dataesr/scientific-paragraphs-categorization huggingface dataset:
When performed properly, this technique can improve the outcome of the procedure (84%). The software to plan and simulate the treatment was considered useful (77%) and allowed to shorten the learning curve, especially in placing the needles correctly (84%). When the software (Echolaser Smart Interface-ESI, Elesta S. p. A. , Calenzano, Italy) gave the indication to insert more needles, it was advised to follow the recommendation rather than use only one needle and perform multiple reinsertions (>75%). Furthermore, applying a fiber positioning aid such as a template or a grid can be helpful (>75%). Anesthesia must be performed (77%). Lidocaine should be administered locally to skin and periprostatic tissue (>75%). The standard use of sedatives during the procedure is still controversial.
In fact, while most studies reported a fixed 3 W power protocol  [5,7e9] , two studies explored the possibility to start with higher power (4. 5e5 W, then reduced to 3 W) that led to a reduction of mean operation time  [1, 6]. About this, one expert reported his personal experience using 7 W power, leading to a faster treatment without provoking discomfort to patients. Surely this suggestion will be topic of future studies. Another important aspect is the use of multiple needles or one needle per lobe. Sometimes the planning software (Echolaser Smart Interface, Elesta S. p. A. , Calenzano, Italy) indicates to insert more needles to extend the treatment area, especially in large prostates and with a hyperplastic median lobe. After discussion about outcomes of the two alternatives, experts agreed on inserting more needles when the software recommended it even if it implies a higher procedural cost.
Gene-Expression analyses of H3. 3K27M-pDMG transcriptomic cohorts For cohort 1  34  , HTSeq gene counts and somatic vcf of St Jude's pDMG samples were downloaded from https://platform. stjude. cloud/. DESeq2 (v 1. 36)  70  was used to normalise the data with the variant stabilisation transformation (vst)  71. ACVR1 mutation status was assessed using tabix 72 (v 1. 15. 1) to query the region of the ACVR1 gene chr2:157,736,251-157,876,330 (hg38). Identified variants were manually curated. PROGENy (v 1. 18. 0)  35  was used to infer TGF-β/BMP pathway activity with the "top" parameter set to 100 (default value). For cohort 2 1 , gene expression (z-score) and tumor variants were downloaded on https://pedcbioportal. kidsfirstdrc. org/ from the dataset "phgg_jones_meta_2017". Samples were filtered based on the following location: brainstem or midline, and the following histone mutation: WT, H3.
1K27M and H3. 3K27M. Only the 4 datasets with ACVR1 mutant samples were kept for the analysis to avoid biases: "PMID:21931021|PMID:24705251", "PMID:21931021|PMID:22286216", "PMID:22389665|PMID:24705252", "PMID:24705251". TGF-β/BMP pathway activity was also inferred using PROGENy, but the "top" parameter was set to 178 genes: as half of the top 100 genes of the PROGENy model for the TGF-β/BMP pathway are not covered in the cohort 2, we identified the (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. top 100 genes with the highest absolute coefficient in PROGENy's model to compute pathway activity with the same number of genes in both cohorts. For both cohorts, Principal Component Analysis (PCA) was performed using FactoMineR (v.
scRNA-seq analyses of H3. 3K27M ACVR1 WT DMG Using the scRNA-seq data published by [Jessa et al. , 2022] (GSE210568)  29  , we selected H3. 3K27M-ACVR1 WT pDMGs localized either in the pons or in the thalamus (10 samples). The same processing steps as the authors were performed except for the regression of mitochondrial proportion and the number of UMIs. Normalization was performed with the LogNormalize function of Seurat  75. All samples were filtered to keep tumoral cells as identified by the authors. As a readout of BMP pathway activity, we used PROGENy to infer the TGF-β/BMP score. We then stratified cells into TGF-β-High and TGF-β-Low groups using the 95th quantile as cutoff. FindMarkers with default parameters was used to identify differentially expressed (DE) genes (FDR <= 0. 05) in each group.
Statistical analyses Data are represented as means ± std. Sample size and replicates are stated in the corresponding figure legends. Using GraphPad Prism 9 software and R (4. 2. 0), the statistical significance between two groups were determined by one-tailed Wilcoxon signed-rank tests, apart from the proportion of Ki67 stained cells, which was assessed using Fisher's exact Test. The following symbols used to denote (<0. 05: *; <0. 01: **; <0. 001: ***; <0. 0001: ****). teams from IHOPe and HFME for their support and contributions, as well as all the facilities from the CLB and CRCL. We are grateful to Séverine Tabone-Eglinger, Loïc Sebileau and Anne-Sophie Bonne for their help with the management of regulatory procedures. P. H. and M. H. received financial support from the Dev2Can LabEx and ITMO Cancer of Aviesan, respectively.
Acknowledgements We thank the patients and their families who consent to participate in this study, as well as charities that support this work, including the  Ligue Nationale contre le Cancer , and the  Ligue Départementale contre le Cancer de Haute-Savoie et de l'Ain. Our warmest thanks go to Augustine and its Wonder team ("Wonder Augustine" charity) that support this work since the initiation, to  Léonie  (" Au Pays de Léonie ") and to " Les Etoiles Filantes ", which has funded all the omics analyses. We also thank clinical.
Data availability Raw bulk RNA-seq and Visium data generated in this study will be available via GEO. RNA-seq data of pDMG samples from cohort 1 were obtained from St. Jude Cloud 46 (https://www. stjude. cloud). Cohort 2 of glioma samples 1 can be accessed on https://pedcbioportal. kidsfirstdrc. org/ with the following dataset id: "phgg_jones_meta_2017". The scRNA-seq cohort of H3. 3K27M ACVR1 WT pDMGs is available on GEO (GSE210568) and https://zenodo. org/record/6929428.
using default parameters. Genes with corrected pvalue (Benjamini-Hochberg) < 0. 05 and |log2FoldChange (LFC)| > log2(1. 5) were considered DE. EnrichR package (3. 0) 76 was used for overrepresentation analysis using the following databases: Gene Ontology (GO) Biological Process 2021, GO Molecular Function 2021, GO Cellular Compartment 2021, KEGG 2021 Human, MSigDB Hallmarks 2020 and ChEA 2016. Enrichment significance was assessed by Fisher's exact test, and p-values were corrected with the Bonjamini-Hochberg method.
On the contrary, the other studies, which showed signi cant modulation of reaction times depending on the emotional context, used transitive motor tasks. Consequently, such studies dealt with the motivational direction theoretical model as well as with the affective meaning of the intended response goal model, which differs from the paradigm used in the present study. Secondly, the present study also differs from previous work in that the participants were given instructions about the movement velocity (i. e. , "please perform every pointing movement as quickly and as accurately as possible"). It could be hypothesized that the temporal pressure contained in the instructions given for the present study has had more impact on the reaction times than the emotional conditioning. Finally, we used pictures coming from the IAPS database and displayed them on a 380*213 mm LED screen that was positioned about 75 cm from the participants' eyes.
1 ). For each movement, a pleasant, neutral or unpleasant affective emotional picture coming from the International Affective Picture System (IAPS) database was displayed on the screen before one of the two targets was lit up (with a 1-3 s SOA). Participants were asked to perform pointing movements "as quickly and as accurately as possible when a target was illuminated", in six experimental conditions (2 Target Distances × 3 Affective Picture Content stimuli). A total of 90 movements per participant (15 movements × 6 experimental conditions) were randomized. Before data recording was initiated, each participant performed six-movement tests which always occurred in the following order: three tests in the 'close × neutral' condition, three tests in the 'distant × neutral' condition (here, the neutral picture was always the same -number 7705 in the IAPS -and was not used later during data acquisition).
Emotional pictures The affective emotional stimuli used to induce emotional states during the voluntary arm pointing movements comprised 45 digital pictures for each gender selected from the IAPS database. women. The scores of the computerized 9-point version of the Self-assessment Manikin (SAM) scale were used to control the 15 pleasant, neutral and unpleasant pictures in the affective dimension according to gender  [74]. An evaluation session was conducted for each participant at least 48 hours before the experimental session to ensure that the affective perceptions of each picture in each volunteer participant were really in accordance with the expected experimental condition. Potential effects of arousal on posture and movements were carefully prevented by choosing pictures with the highest pleasant arousal, the highest unpleasant arousal, whereas neutral pictures were based on the recommendations speci ed by Bonnet et al.
Nonetheless spatial transcriptomics is a powerful tool, how to apply it to understand the metabolic dynamics in healthy and infected tissues is not intuitive. Although genes composing the metabolic pathways are fairly well annotated and flux balance analysis-based approaches have made a lot of progress in determining metabolic networks and capture partly metabolic diversity  [54] , there are major concerns related to these approaches. One above all is that more and more studies have reported a profound discrepancy between gene expression and proteome datasets, as well as predicted metabolic pathways and metabolomic data especially in tissues that operate outside the steady state  [55, 56]. Combinatorial analysis of various -omics might solve this complex problem, however no single method has yet been defined as standard for this task  [54].
First, cells are not homogenous "bags of small molecules and proteins", but their metabolome and proteome are highly variable depending on their biological state and the environment in which they reside. Also, subsets which appear to be highly comparable phenotypically or functionally might rely on very different metabolic programs. Another important point is the isolation processes currently used to get pure populations. Given the unstable nature of the metabolome, isolating cells might considerably impact the measurements of various metabolites and consequently alter the interpretation of their metabolic state. Moreover, despite the characterization of new diet-and microbe-derived small molecules and consequent enrichment and refinement of available databases, there is still not an accepted analysis pipeline that allows to 1) discriminate microbe-from host-derived metabolites; 2) analyze the spatiotemporal aspects of immunometabolism; 3) compare datasets produced by different sources.
Acknowledgements We thank  Marco Giamp  a from the  VIB in Leuven  for critically reading the review,  Shah Dhruvi ,  Susanna NG  and  Marius D€ oring  for reading, editing, and commenting the manuscript. L. S. is supported by the  Max-Eder Grant for junior  group leader ( Deutsche Krebshilfe)  and core fundings from the  Institute of Clinical Chemistry and Clinical Pharmacology at the University Bonn. C. D. thanks the  Institut Pasteur  and  INSERM U1224  for the core funding provided to the  Immunobiology and Therapy Unit.
Owing to the structured management pathway for rare diseases in France  (13) , this study was able to generate data about diagnosis experience based on a survey carried out in a large population of patients with rare endocrine diseases within the FIRENDO network and its partnering patient support associations. Results from 614 patients and relatives covered 35 different diseases. Participants represented a panel of FIRENDO users and patient association website users, and therefore may not be fully representative of all endocrine J o u r n a l P r e -p r o o f rare disease patients in France. Out of all the quantitative data from the online questionnaire, a subset of 425 patients, in 7 disease categories with at least 30 respondents each, was more particularly analyzed in the present study.
By exploiting a relationship between the directly reshaped matrix and integration of unfolding matrices, AITT can estimate effectively the underlying TT-cores with low cost. Nevertheless, it is worth noting that the framework of both iTTD and AITT is not really online streaming learning, but incremental batch learning. Recently, we have introduced an adaptive TT method called TT-FOA capable of tracking the low-rank components of high-order tensors in online settings  [14]. Its design is useful for scenarios where a single data sample is acquired at a time. Despite advantages in some respects, all the existing dynamical/incremental/adaptive TT methods above are not suitable for handling streaming tensors with missing values. In parallel, many tensor completion algorithms have been proposed in the literature  [15].
We compare ATT with other online tensor completion algorithms: TT-FOA  [14] , TeCPSGD  [23] , ACP  [26] , and ATD  [26]. TeCPSGD is dependent only on a regularization parameter µ which is set at 0. 1. We set the forgetting factor λ at 0. 7, 0. relative errors (RE) than TeCPSGD and ATD, but demonstrated faster runtimes than both methods in most cases. ACP is the fastest adaptive tensor-based method for this application, but its estimation accuracy for cases of highly incomplete observations was lower that of the proposed ATT method, particularly when dealing with Hall and Lobby datasets. TT-FOA was unable to perform online video completion effectively. Notably, with the same space (memory) complexity, the ATT method provides a lower-rank representation for video sequences than the CP and Tucker-based methods.
Acknowledgements We are indebted to  C. Rampon  for allowing us to use the Ethovision Software as well as  Ouria Dkhissy Benyahya  and members of the Blader team for helpful discussions. We thank  M. Halpern  and  K. Soanes  for sharing probes. This work was supported by the  Centre National de la Recherche Scientifique (CNRS) ; the  Institut National de la Santé et de la Recherche Médicale (INSERM) ;  Université de Toulouse III (UPS) ;  Fondation pour la Recherche Médicale  (FRM;  DEQ20131029166 );  Fédération pour la Recherche sur le Cerveau (FRC) ;  Association pour la Recherche sur le Cancer (ARC) ;  Association Rétina France and the Ministère de la Recherche. We would like to thank  Brice Ronsin ,  Stéphanie Bosch  and the Toulouse RIO Imaging platform;  Stéphane Relexans ,  Aurore Laire  and  Richard Brimicombe  for taking care of the fish as well as  Sophie Polès  for technical help.
Acknowledgments Paola JUBAN was granted by  KIM RIVE  project ( Key Initiative Muse Risks & Vectors ) from  Montpellier Université d'excellence (MUSE). All experiments on G. p. gambiensis have been performed on the Baillarguet insectarium platform (https://doi. org/10. 18167/infrastructure/00001), member of the National Infrastructure EMERG'IN and of the Vectopole Sud network (http://www. vectopole-sud. fr/). The Baillarguet insectarium plateform is led by the joint units  Intertryp (IRD, Cirad)  and  ASTRE (Cirad, INRAE). Mice were kept under strict ethical conditions according to the international guidelines for the care and use of laboratory animals. The experiments designed for this study were approved by the regional  Ethic Committee for Animal Experimentation   CEEA-LR  36 under project number APAFiS # 34149  and authorized by  French Ministry for Higher Education and Research.
Besides, the present reaction conditions in D 2 O were identical to those of a previous study in which lipolysis was monitored by FTIR  (Sahaka et al. , 2023). Thus, NMR and FTIR analytical monitoring could be compared. The 1 H acquisition time was 340 ms, the spectral width 20 ppm, and 32 scans were accumulated for a total duration of 2 min per spectrum. One 1 H NMR spectrum was recorded before the addition of the enzyme. After enzyme addition, a series of 2-minutes spectra were recorded for 7 h and a final spectrum was recorded after 16 h 37 min of incubation. All spectra were recorded at 37 • C, on a Bruker Avance III 600 MHz spectrometer equipped with a TCI cryoprobe, using Topspin 3. software. Fourier transforms were performed with nmrPipe software  (Delaglio et al. , 1995) , the data were then exported in text format and integrated into Spectra Manager V.
Characterization of galactolipid-bile salt micellar organization (aggregates size) The supramolecular organizations formed by C8-MGDG, bile salts and lipolysis products before and during the lipolysis reaction were characterized using DOSY-NMR with bi-polar PFG stimulated echo experiments. Two pairs of bipolar square-shaped z-gradients of 2. 8 ms (δ) were used to encode and decode the z-axis particle position, spaced with a delay (Δ) of 200 ms. A series of 10 spectra were recorded with gradient powers (G) ranging from 98 % to 2 % of the maximum gradient strength (0. 5 T. m -1 ) using a quadratic ramp. The spectra were transformed in Topspin 4. 3 and nmrPipe  (Delaglio et al. , 1995) , and the diffusion analysis was performed in Dynamic Center 2. 8 and Octave  (Eaton et al. , 2016). For each of these 10 spectra, the signal integral of the abovementioned assigned 1 H resonances were quantified as function of gradient power (PFG -NMR).
Acknowledgements and funding sources We thank the animal and imaging facilities of the  IBPS (Sorbonne Université, Paris, France ). We thank  Nathalie Rouach  for the GFAP-EGFP mice,  Hervé Le Corronc  and  Thomas Panier  for the discussion and the 3D printing of the light sheet chamber, respectively. This work was supported by the  Agence Nationale de la Recherche  ( ANR-17-CE37-0010-03 ;  ANR-20-CE14-0025-02 ),  France Alzheimer  individual fellowship ( 2021-2022 ),  Japanese society for promotion of science (JSPS ) 2022 summer grant,  Grant-in-Aid for Challenging Research (Exploratory) in Japan  (grant number  21K19464 ), the  i-Bio initiative grant  of  Sorbonne Université.
Virological data Out of the 252 cases included in this study, 148 (58. 7 %) of them were sampled by sentinel GPs. Sampled and non-sampled cases had similar clinical characteristics, with the exception of the vaccination status, with a higher proportion of vaccinated cases observed in the sampled group (p = 0. 002) (Table  3 ). Out of the 148 sampled cases, 146 were tested and 11. 6 % (n = 17) had a laboratory confirmation of mumps, which is an estimate of the positive predictive value of the clinical definition followed by the French GPs Sentinel network. Age (between 20 and 29 years old), presence of complications and an exposure to a suspected mumps case within the 21 days prior the current episode were significantly associated with mumps virological confirmation (Table  4 ).
Authors' contributions PPM, FHD et TB designed the study. PPM, FHD and CS undertook the statistical analysis. JH and JD were responsable for the virological analyses and prepared the virological databases. PPM, FHD, OG, SM and TM were responsable for the management of the epidemiological and the virological databases. PPM, FHD et TB wrote the draft manuscript and all authors participated in the enhanced mumps surveillance, revised and approved the final version.
The p values thus obtained are adjusted for multiple testing using the Benjamini and Hochberg procedure. Gene network analysis by WGCNA: A major caveat for differential analysis like DESeq2 is that it treats each gene as a separate entity and assumes independence of genes. However, in order to gain an insight into complex biological mechanisms of regulation and co-expression. In order to visualize the changes in genes as modules of a network, we used the WGCNA (Weighted Genes Co-expression Network Analysis) pipeline to analyze gene groups in modules (https://cran. rproject. org/web/packages/WGCNA/index. html)  (97). We selected the top 10% of the most variable genes in the entire dataset across the experiments using a standard variance calculation. For a (𝑛 × 𝑛) count matrix, an adjacency matrix is measured as a weighted Pearsons' correlation: 𝑠 !" = 1 + 𝑐𝑜𝑟𝑟(𝑔𝑒𝑛𝑒 ! , 𝑔𝑒𝑛𝑒 " ) 2 Relying on the adjacency matrix, clustering is based on proximity of pairs of genes.
Acknowledgements We thank  Drs N. Kupperwasser  and  A. S. Armand  for critical reading of the manuscript and suggestions during the course of this study, and  N. Servel  for assistance in Sodium-dependent Pi transport measurements. We thank the viral production, Imaging, Genomics and animal house facility (LEAT) platforms of the SFR Necker. This work was supported by FRM (F. O and M. R. B),  HFSP  (F. O),  ATIP-AVENIR Program  (F. O),  AGEMED-INSERM  (F. O), ANR (F. O and G. F),  FSER  (F. O) and  EMERGENCE Ville de Paris  (F. O).
ACKNOWLEDGMENTS We thank the staff of the  Regional Center of Hemotherapy of the Garrahan Hospital (Buenos Aires). We greatly thank  Claire Lastrucci  for illustration of the graphical abstract. In addition, we are grateful for the editing service provided by Life Science editors. This work was supported by the  Argentinean National Agency of Promotion of Science and Technology  ( PICT-2019-01044  and  PICT-2020-00501  to LB); the  Argentinean National Council of Scientific and Technical Investigations (CONICET ,  PIP 11220200100299CO  to LB); the  Centre National de la Recherche Scientifique ,  Université Paul Sabatier , the  Agence Nationale de Recherche sur le Sida et les hépatites virales (ANRS)  ( ANRS2018-02 ,  ECTZ 118551/118554 ,  ECTZ 205320/305352 ,  ANRS ECTZ103104  and  ECTZ101971  to CV); and the  French ANR   JCJC-Epic-SCENITH ANR-20-CE14-0028  and  CoPoC Inserm -transfert  MAT-PI-17493-A-04  to RA.
Study Design and Data Collection We designed a multicenter, nested case-control study using the data from the EBMT ProM-ISe registry, which prospectively collects the transplant-related data of every allo-HCT recipient in Europe. Each patient signed informed consent forms for data collection in retrospective studies performed from the ProMISe registry. This conforms to standards currently applied in the Netherlands where the ProMISe registry is placed. Two specific supplementary case report forms were created to collect the clinical, biological, and immunological data, data on PCP prophylaxis, and day 30 and day 90 outcomes for PCP cases and controls. The case report forms for controls provided a date of inclusion for each patient, calculated at the same delay from transplantation as the delay between transplantation and PCP of the matched case.
For PCP cases, we included the first episode occurring within 2 years after transplantation, between March 1, 2016, and May 4, 2018. Patients with pretransplantation PCP were not excluded if the post-transplantation PCP episode fulfilled the criteria for study inclusion. Two controls per case were selected by the EBMTÀInfectious Diseases Working Party data office from the ProMISe registry among allo-HCT recipients who had not developed PCP after HCT. The controls were matched for the center, transplantation date, and underlying disease.
If a control later developed PCP, the control was censored for survival at the time of PCP. Factors associated with 30-and 90-day mortality were investigated among the PCP cases. Probable PCP cases were compared to proven cases using logistic regression. A Type I two-sided error =. 05 was considered significant. The data were analyzed using SAS v 9. 4 (SAS Institute Inc. , Cary, NC, USA software).