dataesr/scientific-paragraphs-categorization huggingface dataset:
Anti-HS was revealed by AF488 goat anti-mouse IgM (Invitrogen, A10680, 2 mg/ml) or AF555 goat anti-mouse IgM (Thermo Fisher, A28180, 2 mg/ml; 2 hours, 4 C). After cells' exposure to anti-thrombin III (AT III; Abcam, AB62542, 10 mg/ml; 2 hours, RT),  19  AT III was stained with anti-AT III (Invitrogen, MA534940, 5 mg/ml; overnight, 4 C) and revealed by AF647 goat anti-mouse IgG (Invitrogen, A-21235, 2 mg/ml; 1 hour, RT). Nuclei were stained with 4 0 ,6-diamidino-2-phenylindole (Sigma, D9542, 2 mg/ml). The whole slides were scanned with a Zeiss Axioscan Z1 (20Â/numerical aperture, 0. 8), and percentage area of staining, normalized to nuclei number and expressed in mm 2 of positive areas, was quantified using ImageJ software (NIH, version 1. 52, 2018). Illustrative photomicrographs were performed with confocal microscopes (Spinning Disk, Zeiss Axio Observer Z1-Yokogawa CSU-X1, and ZEISS CLSM 710).
Statistical analyses Statistical analysis was performed with R software (version 3. 6. 3. ), using the "compareGroups 4. 0" package, and GraphPad Prism software (version 9. 3. 0), also used for graphical representations. Patients' groups were compared with baseline variables by c 2 or Fisher exact tests (categorical data) and Student's t tests or Mann-Whitney test (continuous data), according to the sample size and the distribution of the variables. When >2 groups were compared, 1or 2-way analysis of variance tests were performed on continuous data, according to their respective distributions. Clinical results are presented as medians with interquartile ranges. Pearson correlation tests were used to compare semiquantitative and quantitative JM403 staining tests, with a significant relationship being retained at a value > 0.
ACKNOWLEDGMENTS This work was supported by grants from the  "Association pour l'Information et la Recherche sur les maladies Rénales Génétiques " (2018-2  AIRG-France ), the  Francophone Society of Nephrology, Dialysis and Transplantation  ( Astellas_SFNDT_2020 ), the  "Agence nationale pour la recherche"  ( EJP RD JTC2022 ), and  Lille University Hospital. We sincerely thank  Elise Bouderlique ,  Antonino Bongiovanni ,  Amandine Ydee ,  Solenne Audry , and  Brenda Lammens  for their support in slide preparation and optimization of immunofluorescence and immunohistochemistry labeling ( Lille University Hospital, Pathology Department ). We are grateful to  Véronique Fremeaux-Bacchi ,  Victoria Poillerat ,  Anna Duval , and  Tania Rybkine , from the  Complement and Diseases team  ( UMRS 1138 ,  Cordeliers Research Center, Paris, France ),  Bernard Van Der Berg  ( The Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands ), as well as  Fadi Fakhouri  and  Muriel Auberson  ( Lausanne University ) for advice and the fruitful discussions.
We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network. It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations. We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent. We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.
There is now a substantial body of literature on the genomic diversity and global population structure of malaria parasites, on within-host genetic variation and what this tells us about superinfection and cotransmission, on the identification and monitoring of parasite drug resistance loci, on genetic variation in malaria vaccine antigens, and on methods of analysing genetic relatedness to understand patterns of malaria transmission. A useful summary of the current state of the field can be found in the recent review by Neafsey et al. 2. This rapidly growing area of research is underpinned by open data on genome sequence variation in natural parasite populations. Here we report a new release of curated open data on Plasmodium falciparum genome variation from the MalariaGEN network  3. It includes samples featured in previous MalariaGEN data releases including the Pf3k Project 4 , the Plasmodium falciparum Community Project 5 and the GenRe Mekong Project 6.
To avoid confusion between different MalariaGEN datasets we now identify each by a version number. In this new nomenclature, the previous version 5 is called Pf6, and the version described here is called Pf7. Whole genome sequencing of all the samples in the Pf7 dataset was performed at the Wellcome Sanger Institute and a standardised analysis pipeline was used for variant discovery and genotyping. The Pf7 analysis pipeline was broadly similar to that used for the Pf6 dataset with some improvements that are described in more detail below. Sequence data and genotype calls were returned to partners for use in their own analyses and publications in line with MalariaGEN's guiding principles on equitable data sharing  3. The Pf7 dataset comprises 20,864 samples of P. falciparum collected by 82 partner studies from 33 countries in Africa, Asia, South America and Oceania between 1984 and 2018 (Table  1 , Supplementary Tables  1  and 2 , Supplementary Figure  1 ).
Compared to the Pf6 dataset, this includes 13,752 new samples, 33 new partner studies and 5 additional countries. The majority of new samples (12,146) were collected since 2014, but there were also 379 samples collected prior to 2000 (Supplementary Figure  2 ). The most significant technical advance in the Pf7 dataset is that most of the new samples (12,891/13,752, 94%) came from the MalariaGEN SpotMalaria Project 7. SpotMalaria was designed to simplify and standardise the process of collecting dried blood spot (DBS) samples for parasite genetic analysis. The SpotMalaria protocol ensures that the vast majority of DBS samples are suitable for targeted genotyping of drug resistance loci, e. g. by amplicon sequencing, and that a significant proportion of samples are also suitable for whole genome sequencing.
This requires an intermediate step known as selective whole genome amplification (sWGA), which makes it possible to obtain parasite genome sequence data from a very small sample, but at the cost of introducing considerable variability in sequencing coverage across the genome. This is the first study to analyse a large number of sWGA P. falciparum genomes and therefore it was important to establish that sWGA was not introducing significant biases, and to adapt our methods for calling structural variations which are particularly sensitive to artefactual variation in sequencing coverage. We have performed a number of analyses to make the Pf7 dataset as useful as possible for a broad range of users. These include descriptions of global population structure, geographic Table  1. Counts of samples in the dataset.
Countries are grouped into ten major sub-populations based on their geographic and genetic characteristics. For each country, the table reports: the number of distinct sampling locations (first-level administrative divisions); the total number of samples sequenced; the number of high-quality samples included in the analysis; the percentage of samples collected between 2016-2018, the most recent sampling period in the dataset; and the percentage of samples which are new since the Pf6 release. There are 20,704 samples from natural infections with validated metadata and 160 classified as unverified identity, where this information is not available. The breakdown by admin division is reported in Supplementary Table  1   patterns of drug resistance, haplotypic analysis of drug resistance loci, hrp2 and hrp3 deletions that can cause failure of rapid diagnostic tests, and variation in the C-terminal of the csp antigen used in the most advanced malaria vaccines.
These analyses are not intended to be comprehensive and technical users of the dataset can download the analysis-ready dataset for more specialised or detailed investigations. A high level view of the Pf7 dataset can be obtained from the data exploration tool at the MalariaGEN website. This shows the locations and years where the samples were collected, and the genotype-inferred drug resistance status of each sample. Most importantly it names the investigators who led the studies that contributed the samples at each location and thus made this global dataset possible.
A total of 3,125,721 SNPs (of which 2,513,888 were biallelic) and 2,742,938 non-SNPs, i. e. short indels or SNP-indel combinations, passed all these filters. Some of the variant positions that were classified as SNPs in Pf6 are now classified as non-SNPs because they additionally include indel alleles. We performed quality control checks to remove samples with: (i) unverified or incomplete sample collection information; (ii) evidence of co-infection with other Plasmodium species; (iii) more than one technical replicate or time course sampling; (iv) low coverage; (v) a higher than expected number of singleton SNPs. In total, we retained 16,203 high-quality samples (Table  1 ). This analysis-ready dataset with details of all participating partner studies and a python package providing convenience methods for accessing is available here.
Haplotype analysis of kelch13 and crt drug resistance loci Previous reports have shown that the current wave of multidrug-resistant P. falciparum in Southeast Asia is driven by the KEL1 lineage of the kelch13 artemisinin resistance locus  [9] [10] [11] [12]  and is associated with multiple new mutations in the crt resistance locus  9. This dataset confirms the dramatic increase of KEL1 in Cambodia, Eastern Thailand, Laos and Vietnam that has occurred over the past ten years (Supplementary Figure  9 ). Analysis of the crt locus in samples with the K76T resistance variant reveals a major cluster of haplotypes on a common genetic background, the one observed in a widely used lab strain isolated in Asia in 1980 and commonly referred to as Dd2 (Figure  3A , Supplementary Table  5 ). In addition to the original Dd2 haplotype, we observe 31 additional mutations.
e. different from the 3D7 sequence used in the vaccine design, at amino acids 301, 317, 318, 321 and 361 (Supplementary Figure  10 ). We found a total of 248 unique amino acid haplotypes of csp 277-397 out of 11,254 samples with no ambiguous calls. Amino acid haplotype sequences for the c-terminal region of csp for all samples can be found at the MalariaGEN website. Surprisingly, the most common haplotype in the dataset and the one with the second lowest number of differences from all other unique haplotypes is the one observed in lab strain Dd2, being found in 2,760/11,254 (25%) of the samples and having a mean of 4. 7 differences from other haplotypes (Figure  4a ). In contrast, the 3D7 haplotype used for both csp-based vaccines is only found in 3% of samples and has on average 6. 9 differences from all other haplotypes.
Discussion The Pf7 dataset increases the amount of curated open data for population genomic analysis of P. falciparum by almost threefold, and greatly increases the number of samples collected within the last five years. With denser geographical coverage it is possible to undertake higher resolution analysis of epidemiological variation within a region, e. g. we observe considerable heterogeneity of inferred chloroquine resistance in West Africa (Figure  3 ), and it also allows us to identify new sub-populations with distinctive epidemiological features, e. g. we find two sub-populations in south Asia that have contrasting drug resistance profiles. There is useful historical information to be obtained from older samples that are included in this new data release, e. g. some samples collected in Cambodia in the early 1990s appear to be resistant to both piperaquine and mefloquine, which is highly relevant to the ongoing evolution of multidrug resistance to artemisinin combination therapy in Southeast Asia.
We also see evidence of a recombination with chromosome 11 which results in a hybrid chromosome comprising mostly chromosome 13 sequence but also a section of the 3' end of chromosome 11. This is the most common deletion type, being seen in 151 samples from 14 different countries. Because the recombination occurs between highly similar sequences of a set of three orthologous ribosomal RNA genes found on both chromosomes, it is not possible to identify the exact breakpoints. field. We and others have previously described successful whole genome sequencing of P. falciparum from DBS after selective whole-genome amplification but it was unclear how well this methodology would perform at scale. Here we show that the SpotMalaria protocol for sWGA of DBS samples allows us to generate whole genome sequence data of sufficient quality to genotype the vast majority of SNPs with sufficient accuracy and reliability for large-scale population genomic analysis.
falciparum. Information about the processes and methods of the SpotMalaria Project can be obtained at the MalariaGEN website The Pf7 dataset includes a range of analyses and sample annotations that are intended to increase the utility of the data for researchers working on practical problems in malaria control. Compared to the Pf6 dataset, we have made improvements to methods for calling CNVs at the mdr1 and pm2 drug resistance loci and for calling hrp2 and hrp3 deletions that can affect rapid diagnostic tests. Other new analyses included in Pf7 include more detailed descriptions of: (a) hrp2 and hrp3 deletion breakpoints; (b) drug resistance locus haplotypes and in particular newly emerging crt haplotypes; (c) profiles of variation in the csp vaccine antigen and the vaccine candidate eba175.
In future releases we aim to improve and expand analyses that are relevant to malaria control programmes and policymakers. The Pf7 dataset focuses entirely on genome sequencing data, but there is a growing body of data from amplicon sequencing and targeted genotyping approaches that is highly informative about multiple aspects of P. falciparum population genomics. For example, the GenRe-Mekong Project has used the SpotMalaria platform combined with amplicon sequencing to enable malaria control programmes in the Greater Mekong Region to conduct national genomic surveillance of multidrug resistance  6. In future data releases we aim to integrate data from these different sources to greatly increase sample size and geographical coverage, and thus improve the resolution of population genomic analysis.
F WS was calculated using custom python scripts using the method previously described 7. Nucleotide diversity (π) was calculated in non-overlapping 25kbp genomic windows, only considering coding SNPs to reduce the ascertainment bias caused by poor accessibility of non-coding regions. LD decay (r 2 ) was calculated using the method of Rogers and Huff and biallelic SNPs with low missingness and regional allele frequency >10%. Mean F ST between populations was calculated using Hudson's method. To call duplication genotypes around mdr1 and plasmepsin 2-3 from binned coverage, we adapted the GATK GermlineCNVCaller (gCNV) pipeline, which features a probabilistic Bayesian model that jointly infers both copy-number activity and a model for denoising sequencing systematics. After breakpoint genotypes were called, we performed an initial, permissive round of annotation-based call filtering, using hard cuts to identify failing samples and demarcate duplication and reference genotypes.
Data availability • Sample provenance and sequencing metadata: sample information including partner study information, location and year of collection, ENA accession numbers, and QC information for 20,864 samples from 33 countries. • Measure of complexity of infections: characterisation of within-host diversity (F WS ) for 16,203 QC pass samples. • Drug resistance marker genotypes: genotypes at known markers of drug resistance for 16,203 samples, containing amino acid and copy number genotypes at six loci: crt, dhfr, dhps, mdr1, kelch13, plasmepsin 2-3. • Inferred resistance status classification: classification of 16,203 QC pass samples into different types of resistance to 10 drugs or combinations of drugs and to RDT detection: chloroquine, pyrimethamine, sulfadoxine, mefloquine, artemisinin, piperaquine, sulfadoxinepyrimethamine for treatment of uncomplicated malaria, sulfadoxine-pyrimethamine for intermittent preventive treatment in pregnancy, artesunate-mefloquine, dihydroartemisinin-piperaquine, hrp2 and hrp3 gene deletions.
30 Supplementary data to: Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. https://doi. org/10. 6084/m9. figshare. 2167432130 Data are available under the MalariaGEN terms of use for the Pf Community Project: https://www. malariagen. net/data/terms- use/p-falciparum-community-project-terms-use. Depending on the nature, format and content of the data, appropriate mechanisms have been utilised for data access, as detailed below. This project contains the following underlying data that are available as an online resource: https://www. malariagen. net/ resource/34. Data are also available from Figshare. Figshare.
We aimed to investigate the structure and evolution of this field in a physio-pathological context, and then we focused our review on flow cytometry analysis of Ca 2+ fluxes in PBMCs. Methods: From 1984 to 2022, 3865 articles on inflammation and Ca 2+ signaling in PBMCs were published, according to The Clarivate Web of Science (WOS) database used in this review. A bibliometric study was designed for this collection and consisted of a co-citation and bibliographic coupling analysis.
Collecting scientific literature data Clarivate Web of Science © was used to collect data (Copyright Clarivate 2022WoS). It is a selective, structured, and balanced database with complete citation links and enhanced metadata. It can inform about citation indexes representing the connections between scholarly research articles in globally significant journals, books, and proceedings chapters. Exported data included the complete set of references enabling in-depth analysis of the intellectual structure. We applied the following query to article titles and abstracts: [pbmc OR "peripheral blood mononuclear cells" OR lymphocyte OR monocyte* OR macrophage*] AND ["Ca 2+ " OR calcium] AND [physiological OR inflammat* OR ischem*]  We included all articles, proceeding chapters, meeting abstracts, and books.
The query ranged from 1984 to 2022, and 3865 articles were collected. All data were exported from the WoS database on July 22, 2022. Further analysis of the field, focusing on the evolution of Ca 2+ analysis by flow cytometry, was carried out based on the following query applied to abstracts and titles: [pbmc OR "peripheral blood mononuclear cells" OR lymphocyte* OR monocyte* OR macrophage*] AND ["Ca 2+ " OR calcium] AND [physiological OR inflammat* OR ischem*] AND  [cytometry]  We included all articles, book chapters, and meeting abstracts. The query ranged from 1993 to 2022, and 185 articles were obtained.
Funding The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This project was funded by grants from the  Fondation de l'Avenir  ( n°AP-RM-20-008 ), from the  French National League of Basketball , from the  Agence Nationale de la Recherche  ( ANR-20-CE14-0013-01 ) and  Fedeŕation Francaise de Cardiologie  ( FFC-BOCHATON-Dotation 2020 ). The Ph. D. salary of LC (Cifre, Olea Medical) is co-funded by the  French Ministry of Higher Education and Research (ANRT).
Data and sample collection One hundred and eleven male common quails were collected from two Spanish locations in 2018, 2019, and 2021: croplands near Alp, a village located in the Pyrenees of Catalonia, and croplands located in the middle of Mallorca Island, near Sineu and Vilafranca de Bonany villages (Figure  1 ). Quails were captured by spreading a 10 × 12 m net horizontally over the cereal plots during the reproduction period  (Rodríguez-Teijeiro et al. , 2010). Two days were chosen in the middle phase of their stay in the breeding area (April-July both inclusive), and the maximum number of males in the study area were captured. We distinguish two age categories for all quails: juveniles, born in the breeding season, and adults born in the previous year's breeding season. All individuals were ringed.
Acknowledgment We would like to thank all the confirmed and suspected cases and contacts, and the healthcare workers who participated in the outbreak investigations. We thank the  Central African Ministry of Public Health and Population  and the national World Health Organization team for their collaboration and constant support for the investigation of mpox outbreaks. Financial support for this study was provided by the  French Agence Nationale de Recherche  ( ANR 2019CE-35 ), the  PTR (Projets Transversaux de Recherche   PTR 218-19 ) fund from  Institut Pasteur Paris , the  INCEP - TION  project  ( PIA/ANR-16-CONV-005 ) and the  SCOR Foundation for Science.
Data Source and Study Design This study was a retrospective, nationwide cohort study using administrative claims obtained from the French national health data system, Système National des Données de Santé (SNDS). The SNDS contains health records of an estimated 65 million insured individuals. The French national health system offers universal coverage, so this is a representative sample of the whole population. SNDS data are linked via unique identi ers to primary care, hospital, pharmacy, and death registration databases, allowing for the linkage of patient treatment history, treatment patterns, and hospitalization based on International Classi cation of Diseases, 10th revision (ICD-10) codes. The study period ran from January 1, 2011 through December 31, 2019. The index date was de ned as the date of the rst allo-HSCT procedure between January 1, 2012 and December 31, 2018.
Study Population Patients (aged 18 years and above at the index date) who underwent allo-HSCT for any hematological malignancy between January 1, 2012 and December 31, 2018 were eligible for the study. Patients were excluded if they had an allo-HSCT prior to the start of the study or multiple allo-HSCT procedures during the study period. All patients were required to have at least 12 months of baseline data prior to the allo-HSCT and 12 months of possible follow-up data (unless they died). Eligible patients were identi ed in the database using the common classi cation of medical procedure codes or, where applicable, diagnosis-related group or ICD-10 codes. Using ICD-10 codes, patients were divided into 1 of 4 categories by GVHD type: aGVHD, cGVHD, a + cGVHD, or no GVHD (Supplementary Table  1 ).
Statistical Analysis Continuous variables were summarized descriptively with mean, standard deviation (SD), median, minimum and maximum, and lower and upper quartiles (Q1; Q3). Frequencies and percentages were reported for categorical variables. The chi-square test was used for categorical variables. The crude mortality rate was calculated as a ratio of the number of deaths during the follow-up period divided by the total person-years in the given cohort. The crude rates of HCRU and of severe infections were calculated as the total number of events divided by the person-years. A mean value was then estimated for each cohort. No imputed data were used for missing values for outcomes assessments. Statistical analyses were conducted using SAS (version 9. 4 TS1M4). Percentages were based on available observations (known values), and outliers were included in ranges and percentiles.