dataesr/scientific-paragraphs-categorization huggingface dataset:
Our results show that infections of USUV and WNV among humans, dogs, horses, birds and mosquitoes repeatedly occurred in the study area in recent years. In comparison with our mosquito surveillance data from 2015  [26] , we identified two sites with WNV and USUV detection in different years, suggesting a high suitability of those sites for future surveillance studies (Supplementary Table  S1 : mosquito collection sites). Moreover, the combination of genetic data from other studies and ours show the presence of the same lineages for both WNV and USUV in the same region in 2015, 2018 and 2020. More precisely, the cluster of WNV Lineage 1 found in mosquitoes in 2018 has also been detected in Camargue in a horse in 2015 (Figure  2A ) and in mosquito excreta in 2020 (a different genomic region than that used in our analysis, GenBank accession OK489805.
1  [41] ). The same cluster had been detected in equines in the region in 2000 and 2004 (Figure  2A ). Thus, after an 11-year period without detection, viruses belonging to the same cluster within WNV Lineage 1 have been repeatedly detected since 2015 in both vertebrates and mosquitoes. Similarly, the same USUV lineage was detected in mosquitoes from Camargue in 2015 (a sequence from a different genomic region than that used in our analysis was obtained)  [26]. Thus, similarly to WNV, USUV Africa 3 The phylogenies were inferred based on a partial sequence of the NS5 or the NS3 genes for WNV and USUV, respectively. The tree was rooted with a sequence of Japanese encephalitis virus (AF075723) for WNV sequences. The tree was rooted with a sequence of lineage Africa 1 for USUV. One hundred bootstrap datasets with random sequence addition were computed to generate a consensus tree drawn.
Numbers along branches are bootstrap values. Scale bar indicates substitutions per site. Sequences in blue come from France. French sequences identified in this study (red) are all from mosquito samples and are available in GenBank. The WNV sequence from a horse from the Camargue region in 2015 and obtained by other authors appears in green to facilitate comparison  [32]. Sequences from the Camargue area are marked with a black circumference. The year of collection is stated on the sequence name, generally after the country name. Lineage has been detected in C. pipiens populations in Camargue in 2015, 2018 and 2020. The repeated detection of the same lineages over several years is notable, given the usual low prevalence of these viruses, the detection of other lineages in the study area  [26]  and the lack of mosquito surveillance data in 2016 and 2017.
Statements Ethical statement: The study of human samples was approved by Montpellier University Hospital Review Board (2019-IRB-MPT-05-06) and was performed in line with the regulations outlined in the Declaration of Helsinki. Data was anonymised for publication purposes. Animal sampling were performed according to national and institutional guidelines (the sampling protocols were validated by the ethics committee of VetagroSup, agreement number 1534), informed written consent from animal owners was obtained and sample collection was performed by veterinarians. Funding.
statement: This study was funded by the ANR (French National Research Agency; reference ANR-16-IDEX-0006), the KIM RIVE initiative, the Labex EpiGenMed "Investissements d'avenir" programme (reference ANR-10-LABX-12-01), and Montpellier University of Excellence (MUSE; ArboSud project). Moreover, SG was recipient of funding from the Direction Générale de l'Alimentation from the French Ministry of Agriculture and Food. Horse serosurveys were funded by the Horse and Riding Institute, IFCE, and the EPERON fund (Encouragement aux Projets Equestres Régionaux Ou Nationaux) (OpIUM project).
Measures and data collection: All the participants were provided with information about the study and were asked to provide written informed consent (in Pashto language). Face to face interviews and anthropometric measurements were conducted by trained health staff using standardized questionnaires. Training of health staff for interviews and study procedures was conducted in the medical faculty. Interviews and all the study procedures of the participants were undertaken in the medical research unit following Standard Operating Procedures (SOPs) speci cally developed or adapted for the study. Table  1  summarises all the measurements of data collection in the study. Non-dietary questionnaire and anthropometry: A standardized questionnaire was developed from other studies conducted in collaboration with IARC (6,7) and administered by trained health workers in the research centre.
Waist/hip ratio (WHR) was calculated from these measurements. For abdominal obesity, a cut-off point of 80cm and 94cm and for waist/hip ratio a cut-off point of 0. 85 and 0. 90 were considered for women and men, respectively. Bioelectric impedance analysis (BIA) was used (Nutriguard Data Input device) to estimate body composition, particularly body fat. All the BIA measurements were performed while the person was lying in the supine position. To determine body fat (in kg and percent), lean mass (fat-free mass), body water, plus body cell mass (BCM) and extra-cellular mass (ECM), four electrodes were placed on the right hand, wrist, foot, and ankle and were connected to a generator applying an alternating electrical current of 0. 8 mA and 50 kHz. Participants were also asked about changes in their body weight during the last year, weight control methods and body silhouette at various ages.
Dietary Assessment: For a comprehensive assessment of dietary intake, a detailed country-speci c food frequency questionnaire (FFQ) was developed which included all local food items relevant to the population. Data from previous dietary monitoring surveys have been used to select the food groups of interest  (5). In addition, a research team of nutritional epidemiologists from IARC (International Agency for Research on Cancer) and Afghanistan checked the food list derived from these existing resources to optimize the food list and examples to be included further considering usual foods commonly consumed in Afghanistan. The food list of the nal questionnaire consisted of different food items/categories (combining foods with similar food composition) and different consumption frequency categories (number of times per day, per week, per month, rarely or never).
The research team will also compile Food Composition Tables. For the compilation of the food composition tables we will use the indirect method based on pre-existing data from literature and local/neighbouring regions. Our data will be compiled according to international standards and guidelines for food composition data set by the The dietary intake assessment was performed by trained health staff who asked the participants to report their habitual consumption frequency of the different foods listed in the FFQ during the last year. The food portion photograph book showed life-size colour photographs of foods in four portion sizes with photographs of utensils. The frequency categories included in the questionnaire were: Never, < 1 time per month, 1-3 times a month, once/week, 2-4 times/week, 5-6 times/week, once/day, 2-3 times/day, 4-5 times/day and 6 times/day.
DBS can be used for molecular biology techniques and other diagnostic assays. All of these collection cards can reduce the cost and di culty of cold chain shipping of samples and can be shipped as nondangerous goods at room temperature  (14, 15). Blood samples were collected in TFN and GenSaver cards, stool samples were collected in GenSaver and GenCollect cards and urine samples were collected in GenCollect cards. 99. 5% of the participants provided with both types of blood cards. For GenCollect 82% and for GenSaver 83% of the participants provided stool samples. Urine cards were prepared only for the rst hundred participants as a sample. Before sample collection the following data were recorded from all subjects: date and time of sample collection, date and time of preparing and packing biospecimen collection cards, fasting status (blood samples were only collected during fasting), time since last meal or drink, diet on previous day given that intake of some foods may affect biological measurements, smoking status, last menstrual cycle (women only), and use of any type of drugs or dietary supplements (i.
Samples were centrifuged and analysed using an enzymatic photometric test method within one hour of sample collection. Participants with a fasting plasma glucose level of >115 mg/dL or on antidiabetic medicine were considered diabetics. Dyslipidaemia was de ned as triglycerides >200 mg/dL, total cholesterol >200 mg/dL, LDL-C >130 mg/dL or HDL-C <40 mg/dL (16-18). Future biomarker analyses: The establishment of a biobank, which includes DBS, DUS and dried stool samples will be of great value to perform high-quality biomarker-based research, such as metabolomics and microbiome analyses on stool and blood samples and DNA extraction from DBS for genetics and epigenetics studies. All questionnaire data and biological samples were centralized at the International Agency for Research on Cancer in Lyon, France.
Statistical analyses We will assess the association between demographic risk factors, dietary patterns and biological markers and metabolic health. All potential confounders available will be adjusted for in each analysis. Logistic regression and standard normal regression will be used to study the association between the exposures of interest and the risk of obesity. Statistical analyses are performed at Kandahar University and at IARC by STATA version 14, SPSS version 23 and SAS 9. 4.
Acknowledgments The authors thank all the study participants, data collectors, technical staff and the academic staff of  Afghanistan National Agricultural Sciences and Technology University (ANASTU) :  Abdullah Baryal ,  Halima Rashad ,  Azad Afghan ,  Khalid Akbari ,  Sayed Shah ,  Mohammad Tahir Motwahir ,  Rashid Ahmad Sahrai ,  Naqibullah Mojadidi ,  Mohammad Musa Daudzai ,  Sultan Mohammad Sirat , and  Noorulhaq Mohammadi.
The importance did not escape notice as reported by Armitage in 1959, Meier pointed out that the mean life limited to a time T was an alternative actuarial method to compare survival curves  35. Thus, the paper trail shows RMST fundamentals were well established more than 60 years ago. 3. Gini's mean difference is even older: in 1912, Corrado Gini presented his monography on the variability and mutability contributing to distributions and statistical relations, within which the GMD (Δ) was formally established as la differenza media tra più quantità, i. e. the average difference between multiple quantities  14. Gini derived in 1914 an index that scaled Δ with twice the mean value of the quantities from which Δ was computed, G = Δ/(2μ)  36. The unitless G index, also called Gini coefficient or Gini index, is widely recognized in numerous domains, ranging from social sciences to mathematical physics  [37] [38] [39] [40] [41] [42] [43] [44]  , whereas Δ, expressed in the same units as its computing quantities, has been rediscovered  45, 46  , and, since 2015 has been integrated in a major statistical modeling package  15.
Although delayed for Covid and lack of funding, we have no doubt that the new planned study will someday come to completion. 8. Limitations of the present study includes its retrospective nature. Despite the utmost care given to abstraction and data analysis (master thesis in Supplemental Material), source errors and miscoding transcriptions are inherent. Small study size restricts the possibility of more advanced modeling. Treatments occurred over a long period, staging and management changed over time. Other weaknesses are highlighted in comparison with the published SNUH study, which had systematic advanced preoperative imaging and biological markers, much of which were missing in our dataset. Quality of life of patients were not assessed. There are some weaknesses in the GMD. It does not indicate the direction of the differences, but that is quite minor, a look at RMST would immediately show which values are larger.
Materials and methods We retrieved the records of women who had been referred for treatment between 1980 and 2009 to the radiotherapy department of the Universitair Ziekenhuis Brussel (UZ Brussel). Patients were selected according to the following criteria: women diagnosed with a histologically confirmed non-metastatic primary breast carcinoma who underwent surgery of the breast with axillary lymph node exploration, in whom chemotherapy was given prior to surgery. Records of patients without information on number of positive nodes and number excised were excluded. Age was not used for selection. Randomization was not performed. The study retrospectively collected non-experimental data already recorded in charts. Informed consent to participate was waived and approved by the Universitair Ziekenhuis Brussel (UZ Brussel).
All methods were carried out in accordance with relevant guidelines and regulations. All experimental protocols were approved by the Institution Review Board of the Universitair Ziekenhuis Brussel. Data. The data abstracted were: patient's age, menopausal status, dates of diagnosis, surgery, follow-up and occurrence of events, tumor laterality, tumor location, histopathology, histological grade, neu status, estrogen receptor (ER) and progesterone receptor (PR) status, preoperative T, N, and M stage; type of preoperative chemotherapy, number of chemotherapy courses; type of surgery, tumor size assessed by surgical pathology, number of lymph nodes examined (ntot), number of positive nodes (npos); postoperative radiotherapy given or not, type of radiotherapy equipment, doses delivered, whether treatment fields included the internal mammary and/ or axillary-supraclavicular regions; adjuvant chemotherapy, and adjuvant hormone therapy.
For patients with bilateral tumors, only the first chronological entries were abstracted. The specific organization of the patient's database, the coding, the extraction procedure, and the related computational details are provided in the master thesis in Supplemental Material. The number-based classification pN assigned npos of 0, 1-3, 4-9, and 10 + , to pN0, pN1, pN2, and pN3, respectively. The ratio-based classification LNRc assigned ratios npos/ntot of 0, (0, 0. 20], (0. 20, 0. 65], and (0. 65, 1. 00], to Lnr0, Lnr1, Lnr2, and Lnr3, respectively  21. We used the term "nodal quanta classes", quanta short for quantified, to bring to the fore that in this study "pN" and "Lnr" are labels for numerical quantities. Clinicalpathological classifications such as N-stage mix numerical classes with several different qualitative classifiers such as fixed, matted, internal mammary; the study used the mixed clinical ordinal N-stage as a covariate.
All statistical analyses used version 4. 1. 2 of the R project  58. The AIC, Gini's mean difference and its bootstrap standard error were computed using in-house scripts. The net reclassification improvement used the package survIDINRI 57. Harrell's g-index was computed with the function cph of the package rms  15. Computation of RMST and other metrics used the 2021's version of the package survival  52.
These data were then subsequently used to benchmark FLUKA code predictions  (34). The 11 C ion beam was generated via an in-flight fragmentation method in HIMAC's secondary beam course, exploiting the interaction of the synchrotron accelerated main ( 12 C ion) beam with a beryllium target  (35) (36) (37) (38) (39) (40). Although this method achieves production rates of almost 1%, which are deemed sufficient for testing purposes, the radioactive ion beams produced are considerably broad and feature larger momentum spreads than the projectile beam  (36, 38). Moreover, the production method is also characterized by the presence of impurities in the secondary beam, originating from the projectile fragments. In the presented case, the impurity level reached about 7%  (34). To support this approach and to allow detailed analysis, a Monte Carlo code simulation data can provide a valuable insight into carbon ion hadrontherapy treatment planning, verification, optimization and eventually its outcome  (25, (41) (42) (43) (44) (45) (46) (47).
Recent developments in the FLUKA code have enhanced the accuracy of the models governing ion transport and interactions, resulting in an improved reproduction of the fragmentation mechanisms and thus a more reliable dosimetry and imaging estimate  (48) (49) (50). Furthermore, the recently developed FLUKA PET tools enable the simulation of a PET scanner performance as well as signal acquisition throughout and after the irradiation, providing a more direct assessment of the imaging gain  (51, 52). A recent example of image performance evaluation used a SIEMENS Biograph mCT PET scanner from Heidelberg Ion Therapy Center as model, as well as a synchrotron-like irradiation with either 11 C or 12 C ions, simulating SOBP of comparable dose and range delivered to an antropomorphic head voxelized structure  (52).
In the prospect of producing high intensity mass separated 11 C beams, a boron nitride (BN) ISOL-type target was developed and characterized  (99). The target was manufactured to provide a controlled microstructure, for short diffusion and effusion times, to enhance the isotope release properties. The isotope release is often considered as a bottleneck in intense RIB production  (100, 101). Furthermore, it is foreseen to operate this target with a controlled oxygen leak to extract 11 C in the form of CO. Molecular isotope extraction further increases the release efficiency, as carbon is very refractory and easily forms strong bonds with hot metal surfaces. The expected in-target production yields for the different target-driver combinations can be calculated. For this purpose, simulations were performed with the particle physics Monte Carlo simulation code FLUKA  (48, 49).
Measurement data was taken at ISOLDE to quantify the behavior and limitations of the Penning trap and EBIS under the extreme conditions of high-intensity, low repetition-rate beams and constraints due to molecular beams. The assumed requirements of the charge breeding stage are summarized in Table  6 , and as seen the targeted output intensity is larger compared to the one introduced in Figure  2 , as a margin to account for the fact that matching this type of injector to a synchrotron was not yet tested as a whole. All measurements were performed with stable beams, either from the ISOLDE General Purpose Separator GPS  (114) , or from the local off-line surface ion source in front of the Penning trap (only K, not CO) (115). 13 CO + beams were produced in an ISOLDE target ion-source unit by injecting 13 CO gas into a Versatile Arc Discharge Ion Source VADIS (116) via a leak.
Birmingham, AL, USA) or detection antibody biotinylated antirabbit IgG (1/5,000; Jackson ImmunoResearch, West Grove, PA, USA) followed by HRP-streptavidin (1/200; R&D Systems, Minneapolis, MN, USA). Enzymatic activity was measured by adding tetramethylbenzidine (TMB; Pierce Endogen) and stopped by 1 N H 2 SO 4. Optical density (OD) of each well was monitored at 450 nm with a FlexStation 3 ELISA reader (Molecular Devices, Eugene, OR, USA) and Ascent Software version 2. 6. EC50 was calculated by sigmoidal dose response (Prism 9 software). For the NAb assay, serum-purified W614A-3S-specific Abs were obtained as described  (9). A pool of 4-5 sera was used for mouse purified NAb evaluation. Viral titration of infectious molecular clones or pseudotyped viruses and TZMbl neutralization assays were performed as previously described  (15).
Thirty cycles of PCR were performed using the Biomark microfluidic chip (Fluidigm). Automated data analysis was performed with the Singular Analysis Toolset (v3. 6) compatible with R software. We merged data from two chips (of two experiments) per condition (n = 184-188 cells). A multidimensional scaling analysis was performed without significant difference between chips. Results of negative control (no cells) or positive control samples (10 cells) and probe controls or non-amplified probes were removed before analysis using UMAP regression, heatmap after standard normalization, FlowSOM Elbow Metaclustering, and volcano plot EdgeR analysis (OMIQ Data Science Platform).
V(D)J Repertoire and Gene Expression Profiling W614A-3S-specific IgG1 + GC and NGC B cells at W11 were loaded according to the manufacturer's instructions for the chromium single-cell V(D)J reagent kits (10x Genomics) to attain between 500 and 10,000 cells per condition. Library preparation for V(D)J sequencing was performed according to the manufacturer's protocol [chromium single-cell V(D)J enrichment kit, mouse B cells] prior to sequencing on the Illumina MiSeq. Quality of raw reads was assessed using the FastQC 0. 11. 8 quality control tool, and clonotype quantification was performed with the Cell Ranger 3. 1. 0 V(D)J pipeline. Only 433 clonotypes defined as IgG protein sequences with exactly one heavy and one light chain were considered in the analysis. CDRH3 and CDRL3 sequence alignments were performed with Unipro UGENE software.
In order to study antigen-specific B cells, we measured W614A-3S-specific B cells in draining lymph nodes (dLNs), using W614A-3Sbiotinylated ovalbumin (Ova). Flow cytometry analysis of W614A-3S-biotinylated Ova staining of B cells in either PBS or W614A-3S formulated in SQE or Alum is shown in Figure  2C. Despite background staining in control PBS-injected mice, we were able to identify the W614A-3S-specific B cells in mice over time with both the SQE and Alum formulations (Figures  2C, D ). No significant difference in the absolute numbers (nor frequency; data not shown) of W614A-3S-specific B cells between SQE and Alum conditions was observed at both time points (Figure  2D ). In conclusion, we found that SQE formulation, W614A-3S conjugated with a carrier protein, induced bNAbs while the Alum formulation did not with a similar amount of W614A-3Sspecific B cells.
Our study challenges HIV vaccine development and discovery of formulation that could program B-cell differentiation favoring bNAbs. These data have been used in Go/No-go criteria for a clinical study. Indeed, an experimental medicine study using W614A-3S-CRM197 vaccine candidate (VAC02, Minka Therapeutics, France) is ongoing with the hope to speed up HIV vaccine research (ClinicalTrials. gov NCT04753892). acquisition, analysis, and interpretation. SB, KA, and JN compiled and analyzed the single-cell repertoire data. ES and DK were responsible for adjuvant production and quality control. MB and GS were responsible for the neutralization assays and analysis. BC, PD, GS, DK, and VV provided financial support. BC and OB wrote the manuscript. All authors contributed to the article and approved the submitted version.
FUNDING This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement no. 681137. BC's laboratory has received funding from the Fondation pour la Recherche Medicale "Equipe FRM 2020" award. GC's laboratory thanks the Fondation Dormeur, Vaduz, for funding laboratory instruments relevant to this project. High-throughput sequencing has been performed by the ICGex NGS platform of the Institut Curie supported by the grants ANR-10-EQPX-03 (Equipex) and ANR-10-INBS-09-08 (France Geńomique Consortium) from the Agence Nationale de la Recherche ("Investissements d'Avenir" program), by the Canceropole Ile-de-France, and by the SiRIC-Curie program -SiRIC Grant "INCa-DGOS-4654".
ACKNOWLEDGMENTS We thank  Maxence Mouille  for technical help. Monoclonal antibodies were kindly provided by  Polymun Scientific Immunbiologische Forschung GmbH  ( 10E8  and  PG9 ) and  Michel Nussenzweig ,  Rockefeller Foundation  ( 10-1074 ); plasmids of ConM and ConS by  Rogier Sanders AMC  and plasmids of other viruses by  NIH HIV repository.