dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank  Erik Geibrink  for technical support and  @AndreJ  (https://gis. stackexchange. com/questions/253923/how-to-fix-the-reprojection-from-ease-2-grid-product-smap-togeographic-coordina) for providing valuable code ideas for working with  NASA NEE data. The work was financially supported by the  Swedish Research Council  (grant no. 2016-05275  and  325-2014-6898 ,  JPI Climate initiative ) and  RSF  (grant no. 18-17-00237 ).
The Andromeda search engine was used to match MS/MS spectra against the Uniprot human database (https://www. uniprot. org/). Enzyme specificity was set as Cterminal to Arg and Lys, cleavage at proline bonds and a maximum of two missed cleavages are allowed. Carbamidomethylation of cysteine was selected as a fixed modification, whereas N-terminal preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this this version posted October 15, 2020. ; https://doi. org/10. 1101/2020. 10. 15. 341123 doi: bioRxiv preprint 14 protein acetylation and methionine oxidation were selected as variable modifications. The "match between runs" feature of MaxQuant was used to transfer identification information to other LC-MS/MS runs based on ion masses and retention times (maximum deviation 0.
Mice and human mRNA DPYD expression analysis Genenvestigator 7. 5. 0 (https://genevestigator. com/gv/) is a search engine that summarizes data sets in metaprofiles. GENEVESTIGATOR® integrates manually curated and quality-controlled gene expression data from public repositories  (Hruz et al. , 2008). In this study, the Condition Tools Search was used to obtain DPD mRNA levels obtained from human (Homo sapiens) and mice (Mus musculus) in various anatomical parts. Mean of logarithmic level of expression obtained from AFFIMETRIX expression microarrays was used to generate a cell plot from selected results related to macrophages and monocytes. The lowest and the highest expression results in both series (human and mice) were used to evaluate the expression level in the dataset. Cell plot was generated using the JMP software (SAS).
Acknowledgments AM is supported by the  ATIP/Avenir Young group leader program  ( Inserm and La ligue  nationale contre le cancer). KG is supported by the  ITN  ( International Training Network )  Phys2Biomed  project which is funded from the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No  812772. The authors would like to thank  Xavier Fonrose ,  Edwige Col  and  Floriane Laurent  for their technical assistance. The authors thank the zootechnicians of PHTA facility for animal housing and care. preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Data availabilty All MS proteomics data were deposited on the Proteome-Xchange Consortium website (http://proteomecentral. proteomexchange. org) via the PRIDE partner repository, data set identifier: PXD006354. Disclosure of interest: The authors declare no competing interests related to this study. Life Technologies Cat#:PA522302 Anti-βactin (immunoblots) Sigma Aldrich Cat#:A2228 Anti-HIF1α (immunoblots) BD Bioscience Cat#:610958 Anti-HIF2α (immunoblots) Clinisciences Cat#:sc-46691 Anti-eIF4E (immunoblots) Clinisciences Cat#:sc-9976 Anti-eIF4E2 (immunoblots) Clinisciences Cat#:GTX82524 Anti-CD68 (immunochemistry) Dako Cat#:M0876 Ant-CD163 (immunochemistry) AbD Serotec Cat#:MCA1853 Anti mouse IgG HRP Life technologies Cat#:G21040 Anti Rabbit IgG HRP Life technologies Cat#:G21234 Anti mouse IgG alexa Fluor 488 Invitrogen Cat#:A11029 Anti rabbit IgG alexa Fluor 546 Invitrogen Cat#:A11010.
(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. bioRxiv preprint doi: ; https://doi. org/10. 1101/2020. 10. 15. 341123 this version posted October 15, 2020. The copyright holder for this Gimeracil GSK126 HEPES (1M) Histopaque-1077 Hoescht 33342 Human serum from male AB plasma (SAB) Leupeptin McCoy's 5A (modified) medium, glutaMAX supplement MEM Non-Essential Amino Acids solution (100X) Opti-MEM I medium, glutaMAX supplement Pepstatin A RPMI 1640 medium, glutaMAX supplement TrypLE Express Enzyme (1X), phenol red Ultrapure DNase/RNase-free distilled water Deposited Data Proteomic data Experimental Models: Cell Lines CT26 WT HT-29 LoVo RAW 264. 7 RKO Mouse dpyd reverse Mouse gusb forward (housekeeping gene) Mouse gusb reverse (housekeeping gene) Mouse hprt1 forward (housekeeping gene) Mouse hprt1 reverse (housekeeping gene) siCTL (Non-targeting pool) siRNA human DPYD siRNA human EIF4E siRNA human EIF4E2 siRNA human EPAS1 (HIF2a) Recombinant DNA pLenti-C-DPYD-mGFP-P2A-Puro plasmid pLenti-C-DPYD-mGFP-P2A-Puro plasmid Software and Algorithms Graph Pad Prism 7 JMP 14 ATCC Mouse dpyd forward Sigma Aldrich Clinisciences Life Technologies Sigma Aldrich Invitrogen Sigma Aldrich Sigma Aldrich Life Technologies Life Technologies Life Technologies Sigma Aldrich Life Technologies Life Technologies Life Technologies PRIDE ATCC ATCC ATCC ATCC Eurogentec Eurogentec Eurogentec Eurogentec Eurogentec Eurogentec Horizon Discovery LTD Horizon Discovery LTD Horizon Discovery LTD Horizon Discovery LTD Horizon Discovery LTD OriGene OriGene GraphPad Software Inc SAS Biorender Biorender Cat#:SML2075-5MG Cat#:HY-13470-5mg Cat#:15630056 Cat#:10771-6X100ML Cat#:H3570 Cat#:H4522-100ML Cat#:L5793-5MG Cat#:36600088 Cat#:11140035 Cat#:51985026 Cat#:P5318-5MG Cat#:61870044 Cat#:12605036 Cat#:10977035 PXD006354 Cat#:CRL-2638 Cat#:HTB-38 Cat#:CCL-229 Cat#:TIB-71 5' -TCGCGTGTTCATCGTCTTCA -3' 5' -ATAACCTTCCGTGGCGAGAG -3' 5' -GGGACAAAAATCACCCTGCG -3' 5' -GCGTTGCTCACAAAGGTCAC -3' 5' -AGCCCCAAAATGGTTAAGGTTG -3' 5' -ATCCAACAAAGTCTGGCCTGT -3' Cat#:D-001810-10-05 Cat#:L-008376-00-0005 Cat#:L-003884-00-0005 Cat#:L-019870-01-0005 Cat#:L-004814-00-0005 Cat#:RC216374L4V Cat#:PS100093V Other iScript Ready-to-use cDNA supermix Biorad Cat#:1708841 iTaq universal SYBR green supermix Biorad Cat#:1725124 HypoxyLab Station Oxford Optronix MicroBCA kit Life Technologies Cat#:23235 MycoAlert kit Lonza Cat#:LT07-118 NucleoSpin RNA (50) Macherey Nagel Cat#:740955.
Interbreeding experiments were unsuccessful at triggering auxosporulation between strains of these blue Haslea species, suggesting they belong to different taxa according to the concept of biological species  [19, 21, 23]. In 2009, we observed blue diatoms in water samples from La Gomera, an island from the Canary Archipelago. Based on their morphology, they appeared to belong to a new species thereafter called Haslea silbo sp. nov. Several subsequent findings suggested that this species is a cosmopolitan taxon found in different geographic locations on both sides of the Atlantic Ocean. Preliminary characterization of this species and its blue pigment were done in the past  [3] , without the formal description being provided. Here, we present data collected during a decade of research on Haslea silbo sp.
The PCR products were visualized in a 1% agarose gel and then purified with StartaPrep PCR Purification Kit (Agilent Technologies, Inc. , Santa Clara, CA, USA). The purified products were sent for Sanger sequencing (Macrogen©, Amsterdam, The Netherlands). All sequences were checked, edited, and assembled (5 -3 and 3 -5 ends) using Sequencher 4. 1. 4. In the case of NCC 456 and SZCZMV2009, molecular barcodes have been obtained using next generation sequencing, as described below. All DNA sequences have been submitted to GenBank and obtained registration number.
Next Generation Sequencing Clones NCC456 and SZCZMV2009 were cultivated under the conditions described above. DNA was extracted following Doyle and  Doyle (1990)   [28]. Sequencing was conducted at the Beijing Genomic Institute Shenzhen facilities (Hong Kong, China). NCC456 was sequenced in 2015 on an Illumina Hiseq 4000 (22 million 150 bp paired-end reads, 250 bp insert) and SZCZMV2009 was sequenced in 2019 on a BGISEQ-500 (60 million 100 bp paired-end reads). Data were assembled using SPAdes 3. 14. 0 [29]  with a k-mer of 85, and verified with Consed  [30]. ORFs and genes encoded in the organelle genomes and plasmids were identified as previously described  [31]  and tRNA genes were localized with tRNAscan-SE 1. 23  [32]. GenBank files were generated using Sequin 13. 70 and were used to create maps using OGDRAW  [33].
Phylogenetic Analysis A maximum likelihood (ML) phylogeny was inferred from the partial rbcL gene using sequences obtained from PCR amplifications, extracted from complete plastid genomes or downloaded from GenBank. The rbcL sequences of the Naviculaceae Seminavis robusta Danielidis and Mann and Trachyneis sp. , were added as outgroups. Sequences were aligned using MAFFT  [35]  and trimmed to a final length of 597 bp. The phylogenetic analysis was conducted using RAxML 8. 0  [36]  and data partitioned by first and second codon positions. The best tree out of 100 was computed for 1000 bootstrap replicates.
Molecular Signature The ITS1-5. 8S-ITS2 sequences are available in Genbank as HE663060 (K-1283) and HE978358 (K-1289). The rbcL sequences are available as HE663065 (K-1283), HE978358 (K-1289) (Canary Islands), MH355570 (NaS3), and MG189641 (BIOTAII-43). SSU and psbC partial sequences have also been obtained on BIOTAII-43 and registered as MG189639 and MG189640, respectively. For NCC456 and SZCZMV2009, complete organellar genomes and the cluster of nuclear rRNA genes were deposited in GenBank under accession numbers MW645081 (mitogenome NCC456), MW645082 (plastid genome NCC456), MW645083 (mitogenome SZCZMV2009), MW645084 (plastid genome SZCZMV2009), MW679567 (rRNA NCC456), and MW679566 (rRNA SZCZMV2009).
Comparison with The Mitochondrial Genome of H. nusantara The whole genome alignment obtained from progressiveMauve is shown in Figure  14. The gaps observed when comparing H. silbo NCC456 and SZCZMV2009 represent the differences in intron contents, which also discriminates both of them from H. nusantara. The portion displayed in green corresponds to a change of strand of orf224 in H. silbo compared to the corresponding orf226 in H. nusantara. A comparison with the genome of H. nusantara (MH681882) and blastp analyzes of ist content showed that it also displays a fusion of nad6/nad2, although not indicated on GenBank. However, the fusion of rps13/cox3 differentiates H. silbo from H. nusantara, in which both genes are distinct. orf790) displaying similarity with mitochondrial intron-encoded RTs from other diatoms.
Comparison with The Mitochondrial Genome of H. nusantara The whole genome alignment obtained from progressiveMauve is shown in Figure  14. The gaps observed when comparing H. silbo NCC456 and SZCZMV2009 represent the differences in intron contents, which also discriminates both of them from H. nusantara. The portion displayed in green corresponds to a change of strand of orf224 in H. silbo compared to the corresponding orf226 in H. nusantara. A comparison with the genome of H. nusantara (MH681882) and blastp analyzes of ist content showed that it also displays a fusion of nad6/nad2, although not indicated on GenBank. However, the fusion of rps13/cox3 differentiates H. silbo from H. nusantara, in which both genes are distinct.
illustrate this reduction in cell size because of the MacDonald-Pfitzer rule for the clone K-1285 between July 2009 and January 2012. The differences in the colour of the apices reflects the production of the marennine-like pigment, which seems triggered by higher light conditions. As size diminished, frustules often exhibited deformities, as seen in LM on Figure6picturing (clone K-1285) and SEM on Figure7a,b (clone K-1289). 3. 1. 2. HolotypeAccession numbers CAT 2472 and CAT 2473 for a permanent slide of the K-1285 clone and an acid-cleaned sample of K-1285 kept in 70% ethanol, respectively, deposited at the Natural History Museum of Denmark, University of Copenhagen. Some valve parts of this type material are shown in Figures2-4.
R PEER REVIEW 13 of 28 Funding: This study was supported by the  European Commission  under the Community's  Seventh Framework Program BIOVADIA  (contract No. FP7-PEOPLE-2010-IRSES-269294 ,  Biodiversity and Valorization of Blue Diatoms ), the  Horizon 2020 Research and Innovation Program GHaNA  (The  Genus Haslea, New marine resources for blue biotechnology and Aquaculture , grant agreement No [ 734708/GHANA/H2020-MSCA-RISE-2016 ] J. -L. M. ) and also the 2017-2021 research funds granted for implementation of a co-financed international research project from  Polish Ministry of Science and Higher Education. Partial support was also provided by  Natural Sciences and Engineering Research Council of Canada   Discovery Grant  awarded to I. K. Funding was provided by the  Canadian Museum of Nature  to M.
This combination allows us to represent some elements that are usually left out in similar simulation models of fertility behaviour, while still founding our model on solid theoretical grounds. We start by introducing the basic operation of the model through an example and follow this with a more detailed technical description. Additional technical details can be found in the Appendix. The R code and data necessary to reproduce all the results presented in the paper can be obtained at https://github. com/dciganda/comfert_origins.
Here we search for the combination of parameter values that reduces the distance between the model output and observed data from Spain. Specifically, let X ⊂ R q be the parameter space, where q is the number of parameters. At a given combination of parameter values θ ∈ X, we compute Δ θ the mean squared error (MSE) at this location as a weighted mean of the MSEs for three vectors:. Age-specific fertility rates (ASFRs) between ages 14 and 50 for the period 1960-2016; available from the Human Fertility Database (2011). Average ideal number of children; obtained from Sobotka and Beaujouan (2014). Cohort completed fertility by education; obtained from  Zeman et al. (2014). The objective of the estimation procedure is to find the region of the parameter space where the distance Δ θ is smallest.
The basic idea is to proceed sequentially, taking a sample of k locations θ 1 , … , θ k from X and computing Δ θ1 , … Δ θk. This evidence is then used to decide where to search next in the parameter space. The distance Δ θ is then computed on a new set of locations to be explored. To avoid the need to compute the model at each of these new points, at this stage the model is substituted by an emulator (i. e. a model of the functional relationship between the model parameters and the distance). Specifically, we fit a Gaussian process regression using the R package mlegp  (Dancik and Dorman 2008). (For the use of Gaussian process emulators in the context of demographic simulations, see  Hilton and Bijak 2017). The emulator provides predictions of the distance at any combination of parameters, and the decision of where to search next is made using a specific selection criterion or acquisition function.
Median hemoglobin level, leukocytes count, absolute neutrophil count (ANC), lymphocytes count and platelets count were 9. 35 g/dL (IQR, 8. 85-10. 1), 4. 8 G/L (IQR, 2. 0-8. 0), 1. 78 G/L (IQR, 0. 75-4. 7), 0. 88 G/L (IQR, 0. 65-1. 12) and 66 G/L (IQR, 31. 5-246) respectively, at time of AFMT (Supplementary Fig. 1 ). The median AFMT product retention time was longer than expected (188. 50 min [range 48-288] and 138 min [range 41-245] for the first and second AFMT, respectively, instead of the recommended 120 min) demonstrating the feasibility of the enema procedure and the absence of discomfort for the patients. In order to assess the acceptability of the procedure, treated patients' quality of life (n = 25) was evaluated throughout the clinical study. The data showed that the results of the questionnaire after AFMT (V3) were similar or tended to improve, compared to those at V2 before AFMT (especially self-care, usual activities and anxiety, and depression parameters), which highlights the absence of a negative impact of AFMT on the overall health of patients (Supplementary Table  2 ).
2 ). Finally, we observed that among the 19 per-protocol patients that received antibiotics, patients' receiving carbapenems (imipenem-cilastatin or meronem) have decreased α-diversity indexes at V2 compared to patients receiving piperacillline-tazobactam alone, that persist at V3 after AFMT (Supplementary Fig. 4 ). MDRB decolonization. Evaluation of AFMT efficacy in MDRB eradication was evaluated as a co-primary outcome. To evaluate the presence of antibiotic resistance through metagenomic sequencing, we mapped the total sequencing reads on the MEGARes antibioresistance gene database. We found evidence that IC and associated antibiotic treatments induced a significant increase in the median number of reads mapped against antibiotic resistance genes from V1 to V2 (166,158 versus 352,140 reads, p = 0.
We observed a significant increase of median fecal neopterin levels after IC (V1: 1. 05 ng/g of feces versus V2: 23. 45 ng/g of feces; p = 0. 0002), highlighting the expected inflammatory intestinal status of patients after IC and antibiotic therapy. Levels were significantly decreased and returned to baseline following AFMT (V3: 1. 58 ng/ g of feces; p = 0. 0003 compared to V2). These variations were in line with C-Reactive Protein variations. As a mirror of local immunity, secretory IgA was also measured in feces, and similar trends were observed (Median V1: 1. 21 mg/g of feces; V2: 2. 55 mg/g of feces; V3: 1. 72 mg/g of feces). Altogether, these data clearly point out to the absence of deleterious inflammatory reaction, both locally and systematically, after AFMT. Previous studies have reported that oxidative stress is closely related to the occurrence and development of cancers  18  and is also associated with gut dysbiosis.
This approach is currently being evaluated with FMT capsules for colon delivery in order to ease the administration of the product in a similar setting (Clinicaltrials. gov identifier: NCT04150393). Further clinical investigations will be required to evaluate the beneficial impact of this strategy implemented after each cycle of chemotherapy and HCT conditioning. Overall, AFMT appears to be safe and effective for gut microbiota restoration in patients receiving IC and antibiotic for AML. Besides this particular setting, providing patients with a drug that may modulate inflammation and better potentiate other anti-cancer treatments is of considerable interest.
Methods Study design. ODYSSEE was a phase I/II single-arm, multicentre, prospective, interventional trial in hospitalized patients with AML/ high-risk myelodysplastic syndrome to assess the feasibility and tolerance of AFMT in the setting of IC and antibiotic therapy given during aplasia. All patients were pre-evaluated within clinical practice before the official start of enrollment. All enrolled subjects gave their written informed consent to participate in the study. The study was approved by the ethics committee "Comité de protection des personnes Ile de France V" on April 5th, 2016, was conducted in full compliance with ICMJE guidelines and was registered in ClinicalTrials. gov (Identifier: NCT02928523). While study was submitted for registration on May 26, 2016, before the first patient inclusion on June 2016, there was a delay in the approval during the registration process while some innovative aspects were clarified and the study was finally registered on October 10, 2016.
Patient's vital signs (blood pressure, pulse, temperature, respiratory rate) were monitored during all the time of the transplantation process, until the expulsion of the remaining transplant but at least 2 h after AFMT. Among the 25 treated patients, a major protocol deviation was reported in five: four patients could only receive AFMT after the first consolidation chemotherapy due to AFMT contraindication in two patients (anal fistula (n = 1) and colitis (n = 1)) and for logistical organization in two others. For one patient, the period between V2 and AFMT was 35 days, due to an infectious event requiring prolongation of antibiotics, with a potential impact on the primary endpoint. Twenty patients were thus considered as per protocol. All figures and tables will present the data obtained from these patients, unless specified.
Follow-up. Feces and blood were collected for the same analyses as before, prior to the initiation of consolidation chemotherapy (Visit V3), and at the end of the hospitalization (Visit V4). The quality of life of patients was assessed at each visit (V1 to V4), using an EQ-5D-5L questionnaire (evaluating the mobility, self-care, usual activities, pain/discomfort, anxiety, and depression). Finally, after 6 months (Visit V5) and 1 year (Visit V6), clinical information and safety assessment were recorded (see Fig. 1  for study flow chart). In addition, centers were contacted in September 2019 to collect long-term follow-up data regarding survival or death, including date of relapse, date and causes of death, undertaking or not and date of alloHCT and the occurrence or not of acute and chronic graft versus host disease (GvHD) after alloHCT.
1,500,000 paired-end sequences per sample. Taxonomic profiling was then performed with Kraken v. 0. 10. 5-beta  40 and the RefSeq genomic database (release 84, 2017, http:// www. ncbi. nlm. nih. gov/refseq/). The measure of αand β-diversity indexes was performed in R Statistical Software (R Core Team 2015, version 3. 4. 4, http://www. R-project. org) using vegan v2. 4-2 and phyloseq 1. 19. 1 packages. Gene-based analyses were performed using the Integrated Gene Catalogue (IGC)  41. Finally, antibiotic resistance analyses were performed through gene mapping with Bowtie 2 v2. 3. 0 on MEGARes v1. 0. 1 (https://megares. meglab. org/) database. Clinical outcomes. The co-primary outcomes of the study were to evaluate the efficacy of AFMT in dysbiosis correction and MDRB eradication. The main secondary outcomes were (a) to define a dysbiosis biosignature using combination of biological parameters, (b) to evaluate the effect of dysbiosis correction on patient clinical status, (c) to assess the short and mid-term safety of AFMT in this immunocompromised population and (d) to evaluate the feasibility of the AFMT procedure and acceptability by the patient.
Acknowledgements MaaT Pharma  was the sponsor of this study and in collaboration with the investigators, was responsible for study design, the collection of data and the analysis of data. MaaT Pharma  was not involved in the interpretation of data, writing of the report, and the decision to submit the paper for publication. The corresponding author had full access to all data and had the final responsibility for the decision to submit for publication with the agreement of all other authors. JD would like to acknowledge the suport of the  European Commission  under ERC-2017-AdG n. 788191-Homo. symbiosus. We are grateful to  Prof. Junia V. Melo  ( University of Adelaide, Australia ) for critical reading of this manuscript. Also, we thank  Dr Myriam Labopin  ( Service d'hématologie clinique et de thérapie cellulaire, Hôpital Saint Antoine, APHP, Sorbonne Université, INSERM UMRs 938, Paris, France ) for help with the statistical analyses.
Paulus Mulder ,  Thomas Duflot ,  Nicolas Perzo  and  Jérémy Bellien  for critical commenting on experiments;  Gaëtan Riou  from CyFlow flow cytometry and cell analysis facility platform ( Institute for Research and Innovation in Biomedicine, IRIB)  for his help in performing flow cytometry experiments and analysis;  Manon Lefrançois ,  Florian Vallin  and  Paul Rouault MSc  students for experimental help. We thank the  ENCODE Consortium  and the  Bradley Bernstein, Broad Institute of MIT and Harvard ENCODE production laboratory  for generating the GSE29611 ChIP-seq data sets, and more particularly for generating respectively GSM1003536 and GSM1003564 human CD14+monocytes H3K4me3 and H3K27me3 ChIP-seq data sets.