dataesr/scientific-paragraphs-categorization huggingface dataset:
The HSP. hi macrophages belong to the Cluster 8 macrophages identified previously that had M2-associated functions. [14] The StemLike macrophages are similar to cancer stem cells with protumorigenesis properties. [14, 16] Therefore, the percentage changes in macrophage subpopulations by Mito-ATO treatment were favorable to the antitumor response. To uncover mechanisms underlying the reduced G-MDSC percentages in TIME from mice treated with Mito-ATO, we first determined the gene expression differences associated with mitochondrial metabolism, glycolysis, and apoptosis within G-MDCSs in the mouse tumors relative to G-MDSCs in normal tissues. By analyzing a publicly available scRNA-seq dataset of mouse normal tissues and the corresponding tumors,  [17]  we found that G-MDSCs from tumor-bearing mice upregulated genes for glycolysis and suppressed proapoptosis genes in G-MDSCs in the TIME when compared with those in normal tissues (Figure  7 ).
Gene expression of three mitochondrial complexes (I, III, and IV) in CD4IL2RALO Tregs were all significantly decreased by Mito-ATO treatment (Figure  12D ). Genes for OXPHOS and glycolysis were also significantly downregulated in the Mito-ATO group compared with the control group (Figure  12D ). Coordinately, proapoptotic genes were upregulated in the Mito-ATO group (Figure  12D ). Gene expression changes associated with these pathway activity changes in CD4IL2RALO Tregs are included in Figure  13. These data suggest that mitochondrial function and energy generation were severely impaired by Mito-ATO in the CD4IL2RALO Tregs, resulting in growth inhibition of these cells and also potentially promoting increased apoptosis. Using publicly available scRNA-seq datasets of mouse normal tissues and tumors,  [17]  we compared the tumor CD4IL2RALO Tregs to normal tissue CD4IL2RALO Tregs for possible changes of the above-referenced key pathways we identified in our studies.
t. were started every other day for a total of three injections. Development of the treated and nontreated tumors in the same animal was monitored. Both tumor burden and tumor numbers were recorded. Body weights were monitored every week. To deliver Mito-ATO systemically by oral gavage, LLC-Luc cells (2 × 10 5 ) cells were injected either orthotopically or into the left ventricle. One day after the inoculation, C57BL/6J were given daily oral gavage of Mito-ATO at a dose of 600 μg (or 30 mg kg -1 body weight). Quantitative data for bioluminescence imaging of the orthotopic growth (n = 8 per group) or brain metastasis (n = 7 per group) of LLC-Luc cells were collected. In experiments where Mito-ATO was combined with anti-PD-1 treatment, five-week-old female C57BL/6J mice were purchased from Jackson Laboratory.
These flow cytometry antibodies were purchased from either Biolegend, eBioscience, or BD Biosciences. Cells were analyzed using an LSR Fortessa X-20 flow cytometer (Becton Dickinson). Data were analyzed using FlowJo software (Treestar, Inc. ). Apoptosis Measurement: To analyze levels of apoptosis induced by Mito-ATO in vivo, seven-week-old SV129 mice were inoculated with LKR13 (2 × 10 6 ) tumor cells on the right abdomen. Eight days postinoculation, Mito-ATO (5 × 10 -3 m) was i. t. injected into tumor. Forty-eight hours later, mice were euthanized, and tumors were incised and dissociated into single cells suspension. Cells were first stained with cell-type-specific phenotypic and apoptotic markers and subjected to flow cytometric analysis. The levels of cell apoptosis were determined by FlowJo software.
0 × 10 4 cells. The scRNA-seq libraries were generated by Chromium Single Cell 3′ v3 Reagent Kits (10× Genomics) and sequenced using NextSeq 500/550 High Output Kits v2 (150 cycles) (Illumina) according to the manufacturer's protocol. There were two replicates for each experimental group. The standard quality control procedures were followed to filter out the dead cells or unhealthy dying cells according to the widely used procedures practiced in the single-cell RNA-seq research field (the related publication can be found in the following github website (https://github. com/hbctraining/scRNA-seq_online/blob/master/lessons/04_SC_quality_ control. md)). In general, UMI (Unique Molecular Identifier) counts per cell should be above 500. Here, more stringent filtering criteria were used. The range of UMI counts for the G-MDSC cell population in the studies ranged from 1572 to 28 256.
The mean of UMI counts for the G-MDSC population in the studies was 8328. These data indicate that for the G-MDSCs the general quality control filtering criteria were exceeded. Raw sequencing data were demultiplexed and converted to genebarcode matrices using the Cell Ranger (version 2. 2. 0) mkfastq and count functions, respectively (10× Genomics). The mouse reference genome mm10 was used for alignment. Data were further analyzed in R (version 3. 4. 0) using Seurat (version 3). The number of genes detected per cell, the number of unique molecular identifiers, the percent of mitochondrial genes were plotted, and outliers were removed (cells that expressed less than 200 and more than 2500 genes) to filter out doublets (two single cells) and dead cells. Differences in the number of unique molecular identifiers and percent of mitochondrial reads were regressed out.
Raw unique molecular identifier counts were normalized and log transformed. To analyze the sequenced CD45 + cells from mouse lung tumors, the Seurat R package3 was utilized to perform fine clustering of the single cells. [37] The gene expression data from all single cells were aligned and projected in a 2D space through uniform manifold approximation and projection to allow identification of the cell populations among the CD45 + cells. Differential gene expression analysis of scRNA-seq data was performed as follows: Before the differential expression analysis, the computational imputation of zero values was performed to correct for the influence of dropout events (i. e. , failure in detecting expressed genes due to low sequencing depth of single cells). Computational methods described previously were utilized  [38]  to perform imputation and other data processing procedures.
Flow cytometry analyses Reactivation assay: J-Lat A1 cells were collected and resuspended in PBS-EDTA (0. 5 mM). Data were collected and analyzed with a BD Accuri C6 cytometer and software CFlow Plus. At least 10,000 events in P1 were collected, the GFP-positive population was determined using a GFP-negative population arbitrary and the same gate was maintained for all conditions. Analysis was performed on the whole GFP-positive population. Cell cycle assay: J-Lat A1 cells were seeded into 12 well plates, then transduced with VLPs for 48 h. The cells were then treated with 330 nM Nocodazole for 18 h prior fixation in 70% ethanol. Following treatment for 30 min at 37 °C with 0. 2 mg/ml RNase A and 50 µg/ml propidium iodide in buffer H (20 mM HEPES, 160 mM NaCl, 1 mM EGTA), cells were analyzed for their DNA content using the LSR Fortessa cell analyzer (BD Biosciences).
Immunofluorescence Hela cells were transfected with TASOR-FLAG (WT or mutant). 48 h post transfection, cells were fixed with 4% PFA for 15 min and then permeabilized with PBS-Triton 0. 1% for 10 min at room temperature. A saturation step was performed for 1 h with PBS BSA 3%. After PBSmediated washes, cells were incubated with an 1/500 anti-TASOR (HPA006735-Merck) for 1 h at RT. Cells were then washed three times with PBS, then anti-rabbit Alexa 594 was added at a dilution of 1/1000 for 1 h at room temperature in a dark chamber. DNA was stained with Hoechst 33258 (382061-Sigma). After three PBSmediated washes, the coverslips were mounted on slides with the use of ProLong ™ Diamond Antifade Mountant (P36970-ThermoFisher). Imaging was performed with a Spinning-Disk LEICA confocal microscope from the IMAG'IC core facility at Institut Cochin.
1%, were used: anti-Flag M2 (F1804-200UG, lot SLCD3990, Merck) 1/1000; anti-TASOR (HPA006735, lots A106822, C119001, Merck) 1/1000 -for IF assays 1/500, anti-MPP8 (HPA040035, lot R38302, Merck) 1/1000; anti-MORC2 (PA5-51172, ThermoFisher) 1/1000; anti-Actin (AC40, A3853, Merck) 1/1000; anti-CDK1 (Cdc2p34  (17) , sc-54, Santacruz), anti-CDK2 (M2, sc-163, Santacruz), anti-Cyclin A (H-432, sc-751, Santacruz), anti-Cyclin B1 (H-433, sc-752, Santacruz), anti-SAMHD1 (SAB1400478, Sigma), anti-phospho-SAMHD1 (D702M, 89930, Cell signalling), anti-GAPDH (6C5, SC-32233, Santa Cruz). All secondary antibodies anti-mouse (31430, lot VF297958, ThermoFisher) and anti-rabbit (31460, lots VC297287, UK293475 Ther-moFisher) were used at a 1/20000 dilution before reaction with Immobilon Forte Western HRP substrate (WBLUF0100, Merck Millipore).
28 Of the few studies focused on risk of SPM after RAI for DTC in young patients, an increased risk for leukemia has been reported, specifically myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). 6, 7, 22 The results for solid malignancies have been less consistent, suggesting increased risks of salivary gland and kidney cancers  6, 7, 10, 18, 29, 30  ; however, they were limited by short follow-up, small sample size, and lack of consideration of a minimal 5-year latency period between radiation exposure and solid malignancy development. 31, 32 re, we aimed to estimate risk of SPM associated with RAI treatment for DTC in childhood and young adulthood (age , 45 years) using the US SEER cancer registry database (1975-2017). In addition to confirming the more well-established association of RAI treatment and leukemia risk, the inclusion of nearly 10 more years of follow-up compared with earlier SEER-based studies on this topic  6, 7  allowed for more precise assessment of solid malignancy risks.
SIRs are the observed divided by expected number of cancers. 4] [45] [46]  To evaluate confounding by smoking, we compared SIRs for smoking-related versus nonsmoking-related cancers. 47 We also estimated the standardized mortality ratio (SMR) for chronic obstructive pulmonary disease (COPD), a smoking-related but not radiation-related outcome. 48 mulative incidence. We estimated cumulative incidence of second solid and hematologic malignancies by time since DTC diagnosis, accounting for competing risk of death and other cancers, that is, hematologic malignancies were treated as competing risk for solid malignancies and vice versa. Analyses were conducted using SEER*Stat (version 8. 3. 8), the AMFIT module of Epicure (version 2. 00. 02), and STATA (stcompet function). 49.
Characteristics of Differentiated Thyroid Cancer Patients Age , 45 Years in SEER 9 (1975-2017) Database aBefore exclusions on the basis of minimum latency period. The characteristics of the cohort after exclusion of 5-and 2-year latency period are reported in the Data Supplement. 0. 10) for those not treated with RAI. At 20 years, it was 0. 67% (0. 49 to 0. 88) and 0. 37% (0. 27 to 0. 50), respectively (Fig3).
Trends in RAI therapy for nonmetastatic differentiated thyroid cancer in patients younger than 45 years in the SEER 9 (1975-2017) database, overall and by tumor size at diagnosis. 1988: change in SEER coding definitions for radiation therapy for DTC and first availability of tumor size information. 2009 and 2015: years of publication of ATA guidelines recommending against routine use of RAI for low-risk DTC. ATA, American Thyroid Association; DTC, differentiated thyroid cancer; RAI, radioactive iodine.
Trends in RAI therapy for nonmetastatic differentiated thyroid cancer in patients younger than 45 years in the SEER 9 (1975-2017) database, overall and by tumor size at diagnosis. 1988: change in SEER coding definitions for radiation therapy for DTC and first availability of tumor size information. 2009 and 2015: years of publication of ATA guidelines recommending against routine use of RAI for low-risk DTC. ATA, American Thyroid Association; DTC, differentiated thyroid cancer; RAI, radioactive iodine. 0. 6 RAI Use Proportion 0. 4 0. 2 1988 2009 2015 1975 1980 1985 1990 1995 2000 2005 2010 2015 2017 Year of Treatment All sizes < 1 cm ≥ 1 cm FIG 1. 60,61.
In an 11-year follow-up survey conducted in the Japanese general population, the group of patients with low levels of NK cell cytotoxic activity had a higher risk of cancer  (31). Along the same lines, low NK cell counts, rather than CD4 + or CD8 + T cells in peripheral blood are associated with lower overall survival in patients with follicular lymphoma  (42). Many studies have also reported defective blood NK cell function in patients with solid tumors. Our analysis of predefined NK and CD8 + T-cell signatures in multiple public transcriptome data from the TCGA database, which includes over 10,000 tumor samples corresponding to 33 different cancer types, showed that most tissues infiltrated by NK cells were also infiltrated by T cells. Contrary to the findings for ILC1, the NK signature was strongest in hematopoietic cancers (acute myeloid leukemia (AML) and B-cell lymphoma), followed by solid cancers, including kidney renal clear cell carcinoma, testicular germ cell tumors, mesothelioma (a very rare form of cancer affecting the membranes lining internal organs, such as the pleura, peritoneum and pericardium), thymoma, cervical squamous cell carcinoma, endocervical adenocarcinoma, lung cancer and gastric cancers (esophagus, stomach, pancreas)  (43)  (see Table  1 ).
PDGF-DD is secreted by various tumors and promotes cell proliferation, stromal cell recruitment, angiogenesis, epithelialmesenchymal transition and metastasis  (152, 153)  (see Table  2 ). Barrow and coworkers recently identified transcriptional signatures unique to PDGF-DD-activated NK cells and established the abundance of this signature in The Cancer Genome Atlas (TCGA) low-grade glioma (LGG) and bladder cancer (BLCA) datasets with CIBERSORT. They found that tumors of patients enriched in PDGF-DD-activated NK cell or memory CD8 + T-cell phenotypes were associated with a more favorable prognosis in LGG, but with a poor prognosis in BLCA  (104, 105). Nidogen 1 (NID1) is an extracellular matrix protein (  148 ) that promotes epithelial-mesenchymal transition (EMT) and metastasis in ovarian cancer.
Furthermore, the reactivity of CIML NK cells against HuT-78 lymphoblasts in the presence of AFM13 (CD16/CD33) is moderately higher than that of freshly isolated NK cells  (183). However, TriKEs composed of one scFv against CD16, another against CD33 and a human IL-15 crosslinker promote NK cell effector functions, and also increase NK cell expansion and persistence in vivo in mouse preclinical models of AML and ovarian cancer  (184, 185). Thus, co-engagement of the ITAM and JAK/STAT pathways renders the NK cell response more potent. The humanized TriKE CD16/IL-15/CD33 is currently under evaluation in a phase I/II trial for the treatment of high-risk myelodysplastic syndromes, refractory/relapsed AML and advanced systemic mastocytosis (NCT03214666). NKp46 appears to be a particularly interesting potential target, as it is persistently expressed on tumor-infiltrating NK cells, whereas NKp30, CD16 and NKG2D are frequently downregulated.
FUNDING The  EV laboratory at CIML and Assistance-Publique des Hopitaux de Marseille  is supported by funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (TILC, grant agreement No. 694502  and  MInfla-TILC , grant agreement No. 875102 -MInfla-Tilc ), the  Agence Nationale de la Recherche  including the  PIONEER  Project ( ANR-17-RHUS0007 ),  MSDAvenir ,  Innate Pharma  and institutional grants to the  CIML (INSERM, CNRS , and  Aix-Marseille University)  and to  Marseille Immunopole. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication. HMK is recipient of a PhD grant from ' Institut Cancer Immunologie '.
RESULTS Only specimens meeting the study inclusion criteria were included in the analysis (Fig. 1 ). Characteristics of women enrolled in the study. A total of 456 women were enrolled in this study; 347 patients met the inclusion criteria with all data available for the analysis. The demographic characteristics associated with these 347 specimens prospectively analyzed in this study are presented in Table  1. Most of the samples (61. 7%) were collected from the gynecological emergency ward, from the family planning department, and from hospitalized and outpatients, represented by 6. 3%, 7. 5%, and 24. 5% of the total study population, respectively. According to NS interpretation (positive, negative, or intermediate) after an expert reading by the technician, among the 347 women selected for vaginosis, there were 144 patients (41.
1% compared to the NS determination. This new test presents a higher sensitivity compared to previous molecular tests evaluated  (24). Indeed, the Aptima BV test assessed during this study presents a 91. 1% sensitivity and a 94. 4% specificity, whereas the Aptima IVD, BD Affirm, and Hologic ASR revealed 84. 4%, 86. 7%, and 75. 6% sensitivity, and 86. 3%, 60. 6%, and 81. 8% specificity, respectively  (24). Recent research by Frederick et al. has indicated more complex process implicating the role of bacterial pathogens in the etiology of BV  (27) (28) (29). Many of these organisms, such as Atopobium vaginae, Prevotella species, and others, can be detected only by amplification tests  (18). Indeed, despite the increasing use of MALDI-TOF technology in microbiology laboratories (with large databases), the identification of these fastidious microorganisms remains challenging, necessitating anaerobic prolonged cultures, not compatible with the delay of results (turnaround time) in the routine clinical practice of BV diagnosis  (30).
MATERIALS AND METHODS Study design. This study was designed as a monocentric, retrospective, observational study of adult women. From May to August 2019, we enrolled outpatients and inpatients, including nonpregnant women over18 years of age with vaginosis symptoms consulting at Nantes University hospital. Ethics approval. According to the French and European legislation, the use of data in this monocentric study does not need approval from the ethics committee. This study was recorded at Nantes University hospital by the local data privacy officer under the reference: TS005. BIO. AP. 2019_14. Samples for this study, results, and data had been recorded during normal medical care of patients by professionals who are following them. All the data collected for this new study from patient medical folders has been filed in a board under an anonymized code which cannot be tied to the patient.
Three outliers were excluded from the model on GPx as they were highly influential in the model, and exceed the mean ± 3 times the standard deviation. Linear mixed models were further used to specifically test whether Se and Hg concentrations showed a change from the first to the second sampling period in chicks divided based on the progress of the disease (always healthy, get sick, always sick, improved; as described in detail in  Sebastiano et al. (2019). These models were only run on control chicks (chicks that were not included in the experiments). The skull length was included as a covariate to correct for the age of the chicks, while the ID of the chicks was included as a random factor. All data transformation and violation of models' assumptions are reported throughout the manuscript.
Acknowledgments We thank the  CNRS, DEAL Guyane , the  MNHN of Paris , the  CEBC , the  LIENSs laboratory at University La Rochelle , the  University of Antwerp , the  FWO , the  GEPOG , the  Institut Pasteur de Guyane , and the  King Leopold III Fund  for funding, logistic support, and access to the  Grand Connétable Nature Reserve. The authors are grateful to  Carine Churlaud  and  Maud Brault-Favrou  from the  «Analyses Elémentaires» platform (LIENSs)  for their support during trace element analysis. Thanks are due to the  CPER (Contrat de Projet Etat-Région)  and the  FEDER (Fonds Européen de Développement Régional)  for funding the  AMA and ICPs of LIENSs laboratory. The  Institut Universitaire de France (IUF)  is acknowledged for its support to PB as a Senior Member. We are especially grateful to  Grand Connétable  reserve staff ( Kévin Pineau ,  Alain Alcide ,  Jérémie Tribot ) and to  Jonathan Simon  for their great help in the field.
Regression in male Znrf3 cKO adrenals is correlated with macrophage infiltration and fusion To further gain insight into the underpinnings of the regression phenomenon, we analysed global gene expression by bulk RNA sequencing of control and Znrf3 cKO male adrenals at 4, 6 and 12 weeks. Gene set enrichment analysis (GSEA) of the RNA sequencing data using the C5 Gene Ontology database (MSigDB) showed that at 12 weeks, the 34 most significantly enriched gene sets were all related with immune response and inflammation (Fig  2A ). Most of these gene sets were either not (FDR >0. 05) or negatively enriched at 4 weeks and showed an intermediate enrichment score at 6 weeks. This suggested that ablation of Znrf3 resulted in the progressive establishment of a proinflammatory environment. Consistent with this idea, a large number of proinflammatory cytokines and chemokines genes were progressively upregulated at 6 and 12 weeks  (Fig 2B and Fig S2A).
Phagocytic macrophages signatures are prominent in male ACC patients and associated with better prognosis To further evaluate the role of macrophages in ACC progression, we evaluated their infiltration within human ACC. For this, we used RNA sequencing data from the TCGA consortium (79 sequenced ACCs) and evaluated expression of a 10-gene signature (based on single cell RNA sequencing data from mouse adrenals (  51 )) as a proxy to general macrophage infiltration. Interestingly, tumours of the good prognosis group, defined as C1B (  27  Altogether, these observations suggest that phagocytic macrophages, which are more prominent in male than female ACC patients, are associated with senescence, global innate and adaptive immune response and better prognosis.
Although MERTK expression did not correlate with the presence of macrophages in ACC patients (not shown), we show that increased expression of the phagocytic CD68/TREM2/TYROBP signature is correlated with better prognosis, within the TCGA cohort. This strongly suggests that phagocytosis plays a central role in the tumoricidal activity of macrophages in ACC. Interestingly, scRNA sequencing in human and mouse colorectal cancer identified a population of C1QC + TAMs, characterised by high levels of C1QA/B/C, TREM2 and MERTK expression, which were associated with potential recruitment and activation of T cells, phagocytosis and better prognosis  (53, 56). Although we did not analyse macrophages by single cell RNA sequencing in Znrf3 cKO adrenals, our bulk RNA sequencing data show strong up-regulation of all these markers (Fig 3B ), which are mostly expressed by macrophages in scRNA seq datasets from wild-type mouse adrenals (Fig  S8A ).
For double-immunohistochemistry experiments, HRP was inactivated by incubation with 0. 02% HCl for 20 min after detection of the first antibody to avoid cross-reaction. Nuclei were counterstained with Haematoxylin for brightfield images or Hoechst for fluorescence (Thermo Fisher 33342). Slides were mounted using a 50/50 PBS-Glycerol solution. Images were acquired with a Zeiss AxioImager with Apotome2 or Zeiss Axioscan Z1 slide scanner. Images were minimally processed for global levels and white balance using Affinity Photo® and Affinity Designer®. Image settings and processing were identical across genotypes. Quantifications were performed on scanned whole adrenals (Axio Scan Zeiss scanner, 20× images) using the QuPath software version 0. 3. 1 (Bankhead et al 2017). Briefly, annotations were made of whole adrenals or just the adrenal cortex, and the positive cell detection feature was used to identify positive cells.