed in hypodiploid ALL with decreasing survival with lower MN  20  and similar to AML SCT, did not improve survival. 40, 41 spite being the largest study of hypodiploidy in pediatric AML to date, the cohort may be too small to demonstrate significant differences in outcome. The size of the study limits the number of covariates applicable for multivariate analyses, and hence the dataset neither allowed adjustment for all high-risk features nor did it allow us to stratify the patients based on all established co-occurring translocations.
Acknowledgments The authors thank all contributing study groups for their benevolent participation and cooperation (a full list appears in Supplemental data). This work was presented as an award-winning poster abstract at the 60th annual meeting of the  American Society of Hematology ,  San Diego ,  1-4 December 2018. This work was supported by grants from the  Danish Cancer Society  ( R165-A10463 ) and the Else & Mogens Wedell-Wedellsborg foundation.
BACKGROUND: Clinical examination is the gold standard for surgical indication. Electromyogram and conventional MRI are insu cient to understand the highly variable clinical presentation of neonatal brachial plexus (BP) lesions. Diffusion Tensor Imaging is based on motion of water molecules and can explore nerve function. PURPOSE: This pilot study of healthy subjects aimed to develop a new method for BP exploration using MRI. The main objective was to obtain complete and accurate BP mapping using DTI and MRI tractography. METHODS: Six healthy volunteers had MRI (3T PRISMA) with anatomical 3D STIR, SPACE and RESOLVE diffusion sequences. Image analysis and processing was performed with MATLAB software. Diffusion parametric maps of fractional anisotropy (FA) were extracted from RESOLVE acquisitions.
A reproducible method for root volume and angle measurements was created using 3DSlicer. Regions Of Interest were segmented on Mean B0 sequences. FA measurements were obtained with ROI on Mean B0 sequences. RESULTS: RESOLVE sequence was adapted to the BP. Mean FA was 0. 30. Angle measurements on 3D STIR SPACE sequences showed increasing values from proximal to distal roots with an ICC of 0. 6. Volume measurements on anatomical sequences varied widely from one root to another but no signi cant difference was shown on laterality. CONCLUSION: A new and reproducible method for BP exploration was developed using MRI RESOLVE diffusion sequences. Complete mapping was obtained despite low track density imaging resolution. The whole BP was visualized. Extraction of diffusion, volume and angle parameters of the plexus roots, and script creation for image processing was adapted to the healthy BP.
b. Data analysis Corrections of geometric distortions for diffusion acquisitions were carried out using "Topup" tool from the FSL library (v5. 0; FMRIB, UK). STIR SPACE anatomical sequence denoising was carried out on MATLAB software  [4]. Mean B0 sequences were recalibrated on anatomical sequences for better anatomical accuracy of diffusion imaging. This gave better signal-to-noise ratio (SNR) of diffusion images and better contrast mandatory for segmentation.
c. Manual segmentation Anatomical sequences were obtained with good resolution (Fig. 2  Example of Anatomic T2 SPACE with inversion recuperation pulse sequences with bundles from proximal to distal (from a to c), left plexus (a,b,c), right plexus (d,e,f) with medullar view (f)). In order to obtain proximal root volume, segmentation was performed on STIR SPACE 3D anatomical sequences (Fig. 3  Measurement of C5-T1 roots volumes. A landmark was positioned on the incus of the vertebra overlying the root of interest de ning a multi-cut landmark. A one-centimeter section was then segmented with the "segment editor" function at one-centimeter from the previously positioned mark). Root volume measurements were carried out using 3D Slicer software. A landmark was positioned on the uncus of the vertebra overlying the root of interest de ning a multi-cut landmark.
d. Parametric map creation A mask was created on ITKsnap [28] (www. itksnap. org) software to enable the MRtrix tractography software (v3. 0. 1). The mask aimed to limit the calculation time and exclude the pineapple pad area from the parameters to extract. MRtrix software calculated the diffusion tensor based on empirical calculations of signal strengths  [6]. FA maps were extracted (Fig. 4   FA measurements of diffusion parameters were carried out using the 3D Slicer software by positioning the 1% and 5% ROIs on the parametric map of FA.
g. Diffusion and tractography algorithms The distribution of ber orientations was represented by spherical harmonics (Fig. 6  Orientation of bres estimed by Constraint Spherical Deconvolution (CSD)). Tractography images (Fig. 7  a. Tractogram using a deterministic approach of the medullary emergence from the roots to the peripheral nerves. b. Track Density Imaging reconstructed from gure 6. a ) were obtained with MRtrix simple deterministic tractography. Different algorithms were tested in order to achieve the most e cient plexic ber mask possible. To the best of our knowledge, there is no brachial plexus code or atlas; the main limitation being inter-subject anatomical variability.
ICC<0. 5 represented poor agreement, ICC between 0. 50 and 0. 75 represented moderate agreement and ICC between 0. 75 and 1. 00 represented excellent agreement. The ICC function of the irr package was used to measure the ICC and obtain the degree of agreement between the three repeated measurements. Analysis of the FA parametric maps was carried out with the LMM, with as xed factors of the xed effects the ve levels of plexus roots and the two methods of measuring the FA parameters and their interactions.
The FA values were obtained on the 60 healthy proximal roots. No laterality effect was found. The mean FA was 0. 30 [0. 25-0. 34] consistent with data in the literature  [20, 26]. FA values between 0. 25 and 0. 30 were reported for healthy roots using planar echo imaging  [26]. A mean FA of 0. 34 ranging from 0. 27 to 0. 43 was reported using 1. 5 and 3 Tesla MRI  [20]. Several authors measured FA of peripheral nerves including the median, ulnar, radial and common tibial nerves  [10, 21]. The mean FA measurements obtained for these roots was higher than for the brachial plexus, without possible comparative statistical analysis. The results obtained by the two FA measurement methods were similar. The segmentation method with a 5% radius brush was faster than the 1% radius brush. It will probably be preferred in automatic script development for the segmentation of the plexus roots.
Conclusion A new and reproducible method for BP exploration was developed, using MRI RESOLVE diffusion sequences. Complete mapping was obtained but a low resolution of track density imaging did not allow to exploit distal nerves. Functional data were obtained through diffusion parameters. The whole BP was visualized from proximal to distal and allowed to measure anatomical data. Extraction of diffusion, volume and angle parameters of the plexus roots, and the creation of new scripts allowing image processing was adapted to the healthy BP in young adults. with pineapple pad  [17]  Figure  2  Example of Anatomic T2 SPACE with inversion recuperation pulse sequences with bundles from proximal to distal (from a to c), left plexus (a,b,c), right plexus (d,e,f) with medullar view (f).
Study Population This study was performed in accordance with the Declaration of Helsinki of the World Medical Association revised in 2013 for experiments involving humans and declared to the "Commission Nationale Informatique et Libertés" (authorization number 1118523; 9 March 2020). Participants were systematically informed that their data were being collected for an anonymous retrospective study and that they could refuse to participate in the study (i. e. , non-opposition statement). All consecutive patients with high-tumor-burden FL treated between July 2010 and September 2016 were retrieved from our institutional database. Patients were included in this study when they met the following criteria: (i) patient had a grade 1-2 or 3a FL confirmed on biopsy, with a high tumor burden according to GELF criteria (Groupe d'Etude des Lymphomes Folliculaires); (ii) patient was treated using immunochemotherapy for induction, followed by rituximab as maintenance therapy; and (iii) patient had undergone baseline 18F-FDG PET/CT within one month prior to treatment.
This initial search retrieved a total of 88 patients. Patients were further excluded when (i) they had no accurately delineable lesions on baseline CT or (ii) when no 18F-FDG PET/CT examination performed less than one month before treatment was available for review. In total, 72 patients were ultimately included in the study. For all patients, clinical, biological, and imaging data were recorded. They included the patient's age, gender, Eastern Cooperative Oncology Group (ECOG) performance status, B symptoms, serum level of B2-microglobuline and platelets, presence of circulating tumor cells, the longest diameter of the largest involved node (LoDLIN), presence of extra-nodal involvement, FLIPI and FLIPI2 scores with FLIPI risk category (FLIPI RC), maximum standardized uptake value (SUVmax), and T-MTV on baseline 18F-FDG PET/CT images.
18F-FDG PET/CT Acquisition and Analysis All patients underwent a skull-base-to-proximal-thigh 18F-FDG PET/CT examination, 60 min after intravenous administration of 5 MBq/kg of 18F-FDG. 18F-FDG PET/CT examinations were performed using a Philips Gemini Dual system (Philips Healthcare, Eindhoven, the Netherlands). CT data of PET/CT examinations (120-140 kV, 100-150 mAs) were reconstructed using filtered back projection (FBP) and a medium smooth filter kernel (B30) on a 512 × 512 matrix (voxel size in axial plane, 1. 17 × 1. 17; thickness, 6. 5 mm). 18F-FDG PET/CT examinations were retrospectively reviewed by two nuclear medicine physicians (F. G. and D. M. ) with, respectively, four and nine years of experience in nuclear medicine, blinded to patient outcome on a dedicated interpretation console (AW Server, General Electric Healthcare, Milwaukee, WI, USA) with PET/CT images scaled to a fixed standard uptake value (SUV).
CT Texture Analysis CT TA was made on pretreatment unenhanced CT images extracted from baseline 18F-FDG PET/CT examinations using a commercially available version of TexRAD software (TexRAD Ltd. , London, UK). A radiologist (C. D. ) with six years of experience in oncological imaging selected the image displaying the largest cross-sectional area and placed a region of interest (ROI) encompassing entirely each target lesion (Figure  1 ). One to five target lesions were analyzed for each patient. CT TA was made using a two-step procedure. First, a Laplacian-of-Gaussian spatial band-pass filter was applied in order to allow extraction of features at fine (SSF = 2, object radius of 2 mm), medium (SSF = 3-5, object radius of 3-5 mm), and coarse (SSF = 6, object radius of 6 mm) scales. Then, five parameters were obtained from the quantification of the histogram distribution within the ROI.
Patient Characteristics Eighty-eight patients were eligible for the study. Sixteen patients who did not have a 18F-FDG PET/CT examination within one month prior to treatment were excluded. The final population included 72 patients (43 men and 29 women) with a median age of 61 years. The main clinical, biological, nuclear medicine, and radiological characteristics of patients are reported in Table  1. The FLIPI, FLIPI2, and PRIMA-PI scores were, respectively, low for 10 (14%), 2 (6%), and 11 (22%) patients; intermediate for 28 (39%), 20 (57%), and 13 (27%) patients; and high for 34 (47%), 13 (35%), and 25 (51%) patients. FLIPI2 and PRIMA-PI were not available for all patients due to missing data (mainly information on bone marrow involvement). The median T-MTV on baseline 18F-FDG PET/CT was 381 cm 3 (range: 12-3329 cm 3 Q1-Q3: 155-807 cm 3 ), and 29 patients (40%) had a T-MTVT over the threshold of 510 cm 3.
These same cytokines and chemokines were also increased in the serum from uninfected CoH vs. SPF mice (Figures  2A  and 2B ), which is consistent with our previous findings. 12  These data suggest that CoH mice are primed to respond more vigorously and quickly during a systemic UPEC infection. To determine how immune cell numbers in SPF and CoH mice were affected by the systemic UPEC infection, CD4 T cells, CD8 T cells, B cells, NK cells, CD11b + CD115 + monocytes (hereafter referred to as CD115 + monocytes), and neutrophils in the spleens and blood of SPF and CoH mice were quantitated before and 24 h after systemic UPEC infection. Prior to infection, the number of each cell type-except for B cells-was increased in CoH mice (Figures  3A  and 3B ). Following infection, T cell and B cell numbers were maintained in both SPF and CoH spleens, while NK cell numbers decreased slightly (but significantly) in CoH mice (Figure  3A ).
Depletion of either CD4 or CD8 T cells did not influence resistance of CoH mice to infection, suggesting that these populations of cells do not meaningfully contribute to the survival advantage seen in CoH mice following systemic UPEC infection. By contrast, susceptibility of CoH mice to UPEC infection was significantly increased after removal of CD115 + cells (Figure  4C ), suggesting that these cells are necessary mediators of the survival advantage for UPEC-infected CoH mice. To determine the contribution of monocytes in the accelerated UPEC clearance seen in CoH mice, we next depleted CD115 + cells from CoH mice and determined bacterial titers in blood, spleen, liver, and kidney of these mice, as well as SPF mice and cIgG-treated CoH mice, 24 h after infection. While the UPEC burden was significantly lower in cIgG-treated CoH mice compared with SPF mice (which is also consistent with the clearance data shown in Figure  1B ), the UPEC burden in CoH mice depleted of CD115 + cells was not statistically different from that seen in SPF mice (Figure  4D ).
*p % 0. 05, **p % 0. 01, ***p % 0. 005, and ****p < 0. 0001 as determined by nonparametric Mann-Whitney test. Transcript (normalized copies per million [nCPM]) data in (F) were obtained from 3 to 4 mice per group. Flow data in (E) were combined from two experiments using a total of 9 mice per group, in (F) were combined from three experiments using a total of 25-26 mice per group, in (G) were combined from three experiments using a total of 8-9 mice per group, in (H) were combined from two experiments using 3 mice per group. Each symbol in (A and E-H) represents a mouse and bars indicate means with SEM. reported here with increased presence of monocytes positively affecting survival in microbially experienced mice. In addition, classical monocytes account for $85% of the total circulating monocytes in humans during physiological conditions.
Data and code availability d The bulk RNA-seq data generated have been deposited at the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO) under accession number GSE237883 and are publicly available as of the date of publication. Any additional details regarding these data will be made available upon request. d This paper does not report original code. d Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request.
Measurement of cytokines and chemokines Blood was collected from SPF and CoH mice prior to and either 3 h or 24 h post UPEC infection, and serum was separated and collected by centrifugation of samples at 13,000xg for 1 min. Serum cytokines were quantitated by ProcartaPlex immunoassays (ThermoFisher) using a Luminex 200 with Bio-plex Manager Software 5. 0. The amount of TNFa present in culture supernatants from in vitro/ex vivo assays was quantitated by ELISA (Biolegend ELISA MAX standard set mouse TNFa; cat. No 430901).