dataesr/scientific-paragraphs-categorization huggingface dataset:
Prediction of Transcription Units and Detection of Regulatory Genomic Sequences The Rta transcription units encompassing the genes identified as phosphatases using our functional annotation procedure were defined according to DOOR  (Mao et al. , 2009) , a database of computationally predicted operons covering 2072 bacteria genomes. The operon prediction program used to generate this database has been described by  Dam et al. (2007)  and was ranked to be the best among 14 methods by  Brouwer et al. (2008). The prediction accuracy was estimated to be higher than 80% for genomes where only few operons were already known. Putative transcription factor (TF) binding sites were searched for in the non-coding genomic regions located upstream of the Rta phosphatases CDS, or upstream of the first gene of the operons to which they were predicted to belong.
For that purpose, we detected significant similarities between these non-coding genomic sequences and sequence profiles describing the binding specificity of known TFs of E. coli K-12 (86 PSSMs provided by RegulonDB,  Huerta et al. , 1998) , using the program matrixscan available on the RSAT web server  (Turatsinze et al. , 2008). Owing to the AT-richness of the prokaryotic regulatory regions whatever the GC content of the genomes  (Cordero and Hogeweg, 2009) , the large and experimentally validated dataset provided by RegulonDB constituted a reference for the identification of TF binding sites in bacteria. Pairwise hit p-values were estimated according to an organism-specific Markov model of order 1, precalibrated on all the non-coding upstream-gene sequences of Rta and representing their global oligonucleotide composition (i.
Prediction of Protein Subcellular Location and Export Pathway The subcellular locations of Rta phosphatases were predicted from their amino acid sequences using the program PSORTb v3. 0  (Yu et al. , 2010)  with Gram-negative bacteria models. In addition, the presence of N-terminal signal peptides, the position of their cleavage site, and the corresponding export pathway were investigated by PRED-TAT  (Bagos et al. , 2010). Theoretical isoelectric point and molecular weight of the predicted precursor and mature protein forms were computed from their respective The sequence lengths (in amino acids) are given between parentheses. For each profile accession (CDD, version 3. 14), the boundary positions of their hit detected by RPS-Blast on the corresponding reference sequence are indicated between brackets.
Molecular Homology Modeling and Analysis of Protein Surface Properties The protein structures of Rta phosphatases were modeled using the HHpred server (version 5)  (Meier and Söding, 2015). The HMM-HMM similarity search was done against the PDB70 database, as available on the 3rd of January 2015. Models based on optimal multiple templates were automatically built using MODELLER  (Šali and Blundell, 1993). The quality of the models was checked by Verify3D  (Lüthy et al. , 1992). Structures and models were superimposed with Matras  (Kawabata, 2003). The 3D coordinate files of the protein models are provided in Supplementary Data Sheet 1. Electrostatic potential maps of 3D structures and models were computed and drawn using the APBS plugin  (Baker et al. , 2001)  in the PyMOL Molecular Graphics System (version 1.
Genomic Organization, Regulatory Sequences, and Predicted Cellular Location of Rta Phosphatases The phoD gene was located on the direct DNA strand, while the 4 phoX genes were located on the reverse strand (Table  2 ). These 5 genes were distant from each other on the genome, i. e. , there was no joint organization as gene clusters or operons. The phoX2 gene was predicted as part (3 ′ -end) of an operon in the DOOR database  (Mao et al. , 2009) , together with two other genes: from 5 ′ (locus tag Rta_37630) to 3 ′ (Rta_37620), the protein sequences corresponding to these genes were described as (1) uncharacterized (Uniprot accession F5Y2Z8; similar to non-heme di-iron oxygen transport proteins, CDD profile pfam01814) and (2) cytochromes P450-like (Uniprot accession F5Y2Z7), respectively. The 4 other phosphatase-encoding genes were considered as complete transcription units.
Genes are located on direct (D) or reverse (R) DNA strands; the CDS start and end refer to base positions on the direct strand. Operon-included region is indicated by an asterisk (according to the predicted list of operons available in the DOOR database  (Mao et al. , 2009). Transcription factor (TF) names are those used in RegulonDB  (Huerta et al. , 1998) ; Fur, Ferric uptake regulation; PhoB, phosphorus uptake and metabolism regulation; Cra, Catabolite repressor regulator; FhlA, Formate hydrogen lyase activator; FadR, Fatty acid degradation and metabolism regulator. In order to predict the regulatory pathways controlling the expression of phosphatases in Rta, and assess whether they were expressed constitutively or under controlled regulation and in the latest case which environmental parameters may impact their transcriptional regulation, we looked for putative regulatory elements.
Recombinant Expression of Rta Phosphatases in E. coli; Phosphatase and Calcification Activities Recombinant expression was achieved for 3 of the 5 Rta phosphatase genes: phoD, phoX1, and phoX3. E. coli phoA was also cloned in the same vector and tested for expression as a control. On SDS-PAGE, an intense band was systematically observed for each transformed strain in the "IPTG" condition that was absent from the "no-IPTG" condition (Supplementary Image 2). These proteins had apparent molecular masses close to those predicted by in silico analyses for the different phosphatases. For E. coli phoA, the overexpression of PhoA was confirmed using Western blot with a commercial anti E. coli alkaline phosphatase antibody (data not shown). Two proteins were clearly visible for PhoA after an induction time of 4 h, corresponding to the expected molecular weights of the precursor and mature forms of this protein.
These data support the existence of a relationship between the availability of Ca and P in the environment and the relative abundance of the phosphatase gene families. However, the taxonomic scope of studies on ocean surface waters was limited by the numerical domination of microbial phototrophs, in particular Cyanobacteria, and heterotrophic Alpha-and Gamma-proteobacteria in these environments. Here, in order to limit the bias due to a limited taxonomic sampling, we annotated the phosphatase genes in the large amount of available bacterial complete genomes. This dataset comprised 3630 genomes from 33 phyla. Eight families, either alkaline or acid phosphatases, were annotated according to the procedure previously applied to Rta genome. Compared to the statistical trends that emerged from the analysis of bacterial genomes, the functional potential of the Rta genome for phosphatases exhibited atypical features: (i) among the 12 bacterial genomes with at least 4 PhoX genes, Rta was the only member of Proteobacteria, a phylum which was represented by 1794 genomes; (ii) while 62% of the bacterial genomes had at least one gene of alkaline phosphatase (71% of the 261 Betaproteobacteria genomes), only 4% (1% for Betaproteobacteria) had at least 5 genes, similarly as Rta; (iii) although it was absent in Rta, the PhoA family was the most widely represented with 35% of the bacterial genomes exhibiting at least one gene of this family.
It was less than 25% for each other family, either alkaline or acid, e. g. , 22 and 17% in the case of PhoX and PhoD, respectively. Among the genomic features of bacteria, the linear correlation between the genome size and the global number of genes (abundance) was well known  (Hou and Lin, 2009 ) (Supplementary Image 3; R 2 = 0. 97). Though the abundance of phosphatase genes was related to the genome size in our dataset (Kruskal-Wallis test, p < 2. 2e-16), Rta represented the bacterial genome with the highest density of PhoX genes (Supplementary Image 4). In addition, only 0. 9% of the bacterial genomes had a higher density of alkaline phosphatase genes than Rta. The variable physicochemical properties of Rta phosphatases suggested a functional diversification of the assimilation of organic P substrates, driven by P-depleted conditions.
Due to the limited power of our association study and the potentially high false negative rate due to population structure correction, and because we aimed to test any major emerging candidate experimentally, we selected a relatively non-conservative 10% false discovery rate (FDR) as our threshold for significant association (we thus expect that 10% of the significant SNPs are false positives). Using this criterion, we identified two chromosomal regions associated with root length in -Zn conditions. On chromosome 2, the significant peak (P-value = 3. 27 Ã 10 -7 ; FDR % 7%) was located in a region with a cluster of similar genes encoding a Cysteine/Histidine-rich C1 domain family (At2g21810). It was detected on the last day of the time course (day 7). These proteins require Zn ions for their function  [25]  (pfam, PF00130).
In particular, our study revealed a significant association between the AZI1 locus and primary root length in Arabidopsis accessions grown in -Zn condition, as well as an intriguing AZI1 dependent interaction between Zn levels and the AzA pathway. One interesting question is whether the AZI1 function that relates to abiotic factors is specific to Zn or not. While there has been one report in which it was shown that ectopic expression of AZI1 improved Col-0 seed germination under high salinity stress condition and azi1 mutants were overly sensitive  [14] , many leads point in the direction of a largely Zn specific function: Significant associations close to the AZI1 locus were neither found in the GWAS for accessions that were grown at the same time on +Zn (S5 Fig) , nor in other published root GWAS datasets for growth on MS medium  [40] , under different nitrogen conditions  [41] , under NaCl stress  [42] , and under Fe deficiency  [39].
Rice seedlings were grown in a growth chamber under the following environmental conditions: light/dark cycle of 14/10 h, temperature of 28/25 ˚C, and RH of 80%. GWAS root trait quantification was conducted using the BRAT software  [40]. Root length in assays involving mutant and transgenic lines, as well as rice plants was measured using Ima-geJ software, version 2. 0. 0 (http://rsb. info. nih. gov/ij/). Statistical differences between genotypes were calculated using t-test analyses and ANOVA with subsequent post hoc tests using Graphpad Prism (GraphPad Software Inc. , San Diego, CA, USA) or Microsoft Excel (Microsoft, USA).
GWA mapping For GWAS, mean total root length values of 231 natural accessions were used (S1 and S2 Tables). The GWA analysis was performed in the GWAPP web interface using the mixed model algorithm (AMM) that accounts for population structure  [23]  and using the SNP data from the RegMap panel  [61, 62] [19]. Only SNPs with minor allele counts greater or equal to 10 were taken into account. The significance of SNP associations was determined at 10% FDR threshold computed by the Benjamini-Hochberg-Yekutieli method to correct for multiple testing  [24].
Variance component analysis Using a Multi-trait mixed model (  [63] ) we decomposed the variance of the root length response under plus/minus Zn Conditions for each day into a genetic term, the G X E interaction and an environmental term. The respective variance parameters were estimated in a null model without single marker effects and a global Kinship estimated from all markers. The analysis has been performed in R (R Development Core Team 2008). The respective R scripts are available at https://github. com/arthurkorte/MTMM.
Acknowledgments The authors are thankful to  Prof. Peter Urwin  ( University of Leeds, UK ) for providing seeds of azi1 mutant and  Dr. Youssef Belkhadir ,  Dr. Hironaka Tsukagoshi ,  Dr. Zaigham Shahzad ,  Dr. Fan Lin  and  Dr Benoit Lacombe  for helpful discussions and suggestions. We are also grateful to  Bonnie Wohlrab ,  Christian Go  ¨schl and  Mushtak Kisko  for technical assistance.
This work was funded by the  "Institut National de la Recherche Agronomique -Montpellier -France" INRA (HR) ,  Region Languedoc-Roussillon: Chercheurd'Avenir/Projet Cofinancepar le Fonds Europeen de Developpement Regional (HR) , and supported by funds from the  Austrian Academy of Science  through the  Gregor Mendel Institute (GMI) , the pathway in the root, which is zinc-dependant. basis to design new strategies for improvement agricultural crop species able to modulate growth and defence. Salk Institute for Biological Studies  and an  Austrian Science Fund (FWF)  stand-alone project ( P27163-B22 ) (WB). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
1b ). At each site, between six and ten cores were drilled. All samples were magnetically oriented but sun orientation was preferably used whenever possible. We obtained new high-quality directions that improve the statistical coverage for paleosecular variation in the area. The compilation of former paleomagnetic studies 13 , added to new K-Ar radiometric ages  19, 20  provide an integrated paleomagnetic dataset for the eastern Caribbean that constrains the time-averaged field in this area.
Results Paleomagnetic directions. The Characteristic Remanent Magnetization (ChRM) was determined from both alternating field (a. f. ) and thermal stepwise demagnetization diagrams using principal component analysis  22, 23  and the Paleomac software  24. Typical demagnetization diagrams for normal and reverse polarity samples are shown in Fig. 2. Most samples were totally demagnetized (i. e. with more than 95% NRM lost) after peak a. f. 70 mT or thermal demagnetization to 580 °C. In a few cases, a small residual NRM beyond 580 °C required additional temperature steps up to 610 °C. A tiny portion of Ti-hematite could be responsible for unblocking   65. Regional setting of Guadeloupe archipelago with the main faults affecting the area  66. Bathymetry image is from GeoMapApp (http://www. geomapapp.
org) using bathymetry data of Smith and Sandwell  67. Black square: location of Basse-Terre Island. (b) Shaded Digital Elevation Model (illumination from NW, data from the Institut Géographique National, map generated with ArcGis 10. 1 software) of Basse-Terre Island, with the sites of samples analyzed in this study. K-Ar ages of the volcanic massifs compiled in Ricci et al. 20. temperatures above 580 °C and stronger resistance to a. f. demagnetization. Forty per cent of samples carried a secondary magnetization component that was removed by a 15 mT a. f. or after heating at 300 °C. The characteristic direction of remanence was very well defined for ninety five percent (95%) of samples with demagnetization diagrams decreasing linearly towards the origin. The remaining 5% of the samples exhibited an erratic behavior and were therefore rejected.
4°) obtained for the thirteen lava flows of the present study is in poorer agreement with the expected geocentric axial dipole field direction and suggests that a larger flow number is required for adequate calculation of the time-averaged field, as previously mentioned by Tanty et al. 21. In order to integrate the Basse-Terre Island data into a more regional perspective we added the paleomagnetic directions of the individually dated flows from the nearby Martinique Island  21. We restricted this regional dataset to the Brunhes chron (<0. 78 Ma) that contains the highest measurement density with 46 independent directions. The results are presented in Fig. 8  in terms of VGP latitude and inclination anomaly (the inclination deviation from the geocentric axial dipole inclination at the site) as a function of time.
The Pringle Falls event has been more recently observed in sediments from site 919 in the northern Atlantic Ocean  52. Based on anomalous inclination values, several excursions have been proposed within the 205-225 ka interval that were interpreted as a 20 kyr long period of directional instability during the low paleointensity interval documented in the East Pacific Rise sea floor magnetization  53  as well as in the Sint-2000 and Piso-1500  54  composite curves of relative paleointensity  55. In the present dataset, the 320 ka old large directional changes were only detected at Martinique. Excursion 9b discussed by Lund et al. 56  has a similar age, but there is no consensus about its existence, despite one transitional flow found in Argentina (Meseta del Lago Buenos Aires) and dated by Brown et al.
14  to check for consistency of geochronological data with flow polarity. However, the small number of samples as well as the absence of detailed rock magnetic investigation did not meet the requirements for a reliable paleosecular variation study. In this study, we analyzed a total of 118 samples using both alternating fields (a. f. ) and thermal stepwise demagnetization techniques in the magnetic shielded room of the Institut de Physique du Globe de Paris. Natural Remanent Magnetization was measured using Agico JR-5 and JR-6 spinner magnetometers. Eleven a. f. demagnetization steps were systematically performed at 04, 08, 12, 16, 20, 25, 30, 40, 50, 60 and 70 mT. Thermal demagnetization was carried out at 14 temperature steps (120, 180, 240, 280, 320, 360, 400, 440, 480, 500, 520, 540, 560 and 580 °C) and two additional heating steps (595 and 610 °C) were used for eleven samples.
Measurements of low field thermomagnetic susceptibility (κ) were conducted on 1 cm 3 sample powders from each flow using an Agico KLY-3 equipped with a CS-3 furnace. Heating-cooling runs were performed in air atmosphere from 20 °C to 630 °C to detect mineralogical changes. Hysteresis loops and high-resolution acquisition curves of Isothermal Remanent Magnetization (IRM) were conducted for one representative sample from each flow using an Alternating Gradient Force Magnetometer (AGFM, Princeton Measurements Corporation) in a 1 Tesla maximum field. The IRM acquisition curves were unmixed using the CLG function  28  in order to isolate magnetic components with different coercivities. Finally, microscopic observation and semi-quantitative chemical data were collected on thin sections from sites GU41, GU44, GU48, GU52 and GU53 (Fig.
Conclusion The paleomagnetic directional dataset for Basse-Terre Island (Guadeloupe, F. W. I) now includes 44 distinct directions from lava flows covering the last 2 Myr, of which 39 were dated by K-Ar technique. The overall mean direction (D = -1. 2° and I = 31. 4°) is indistinguishable from that of the geocentric axial dipole (D = 0°; I = 29. 8°). The VGPs dispersion (Sb) of 10. 2° and 9. 6°, for the all Basse-Terre flows and only those restricted to the Brunhes chron, respectively, is lower than in PSV models (e. g. TK03  61  , C1  8  ). Nevertheless, the significant number of data (N = 39 and N = 32, for all flows and Brunhes chron only, respectively), allows us to consider these values as a reference for Guadeloupe Island. In a regional perspective, the PSV records from Guadeloupe and Martinique islands indicate an episode of high amplitude secular variation at around 205 ka that we link to the extended period of low dipole intensity during the 205-225 ka interval  49  with one or more excursions  52  including the Pringle Falls event  49.
Acknowledgements We are pleased to acknowledge  Xavier Quidelleur  ( GEOPS/Paris-Sud ) for the help with sampling and preliminary analyses. We thank  Maxime Legoff  ( IPGP ) for Triaxe analyses and  Stephan Borzenstein  ( IPGP ) for help with SEM observations. The research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  (FP7/2007-2013)/ ERC  advanced grant agreement GA  339899. This is IPGP contribution # 3948.
H. Chan School of Public Health (CR-16330-05). The two Cambodian samples (KH01, KH02) are part of a study registered with ClinicalTrials. gov, number NCT00341003. The use of the Kenya parasite isolate (KE01) was approved under SSC 1131 that was reviewed and approved by the KEMRI Ethics Review Committee and University of Oxford Tropical Research Ethics Committee. The Gabon (GA01) sample was approved by the local ethics committee in Lambaréné, Gabon: CER-MEL (Centre de Recherche Médicale de Lambaréné), Lambaréné, Gabon  3. The isolates Sudan (SD01), Togo (TG01) and Congo (CD01) were culture adapted from diagnostic specimens submitted for routine malaria diagnosis at the University of Tübingen and therefore did not require separate ethical approval. The isolates 3D7, IT, Dd2, HB3, Gb4 and 7G8 are established laboratory strains, and do not require ethical approval.
After resolving overlaps, contigs were ordered using ABACAS2  13  (parameter 1 kb hits, >98% identity, version 2) against the Pf3D7 reference version 3 (from GeneDB  14  ), excluding the sequences where no one-to-one orthologues to other Plasmodium species exist. The apicoplast and the mitochondria were circularized with Circlator  15  (default settings, version 0. 12. 0). Single-base discrepancies and insertions or deletions (indels) up to 3 bp were corrected with iCORN2  16  version 0. 95, with three iterations using the 250 bp Illumina reads. All of the steps after the HGAP assembly were performed using a bash script (IPA v1; https://github. com/ThomasDOtto/ IPA). The Sudan sample (PfSD01) was also assembled with Canu 17 (version 1. 6; parameters: genomeSize 24m errorRate 0. 15).
Removal of contamination To eliminate possible contamination, the GC content for each contig not aligned to a reference chromosome was calculated. Next the number of hits to P. falciparum genes was counted on each contig. If a contig had no hits to a gene, a megaBLAST search (parameter: -F F E-value 1e-10, version 2. 2. 25) against the Pf3D7 reference and the human genome was performed. If a contig had no hits against P. falciparum genes or the human genome, it was BLAST-searched against the non-redundant database at NCBI and excluded if its top Blast hit was to another organism.
9. 1). To compute the global distribution of a novel gene that was absent in Pf3D7, we used the Pf3K dataset (ftp://ngs. sanger. ac. uk/production/pf3k/release_5/). All non-mapping reads were extracted with samtools view -f 12 (version 0. 1. 19-44428cd) from the downloaded bam files. The reads were mapped with BWA-MEM  29  (version 0. 7. 12-r1039) against the nucleotide sequence of PfIT_110029200 (one allele of the novel gene). If 10 reads from a Pf3K sample mapped to that gene it was assumed to be present. The novel gene was further analysed using Pfam  30  and I-Tasser 31 using the webpages from December 2017, with default settings.
Definition of the core genome To define core conserved regions for each chromosome, the consensus sequences for each isolate were mapped with BWA-MEM (as above) against the corresponding Pf3D7 chromosome. The outer limits of the core for each chromosome were defined as the most telomere-proximal position covered by the majority (8 out of 15) of these aligned sequences. Regions of the subtelomeres that bound to heterochromatin protein 1 were obtained from the GEO repository (accession: GSE102695  33  ). To generate the plots of Figure  3B , the above BWA-MEM alignments were used. The leftmost or rightmost position when a mapping was clipped (soft or hard) was used as the point at which synteny was lost. Where there was no clipping at the end of an alignment, (the assembly did not reach into the subtelomere), that isolate at that chromosome end was excluded.
Acknowledgments We would like to thank the patients who contributed samples and the health workers who assisted with the sample collections. We would also like to thank staff from the  Illumina Bespoke Sequencing Team  at the  Wellcome Sanger Institute  for their contribution,  Amanda Lukens  for providing the Dd2 sample,  Eleanor Drury  for DNA extraction and  Alister Craig  for his analysis contribution. We thank the  Pf3k consortium , particularly  Dan Neafsey  and  Dominic Kwiatkowski  for discussions. This paper is published with permission from the Director of  Kenya Medical Research Institute (KEMRI).