dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis Data are presented as mean ± SD. Statistical analyses were performed using SPSS (v19, SPSS Inc. , Chicago, IL, USA) and Stata software (v12, Stata-Corp, Texas, USA). Normality of distribution was assessed by the Shapiro-Wilk test. The primary focus of the analyses was the 12-month change in lipoprotein subfractions' serum levels. Changes over time were tested by a one-way ANOVA with repeated-measures, with the use of Bonferroni post-hoc test. Correlation matrices between lipoprotein subfractions and CVR were constructed using the non parametric Spearman test. In order to minimize the probability of false positives when numerous correlations are calculated, the independent associations of each of the lipoprotein subfractions with CVR (Framingham score or CIMT) were further assessed using a multivariable generalized estimating equations model that controlled for age, gender, body mass index, presence of diabetes, participant's compliance and exercise intensity while accounting for multiple correlations between the repeated measures.
Melanin content Melanin pigments revealed by Fontana Masson staining on 5 mm paraffin skin sections were quantified by image analysis using Histolab software (Microvision instruments, Evry, France). After determination of a threshold of detection of melanin granules, melanin content in the epidermis was quantified as the area occupied by melanin pigment within the cross-section. Melanin content was measured over the epidermal surface, defined by a standardized length (i. e. 6 mm) of dermal epidermal junction. In Fig. 1 , results from the model without fibroblast are expressed relative to those obtained with the model with living fibroblasts. In other figures, melanin content is expressed as the percentage of melanin surface per epidermis surface. Total RNA extraction and quantitative reverse transcription PCR Reconstructed skin sample was rinsed in Dulbecco's PBS (Invitrogen, Cergy-Pontoise, France).
The epidermis and dermal equivalent were separated using fine forceps as previously described  [50]. Disruption of epidermal tissue, total RNA extraction and Dnase I treatment were performed using Rneasy midi-kit (Qiagen, Courtaboeuf, France). 1 mg of total RNA was used for first strand cDNA synthesis using an Advantage RT-for-PCR kit (Clontech, Saint Quentin en Yvelines, France), according to the manufacturer's instructions. Quantitative PCR was performed using the LightCycler and the Light Cycler-Fast Start DNA Master Sybr Green kit (Roche Diagnostics, Meylan, France). Normalization of data was performed using five housekeeping genes (B2M, RPL13A, RPS28, RPS9) and Genorm application. The following oligonucleotide primers were used: Silver sense -59ataggtgctttgctggctgt-39 and antisense 59 -gcaataccttttggcttcca-39; Tyrosinase sense 59-ctcaaagcagcatgcacaat-39 and antisense 59-ccatgtaggattcccggtta-39; Trp-1 sense 59-tctcaggttcaaggctacaaca-39 and antisense 59-ccatgtaggattcccggtta-39; DCT (Dopachrome tautomerase) sense 59-ggcaccggtaccatttgttgtgtc-39 and antisense 59gtagtcatccaagctatcacagacag-3-; Ribosomal protein S28 sense 59-ccgtgtgcagcctatcaag-39 and antisense 59-caagctcagcgcaacctc-39; Beta-2-microglobulin sense 59tttcatccatccgacattga-39 and antisense 59-cctccatgatgctgcttaca-39; Ribosomal protein L13a sense 59-taaacaggtactgctgggccggaaggtg-39 and antisense 59cacgttcttctcggcctgtttccgtagc-39; Ribosomal protein S9 sense 59-gatgagaaggacccacggcgtctgttcg-39 and antisense 59-gagacaatccagcagcccaggagggac-39.
Back Close Full to as "Control-meso"). The sampling session took place every morning at the same time over the duration of the experiments. Each day, three different depths (0. 1, 5 and 10 m depth) were sampled in the six mesocosms using a trace metal clean system of permanent PVC tubing placed at the center of the bags and connected to a Teflon pump. Additional depths (2. 5 and 12. 5 m) were sampled in two dust mesocosms during DUNE-2-R for nutrient determination. Every 48 h, seawater was also collected outside the mesocosms (hereafter referred to as "out") at the same depths in order to test the representativeness of data between the Control-meso and out. June 2008 experiments: Two distinct seeding experiments were conducted with two types of dust. In the first one (10-18 June 2008 hereafter referred to as "DUNE-1-P"), the dust used was previously subjected to physico-chemical transformations through condensation/evaporation cycles that involved HNO 3 and H 2 SO 4 , mimicking atmospheric transport  (Desboeufs et al.
Statistical analysis of biological and chemical parameters in Table -1 ) and PP (3. 89-5. 35 mg C m -3 d -1 ) were initially low, and were slightly higher in DUNE-1-P relative to DUNE-1-Q and DUNE-2-R (p < 0. 05, Table  2 ). The picophytoplanktonic biomass (Chl a < 3 µm) accounted for about 70 % of the total phytoplanktonic biomass before the Q and R seedings (C. Brunet, personal communication, 2013; Giovagnetti et al. , 2013)  (no data for DUNE-1-P). Synechococcus was the most abundant phytoplanktonic organism in the Introduction.
online at http://www. biogeosciences-discuss. net/11/753/2014/ bgd-11-753-2014-supplement. pdf. Acknowledgements. This work is a contribution of the DUNE experiment (a DUst experiment in a low Nutrient, low chlorophyll Ecosystem, http://www. obs-vlfr. fr/LOV/DUNE/index. html) and was funded by the LEFE, UPMC and ANR-DUNE under the contract "ANR-07-BLAN-0126-01". We would like to sincerely thank the "Réserve naturelle de Scandola, Parc naturel régional de Corse", in particular J. M. Dominici, Jo Albertini and collaborators, for professionalism and cooperation in the implementation of the field work in the bay of Elbo. Lars Stemmann and Discussion Paper | Discussion Paper | Discussion Paper | the RadeZoo service from the "Observatoire Océanographique de Villefranche-sur-mer" are acknowledged for providing zooplankton data.
An experimental programme has been started, to study the possible options. Finally, the LNL accelerator complex is undergoing a major upgrade of its control systems in order to integrate seamlessly with the operation of the overall SPES. The new control system (CS) will use modern network technologies to distribute its action on the campus area and will rely on networked services to fulfil its goals. The control software is based on EPICS  [11]. As part of the upgrading process, beam diagnostics software and magnet PS control system are under development. Due to obsolescence of some key components, LLRF (Low Level Radio Frequency) electronics of sc cavities is also being redesigned: a direct sampling digital RF controller is being prototyped and applied to 80 and 160 MHz cavities.
When entering the study, the patients were subjected to a standard clinical eye examination, including determination of Best Corrected Visual Acuity (ETDRS). OCT (Cirrus, Humphrey Instruments, CA, USA), automated visual field analysis, SITA standard 30-2 (Humphrey Instruments, Type 750, CA, USA), digital photo of the fundus and the optic nerve head (Visupac FF 450 plus IR, Germany or Retinal Camera TRC-NW7SF, Mark II, Topcon, Japan), and test for color vision (Farnsworth 15D and Ishihara's test) were also performed. The average peripapillar retinal fiber layer thickness (RNFL) was computed by the OCT software, based on a 512 × 128 scan, centered on the optic nerve. A healthy control group, consisting of 11 age-matched subjects without any systemic or ophthalmic disease, was recruited by advertisement and included in the study.
Medical Data Unlike other works, we try to generalize a procedure to find the rectum's upper limit by considering studies from two different volumetric imaging modalities: ctc and mri. The ctc colonography collection was downloaded from the National Cancer Institute's Image Cancer Archive ( http://cancerimagingarchive. net/ ) whereas the mri acquisitions come from patients from La Timone hospital in Marsille, France. The ctc scans were made by an helicoidal TOSHIBA CT using a 120 kVp protocol. The studies have between 340 and 588 slices, with a 512x512 pixel resolution and a [0. 702, 0. 702, 0. 800]mm average spatial resolution with an Axial-LPI orientation. The mri scans are under a T2 weighted FSE Sagittal protocol, having 110 slices with a 256x256 pixel resolution and a [0. 781, 0. 781, 1.
86 ml). Retention time and full width at half-maximum (FWHM) of the peaks were determined with Chromeleon 6. 80 (Dionex, Sunnyvale, CA, USA) and verified with PeakFit 4. 11 (Systat Software, Inc. , San Jose, CA, USA) using an exponent modified Gaussian model (Equation (  1 )) where Abs norm is the normalized absorbance, h is the amplitude of the peak, w is the width of the peak, s is the distortion of the peak, z is the center of the peak and erf is the error function  (72). Examples of peak deconvolution are given in Supplementary Figure  S2. Abs norm = hw s π 2 exp w 2 2s 2 - V e /V 0 -z s 1 -erf 1 √ 2 w s - V e /V 0 -z w. ( 1 ) Data analysis was performed with QtiPlot 0. 9. 8. 7 (ProIndep Serv S. r. l. , Romania) and OriginPro 9. 1 (OriginLab, Northampton, MA, USA). For each peak, the nature of the species was confirmed by visual inspection of the characteristic absorbance spectrum (i.
Full parameters and results are provided in Supplementary data. 'Radii of gyration' (R g ) were calculated with UCSF Chimera 1. 8. 1  (74) , from structures deposited in the PDB (the results were averaged when multiple models are available), using a Python script written by Dr Eric Pettersen from a Fortran program by Dr Elaine C. Meng, reported in Supplementary data. 'Native mass spectrometry' samples were prepared by annealing oligonucleotides at a 10-M strand concentration in 100 mM ammonium acetate, pH 6. 9. Native ESI-MS were obtained using an LCT Premier mass spectrometer (Waters, Manchester, UK). The ESI source voltage was set to 2. 2 kV with a desolvation temperature of 60 • C, and the sample cone voltage was successively set at 100, 150 and 200 V. The source pressure was adjusted at 35 mbar and monitored with a Center Two probe (Oerlikon Leybold Vacuum, Cologne, Germany).
θ T = (L T 0 -A T )/(L T 0 -L T 1 ) ( 6 ) Melting temperatures were extracted by nonlinear fitting (least-squares method) of the θ T = f(T) plot using a sigmoidal-type Boltzmann function (Equation (  7 )), and then solving T for θ T = 0. 5, where A 1 and A 2 are the initial and final values, respectively, T 0 is the center (i. e. the temperature for which θ = (A 1 + A 2 )/2) and c is a constant. θ T = (A 1 -A 2 )/(1 + exp[(T -T 0 )/c] + A 2 (7) CD experiments were performed with a JASCO J-815 spectropolarimeter equipped with a JASCO CDF-426S Peltier temperature controller, using quartz cells of 10 mm path length. The scans were recorded at 20 • C from 210 to   2). The CD data are blank-subtracted and normalized to molar dichroic absorption ( ε) based on nucleoside concentration using Equation (  8 ), with θ the ellipticity in millidegrees, c the nucleoside concentration in mol l -1 and l the path length in cm (Supplementary Figure  S3 ).
ACKNOWLEDGEMENTS E. L. thanks  A. Marchand  for his help with native mass spectrometry,  W. Palau  and  Dr C. Di Primo  for the kind gift of SL2, SL2 mut and  R06  oligonucleotides and subsequent discussions,  Dr V. Gabelica  for the gift of TG n T oligonucleotides and fruitful discussions,  Dr S. Amrane  and  Dr V. D'Atri  for their insights into quadruplex structures and  Dr M. Renders  for proofreading of the manuscript. J. L. M. dedicates this manuscript to the memory of  Jean-Louis Leroy , who pioneered the use of  SEC  for unusual nucleic acid structures.
We further apply two quantitative and independent methods, ABGD (Automatic Barcode Gap Detection) and GMYC (General Mixed Yule Coalescent) to a dataset of published and newly obtained partial SSU rDNA for a more objective assessment of the species status of these genetic types. Results of these complementary approaches are highly congruent and lead to a molecular taxonomy that ranks 49 genetic types of planktonic foraminifera as genuine (pseudo)cryptic species. Our results advocate for a standardized sequencing procedure allowing homogenous delimitations of (pseudo)cryptic species. On the ground of this revised taxonomic framework, we finally provide an integrative taxonomy synthesizing geographic, ecological and morphological differentiations that can occur among the genuine (pseudo)cryptic species.
g. ,  [27, 28] ), SSU rDNA is still the most widely used marker for putative species delimitation in planktonic foraminifera. Within the 25 morpho-species for which rDNA sequences are currently available, 54 genetic types, variously labeled ''genotypes'', ''types'', ''subtypes'' or ''cryptic species'' have been published so far (NCBI database, January 2013). Apart from one exception (G. sacculifer,  [22] ), all studied morpho-species include two to seven distinct genetic types  [9, 16, 17, 19, 21, 29] , several of which exhibiting a distinct biogeography and/or ecology  [18, 20, 30, 31, 32, 33, 34, 35]. Molecular clocks and biogeographic patterns further suggested that these genetic types have been reproductively isolated for a significant amount of time and should be considered as cryptic or pseudo-cryptic species when subtle differences in shell morphology were additionally detected  [21, 29, 36, 37, 38].
Nevertheless, a number of genetic types within a morphospecies, or a number of ''subtypes'' within a genetic type, exhibit partial or even total sympatric distributions and/or similar shell morphologies  [9, 18, 29, 38, 39]. Many proposed genetic types were defined exclusively on the basis of genetic differences and phylogenetic criteria involving only a single or a few closely related morpho-species, without any additional DNA-independent investigation that may help validating their species status. Such difficulties, associated with the rapid increase of SSU rDNA sequences available, calls for the development of a standardized approach to rationalize species delimitation in planktonic foraminifera. Definitions of the published genetic types over the last 15 years have been optimized on the basis of various phylogenetic inferences mostly applied to isolated morpho-species, because of the high and variable SSU rDNA substitution rates, which induce highly ambiguous sequence alignments when datasets include loosely related species  [17].
Furthermore, sequences that lack genetic type assignation in sequence databases such as GenBank, or for which a genetic type could not be inferred from original publication, cannot be considered for patristic distance calculations. Consequently, we test two independent and complementary automatic methods for molecular operational taxonomic unit (MOTU) delimitations: the Automatic Barcode Gap Discovery (ABGD,  [42] ), which allows calculation of genetic distances within and among genetic types delimitated according to each possible species-level threshold, and the General Mixed Yule Coalescent (GMYC,  [43] ), which uses phylogenetic trees to identify transitions from coalescent to speciation branching patterns. These methods provide alternative delimitations and offer the opportunity to analyze sequences that lack former assignation of their genetic type.
Patristic Distances Accounting for taxonomic synonymies and ambiguous assignations (see Material and Methods), we retained 1217 SSU rDNA sequences from NCBI. Adding the 135 newly obtained sequences from living foraminifera collected in the world oceans (Fig. 1 ), we finally compiled a global dataset of 1352 sequences belonging to 25 morpho-species. Due to lengths heterogeneities of the NCBI sequences, only 714 sequences (corresponding to 395 non-identical sequences) of a homologous block of ,700 bp were used for calculations of patristic distances. As a result of procedure requirement, inter-and intra-type distances could be estimated for 9 out of 25 morphospecies (Fig. 2A ). Inter-type distances are highly variable between morpho-species, their medians ranging from 3. 5% (Turborotalia quinqueloba) to 64% (Hastigerina pelagica).
menardii and Candeina nitida do not hide cryptic diversity given that their total genetic distances are reduced and are of the same range as the intra-genomic distances (Table  S1 ). Likewise, the analyzed sequences of Globoconella inflata correspond to a single species but we note that due to their short length, sequences of the second described genetic type  [21]  were all excluded from the dataset. Overall distances within Neogloboquadrina dutertrei and Beella digitata seem to match intra-species distances but data are too scarce to draw firm conclusions. Conversely, these distances are significantly higher that the intra-genomic distances in Globigerinita uvula and Globigerinita glutinata, suggesting that they may constitute complexes of yet unknown cryptic species. The case of these two latter morpho-species points to a major drawback of the patristic distance approach: it requires a-priori delimitations.
Automatic genetic type delimitation methods Automatic Barcode Gap Discovery (ABGD). ABGD sorts the sequences into hypothetical species based on the barcode gap that can be observed whenever the divergence among individuals belonging to the same species is smaller than divergence among individuals from different species. Since ABGD does not require any prior attribution of taxonomic units, the sequences that lacked genetic type labels in the initial dataset were included in the analysis, which is then run on the same SSU region used for patristic distances calculation (462 non-identical sequences of ,700 bp; 23 morpho-species). No barcode gap was identified for 7 morpho-species (Globigerinoides sacculifer, Beella digitata, Globorotalia tumida, Hirsutella hirsuta, Neogloboquadrina dutertrei, Pulleniatina obliquiloculata and Globoconella inflata).
Based on this method, the sampled material of each of these morpho-species corresponds to a single genuine species (Table  1 ). In G. inflata, however, we cannot exclude that our dataset contains only sequences from one of the two types identified by  [21]. For 6 morpho-species (Orbulina universa, Turborotalia quinqueloba, Truncorotalia truncatulinoides, Neogloboquadrina pachyderma, Neogloboquadrina incompta, and Globigerinita uvula), ABGD identifies only one species delimitation optimum (i. e. , one MOTUs richness plateau). For the remaining 8 morpho-species, it identifies several species delimitation optima. As other delimitation optima lead to misassignment of clones from the same individual into distinct MOTUs, we retain the one-MOTU delimitation in Globorotalia ungulata, Menardella menardii and Globoquadrina conglomerata, and the four-MOTUs delimitation in Globigerinita glutinata.
To avoid long calculation time and ambiguous alignments, we divided the dataset into 5 subsets of sequences, each of them incorporating sequences belonging to 3 to 7 morphospecies following  [17]. For 3 ultrametric trees (''Spinose A'', ''Non-spinose A'' and ''Non-spinose B''; Figs. 3  and 4 ; Table  2 ; Figure  S1 ), the likelihood of the GMYC model is significantly higher than that of the null model and thus supports the hypothesis that those trees include several biological species. The GMYC method applied to the tree ''Spinose A'' lead to an estimate of 19 putative species, 2 of which containing a single individual (Fig. 3 ). Isolated sequences AJ229109 (Orbulina universa), Z839665 (Globigerinoides ruber), JQ004126 and Z83964 (Globigerinoides sacculifer) (Figure  S1 ) correspond to old (submitted to the NCBI database back in 1996) or short sequences (,500 bp).
Given that N. pachyderma phylogram (PHYML) and ultrametric tree (BEAST) recover quite different relationships (File S1), patristic distances were not pertinent for testing GMYC delimitations. In Neogloboquadrina incompta, application of the GMYC method delimitates 2 putative species corresponding to the previously defined genetic types of  [46] , and isolates the sequence AY453130 as a possible third species. It also suggests that there are 2 putative species in Neogloboquadrina dutertrei, one of which containing a single individual (AY241708). The species status of the two isolated and short sequences from N. incompta and N. dutertrei could not be genomic distances and black boxes to overall genetic distances. A: Boxplot distribution using species delimitations and specimens identifications according to NBCI database and literature; B: boxplot distribution using species delimitations and specimens identifications according to ABGD and GMYC analyses.
Pulleniatina obliquiloculata GMYC-delimitated and genetic types defined in the literature lead to overlapping intraand inter-type patristic distances (Fig. 2 ). Even after close examination of the dataset of P. obliquiloculata, we were not able to infer a possible artifact that might explain why species delimitation is unsatisfactory within this morpho-species. Last, likelihoods of the GMYC model are not significantly higher than that of the null model for the trees ''Spinose B'' and ''Microperforate'' (Fig. 3 ; Table  2 ). Validation of the null model would imply that each of those trees would correspond to a single     2 ). Colored branches correspond to GMYC clusters and outer circles correspond to the names of the morpho-species (outer arc) and plausible species (inner arc) (see Table  1 ).
Symbols associated to specific colors indicate clones sequenced from the same individuals. For sequences accession numbers see Figure  S1. doi:10. 1371/journal. pone. 0104641. g004 genetic type, which appears highly unrealistic as it would cluster very distinct morpho-species such as Globigerina bulloides and Globigerina falconensis or Globigerinata glutinata and Globigerinita uvula. Therefore these negative results clearly point to a lack of statistical power of the GMYC method in those still poorlysampled organisms.
Heterogeneity of previous genetic type delimitations Our study shows that the empirical delimitations available in the literature suffer from subjectivity although the heterogeneity of the dataset complicates their review using more objective criteria. Those delimitations are apparently not homogenous: some previously-defined genetic types are likely to correspond to valid taxonomic units whereas others probably represent sub-species or population level structuring. Among the morpho-species for which genetic type delimitation seems accurate, intra-specific distances are quite variable as well as the range of the distance gap between intra-and inter-specific distances (Fig. 2 ). This phenomenon may be the result of the heterogeneity of substitution rates observed between planktonic foraminiferal lineages and even sometimes between more closely related morpho-species  [13].
However, results also demonstrate that GMYC-based delimitations can be heavily impacted by data quality and thus requires thorough inspection. Because the sequence overlap/missing data criteria are less critical than in distance-based methods, the GMYC analysis identifies more putative species than ABGD and patristic distances analyses (Figs. 3  and 4 ; Table  1 ). While GMYC proves useful, we also recover very doubtful results where the GMYC model could not be favored over the null model of a single coalescent population (i. e. , trees ''Spinose B'' and ''Microperforate''; Figs. 3  and 4 , Table  2  and Figure  S1 ). Comparison of these cases suggests guidelines on how to design sequence datasets for GMYC analysis. We note that in our study, the statistically significant GMYC species delimitations tend to be associated with: (i) large datasets involving more than 3 morpho-species; (ii) datasets with few ambiguously aligned regions, i.