dataesr/scientific-paragraphs-categorization huggingface dataset:
i, Assessing genotype calling across souporcell, vireo, and sc_split. We plot true positive versus false positive genotype calls while sweeping the threshold on genotype likelihood. These are compared to a truth set obtained from variant calls on the WGS data j, Each method's genotype calls versus the true genotype of each tool for a synthetic mixture of five HipSci lines with 6% doublets and 10% ambient RNA with a 0. 95 probability threshold for each tool. The facets are the genotype calls made by each tool and the x-axis shows the correct assignments according to the WGS data. We observe that a major error mode for both vireo and sc_split compared to souporcell is that homozygous reference variants are mis-called as heterozygous because ambient RNA is not accounted for in these methods. Plasmodium falciparum in vitro culturing and single cell analysis P.
falciparum strains were maintained in O+ blood in RPMI 1640 culture medium (GIBCO) supplemented with 25 mM HEPES (SIGMA), 10 mM D-Glucose (SIGMA), 50 mg/L hypoxanthine (SIGMA), and 10% human serum in a gas mix containing 5% O 2 , 5% CO 2 and 90% N 2. Human O+ erythrocytes were obtained from NHS Blood and Transplant, Cambridge, UK. All samples were anonymous. Plasmodium culture using erythrocytes and serum from human donors was approved by the NHS Cambridgeshire 4 Research Ethics Committee (REC reference 15/EE/0253) and the Wellcome Sanger Institute Human Materials and Data Management Committee. All P. falciparum clonal strains were obtained from MR4 (BEI resources): 3D7-HT-GFP (MRA-1029), 7G8 (MRA-152), GB4 (MRA-925), SenP011. 02 (MRA-1176), SenTh015. 04 (MRA-1181) and SenTh028. 04 (MRA-1184).
The Wellcome Sanger Institute is funded by the Wellcome Trust (grant 206194/Z/17/Z), which supports MKNL and MH. This work was supported by an MRC Career Development Award (G1100339) to MKNL. We would like to acknowledge the Wellcome Trust Sanger Institute as the source of the human induced pluripotent cell lines that were generated under the Human Induced Pluripotent Stem Cell Initiative funded by a grant from the Wellcome Trust and Medical Research Council, supported by the Wellcome Trust (WT098051) and the NIHR/Wellcome Trust Clinical Research Facility, and acknowledges Life Science Technologies Corporation as the provider of Cytotune (HipSci. org). The Cardiovascular Epidemiology Unit is supported by core funding from the UK Medical Research Council (MR/L003120/1), the British Heart Foundation (RG/13/13/30194; RG/18/13/33946) and the National Institute for Health Research [Cambridge Biomedical Research Centre at the Cambridge University Hospital's NHS Foundation Trust].
Acknowledgments: We acknowledge the  Wellcome Sanger Institute's DNA Pipelines  for construction of the 10x sequencing libraries. We thank  Allan Muhwezi  and  Andrew Russell  for assistance with parasite culture and 10x Single-cell 3' RNA-seq respectively. In addition, we would like to thank  Matthew Young  for useful conversations about ambient RNA,  Mirjana Efremova  for providing information about the maternal/fetal data, and  Katie Gray  for assistance in interpreting the previously unannotated cluster. Author contributions: MKNL and MH conceived of the project. HH developed the methods, software, ran the tests and simulations, and created the figures. MKNL, MH, and HH wrote the manuscript with methods contributions from AT, AK, and MI. AT conducted the Plasmodium wet lab experiments.
Data Availability Maternal Fetal data is available at https://www. ebi. ac. uk/arrayexpress/experiments/E-MTAB-6701/ with accession numbers FCA7474063-FCA7474065. This data is shown in Fig 3, Supp Fig 2. HipSci cell line data will be made available on GEO upon acceptance. This data is shown in Fig 2, Supp Fig 1. Plasmodium data will be made available on GEO upon acceptance. This data is shown in Fig 3, Supp Fig 3.
Funding: The Wellcome Sanger Institute is funded by the Wellcome Trust (grant 206194/Z/17/Z), which supports MKNL and MH. This work was supported by an MRC Career Development Award (G1100339) to MKNL. We would like to acknowledge the Wellcome Trust Sanger Institute as the source of the human induced pluripotent cell lines that were generated under the Human Induced Pluripotent Stem Cell Initiative funded by a grant from the Wellcome Trust and Medical Research Council, supported by the Wellcome Trust (WT098051) and the NIHR/Wellcome Trust Clinical Research Facility, and acknowledges Life Science Technologies Corporation as the provider of Cytotune (HipSci. org). The Cardiovascular Epidemiology Unit is supported by core funding from the UK Medical Research Council (MR/L003120/1), the British Heart Foundation (RG/13/13/30194; RG/18/13/33946) and the National Institute for Health Research [Cambridge Biomedical Research Centre at the Cambridge University Hospital's NHS Foundation Trust].
1. Adaptive integration of life history and behaviour is expected to result in variation in the pace-of-life. Previous work focused on whether 'risky' phenotypes live fast but die young, but reported conflicting support. We posit that individuals exhibiting risky phenotypes may alternatively invest heavily in early-life reproduction but consequently suffer greater reproductive senescence. 2. We used a 7-year longitudinal dataset with >1,200 breeding records of >800 female great tits assayed annually for exploratory behaviour to test whether withinindividual age dependency of reproduction varied with exploratory behaviour. We controlled for biasing effects of selective (dis)appearance and within-individual behavioural plasticity. 3. Slower and faster explorers produced moderate-sized clutches when young; faster explorers subsequently showed an increase in clutch size that diminished with age (with moderate support for declines when old), whereas slower explorers produced moderate-sized clutches throughout their lives.
We used a descriptive approach, acknowledging that experimental studies will be required to test whether personality-related allocation to early-life reproduction represents an investment causally affecting reproduction later in life. We used a longitudinal dataset with 1,209 breeding records of 813 females great tits assayed annually during the reproductive phase for their activity in a small cage  (Stuber et al. , 2013). Our previous studies demonstrated that activity represents a risky behaviour, implying that it allows for an appropriate test of theory (sensu  Carter, Feeney, Marshall, Cowlishaw, & Heinsohn, 2013; Houle, Pelabon, Wagner, & Hansen, 2011). Active great tits-called 'faster' explorers throughout-behave more boldly when confronted with risk of predation  (Stuber et al. , 2013)  and respond more aggressively to territorial intrusions than 'slower' (less active) explorers  (Moiron, Araya-Ajoy, Mathot, Mouchet, & Dingemanse, 2019).
| Modelling age effects Following  Bouwhuis et al. (2009) , statistical analyses fitted linear and quadratic age to simultaneously model pre-peak improvements and post-peak declines in reproduction. All analyses also fitted 'first observed age' and 'last observed age' of reproduction to control, respectively, for selective appearance and disappearance from the dataset of birds differing in average annual reproductive performance; this avoids biases in estimates of within-individual age effects (van de  Pol & Verhulst, 2006). First observed age of reproduction, determined using breeding season and roosting captures (see above), was 1 (n = 598 females; 74%), 2 (n = 190; 24%), 3 (n = 13; 2%), 4 (n = 3; <1%) or 5 (n = 1; <1%). Fewer than 2% of all females (n = 17 of 813 individuals) were (older than) 3 years old at first observed age of reproduction; we therefore pragmatically fitted first observed age as a two-level factor in our analyses (recruited as 1 year old vs.
M. M. was funded by a Marie Skłodowska-Curie Individual Fellowship (PLASTIC TERN, Grant Agreement Number 793550). We thank past members of the Evolutionary Ecology of Variation group (Max Planck Institute for Ornithology) and past and current members of the Behavioural Ecology (LMU) group, Alexander Hutfluss, and all field assistants and students that helped collecting the data. We also thank members of the Evolutionary Ecology of Variation Group at North Dakota University, Pat Monaghan, Samantha Patrick, Neil Metcalfe, John Quinn and two anonymous reviewers for input. All procedures complied with guidelines from the District Government of Upper Bavaria (Regierung von Oberbayern) for Animal Care. AUTH O R S ' CO NTR I B UTI O N SThe study was conceived by N. J. D. , and developed and operationalized with input from all authors.
For pigment analysis and electron microscopy, RCC2288 was grown at 7ºC under continuous light at 100 µE intensity in L1 medium prepared using autoclaved seawater from offshore Mediterranean Sea water diluted 10% with MilliQ water and filtered prior to use through 0. 22 μm filters. Holotype specimens were deposited in O (Natural History Museum, University of Oslo), herbarium acronym follows  Thiers (2019). Sequences. Nuclear 18S rRNA and the Internal Transcribed Spacers (ITS) 1 and 2, as well as the 5. 8S rRNA gene were retrieved from GenBank for strains RCC2288, RCC2497 and RCC2285  (Balzano et al. 2012). For RCC5418 and RCC5150 (M. antarctica), cells were harvested in exponential growth phase and concentrated by centrifugation. Total nucleic acids were extracted using the Nucleospin Plant II kit (Macherey-Nagel, Düren, DE) following the manufacturer's instructions.
The nearly full length nuclear 18S rRNA gene (only RCC5418) and the region containing the Internal Transcribed Spacers (ITS) 1 and 2, as well as the 5. 8S rRNA gene were obtained by PCR amplification using universal primers (Supplementary Table  1 ). PCR products were directly sequenced at the Macrogen Company (Korea) and sequences have been deposited to Genbank under accession numbers MH516003, MH516002 and MH542162. ITS2 secondary structure. The ITS2 secondary structure from the strains listed in Table  1  was predicted using the Mfold web interface  (Zuker 2003)  under the default options with the folding temperature fixed at 37ºC, resulting in multiple alternative folding patterns per sequence. The preliminary structure for each sequence was chosen based on similarities found among the other structures proposed for Mamiellophyceae  (Marin and Melkonian 2010, Simon et al.
org/10. 6084/m9. figshare. 7472153. v1. Phylogenetic analyses. Nuclear 18S rRNA sequences belonging to members of Mamiellophyceae were retrieved from GenBank (http://www. ncbi. nlm. nih. gov/). Two environmental sequences (similar to strain sequences) were included in addition to the sequences obtained from the cultures. Sequences were also obtained for the ITS2 region located between the 5S and 23S rRNA genes. However, no environmental sequences were available to be included in the 18S/ITS phylogenetic analyses. Twenty-seven nuclear 18S rRNA and fourteen ITS2 sequences were aligned with MAFFT using the E-INS-i and G-INS-i algorithms respectively  (Katoh and Toh 2008). Alignments were visualized and manually edited using Geneious 10. 2. 5  (Kearse et al. 2012 ). The ITS2 alignment was further edited on the basis of conserved secondary structures (see above).
Mantoniella baffinensis Etymology: Named for its geographical provenance. Phylogeny and ITS signatures. The phylogenetic tree based on nearly full-length nuclear 18S rRNA sequences obtained from the novel polar strains RCC2288, RCC2285, RCC2497 and RCC5418 (Table  1 ), and environmental sequences retrieved from GenBank indicated that these strains belong to the family Mamiellaceae (Supplementary Figure  3 ). The analysis also recovered the major genera within Mamiellales: Bathycoccus, Ostreococcus, Micromonas, Mantoniella and Mamiella  (Marin and Melkonian 2010). Dolichomastigales and Monomastigales were the basal orders in Mamiellophyceae with Monomastix opisthostigma type species used as an outgroup. Strains RCC2485, RCC2288 and RCC2497 isolated during the MALINA cruise in the Beaufort Sea and strain RCC5418 isolated from Baffin Bay during the Green Edge project Ice Camp formed a well-supported clade together with two environmental sequences (clone MALINA St320 3m Nano ES069 D8 and clone 4-E5), which also originated from Arctic Ocean samples.
Two unknown carotenoids were detected in RC2288, the first one having adsorption peaks at 412, 436 and 464 nm, and the second one at 452 nm (Supplementary Table  5 ). These were relatively minor components comprising 2. 7% and 1. 5% of total carotenoids, respectively and may represent carotenoids unique to M. beaufortii. Environmental distribution. In order to obtain information on the distribution of these two new species, we searched by BLAST both environmental GenBank sequences and published 18S V4 and V9 metabarcode data sets (Supplementary Table  2 ). This allowed the retrieval of a few 18S rRNA sequences with higher than 98% similarity to the gene of RCC2288. Alignment of these sequences with other Mamiellophyceae sequences revealed diagnostic positions in both the V4 and V9 hypervariable regions permitting M.
Flagella with hexaradial oval scales composed of six spokes increasing in number towards the periphery. Six or more concentric ribs divide the scale into segments. Combined nucleotide sequences of the 18S rRNA (JN934679) and ITS2 rRNA (JQ413369) are species specific. Holotype: Accession number O-A10010, plastic embedded specimen, 14 July 2009, from surface water, MALINA cruise leg 1b. Figure 4 shows cells from the embedding. Culture deposited in The Roscoff Culture Collection as RCC2288.
Acknowledgments We thank  Adam Monier ,  Katja Metfies ,  Estelle Kilias  and  Wei Luo  for communicating raw metabarcoding data and  Sophie Le Panse  and  Antje Hofgaard  for assistance with electron microscopy. We acknowledge the support of the BioPIC flow cytometry and microscopy 22 platform of the  Oceanological Observatory of Banyuls  and of the ABIMS bioinformatics platform at the  Roscoff Biological Station.
Batholith emplacements within a continental margin may bear witness of a magmatic input lasting for several million years. Consequently, the geochemical signatures of such sections are complex, and their understanding in terms of petrological processes, is crucial. The Arequipa section of the Coastal Batholith of Southern Peru was discontinuously constructed during several periods of magmatic activity, from the Jurassic to the Paleocene. Thermobarometric data on amphiboles indicates two main levels of emplacement at the batholith scale, the deepest between 5 and 7 km in depth and the second around 3. 5 km. The present day outcropping of these different units at the same elevation argue for a large vertical movement along the Lluclla Fault System between 76 and 68 Ma. Both major/trace element contents and Nd-Sr isotopes show a large variability that is not random.
(ii) The plutonic rocks are partly hosted by a thick Precambrian basement  (Shackleton et al. , 1979). It is also an area allowing the study of a long-lived arc history, and the interaction of arc magmas with an old basement. Moreover, the batholith of Arequipa represents a strong economic interest as it hosts an open-pit of copper and molybdenum mining complex (Cerro Verde Mine). To document the geochemical evolution of this magmatic arc, we analysed major and traces elements (100 samples) and Sr and Nd isotopes (92 samples) were analyzed. We combined these data with ages obtained on the same sample set by in-situ U-Pb zircon method  (Demouy et al. , 2012). In the present study, we propose that the combination of both geochronological The Costal Batholith of Peru is made up of more than 1000 plutons, extending over a 1600 km-long and 60 km-wide array, 150-200 km away from the present-day trench  (Pankhurst et al.
AMPHIBOLE THERMOBAROMETRY We analyzed the amphibole grains of 16 samples from: basement (n: 1), Linga unit (n: 5), Tiabaya unit (n: 5) and Yarabamba unit (n: 1). The data are listed in Supplement B and plotted in Figure  3a  and b and in figure  4  for P/T estimates. The range of temperature calculated is 904 to 662 C°, and the corresponding range of pressure is 3. 3 to 0. 4 kbar (Figure  4 ). The pressures correspond to upper crustal emplacement conditions (up to 13 km), and temperatures are consistent with those indicated in the literature for calk-alkaline magmas  (Ridolfi and Renzulli, 2012). We observe both inter-and intra-plutonic units variations. In Jurassic plutons, amphiboles indicate a 901-692˚C crystallization temperatures range for two different range of pressure: 1. 9-1. 0 kbar for the cumulative 09SD226 rock and 1.
(iii) a high range (P : 1. 2-4. 5 kbar) corresponding to a mafic enclave in Tiabaya NW unit and the basement sample. The major and trace element data is given in Supplement C. TAS diagram shows that the data are in good accordance with the petrographic description (Figure  5a ). As a whole, samples from various periods of activity define trends that partly overlap themselves, fitting the calkalkaline trend (Figure  5b ). The six most mafic rocks (Gabbro & Diorite unit) that plot in the tholeiitic area are cumulative rocks, this explains their higher Fe content regarding the other samples. The A/CNK and A/NK molar ratios of the samples are negatively correlated, defining a large trend from the mafic to the felsic rocks (Figure  5c ). Most of the sample set plot in the metaluminous area, and only the most evolved samples from the Jurassic rock set (quartz-diorites) and the Cretaceous granites display peraluminous affinities.
Sr and Nd isotopic data Whole rock Sr and Nd isotopic data are reported in Supplement D along with Rb, Sr, Sm and Nd concentrations. The 87 Sr/ 86 Srm range is large with values comprised between 0. 70528 and 0. 71788, as illustrated in the Rb-Sr isochron diagram (Figure  7 ). This figure highlights two different set of samples: (i) the first set is made of samples characterized by a narrow range of 87 Rb/ 86 Src ratio (0. 14-1. 18) for a large range of 87 Sr/ 86 Srm ratio (0. 70545-0. 71279), with a scattered repartition. This domain includes all of the Jurassic samples (n: 20), the Cretaceous samples of the Tiabaya NW unit (n: 7), and several samples of the Yarabamba unit (n: 5). (ii) the second set contains According to field, geochronological and geochemical data, all samples that fall along the calculated errorchrons are age-consistent (Figure  7 ).
According to these results, we have performed age corrections for the measured samples. Two scenarios have been investigated: (i) samples that are falling on a single errorchron should have the same initial isotopic ratio. (ii) samples, which have been dated by U/Pb method should be corrected from their own ages, and for the other ones we use estimated ages (both errochrons or regional ages). We have decided to use option (ii) because option (i) is not applicable to Sm/Nd isotopic system and, for example, some of Maastrichtian-Paleocene samples that fall on the estimated errochron gave different U/Pb ages. Following this, initial isotopic ratios ranges are 0. 70428 to 0. 71095 for 87 Sr/ 86 Sri and 0. 51202 to 0. 51253 for 143 Nd/ 144 Ndi (εNd from -10. 4 to +1. 71) for the whole dataset. They are reported in figure  9.
Nevertheless, details on the functioning of the main accident affecting the batholith (Lluclla Fault System in particular) still remain a matter of debate. The movements linked to the faults have caused vertical displacements of the plutonic units that need to be quantified  (Demouy et al. , 2012). The plutonic unit that currently crops out at the surface might have crystallized at different crustal depths, and granitoids barometry can play a critical role in constraining tectonic history  (Smith et al. , 1998). In the Arequipa batholith, the barometric data suggest two main levels of plutonic magma emplacement: a shallowest level (P: 0. 4-1. 6 kbar) for the Yarabamba, Linga and the Gabbros & Diorites units (apart from cumulate 09SD221), and a deepest level (P: 1. 0-1. 9 kbar) for the Tiabaya unit and the cumulative 09SD221 G&D sample.
1 to 1. 6 kbar. Following the estimation from the Linga unit, this indicates an emplacement level between 5-7 km. Starting at 69 Ma, the emplacement of the plutonic rocks occurred at the same level (Linga unit level), north and south of the Lluclla Fault System. This observation suggests that the northeast part of the batholith, that is the footwall of the Lluclla normal fault, was exhumed with a 1. 5 to 3. 5 km vertical movement in less than 10 Ma (between 76 and 68 Ma). The growth of the Coastal Batholith could be responsible of these extensional movements, which has to occur in a convergent geodynamic context. The emplacement of the Yarabamba unit clearly postdates the activity of the Lluclla Fault System at 66 Ma. • Within the whole dataset, the Jurassic rocks display the largest 87 Sr/ 86 Sri and εNd ranges.
Data exploration Previous work on the Southern Peruvian Coastal Batholith proposed a two-step AFC model involving first a lower Precambrian crust and then a middle upper Precambrian crust -to explain the geochemical and isotopic diversity of the different plutonic rocks  (Boily et al. , 1989). Our dataset is clearly not consistent with an AFC model, as explained before. Moreover, regarding isotopes, several samples should have undergone excessive amount of combined assimilation and fractionation to explain their enriched signatures. This is inconsistent with their mafic compositions. In order to assess the questions listed before we have used Rb-Sr plots, in which we have reported the sample signatures (Figure  7 ). This approach allows us to draw some global sketches and isolate groups with specific elemental Rb/Sr ratios and Sr isotopic characteristics.
They are listed hereafter: data isochrones calculated from these ages. We observe that the distribution of the MP-group dataset fits with the domain defined by the calculated isochrones. This suggests that this trend corresponds to an errorchron and not to a mixing-line. The initial 87 Sr/ 86 Sr ratio indicated by the errochron (or whole rock isochron) is 0. 705364 ± 0. 000081. • The Cretaceous (K) group includes the Linga -SJK2 (n: 3) and OPK samples (n: 8). Each dataset plots on a distinct trend. As for the MP-group, we calculated isochrones from the Cretaceous U-Pb ages of the Linga unit. The different trends are consistent with the calculated isochrones, and we consider them as errorchrons. Indeed, the two groups are consistent according to the field, geochemical and petrological observations.
Solid Earth Discuss. , https://doi. org/10. 5194/se-2019-43 Manuscript under review for journal Solid Earth Discussion started: 27 March 2019 c Author(s) 2019. CC BY 4. 0 License. data (U-Pb in-situ on zircon) and extensive geochemical studies (bulk rock major and trace elements and isotopic compositions) is a powerful approach to unravel the magmatic history of the arc system and to understand the contribution of the juvenile and/or crustal reservoirs in magmatic arc rocks. 2. GEOLOGICAL SETTING The subduction along the Western coast of the South American plate is active since the beginning of the Paleozoic (570 Ma; Cawood 2005). Subduction-related magmatism led to the emplacement of granitic intrusions during the Ordovician (468-440 Ma; Loewy et al. 2004), the Carboniferous to Late Triassic period (325-215 Ma around Cuzco in the present Eastern Cordillera; Mišković et al.
Solid Earth Discuss. , https://doi. org/10. 5194/se-2019-43 Manuscript under review for journal Solid Earth Discussion started: 27 March 2019 c Author(s) 2019. CC BY 4. 0 License. samples characterized by a large range of both 87 Rb/ 86 Src and 87 Sr/ 86 Srm ratio. The data align themselves, and these alignments are often interpreted as errorchrons in isochron diagrams.