dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The National Reference Center for Malaria in French Guiana acknowledges its partners involved in diagnosis and care of malaria in French Guiana, who collaborate for several years in malaria surveillance and allow generation of precious data for public health and malaria control. The authors are grateful to  Valentin Joste  for reviewing the manuscript and fruitful discussion. This work was funded by  Santé publique France  ( French Ministry of Health) ,  European Funds for Regional Development, N° Synergie :  GY0012082 , and the  French Ministry for National Education Higher Education and Research.
Introduction Emerging fungal pathogens pose a growing threat to global health, ecosystems, food security and the world economy  [1]. Between 1995 and 2010, the proportion of fungal infections in plants and animals recorded in the ProMED database (the Program for Monitoring Emerging Diseases) increased from 1% to 7% and a positive trend in the proportion of fungi infecting animals and plants was observed over the period 2007-2011 with global fungal disease alerts  [1]. Furthermore, data from a meta-analysis and literature searches have shown shown that fungal infections remain the major cause (65%) of biodiversity loss due to pathogen  [1]. Although fungi have been known for a long time to pose a widespread threat to plants, the impact of fungal infections on animal health has been underestimated until recently, with major declines in wildlife due to fungal emergences  [1].
The infectious agent responsible has been described as a systemic protist and has been termed a "rosette" or "chinook rosette agent" because of the clustered organization of organisms observed in the stained tissues of infected fish  [23]. This first RA-1 isolate of S. destruens was amplified on the CHSE-214 cell line developed from Chinook salmon embryos and held in the American Type Culture Collection (ATCC, Accession Number #50643)  [24]. A few years later, chronic mortalities in subadult Atlantic salmon Salmo salar received as eyed eggs from Finland and reared in spring water on a private farm in northern California, USA, were reported  [25]. Although microscopic examinations suggested that the disease was caused by an organism similar to that described by  Harrell et al. [23] , it was termed "Dermocystidium-like" and a second isolate of S.
destruens, RA-2, was deposited at the ATCC (Accession Number #50644)  [25]. Finally, a third emergence of the disease was reported in the USA in captive subadult and winter-run adult of O. tshawytscha broodstock from Sacramento River maintained at the Bodega Marine Laboratory (BML, Bodega Bay, California) in collaboration with the Coleman National Fish Hatchery (CNFH, California) and several state and federal agencies  [26]. Among the 1991-1994 brood years, disease prevalence peaked at 40. 1% in the 1991 year-class. S. destruens was first detected in a few 1991 brood year salmon (14-16 months old) that had never been transferred to seawater since their arrival from the original freshwater hatchery (CNFH). Subsequently, the parasite was detected in wild adult late-fall-run O. tshawytscha returning to freshwater to spawn in the upper Sacramento River.
Since 1994, surveillance by the California-Nevada Fish Health Center has demonstrated the presence of S. destruens in up to 32% of late-fall-run adult O. tshawytscha returning to Battle Creek on the Upper Sacramento River, suggesting the persistence of the disease in the BML and a potential risk of disease emergence. A third isolate, named RA-3 or BML strain, was isolated from O. tshawytscha infected kidneys, amplified in fish cell lines and also deposited at ATCC (Accession number #50615). For several years, the disease caused by S. destruens was only reported in salmonids reared on the northwest coast of the USA (Washington State and California). However, in 2005,  Gozlan et al. [27]  were the first to describe the emergence of S. destruens disease in invasive populations of Pseudorasbora parva in Europe, but also in the non-native cyprinid Leucaspius delineatus (sunbleak) in England  [27, 28].
, 2017). The similar changes in the biofilm architecture seen in our study suggests that the enhanced action of nystatin by OligoG could also be due to chelation of calcium. Tøndervik et al. (2014)  revealed significant reductions in vegetative cell growth and an inhibitory effect on hyphal growth of C. albicans with OligoG treatment; findings similar to studies showing candidal growth reductions  (Pugh and Cawson, 1980)  and blocked hyphal development in C. albicans  (Gil et al. , 1994)  when treated with EDTA. The results shown in this and previous studies  (Tøndervik et al. , 2014; Pritchard et al. , 2017) , together with the excellent safety profile and high tolerability of OligoG proven through clinical trials, (NCT02157922; NCT02453789;  Van Koningsbruggen-Rietschel et al. , 2020; Fischer et al.
Acknowledgments The GBJ 13/4A strain was kindly provided by the team of  Prof. Henny van der Mei ,  University of Groningen, Netherlands  and the other Candida strains by  Prof. David W. Williams ,  Cardiff University School of Dentistry. We thank  Atos Medical  ( Nottingham, UK ) for the gift of the silicone sheets and  Dr M. Wootton  ( University Hospital of Wales ) for the MALDI-TOF identification.
Gene Forward Primer Reverse Primer Gene Accession Code Nrf2 -AGCGACGGAAAGAGTATGAG-3 5 -GTTGGCAGATCCACTGGTTT-3 NM_001145413. 2 HO-1 -TCCGATGGGTCCTTACACTC-3 5 -TAAGGAAGCCAGCCAAGAGA-3 NM_002133. 2 NQO1 -CAGACGCCCGAATTCAAATC-3 5 -AGGCTGCTTGGAGCAAAATACA-3 NM_000903. 2 IL-1β -AATGATGGCTTATTACAGTGGCA-3 5 -GTCGGAGATTCGTAGCTGGA-3 NM_000576. 3 IL-6 -GTAGCCGCCCCACACAGA-3 5 -CATGTCTCCTTTCTCAGGGCTG-3 NM_000600. 5 TNF-α -GGAGAAGGGTGACCGACTC-3 5 -TGGGAAGGTTGGATGTTCGT-3 NM_000594 18S rRNA -GATAGCTCTTTCTCGATTCCG-3 5 -TAGTTAGCATGCCAGAGTC-3 M10098. 1.
Analysis of Cell Phagocytosis and Cell Apoptosis via Flow Cytometry For the assessment of cell phagocytosis, 1 × 10 6 cells/well THP-1-derived macrophages were treated with rMS 3 h prior to infection with SYTO9-labeled S. aureus. After 1 h infection, macrophages were scraped, washed with PBS, and collected for flow cytometry analysis. To assess cell apoptosis 24 h after rMS treatment, 1 × 10 6 cells/well THP-1-derived macrophages were stained for 10 min in the dark with Annexin V-FITC reagent. Non-adherent and adherent cells were collected and after 3 washes with PBS, cells were analyzed via flow cytometry. All flow cytometric analysis was immediately realized on the BD LSRFortessa TM using FACSDiva 7. 0 software (BD Biosciences, Franklin Lakes, NJ, USA).
Statistical Analyses Values are presented as means ± standard errors of mean (SEM). The imaging flow cytometry results presented are means ± SEM of 3 independent experiments of 100,000 events. Statistical comparisons were performed using a two-tailed unpaired t-test for comparisons between 2 groups, or one-way analysis of variance with Tukey's multiple group comparison test for multiple comparisons. Data analyses were performed with GraphPad Prism statistical software (v8. 0. 2). Differences were considered to be statistically significant at p < 0. 05.
rMS Increased Phosphorylated p62 and Total p62 Protein Expressions Next, we hypothesized that the observed decrease in Keap1 expression and increase in Nrf2 expression levels resulted from rMS modulation of p62 phosphorylation and p62 expression levels. Total protein extracts were collected from THP-1-derived macrophages 1 h after rMS treatment for phosphorylated p62 immunoblotting analysis and 3 h after rMS treatment for p62 immunoblotting analysis. Data analysis showed a significant increase in p62 protein expression, as well as a significant increase in phosphorylated p62 (Figure  3A, B ). Furthermore, confocal images were taken from THP-1-derived macrophages treated with rMS for 3 h. The macrophages were then immunolabeled with a specific p62 antibody, and the nucleus was counterstained with Hoechst33342 (Figure  3C ).
Using Image J software v1. 53k, the number of p62 puncta and the fluorescence intensity of p62 in the puncta were quantified. Our data showed a decrease in the number of p62 puncta per cell in rMS-treated macrophages, along with a decrease in p62 fluorescent intensity within the puncta of each cell (Figure  3D, E ). These results suggest that rMS induces the phosphorylation of p62, which enables the binding of phosphorylated p62 with Keap1, and consequently allows the released Nrf2 to translocate into the nucleus. The phosphorylated p62-Keap1 complex subsequently undergoes p62-dependent autophagy degradation  [21]. rMS treatment for p62 immunoblotting analysis. Data analysis showed a significant increase in p62 protein expression, as well as a significant increase in phosphorylated p62 (Figure  3A, B ).
Furthermore, confocal images were taken from THP-1-derived macrophages treated with rMS for 3 h. The macrophages were then immunolabeled with a specific p62 antibody, and the nucleus was counterstained with Hoechst33342 (Figure  3C ). Using Image J software v1. 53k, the number of p62 puncta and the fluorescence intensity of p62 in the puncta were quantified. Our data showed a decrease in the number of p62 puncta per cell in rMS-treated macrophages, along with a decrease in p62 fluorescent intensity within the puncta of each cell (Figure  3D, E ). These results suggest that rMS induces the phosphorylation of p62, which enables the binding of phosphorylated p62 with Keap1, and consequently allows the released Nrf2 to translocate into the nucleus. The phosphorylated p62-Keap1 complex subsequently undergoes p62-dependent autophagy degradation  [21].
Next, we investigated whether rMS affected oxidative stress by staining rMS-treated THP-1-derived macrophages with CellROX fluorogenic probe, which detected ROS in live cells. Data analysis showed no significant effect of rMS on oxidative stress (Figure  4D ). We then examined the impact of rMS on macrophage phagocytic activity. THP-1-derived macrophages were treated with rMS and incubated for 3 h prior to infection with SYTO9-labeled S. aureus for 1 h. Flow cytometry analysis revealed no significant difference in macrophage phagocytosis activity after rMS as compared to control (Figure  4E ). Furthermore, we assessed the bactericidal activity of rMS-treated macrophages by determining the intracellular survival of S. aureus 24 h after infection. Gentamicin was added to the cell culture medium 1 h after infection to eliminate extracellular bacteria.
Interestingly, in S. aureus-infected cells, rMS treatment specifically inhibited the phosphorylation of p38 compared to control cells. To further validate the findings from the Western blot analysis, we acquired confocal images of THP-1-derived macrophages labeled with a specific phospho-p38 MAPK antibody, counterstained the nuclei with Hoechst 33342, and conducted quantitative analysis using Image J software v1. 53k (Figure  7B ). rMS-treated THP-1-derived macrophages exhibited a significant decrease in the fluorescence intensity of phospho-p38 MAPK compared to control cells or S. aureus-infected cells (Figure  7C ). Additionally, analysis of confocal images revealed a reduction in the nuclear localization of phospho-p38 MAPK in rMStreated macrophages compared to control macrophages or S.
CRISPR genome editing Guide RNAs (20 nucleotides (nt) of crRNA 5' end) design was optimized to maximize cutting specificity using the online CRISPOR software (http://crispor. tefor. net/). For the B6. SJL. CSTE-KO mouse generation, two guides RNA targeting exon 3 of Ctse gene and allowing an 83 nt deletion were selected  11. For the Ptprc gene point mutations, the guides RNA with Cas9 cutting sites located as close as possible to the mutation(s) to introduce (cut-to-mutation distance <10 nt) were selected as HDR efficiency drops with increased cut-to-mutation distance  12. In the cases where cut-to-mutation distance was superior to 10 nt, a silent mutation was added in the repair template sequence between the cutting site and the mutation to reduce this distance. 2′-O-methyl +3′phosphorothioate chemical modifications were introduced on nt 1 to 3 of crRNA and nt 69 to 71 of tracrRNA to increase guide RNA stability  13.
Off-Target mutation detection Prediction of potential Off-Target cleavage sites (OT) were made with CRISPOR software  16  based on sequence similarity and are listed in Supplementary Fig. 3. We first focused on potential OT sites localized on the same chromosome as on-target, as they can be more difficult to eliminate by backcrossing. OT sequences containing 4 mismatches compared to on-target sequences and having one or more mismatches located in PAM proximal sequence (<12 nt) were not considered as they are not likely to happen  17. Potential OT sites containing 3 or less mismatches compared to on-target were checked. Concerning potential OT localized on other chromosomes, we focused on those with up to 3 mismatches and for which all mismatches are in PAM distal position (>12 nt), as they are more likely to occur  17.
Flow cytometry Surface staining was performed on single-cell suspensions from each organ for 30 min at 4°C with the appropriate mixture of antibody (Ab) diluted in staining buffer (PBS supplemented with 1% FCS [Life Technologies] and 0. 09% NaN3 [Sigma-Aldrich]). For intracellular staining, cells were fixed and permeabilized using CytoFix/CytoPerm buffer according to manufacturer's instructions (BD Biosciences) and then stained with the appropriate mixture of Ab for 30 min at 4°C. Antibodies used are listed in the Supplementary Table  2. All analyses were performed on a BD Biosciences FACS Fortessa (BD Biosciences) and analyzed with FlowJo software (Tree Star).
1 epitope. To address the role of mutation A and B in the recognition by the anti-CD45. 1 antibody, we generated 3 mutant mouse models by introducing mutation A (Fig. 2b ), mutation B (Fig. 2c ) or both mutations in B6 mouse. Mutations were introduced in the Ptprc gene by Homology Direct Repair (HDR) using the CRISPR/Cas9 genome editing technology. Guides RNA were selected using the CRISPOR software  16. Template DNAs (ssODN) were designed to introduce mutation(s) of interest as well as silent mutation(s) in order to prevent a new cleavage of the mutated allele by Cas9 nuclease (Fig. 2b-c ). The resulting B6. mut A , B6. mut B and B6. mut A/B F0 mice were back crossed twice with their original wild-type mice before generation of homozygous lines. Sanger sequencing of PCR amplificons of mutation A (Fig.
The regions of potential OT sites were amplified by PCR and Sanger sequenced from the F1 mice used to amplify B6. mut A and B6. mut A/B a. mouse strains, with B6 mouse as control. For each OT site tested, only one fragment was amplified by PCR, with a size similar to the B6 control (Supp. Fig. 2b ). Sanger sequencing of the PCR amplicons confirmed the absence of OT cutting in B6. mut A (Supp. Fig. 2c ) and B6. mut A/B F1 mice (not shown). A nucleotide substitution within OT_mutA_6 sequence was observed from the provided sequence (Supp. Fig. 2c ) but trace data examination shows that it is not due to an OT cleavage but to the quality of sequencing, as chromatograms present double pics at almost each position, for B6 control and B6. mut A mice (Supp. Fig. 3 ).
SJL CD8 memory cells. This difference appears in public database such as Immgen (https://www. immgen. org/) where CD8 T cells from both B6 or B6. SJL origins were used for RNA transcriptomic analysis. To avoid these confounding factors when performing functional or gene expression comparison between wild-type and mutant line, we generated a B6 mouse that expresses the CD45. 1 epitope, using the CRISPR/Cas9 editing approach to introduce a single point mutation(s) in the Ptprc gene of the B6 mouse line. We showed that the introduction of the mutation A (A904G -> K302E), but not the mutation B (T1298C -> V400A; G1311T -> E404D; T1312C -> S405P) was sufficient to generate the CD45. 1 epitope, thus confirming previous results  5, 21. One major disadvantage of the CRISPR/Cas9 editing method is the potential OT cleavage by Cas9 protein due to guide RNA binding to unintended regions of the genome.
Acknowledgements We acknowledge the contribution of  AniRA-Cytometrie  and  AniRA-PBES  facilities of the  SFR BioSciences  ( UAR3444/CNRS ,  US8/Inserm ,  Ecole Normale Supérieure de Lyon, Université de Lyon). The project was funded by the intramural  CIRI  grant:  AO-4-2018.
K E Y W O R D S haemosporidian parasites, mosquito-borne pathogens, Plasmodium, urbanization index, vectorborne diseases found in various climates and habitats, being considered an excellent urban exploiter since their occurrence is routinely tied to human settlements  (Meillère et al. , 2015). Moreover, this species is commonly found to be infected by avian malaria parasites  (Bensch et al. , 2009; Bichet et al. , 2013; Ferraguti et al. , 2018; Marzal et al. , 2011; Valkiūnas et al. , 2006). Marzal et al. (2011)  analysed the prevalence and genetic diversity of haemosporidians in native and introduced house sparrows, showing differences in diversity and prevalence of haemosporidians between native and colonized regions. Here we expand upon this previous study at a global scale using an updated and larger database to evaluate the role of (a) environmental (urbanization index and human density); (b) geographical (altitude, latitude, hemisphere); and (c) temporal (breeding/non-breeding seasons, years elapsed since host introduction) drivers of global variation in prevalence and richness (i.
| Study areas and bird sampling Tshe dataset on prevalence and lineage richness of malaria parasites used in this study was partially compiled by  Marzal et al. (2011)  and further extended to include new data from 436 individuals from 11 additional populations  (Ewen et al. , 2012; Ferraguti et al. , 2018; Garcia-Longoria et al. , 2022; Hellgren et al. , 2011; Ishtiaq et al. , 2007; Marzal et al. , 2011 Marzal et al. , , 2018;; Muriel et al. , 2021). These new data added an extra 20% to the total sample size and included remote and poorly investigated tropical areas of western South America and Southeast Asia (see Supporting Information Table  S1  for further information on the additional localities), thus expanding the global scope of the analyses. Overall, birds were captured by different teams in the framework of different surveys, from 2002 to 2019 at 69 sampling localities distributed over 27 countries (all continents except Antarctica, Figure  1 ).
(2000). For this study, we focused on Plasmodium spp. parasites only and, after parasite genus identification, the identity of the lineages was determined by comparison of the sequences with those available in public databases (i. e. , GenBank DNA sequence database, National Center for Biotechnology Information Blast). For the estimation of parasite lineage richness, sequences differing by at least one nucleotide substitution were considered to represent evolutionarily independent entities (lineages;  Bensch et al. , 2004; Ricklefs et al. , 2005).
| Environmental and time-related variables Geographical variables such as altitude, absolute value of the latitude, and hemisphere (North/South) were recorded for each sample site (Supporting Information Table  S1 ). In addition, an urbanization index for each of the sampled localities was calculated using the Urbanisation score software (available at https://keplab. mik. uni-pannon. hu/en/urban izati on-index). This approach, based on the quantification of the percentage of area covered by different land uses in a defined parcel (e. g. , building, roads, agriculture, vegetation, forest, water, among others), has been extensively used in studies of urban ecology  (Jiménez-Peñuela et al. , 2019; Meillère et al. , 2015 Meillère et al. , , 2017;; Salmón et al. , 2018). Briefly, the software takes satellite images from Google Maps covering an area of 1 km 2 around each bird-sampling point, and these images are divided into 10 the localities included in it (range -3 to +4 for our localities).
, 2021). F I G U R E 1 Distribution of the 69 sampling localities of house sparrows. Red dots represent localities sampled in  Marzal et al. (2011) ; blue dots are new localities included in this study. Light and dark grey areas show countries sampled in native and introduced ranges, respectively, white areas are countries where no data have been recorded (http://dataz one. birdl ife. org/speci es/facts heet/house -sparr ow-passe r-domes ticus/ distr ibution). Map created by QGIS. 3. 12. 0 (2020). QGIS Geographic Information System, Open-Source Geospatial Foundation Project, http://qgis. org. The prevalence of the parasites was estimated using. a bivariate model that utilized a two-column matrix to represent the number of infected birds in a population in relation to the number of uninfected birds.
Na ve Independent models were performed on the native (n = 35) and introduced (n = 34) bird datasets to investigate the effects of environmental, geographical and temporal drivers on the prevalence and number of observed lineages of Plasmodium spp. per locality because significant differences were found between the two populations  (Marzal et al. , 2018; Schrey et al. , 2011). Altitude (continuous), the absolute value of latitude (continuous), urbanization index (continuous), human density (continuous) and reproductive season (categorical: breeding/non-breeding) were included as independent variables. For the introduced bird populations, years since the bird introduction (continuous), and the hemispheres (categorical: North/South) were included to account for (a) colonization time, and (b), differences between hemispheres.
Finally, to determine and graphically represent the degree of associations between the Plasmodium lineage composition in native and introduced populations, we (a) built a heat map showing the frequency of each parasite lineage at each locality (created using the function heatmap. 2 from the package ggplot2), and (b) conducted a correspondence analysis (CA) of each lineage abundance at each sampling locality, which makes no assumption about distributions  (Sourial et al. , 2010). Only localities with more than one infected individual were considered. Axis scores from this ordination represent a gradient of similarity of parasite composition among localities.
| RE SULTS The dataset included samples from 2,220 house sparrows. Overall, 670 birds (30. 2%) were infected by 22 Plasmodium parasite lineages. The number of observed lineages per sampling locality ranged from one to seven (for further information, see lineage richness in Supporting Information Table  S1 ). The most common lineage was SGS1 (found in 31 localities), followed by GRW11 (20 localities), GRW04 (18 localities), PADOM01 (11 localities), PADOM02 (11 localities) and COLL1 (10 localities). All other lineages were observed in fewer than 10 localities. Nine lineages were only found in native populations, and nine only in the introduced populations. Four lineages were found in both introduced and native birds, with SGS1 and PADOM1 mainly recorded in native populations, GRW04 in introduced populations and GRW06 was sporadically observed in both populations (Figure  2 ).
ACK N OWLED G M ENTS This study was funded by projects:  IB20089  from the  Consejería de Economía, Ciencia y Agenda Digital of the Junta de Extremadura and Fondo Europeo de Desarrollo Regional ,  P11-RNM-7038  from  Junta de Andalucía , and PR( 19_ECO_0070 ) from  Ayudas Fundación BBVA a Equipos de Investigación Científica  2019. MF was supported by a  Juan de la Cierva   2017 Formación  contract ( FJCI-2017-34394 ) from the  Ministry of Science, Innovation and Universities , by the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Sklodowska-Curie  (grant agreement No  844285 , ' EpiEcoMod ') and she is currently funded by a  Ramón y Cajal  postdoctoral contract ( RYC2021-031613-I ) from the  Spanish Ministry of Science and Innovation (MICINN). JJP was supported by the  Fundación Tatiana Pérez de Guzmán el Bueno.