dataesr/scientific-paragraphs-categorization huggingface dataset:
The rate ratios (RRs) were calculated using the OpenEpi statistical tool. (11)  Comparative Analysis For the comparative analysis, separate 1:1 propensity score matching was used to balance covariates between the aGVHD, cGVHD, and a + cGVHD groups versus the no GVHD group. The propensity score, de ned as the probability of a patient to develop GVHD conditional on observed baseline covariates, was estimated using a logistic regression model. The baseline covariates explored were hematological condition for the allo-HSCT, age, gender, comorbidities, and preparative regimens. The nal model was chosen based on the Akaike information criterion (a mathematical method for evaluating how well a model ts the data it was generated from) and the sample size retained for each comparison. The nal covariates were selected based on clinical relevance and/or statistical signi cance.
Results A total of 10 579 patients were identi ed in the SNDS database as recipients of allo-HSCT during the study period. After applying inclusion and exclusion criteria, 6 385 patients were included in the study population (Fig. 1 ). The mean age of the overall study population was 51. 1 years and 57. 9% were male. A total of 2 002 patients (31. 4%) experienced aGVHD, 411 patients (6. 4%) had cGVHD, and 1 304 patients (20. 4%) had a + cGVHD. The remaining 2 668 patients (41. 8%) had no recorded diagnosis code for GVHD (Supplementary Table  2 ). Patients with GVHD had lower rates of relapse than those with no GVHD. Overall, 16. 3% of the total study population (1 043 patients) had a relapse (aGVHD 276 patients [13. 7%]; cGVHD 61 patients [14. 8%]; a + cGVHD 220 patients [16. 8%]; no GVHD 486 patients [18.
Acknowledgments This study was funded by  CSL Behring  and conducted independently by  Certara Evidence & Access. Data were provided by the  French Caisse Nationale d'Assurance Maladie (CNAM)  and its staff involved in the project, in particular the DEMEX team. Support during the data application process was provided by the  Health Data Hub, the Ethics and Scienti c Committee for Health Research, Studies and Evaluations (CESREES) , and the  French Commission Nationale de l'Informatique et des Libertés  (CNIL) governing data access and data privacy laws. Medical writing was provided by  Cheryl Jones  from  Certara Synchrogenix , and editorial support was provided by  Synergy Medical Communications. Both were funded by  CSL Behring  in accordance with Good Publications Practice (GPP3) guidelines (http://www.
Statistical analysis The statistical analyses were carried out using the Stata software version 14. The characteristics related to sex, age, presence of splenomegaly and RDT results before and after MTS were compared between groups using chi-square tests. The distribution of FcγRIIA, FcγRIIC, FcγRIIIA and FcγRIIIB genotypes and G3m6 genotypes [(+/+), (+/-), (-/-)] between groups (together and between children) were compared using chi-square independence tests. Also, the genotypic frequencies were tested for Hardy-Weinberg equilibrium (HWE). Since a high level of opsonic phagocytosis of Pf merozoites has been described in young Fulani and related to fewer Pf malaria infections after MTS in this cohort  (Fall et al. , 2023) , the correlation between individual carriage of G3m6 or FcγRIIA, FcγRIIC, FcγRIIIA and FcγRIIIB and the presence of Pf malaria infection before MTS was first studied through a logistic multivariate regression model using the following as covariates: splenomegaly, ethnic group, gender, rural village and age status (adults vs.
Funding This research was supported by a grant from  Labex GR-Ex  and from the  National Geographic Society Committee for Research and Exploration  (Grant  9804-15 ). The  Labex GR-Ex , reference no. ANR-11-LABX-0051 , is funded by the  Programme d'Investissements d'Avenir (PIA)  of the  French National Research Agency , reference no. ANR-11-IDEX-0005-02. The  Université Paris Cité  awarded a PhD scholarship to AKDJF.
Patients We conducted a retrospective study in our tertiary referral center from 2001 to 2020. We have included all the adult patients with a CV receiving the anti-CD20 chimeric monoclonal antibody rituximab and divided them in two groups depending on whether they received flare prevention by plasmapheresis or not. The inclusion was made upon the patients' digital medical files according to the "Programme de Médicalisation des Systèmes d'Information" coding (PMSI), the French hospital system, based on the Diagnosis Related Groups model, and with the agreement of the ethics committee "Comité Local d'Ethique Recherche" (IRB, n • 202000652) and the French personal data protection committee "Commission Nationale de l'Informatique et des Libertés" (CNIL). All patients file were re-analysed by one examiner to assess the correct diagnosis reported on PMSI.
We reported all the demographic characteristics and disease statuses before and after treatment. Among 226 patients extracted from the database, 79 were excluded (64 due to misdiagnosis, 7 because of biologically undemonstrated cryoglobulinemia, and 8 due to lack of information concerning the treatment received). The remaining 147 subjects had cryoglobulinemia vasculitis proven by laboratory evidence but 76 were not treated with rituximab-based therapies. Our work was focused on the 71 remaining patients. The choice between performing PP or not was made on a caseby-case basis, depending on the expected risk of flare effect. In other words, PP was given to patients thought to be at high risk of flare effect. Of note, following a severe flare in 2013 (patient 3), we decided to we decided to be broader in our indications of PP.
Statistical analysis Primary endpoint was flare incidence after rituximab initiation in the two groups. We used GraphPad Prism 8 software (Dotmatics). Categorical variables are presented with absolute number "n" and percentage "%" in each groupe (n (%)). Fisher's exact test was used to compare them. Continuous variables are presented with median number and interquartile range. To compare frequencies in 2 unpaired groups, we used an unpaired Student t-test. Two-tailed nominal P < 0. 05 was considered significant. The Kaplan-Meier method was used to estimate OS and TTNT probabilities from initiation of rituximab. Logrank test was used to compare estimates of hazard functions of the two groups at median.
Within MOVIDA 2, follow-up of each participant started at ART initiation and continued until the last enrolled patient reached the virological evaluation at 24 months, data were therefore collected from June 2017 to July 2020. The MOVIDA 2 study being observational, follow-up and care complied with national guidelines. Following the WHO  [2] , national guidelines recommended initiating ART with a combination of two nucleotide reverse transcriptase inhibitors and one non-nucleotide reverse transcriptase inhibitor. Patients attended weekly visits the first month, and then monthly visits, or bi-monthly if in stable health. The only intervention was the use of DBS for blood sampling. Most demographic data were directly retrieved from the medical file, while data related to ethnicity, distance to care site, professional activity were obtained from the patient at enrolment.
Clinical data were retrieved from the medical file. For HIV VL monitoring, the national algorithm, based on WHO guidelines, recommended HIV VL testing at 6 months of ART, 12 months of ART and then every 12 months afterward. At these timepoints, if the HIV VL was �1,000 copies/mL, the algorithm recommended providing adherence support and repeat HIV VL testing within 3 to 4 months from the initial measurement. If the confirmatory HIV VL was again �1,000 copies/mL, ART modification for a new ART line was recommended; otherwise, no ART modification was required. Adherence to ART was assessed at each clinical visit by self-reporting the number of missed ART doses in the last 4 days (ranging from none to four missed doses).
Ethical considerations The study was reviewed and approved by the Institutional Review Board at the NIHE in Vietnam (02/QD-VSDTTU) and Institut Pasteur in France (2016-10/IRB/1). The protocol was submitted on the clinicaltrials. gov website (NCT03249493). All participants gave their written informed consent before the enrolling. Data processing was authorized by the French legal authority CNIL (DR-2017-046).
Restricting the analysis to the 24 months of ART timepoint, the only two factors that remained independently and significantly associated with higher risk of virological failure were PWID status and late visit attendance (data not shown). Only DBS collected within the interval 2 months prior and 4 months after the time point were considered, proportions are estimated as the ratio between the number of DBS collected divided by the number of patients still followed. 2 At 6 months, four patients had their DBS lost at some point, with no replacement; at 12 months, seven patients had their DBS lost at some point, and two patients had new DBS collected to replace them; at 24 months, one patient had his DBS lost at some point and a new DBS was collected to replace it. 3 Some DBS were lost and therefore not tested (as described before) and others were discarded as they showed signs of humidity making the HIV viral load result uncertain (24, 2 and 5 DBS discarded at 6, 12 and 24 months of ART, respectively) https://doi.
Acknowledgments We are grateful to the following for their cooperation and support in the conduct of this study. The  MOVIDA 2 Study group National Institute of Hygiene and Epidemiology (NIHE) ,  Hanoi , Vietnam:  Anh Duc DANG ,  Huyen Thi Thanh DAO ,  Nhung Thi Hong LE, Phuong Khanh NGO, Binh Thanh NGUYEN, Tuan Anh NGUYEN, Tram Thi Phuong PHAM, Ha Thi TONG, Tram Hong TRAN; Institut Pasteur, Paris, France: Mohand AIT-AHMED, Yoann MADEC, Fabien TAIEB; Vietnam Administration of HIV/AIDS Control (VAAC), Hanoi, Vietnam: Huong Thi Thu PHAN, Long Hoang NGUYEN; Hanoi University of Public Health ,.
We used quality score threshold of 20 and removed the read shorter than 25 pb. The read alignments were performed using the STAR program with the genome reference mouse (GRCm39) and the reference gene annotations (Ensembl). The UMI (Unique Molecular Index) allowed to reduce errors and quantitative PCR bias using fastp and umi-tools. Based on reads alignments, we counted the numbers of molecules by gene using FeatureCount. Other programs were performed for the quality control of reads and for the workflow as qualimap, fastp, FastQC and MultiQC. Differential Gene Expression of RNA-seq was performed with R/Bioconductor package DESeq2. The cut-off for differentially expressed gene was p-value padj (BH) < 0. 1. RNA sequencing data that support the findings of this study have been deposited in sequence Read Archive (SRA) data (https://dataview.
Acknowledgments The authors acknowledge  Jean-Pascal Meneboo ,  Martin Figeac  ( Plateformes Lilloises en Biologie et Santé ( PLBS ) - UAR 2014 -US  41),  Antonino Bongiovanni ,  Meryem Tardivel ,  Nathalie Jouy  (cell imaging platforms/BICeL). Matthieu Corbin  for its contribution to experiments.
statistics generated by the COVID-19 HGI are available online, including per-ancestry summary statistics for African, admixed American//www. covid19hg. org/results/r7/). The analyses described here used the data release 7. If available, individual-level data can be requested directly from https://github. com/ AndrewsLabUCSF/COVID19_heritability)https://github. com/marcoralab/MRcovid); and subtype analyses (https://github. com/mjpirinen/covid19-hgi_subtypes) are available at GitHub.
Data Policy information about availability of data All manuscripts must include a data availability statement. This statement should provide the following information, where applicable: -Accession codes, unique identifiers, or web links for publicly available datasets -A description of any restrictions on data availability -For clinical datasets or third party data, please ensure that the statement adheres to our policy Summary statistics generated by COVID-19 HGI are available online, including per-ancestry summary statistics for African, Admixed American, East Asian, European, and South Asian ancestries (https://www. covid19hg. org/results/r7/). The analyses described here utilize the data release 7. If available, individual-level data can be requested directly from contributing studies, listed in Supplementary Table  1.
We used publicly available data from GTEx v8 (https://gtexportal. org/home/; dbGaP Accession phs000424. v8. p2), the Neale lab (http://www. nealelab. is/uk-biobank/), Finucane lab (https://www. finucanelab. org), FinnGen Freeze 4 cohort (https:// www. finngen. fi/en/access_results), and eQTL catalogue release 3 (http://www. ebi. ac. uk/eqtl/).
Mogamulizumab is a first-in-class defucosylated monoclonal antibody, selectively binding to C-C chemokine receptor 4 (CCR4) with enhanced antibody-dependent cellular cytotoxicity activity. The CCR4 receptor is overexpressed on the malignant T-cells in the skin and peripheral blood of patients with MF and SS. Efficacy of mogamulizumab has been evidenced in an open-label, multinational, phase 3, randomized controlled trial comparing mogamulizumab with vorinostat, an oral histone deacetylase inhibitor and antineoplastic agent, among patients with refractory or relapsed MF and SS (MAVORIC, NCT01728805). It was shown that mogamulizumab significantly prolonged progression-free survival (PFS) compared with vorinostat (hazard ratio: 0. 53, 95% CI [0. 41-0. 69], p < 0. 0001). 11 Based on these positive findings, mogamulizumab was approved in 2018 in the European Union for adult patients with MF and SS who have received at least one prior systemic therapy.
Study design This non-interventional, multicentre, retrospective ('OMEGA') study was conducted in 14 expert centres of the French Study Group of Cutaneous lymphoma (https://www. gfelc. org/). Eligible patients were adults who received mogamulizumab at least once for MF or SS until March 2020. Patients previously enrolled in the MAVORIC trial could be included if they were alive at the end of this interventional study. The study protocol was approved by an independent Ethics Committee (Sud-Est VI, Clermont-Ferrand). According to the French law regarding retrospective studies, all included patients alive at the time of data collection were informed about the study content and had no objections to their personal data being processed. Data were retrospectively collected from patients' medical records until March 2020.
Data collected The following retrospective data were collected: Patient characteristics, type of CTCL, MF or SS, disease history, previous therapies for MF or SS, disease stage at diagnosis and mogamulizumab initiation, use of mogamulizumab including temporary and permanent discontinuations, response to treatment from mogamulizumab initiation to discontinuation or end of study (complete response [CR], (median: 4. 6 months, 2. 1-7. 2), 96. 7% of patients received all the planned mogamulizumab infusions. Among the 109 patients evaluable for effectiveness, ORR was 58. 7% (95% CI [48. 9- ). Treatment response was collected overall and by compartment (skin, lymph nodes, viscera and blood in SS patients) according to European guidelines for response,  6, 13  at any time and for no pre-specified duration from mogamulizumab initiation.
Statistical methods For this retrospective non-interventional study based on available patient medical files, no sample size calculation was requested. Descriptive analysis was performed. Study parameters were assessed using mean and standard deviation or median and interquartile range for continuous variables, and proportions for categorical variables. Two-sided tests with type I error α = 0. 05 were applied when relevant and were considered significant at p < 0. 05. Missing data were not replaced. Statistics were carried out using SAS® software (SAS Institute), version 9. 4. The safety population comprised all included patients having received at least one dose of mogamulizumab. Patients of the safety population who met all inclusion criteria were retained in the overall analysis population, and in patient groups MF or SS.
5 to 72. 6 months depending on patients) which led to heterogeneous effectiveness population. Since 20 patients still alive at the end of the MAVORIC trial were included in the OMEGA study (i. e. 16% of our analysis population), there might be a survivor bias  26  with an overestimation of our effectiveness results. Despite these limitations, our real-life data from a large French population of patients with Sézary syndrome or Mycosis Fungoides, less selective than in clinical trials, were consistent with previous findings and confirmed the effectiveness of mogamulizumab (high level and rapid onset of treatment response, in particular in patients with blood involvement), as well as its manageable safety profile.
E T H IC S S TAT E M E N T The study protocol was approved by an independent Ethics Committee (Sud-Est VI, Clermont-Ferrand). According to the French law regarding retrospective studies, all included patients alive at the time of data collection were informed about the study content and had no objections to their personal data being processed. ORC I D M. Beylot-Barry https://orcid. org/0000-0001-6150-1229 O. Dereure https://orcid. org/0000-0001-8736-1922 A. Pham-Ledard https://orcid. org/0000-0003-2960-6084 V. Braniste https://orcid. org/0000-0003-1992-3609 M. Bagot https://orcid. org/0000-0002-1631-5192.
In daily practice, the availability of Ct values in the QS system, indicating a high Ct value can likely be alerted of possible false positive results. This is an important advantage over FA, which provides only qualitative results. Of note, the QS raw data is not available and replaced by curves improved by the manufacturer. Previous studies of POC PCR have shown the interest of having access to the raw curves  [22]. The 2 viral targets (HSV-1 and PeV) and the 2 bacterial targets (Nm and Sp) were tested positive with 3 cartridges of the 2 SPCR POC assays. QS Ct values were very close (Ct value variation below 2) which is in favor of a high reproducibility of this POC SPCR assay. Surprisingly, internal control Ct values obtained with series of cartridges loaded with same content were sometimes significantly scattered (Ct value variation below 2).
Statistical Analyses Data were entered by using 4D (v6. 4 to v17. 4) and analyzed with Stata SE v15. 1 (Stata Corp. , College Station, TX, USA). Data were analyzed using segmented linear regression with autoregressive error  [42, 43]. We analyzed monthly data to provide optimal precision. The model took into account autocorrelation and the trend before and after PCV implementations, which were considered in the model by including dummy variables for each period. The post-intervention trend change was estimated by comparing observations with the expected trend if the intervention had not occurred. Furthermore, we analyzed the monthly carriage and penicillin nonsusceptibility rates of the emerging serotypes from the late PCV13 period. For these nonvaccine serotypes, we identified knots (specific time points when a trend change occurred) to select the model providing the best fit.
This lipidomic profile was also detected in tumors from mice treated with the new synthetic compound PFM037, structurally and functionally related to SULT2B1b-derived products. PFM037 contributed to monocyte differentiation and induced effective antitumor responses by interfering with LXR signaling. Moreover, it increased the efficacy of immune checkpoint blockers and adoptive cell therapy. Finally, by interrogating available scRNA-seq datasets of tumor-infiltrating immune cells, we reported a significant enrichment of melanomainfiltrating monocytes/macrophages over-expressing the LXR target genes ABCA1 and SCD1 in ICB-resistant patients.
3F ). Then, we compared our transcriptomic results with publicly available datasets, particularly TNF-and NOS-producing DCs (Tip-DCs)  [25] , bone marrow-derived and blood monocytes  [23] , skin-derived macrophages, cDCs and monocyte-DCs  [29] , and lung-derived cDC1, cDC2, inf-cDC2 and monocyte-derived APCs  [24]. Ly6C high CD11c + MHC-II + mono-DCs, as well as Ly6C low cells isolated from SULT2B1b-and Mock-LLC tumors resulted to be closer to the Tip-DCs (Fig. 3A ). By UMAP analyses we identified 4 clusters grouping cells isolated from different organs or pathologic conditions sharing some program commonalities (Fig. 3B ). Cluster 2 grouped our mono-DCs and Ly6C low cells with Tip-DCs  [25] , both groups isolated from tumors. Cluster 0, cells isolated from lung independently of their state of activation  [24].
Expression of LXR/cholesterol genes in myeloid cells infiltrating human tumor samples predicts tumor response to ICBs To find molecular correlates in human tumors we evaluated the expression and clinical significance of LXR/cholesterol synthesis genes in myeloid cells infiltrating human tumors by taking advantage of recently published scRNA-seq datasets of nonsmall cell lung cancer (NSCLC)  [43]  and melanoma samples, the latter from ICB-responder and non-responder patients  [44]. We detected an increased expression of ABCA1 and SCD transcripts, as well as cholesterol synthesis genes, such as HMGCR, in myeloid cells infiltrating NSCLC samples (Fig. 9F ). We observed the expression of ABCA1 and SCD mainly in tumor-associated macrophages (cluster 2) (Fig. 8G ), while HMGCR was mainly expressed in DCs (Fig.
9G ). To correlate myeloid cell infiltration, LXR/cholesterol synthesis pathways and response to immunotherapy, we interrogated the scRNA-seq dataset of melanoma samples of ICB-responder and non-responder patients  [44]  and observed a statistically significant enrichment of ABCA1 and SCD transcripts in monocytes/macrophages of patients not responding to ICBs (Fig. 9H  and Supplementary Table  3 ) (ABCA1 NR vs R = 1. 52; P = 4. 29 × 10 -8 ; SCD NR vs R = 1. 80; P = 2. 93 × 10 -5 ; Wilcoxon rank sum test). Of note, the enrichment of ABCA1 transcripts in monocytes/macrophages of non-responders turned out to be the most significant among all melanoma-infiltrating CD45 + cells (T lymphocytes, B lymphocytes, etc. ; ABCA1 NR vs All = 1. 40; P = 5. 79 × 10 -212 ; Wilcoxon rank sum test) (Supplementary Fig.
For image acquisition and analysis eSlide Manager (Aperio Leica Biosystems) was used. All images were acquired using the Aperio AT2 system (Leica Biosystems). A total area of 97,6 mm 2 (Vehicle) and 104,98 mm 2 (PFM037) of liver was analyzed for each group of mice. Tumor cell quantification (MC38-GFP) was performed by automated image analysis software through the Color Deconvolution Algorithm v9. 1 of the ImageScope program (version 12. 4. 3), following manufacturer's instructions (Leica Biosystems). The images shown were identified as representative area of interest within the total area of the specimen and exported as ImageScope snapshots at 20x magnifications as described  [38]. Analysis of tumor-infiltrating cells by flow cytometry. Mice were challenged with LLC, LLC-Mock, LLC-SULT2B1b and RMA tumor cells (see tumor challenge experiments for details).
7), IFNγ (XMG1. 2), CD19 (6D5), CD49b (DX5) and Ter119, CD26, CD64, MAR-1 all from Biolegends. CD209a (5H10), CCR7 (4b12) and F4/80 (BM8) were from eBioscience. Rat IgG, Rat IgG2a, Rat IgG2b, Rat IgM and Hamster isotype control mAbs were used as controls (Biolegends and BD Biosciences). For intracellular staining, cells were incubated with PMA (100 ng/ml) and ionomycin (500 ng/ml) in the presence of 10 μg/ml of Brefeldin for 4 h. Cells were then fixed using the IC Fixation buffer (eBioscience), permeabilized with 1x Permeabilization buffer (eBiosciences) and stained with anti-IFNγ mAb. Samples were run by FACSCanto flow cytometer and analyzed by FlowJo software gating on live cells. FACS sorting was performed by using the FACSAria Fusion (BD). RNA-seq experiments. FACS-sorted monocyte-DCs and Ly6C low cells were collected in complete RPMI and pelleted.