dataesr/scientific-paragraphs-categorization huggingface dataset:
M. D. declares no conflict of interest. V. C. declares no conflict of interest. C. B-C. has received research support grants from Fondation de France PHRC National, France Parkinson Association; speech honoraria from UCB, Teva, ABBVIE, Aguettant, Orkyn, Zambon and received travel funding ABBVIE, Aguettant, Orkyn, Zambon N. C. has received speech honoraria from Abbvie, Orkyn T. D. declares no conflict of interest. L. D. has received speech honoraria from Abbvie, Orkyn, Zambon, UCB G. D. declares no conflict of interest. E. D. declares no conflict of interest. A. D. d. M. declares no conflict of interest. C. G. received travel funding from Home Air. D. M. declares no conflict of interest. W. M. has received fees for editorial activities with Springer, for consultancy activities from Sanofi, Lundbeck and Affiris, teaching honoraria from UCB and MDS, as well as research support from the Michael J Fox Foundation, the University Hospital Bordeaux, the French Health Ministry, the European Community, ANR, ARAMISE, PSP-France, MSA Coalition, ARAMISE, LABEX Excellence Initiative.
O. R. has received scientific grants from: Agence Nationale de la Recherche (ANR), CHU(FP7, H2020) de Toulouse, France-Parkinson, INSERM-DHOS Recherche Clinique Translationnelle, MJFox Foundation, Programme Hospitalier de Recherche Clinique, European Commission (FP7 & H2020) and has acted as a scientific advisor for: AbbVie, Adamas, Acorda, Addex, AlzProtect, Apopharma, Astra Zeneca, Bial, Biogen, Britannia, Clevexel, Cynapsus, INC Reasearch, Lundbeck, Merck, MundiPharma, Neuroderm, Novartis, Osmotica, Oxford Biomedica, Parexel, Pfizer, Prexton Therapeutics, Quintiles, Sanofi, Servier, Teva, UCB, XenoPort, Zambon. S. T. reports grants from Fondation pour la Recherche Médicale, France Parkinson, Neurodis and personal fees from UCB, Medtronic, Teva, St Jude, Novartis, Aguettant, Zambon, Abbvie, outside the submitted work.
Funding sources for study: The research leading to these results has received funding from the program " Investissements d'avenir "  ANR-10-IAIHU-06 ,  Institut national de la santé et de la recherche médicale (INSERM) ,  Ministère des Solidarités et de la Santé -DGOS, Paris, France Agence nationale de la recherche, PIA 1 "INBS", F-CRIN, Paris, France. We are very grateful to the patients and family members who participated in the study. The authors would like to thank the following contributors:  Carole Dongmo-Kenfack  ( CRA ) and  Minh-ha Morvan (CRA) ,  CIC Neurosciences, Parkinson Expert Center, Pitié-Salpêtrière Hospital, Paris, France  ;  Rachida Bari  ( CRA), Department of Neurology, Caen University-Hospital, Normandie University, Caen, France ;  Nadia Barun  ( CRA ) and  Fanny Huselstein  ( CRA), Department of Neurology, Hopitaux Universitaires, Strasbourg, France Margaux Bonnaire (CRA), Department of Neurology, Hôpital Maison Blanche, Reims, France Morgane Gaboreau (CRA), Service de Neurologie, Hôpital Pellegrin, CHU de Bordeaux, 33000 Bordeaux ,  Univ.
| Recruitment IDI participants were selected through convenience sampling from within or around health establishments after a screener questionnaire established that they met the inclusion criteria. Health establishments were selected by choosing one health centre and one health post per district, favouring those establishments with the highest percentage of children with anaemia out of children evaluated according to most recent data from "Arequipa Red" unpublished sources. The selection The same questions were used across all interactions with caregivers, whether IDIs or FGDs. of one health centre and one health post per district was made to account for variation among establishments as health centres are typically larger, have more resources, and are located in more urbanized areas than health posts.
| Data management and analysis IDIs and FGDs were audio-recorded (verbal consent permitting); also, a member of the field team took detailed notes and reviewed these with the interviewer afterwards. In the few cases that the participant did not give consent for audio-recording but expressed interest in participating in the research, notes were used for analysis in lieu of a transcription. This occurred in five IDIs in four districts-two with caregivers and three with health personnel. For analysis, the research team developed a codebook based on the IDI and FGD guides, in a process similar to structural coding  (Saldana, 2015) , distinguishing codes as either themes related to MNP use or anaemia and other methods of anaemia prevention, each cross-coded with a corresponding level of the SEM.
ACKNOWLEDGMENTS We would like to express our gratitude to  Dr. Ricardo Castillo-Neyra ,  Dr. Michael Z. Levy ,  Katty Borrini Mayorí ,  Lina M. Mollesaca Riveros ,  Amparo M. Toledo Vizcarra , and the entire field team at the  Zoonotic Disease Research Lab in Arequipa  for using their research facilities, for introducing us to the  Arequipa community , and specifically, for assessing us with the help of the field team in recruitment and notetaking for the focus groups and interviews. We would also like to take this opportunity to thank all of the caregivers and health personnel in Arequipa who participated in this study for sharing their time, experiences, and wisdom with us. Funding for this project was provided by the  National Institute on Minority Health and Health Disparities , " Tulane-XavierMinority Training in International Health " through the  Minority Health InternationalResearch Training (MHIRT) Program  ( T37 MD001424 ); the  Stone Center for Latin American Studies at Tulane University  with the Tinker Foundation; the  Fulbright US Student Program ; and the  Wellcome Trust  ( 212712/Z/18/Z ).
| Three-dimensional growth assay DAOY and HD-MB03 3-D cultures were prepared using ultra-low attachment 96-well plates (Corning). Cells (5000) were seeded in 200 µL medium per well. The spheroids were cultured for 8 days and pictures were taken with an AMG Evos microscope 40x objective (Thermo Fisher Scientific Inc). Spheroid areas were measured using ImageJ 1. 51j8 software (National Institute of Health). 30.
YC and MPB designed and performed the experiments. YC, MPB and VP analysed the data. YC and VP wrote the manuscript. SS isolated PCN cells. SG contributed to design the experiments and to the manuscript revisions. YC and ET performed the radioactivity experiments. HE and MFW kindly provided the JPH203 but did not conduct any experiment nor participated to the elaboration of experimental procedures. GP and JP contributed reagents, materials and funding. Besides the financial support of CSM, YC and JP were funded by GEMLUC and MPB, VP and GP by Fondation Flavien. All co-authors contributed in improving the draft manuscript. The authors are grateful to Dr. M. Gettings for editing the manuscript and to all the staff members of Fondation Flavien for their constant efforts and strong support.
Proteomic Analyses Platelets were lysed in radioimmunoprecipitation assay (RIPA) buffer (Sigma) supplemented with protease-inhibitor cocktail (Roche, Mannheim, Germany). A 6-mm 2 area of a 2. 5-µmthick, formalin-fixed, paraffin-embedded (FFPE), tumor-tissue section was preselected on a hematoxylin-and-eosin-stained slide and microdissected with a PALM type 4 (Zeiss) laser microdissector. Tumor proteins were extracted from the tumor and platelet proteomes with formalin cross-link reversion were subjected to mass-spectrometry (MS) analysis, as previously described  (13). The Mascot 2. 5 algorithm identified proteins with the Proteome Discoverer 1. 4 Software (Thermo Fisher Scientific, Illkirch, France) used in batch mode to search the Homo sapiens database (71,663 entries, Reference Proteome Set, release 2017_06) from http://www.
uniprot. org/ website, allowing 2 missed enzyme cleavages. MS and MS/MS mass tolerances were set to 10 ppm and 0. 02 Da. Methionine oxidation, lysine acetylation, and asparagine and glutamine deamidations as dynamic modifications, and cysteine carbamidomethylation as a static modification were sought. Peptides were validated with Proline software (http://proline. profiproteomics. fr/). Only peptides with 1. 0% false-discovery rate (FDR), calculated using the Mascot "decoy" option, and a pretty rank = 1 were retained. Proteins were identified with ≥2 specific peptides and FDR <1. 0%.
Immunohistochemistry Analyses The 2. 5-µm-thick tissues sections were dewaxed, rehydrated and antigens were retrieved in EnVision TM FLEX Target Retrieval Solution Low pH solution (Dako-Agilent, Santa-Clara, CA, US), and immunolabeled in an automated autostainer (Dako-Agilent, Santa-Clara, CA, US) using standard reagents provided by the manufacturer. The sections were incubated with anti-CD41 rabbit polyclonal antibody (HPA031168; Sigma), diluted 1:50, for 60 min at room temperature, then incubated with anti-rabbit IgG conjugated horseradish peroxidase (EnVision Flex/HRP, Dako-Agilent) for 20 min for signal amplification, revealed by 3,3 ′ -diaminobenzidine (Dako). The slides were counterstained with hematoxylin, dehydrated, and mounted. Each immunohistochemical run contained a negative control (buffer, no primary antibody).
Acknowledgements AFM measurements were performed at  NanoLab Nijmegen. Surface X-ray diffraction experiments were performed on beamline ID03 at the  European Synchrotron Radiation Facility (ESRF), Grenoble ,F rance. vSFG IR spectroscopy measurements were supported by the  US Department of Energy (DOE), Office of Basic Energy Sciences,Division of Materials Science  and Engineering and were performed at the  Environmental Molecular Sciences Laboratory ,aDOE office of Science User Facility sponsored by the  Office of Biological and Environmental Research  that is located at  Pacific Northwest National Laboratory (PNNL). PNNL is amultiprogram national laboratory operated for DOE by Battelle under Contract No. DE-AC05-76RL01830.
18/23 received pre-conditioning with azathioprine 3 mg/kg/day, hydroxyurea 30 mg/kg/day, and hyper-transfusion. Graft source was bone marrow, and 20/ 23 donors were mobilized with filgrastim 10 mcg/kg/day x 5 days. PTCy (50 mg/kg/day x2), MMF, and sirolimus were given for GvHD prophylaxis. Cellular subsets analyzed included CD4, CD8, NK, and B cells. Patients deceased or without IR data were excluded. Results: Table  1  shows patient and donor characteristics. Median total nucleated and CD34 cell doses were 4. 9 £ 10(9)/kg and 4. 69 £ 10(6)/kg, respectively. Among engrafted patients, those who received preconditioning had delayed platelet recovery (mean 35 days vs 27, p = 0. 002), but higher median CD4 absolute cell count (cells/mL) at D+30 (43 vs 41), D+60 (190 vs 98), D+90 (229 vs 191), D+180 (304 vs 308), D+360 (1255 vs 394) compared to those without, respectively.
Materials and methods This project is coordinated by IARC and involves scientific teams in four Latin American countries, with one coordinating center in each country and one or more hospitals collaborating with the coordinating center. Through IARC and a central pathology laboratory (the Porter Lab) at the Fred Hutchinson Cancer Research Center (FHCRC) in Seattle, the research teams have harmonized and standardized protocols for recruitment of cases and controls, collection of questionnaire data, collection and storage of blood and urine samples, tumor block fixation and handling, and pathology review. All questionnaires and forms are administered in the local language (Spanish). A central web-based database has been developed.
Storage, management, and quality control of data and biological samples To facilitate data entry and validation, a computerized version of the questionnaire, based on previous BC studies in Mexico,  17, 18  has been developed. Questionnaire data are entered locally using a web-based application and centralized at IARC at regular intervals. IARC conducts consistency checks and quality controls; any queries are resolved directly with the center before files are merged for data harmonization and establishment of the central database. Mirror halves of the blood fractions and urinary samples are stored in local biobanks in each center, and half is stored and centralized at the IARC biobank, in order to minimize the risk of sample loss in case of freezer breakdown or other problems affecting samples in one of the locations, and to facilitate retrieval of samples for PRECAMA-wide projects.
Family history and highpenetrance germline mutations will be explored in relation to the risk of BC in young Latin American women. The establishment of genetic counselling for women with inherited mutations and for their families would also be a priority in infrastructure development. Young women are more likely to have genetic susceptibility to BC  9  with specific germline mutations that could be related to ancestry. Some mutations with high penetrance, such as those in the BRCA1 and BRCA2 genes, have been widely described (80% risk of BC), and other mutations with lower penetrance are known in the Caucasian population,  46, 47  however, there are limited data among Latin American women. Therefore, it will be important to assess the hereditary component in this population.
Acknowledgments The  PRECAMA team includes International Agency for Research on Cancer  (Coordinating Center) Investigators and Staff:  Carine Biessy ,  Magali Olivier ,  Sabina Rinaldi ,  Isabelle Romieu ; Investigators and Staff in Chile:  Maria Luisa Garmendia ,  Jose Luis Soto ,  Eva Bustamante ,  Leonor Moyano ; Investigators and Staff in Colombia:  Alberto Angel ,  Carlos Andres Ossa ,  William H. Arias ,  Gabriel Bedoya ,  Mauricio Borrero ,  Alicia Cock-Rada ,  Israel Díaz-Yúnez ,  Carolina Echeverri ,  Fernando Herazo ,  Ángel Hernández ,  Roberto Jaramillo ,  Edgar Navarro ,  Yorlany Rodas Cortés ,  Gloria I. Sánchez ;  Investigators and Staff in Costa Rica: Bernal Cortés ,  Paula González ,  Diego Guillén ,  Viviana Loría ,  Rebecca Ocampo ,  Carolina Porras ,  Ana Cecilia Rodríguez ; Investigators and Staff in Mexico:  Gabriela Torres-Mejía ,  Isabel Alvarado-Cabrero ,  Angélica Ángeles-Llerenas ,  Jenny Tejeda ; Investigators and Staff in Seattle:  Peggy Porter.
Viable counts on KB plates of initial and final populations were performed to calculate the number of generations. Stability of colony morphologies was confirmed and data from microcosms with >5% smooth colonies were excluded (two cases). Control competition experiments with isogenic WspF DT226-G275 reference strains with and without GFP were used to correct for the cost of the GFP marker. Control competitions were also used to determine the cost of the double deletions and the reporter construct relative to a wild type genetic background, for example an AwsX DY77-Q87 mutant in Dwsp/Dmws background with pMSC was competed with a GFP labeled AwsX DY77-Q87 mutant in wild type background. Competitions were performed in independently inoculated quadruplicates for each strain with the number of replicates based on previous work  (Lind et al.
Computational method Protein-protein molecular docking was performed with the ZDOCK 3. 0. 2 software. 37 ological assembly of the SOD dimer, determined by X-ray diffraction (PBD: 1SDY),  38  was defined as the target while the NMR solution structure of yeast frataxin (PDB: 2GA5)  39  was defined as the ligand. In this procedure, the ZDOCK software searches all possible binding modes in the translational and rotational space between the two proteins and evaluates each pose using an energy-based scoring function. To explore the variability of protein-protein association, 2000 docking poses were calculated and ranked according to the scoring function based on statistical pairwise potentials. 40 Moreover, as protein-protein docking acts with a rigid body, the best predicted docking structure was further optimized with the FF14SB forcefield  41  under Amber software.
The mitochondrial targeting sequence includes the amino acids (aa) from 1 to 40. The mature form sequence was reported to include residues 81 to 210 aa (52 to 172 aa for Yfh1). The other isoforms of human frataxin (56-210 hFxn or 78-210 hFxn) can also be found in the mitochondria. 59 According to the proteomics analysis database (http://gpmdb. thegpm. org), the non-mature forms of both Yfh1 and hFxn are seldom detected. 1] [62] [63]  The mitochondrial and extra-mitochondrial isoforms are identical (hFxn, 81-210 aa), and it has been suggested that after maturation inside the mitochondria, a part of mature hFxn is exported back to the cytoplasm. 61 Sod1 is mainly found in the cytosol at a level of 4,000-120,000 molecules per cell. 64 Only 5% of total Sod1 is localized to the mitochondrial intermembrane space, corresponding to a concentration of 0.
AFM imaging Following EV capture on the gold biochip, glutaraldehyde (0. 5%) was injected for 10 min to fix the captured materials for further AFM experiments operating in air. An injection of water was applied to remove buffer salts from the biochip surface; the biochip was then dried under gentle airflow. AFM imaging was obtained in contact-mode and in air using Vshaped silicon nitride cantilevers (Digital instruments, NP-S10) with a spring constant of 0. 32 N/m. Nanoscale investigations of the biochip by AFM were engaged by rigorously imaging different areas (from 100 µm 2 down to 2 µm 2 zones) of each spot to ensure representative sampling. EV size distribution was measured mainly using AFM images of 5 x 5 and 10 x 10 µm 2. The typical scan rate was 0. 5 Hz for 512 x 512-pixel images. Using Gwyddion software, a height threshold of 3 nm was applied to AFM images, in respect to the ligand-modified biochip surface roughness, to identify/mark the captured EVs prior to their size measurement (see Supplementary data -S2).
Distribution data of Tilia-feeding Phyllonorycter in the Russian Far East have been retrieved from a century-old Tilia herbarium stored in Vladivostok. Overall, 280 typical mines of Phyllonorycter, some with larvae and pupae, were found on 61 out of 799 herbarized specimens of Tilia spp. collected in Khabarovskii krai and Primorskii krai. For the first time, the presence of Tilia-feeding Phyllonorycter has been documented more West -in Amurskaya oblast and Jewish Autonomous oblast. High densities of the leafminer have been recorded on Tilia amurensis sampled in Khabarovskii krai and Primorskii krai between 1937 and 2005 suggesting a population dynamics with recurrent outbreaks. Our results confirm the importance of historical herbarium collections in studying trophic interactions and invasion ecology of folivore organisms.
issikii, as so far it is the only described species known to attack limes in the Russian Far East  (Baryshnikova, 2016). However, in this paper we utilize the neutral name "the lime leafminer" or "Tilia-feeding Phyllonorycter" until more detailed analyses (i. e. DNA barcoding) is done to prove the taxonomic possession of the archival specimens sampled from the herbarium in RFE. Data retrieved from herbarium specimens were used to compute average number of mines per infested leaves and relative number of infested leaves per herbarium sheet (expressed in %). Data on sampling localities were translated to the coordinates for mapping the historical occurrence of Tiliafeeding leafminer in the Russian Far East using ArcGis 9. 3 software. The distribution of Tilia spp. was extracted from various sources  (Pigott, 2012; Koropachinskiy, Vstovskaya, 2012; Zhuravlev, 2019)  Archival specimens of Phyllonorycter immature individuals and their parasitoids have been deposited at Sukachev Institute of Forest, Federal Research Center «Krasnoyarsk Science Center SB RAS», Krasnoyarsk.
issikii distribution is available from North Korea. The reference on its occurrence in the Republic of Korea concerns only the southern part of the Korean Peninsula  (Kumata et at al. , 1983). Overall, data retrieved from the historical herbarium collections deposited in Vladivostok provide evidence for wider distribution range of Tilia-feeding Phyllonorycter in the Russian Far East, at least in the past. Besides Khabarovskii and Primosky krais, the typical mines of Phyllonorycter were recorded more West -in Jewish Autonomous oblast and Amurskaya oblast meaning that the moth was distributed (and probably remains so) across the whole range of its primary Tilia hosts in the Russian Far East. High densities of Phyllonorycter mines on archival Tilia specimens dated back to  1937, 1961, 1992, and 2005  in Khabarovskii krai and Primorskii krai suggest the existence of outbreaks, a fact never reported in the literature from these regions.
Data The dataset contains qualitative description of ES provided by coral reefs, sandy beaches and coastal lagoons in different eutrophication states. Three to four eutrophication states are considered, from non-eutrophic to hyper-eutrophic state. 14 ES are considered: food through fisheries; material; molecules; coastal protection; nutrient regulation; pathogen regulation; climate regulation; support of recreational and leisure activities; contribution to a pleasant landscape; contribution to culture and territorial identity; emblematic biodiversity; habitat; trophic networks; recruitment. The capacity of the ecosystem to provide ES is described for each ES in each eutrophication state using qualitative information collected in the literature completed by expert-knowledge. Data are presented in double entry matrix (ES/eutrophication states) for coral reefs (Table  1 ), sandy beaches (Table  2 ), coastal lagoons (Table  3 ).
Value of the data The dataset is useful for understanding the relations between ecological functions, ecological states and ES. Scientific can benefit from this data to carry out ES assessment or to inform decision-making processes and management strategies regarding eutrophication. Practitioners and policy-makers can benefit from this data to adopt management strategies or measures for biodiversity conservation. The data provide a first overview of the effects of eutrophication on ES bundles and can serve as a basis for a larger database. The data can be used for further insight the trade-offs and synergies between ES and can be used for modelling. The dataset helps to build relationships between disparate data on the effect of eutrophication on ecological function and ES.
The literature review encompassed knowledge obtained and disseminated on a global scale, while expert knowledge focused on data observed on a more local scale, based on their field studies. However, experts had a good understanding of these ecosystems which allowed them to pronounce in a qualitative way where data gaps were identified. All information were compiled within Table  1. Information was then coded to summarize the variation of ES supply between states. Five levels of ES supplied were considered: "0: inexistent", "1: very low", "2: low", "3: medium", "4: high", "5: very high".
The volume for 100 µm was calculated as CSA × 100 µm (µm 3 ). For the myonuclei analysis, area (µm 2 ), maximum diameter length (µm), roundness and angle of the maximum diameter relative to the long axis of the fibres were determined on 2D projections using the analysis particles plugin of ImageJ software. Roundness was calculated as 1/(length of the major axis/length of the minor axis). The sinus value of the angle was calculated. The number of nuclei was counted and illustrated as number of nuclei/100 µm fibre length or as number of nuclei/volume calculated for 100 µm fibre length. The three-dimensional coordinates of the geometric centre of each nucleus were determined on image stacks to measure the nearest neighbour (NN) distance for each myonucleus using the 3D manager plugin of Image J software.