dataesr/scientific-paragraphs-categorization huggingface dataset:
This work has been supported by research grants from the  Ligue Contre le Cancer (JGG) , by institutional funding from  Inserm  and the  University of Strasbourg (JGG)  and by  EMBL  funds (YS). MAK is supported by an  EMBL Interdisciplinary Post-doctoral fellowship (EIPOD) under Marie Curie Actions  (COFUND), and LM is supported by an  INSERM/Region Alsace Ph. D fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
RNA extraction and cDNA cloning BjSultr1;1 and BjSultr1;2 partial cDNAs were amplified by RT-PCR from Brassica juncea mRNA isolated from roots. Total RNA was extracted from roots of sulfur-starved plants using TRIzol reagent (LifeTechnologies), poly A + mRNA was isolated using the Oligotex mRNA Spin-Column system (QIAGEN), and first-strand cDNA synthesis was carried out using the SuperScriptIII firststrand synthesis system for RT-PCR (LifeTechnologies) according to the manufacturer's instructions. Degenerate primers BjSultr1;1 degdir (5'-ACGGAGGAGGGTCCGRTG CAA-3'), BjSultr1;1 degrev (5'-TTYGGGTCGATCACGGCC TGGCA-3'), BjSultr1;2 degdir (5'-GTYTTCGATTGGGGRC GTAR-3'), and BjSultr1;2 degrev (5'-RAGGAAGAGCAATG TCAAGAGA-3'), were designed based on highly conserved regions identified in sequences of sulfate transporter cDNAs of Brassica napus and Arabidopsis thaliana [for BjSultr1;1: BnSultr1;1 (GenBank accession no.
AJ41 6460) and AtSultr1;1 (TAIR accession no. At4g08620); for BjSultr1;2: BnSultr1;2 (GenBank accession no. AJ311388), and AtSultr1;2 (TAIR accession no. At1g78000)]. 5′-and 3′-regions of the sulfate transporter cDNAs were isolated by 5′-and 3′-RACE approach using GeneRacer Kit (LifeTechnologies) according to the manufacturer's instructions. Finally the full coding regions were confirmed by RT-PCR using sequence specific primers obtained from the 5′-and 3′-RACE fragments, and proofreading Pfu-DNA polymerase (Promega). All PCR products were verified by sequencing after cloning into the pCR-BluntII vector (LifeTechnologies), and sequence data were submitted to GenBank (accession no. JX896426, BjSultr1;1; JX896427, BjSultr1;2a; JX896428, BjSultr1;2b; JX896429, BjSultr1;2c). Sequence analyses were performed using ClustalW and neighbor-joining trees were generated using MEGA 5.
At4g20890) and Brassica napus (GenBank accession no. AF258790) as follow: Tub dir 5′-TGTTGTGAGGAAG GAAGCTGAG-3′ and Tub rev 5′-TCCTGTGTACCAATG AAGG-3′. PCR products were separated in agarose gels and stained with SYBR Green I (LifeTechnologies); signals were detected using a laser scanner (Typhoon 9200, GE Healthcare) with a 532 nm laser and a 526 nm filter. For semi-quantitative RT-PCR analyses of the three different variants of BjSultr1;2, the entire ORFs were amplified with BjSultr1;2 ATG 5′-ATGTCTGGGAGAGCTCATCCT G-3′ and BjSultr1;2 STOP 5′-TCAGACCTCGTCGGAGAG TTTTG-3′ primers (producing a fragment of 1968 bp for BjSultr1;2a and fragments of 1959 bp for BjSultr1;2b and BjSultr1;2c). PCR products were then digested with ClaI endonuclease at 37°C for 3 h, and restriction products were separated in agarose gels.
Statistical analysis Statistical analysis was carried out using SigmaPlot for Windows version 11. 0 (Systat Software, Inc. ). Quantitative values are presented as mean ± standard error of the mean (SE). Significance values were adjusted for multiple comparisons using the Bonferroni correction. Statistical significance was at P < 0. 05. Student's t-test was used to assess the significance of the observed differences between control and treated plants. Statistical significance was at P ≤ 0. 001.
On the other hand the coding sequences of the shorter variants, BjSultr1;2b and BjSultr1;2c, share the highest identities with Bra008340 (95% and 99%, respectively). Unfortunately, we failed in finding any information about the sulfate transporter genes of B. nigra (the other B. juncea parent) in public genomic databases. The heterologous expressions of BjSultr1;1, BjSultr1;2a, BjSultr1;2b, and BjSultr1;2c in the yeast (Saccharomyces cerevisiae) double sulfate transporter mutant CP154-7A  [31]  were able to revert the yeast mutant phenotype, allowing it to grow on a minimal medium containing 100 μM Na 2 SO 4 as a sole sulfur source (Additional file 4), confirming the identity of these B. juncea clones as functional sulfate transporters. In order to estimate the apparent k M for sulfate of each transporter we first analyzed the growth curves of complemented yeasts incubated in liquid media containing different sulfate concentrations (from 0 to 100 μM) as sole sulfur sources (Additional file 5).
Large datasets containing many spectra commonly associated with in situ or operando experiments call for new data treatment strategies as conventional scan by scan data analysis methods have become a time-consuming bottleneck. Several convenient automated data processing procedures like least square fitting of reference spectra exist but are based on assumptions. Here we present the application of multivariate curve resolution (MCR) as a blind-source separation method to efficiently process a large data set of an in situ X-ray absorption spectroscopy experiment where the sample undergoes a periodic concentration perturbation. MCR was applied to data from a reversible reduction-oxidation reaction of a rhenium promoted cobalt Fischer-Tropsch synthesis catalyst. The MCR algorithm was capable of extracting in a highly automated manner the component spectra with a different kinetic evolution together with their respective concentration profiles without the use of reference spectra.
Introduction During the last two decades many synchrotron beamlines specialized in X-ray absorption spectroscopy (XAS) have increased their instrumental performance enormously. While recording a single spectrum used to take several tens of minutes, now it can be recorded in less than 10 seconds or even in the order of milliseconds  1. This has opened up the way to perform in situ and operando XAS experiments with the ambitious aim to shed light on transient structures. In such experiments XAS data are collected as a function of time while changing a variable of the experimental condition such as temperature, concentration, or pressure. It has become routine to collect hundreds of spectra on a single sample. These large datasets have to be treated and the conventional scan by scan data analysis methods have become a time consuming bottleneck.
Automated data processing procedures like least square fitting of data with a linear combination (LC) of reference spectra and Principle Component Analysis (PCA) are powerful tools yet have limitations. More precisely LC requires standards and PCA often provides mixed components that are hard to interpret. Here we present the application of multivariate curve resolution (MCR) as a blind-source separation method  2, 3  to process a large data set of an in situ XAS experiment where a sample is under periodic concentration perturbation with simultaneous effluent gas analysis. The advantage of MCR extracted components is that they can be treated as conventional XAS spectra. In a XAS experiment the X-ray energy is scanned over and beyond the absorption edge and the intensity before and after the sample is recorded.
MCR-ALS should hence not be taken as a general or sole solution for blind source separation, although it did perform well in this application compared to independent component analysis (ICA), such as SNICA 2 , in this particular case. The MCR algorithm has been developed, described and discussed in detail by Tauler et al. [19] [20] [21] [22] [23]. Multivariate resolution methods also assume that the experimental data follows Lambert-Beer's law. This assumed linearity between recorded spectral data and component concentrations is widely accepted for XAS data  24, 25. Hence our aim is to extract the concentration C and spectra S matrices from only the experimental data matrix D without using any reference spectra. Before extracting the C and S matrices the number of pure components present in the system needs to be defined.
Conventional versus MCR data processing Conventional EXAFS data processing includes several initial steps such as normalization, background subtraction and edge position correction. Fig. 3  shows the Fourier transforms of the averaged EXAFS spectra (i. e. one cycle) after the preprocessing steps (details given in Supplementary Material). All the transformed spectra are apparently different from each other, meaning that all 30 spectra must be processed and analyzed separately. This is a time-consuming procedure and becomes impractical for large datasets. Note that this is still a relatively small dataset compared to the experimental capabilities of state of the art XAS stations. MCR works differently; here the entire system is represented by the various components present in the system and their concentrations.
Fig. 4  graphically represents the result of the MCR method applied to our XAS data. The commercially available Unscrambler X 10. 2 software was used for the MCR data analysis. We have constrained the MCR analysis to non-negativity for spectra and concentration profiles. Here the data matrix D is expressed by the matrices of "MCR pure component" spectra S and their concentrations C varying with time and the associated residual error E matrix (shown in Supplementary Material). In this particular example only two components and their concentration profiles were, at the first glance, sufficient to represent the data with very little residual error. Therefore compared to conventional EXAFS data treatment, only 2 spectra need to be interpreted instead of 30. In conventional EXAFS data analysis each of the 30 datasets would be compared or fitted with parameters from a proposed structural model.
Alternatively, the spectra can be fitted by a linear combination of chemically pure standard spectra (typical for XANES analysis). By doing so a model is forced into the interpretation such that Furthermore, it has to be mentioned that the averaged dataset, absorption coefficient (mu) as a function of X-ray energy and time, is processed by the MCR-ALS algorithm. The physically more meaningful interpretation is done only after standard EXAFS analysis, in brief Fourier transform, on the MCR-ALS extracted component spectra.
Fig. 5b  shows that there is a significant difference between the components, implying that the two components belong to the substances with different chemical and structural nature. For a better understanding of the chemical meaning of the components, the FT curves of the two components and of the cobalt containing standards are compared (Fig. 6 ). The As explained in Section 2. 5. 3 and in the Supplementary Material, the presence of 3 components can be concluded based on the structure of scores and S/N of loadings in PCA. Also when we increase the number of components to three, the sum of all differences in matrix E is reduced by a factor of 40 (Supplementary Material), but does the increase in the number of components make better chemical sense and does MCR hence provide more detailed information? The next example uses the same XAS data set but separated into 3 components by MCR.
Acknowledgements This publication forms a part of the  inGAP (Innovative Natural Gas Processes and Products) Centre of Research-based Innovation , which receives financial support from the  Research Council of Norway  under contract no. 174893. The authors would like to thank the  Research Council of Norway  for financial support through the  KOSK-II and SYNKNØYT programmes and Statoil for financial support through the inGAP project. The project team of the Swiss-Norwegian Beamlines  is highly acknowledged for experimental assistance. We thank anonymous reviewers for valuable suggestions helping us to improve the manuscript substantially.
Analysis of the samples was done using a one laser BD-Facscalibur cytometer or a Beckman Coulter. For each sample, 500,000 cells were analysed in a FL1 (TO)/FL2 (HE) dotplot for rings (R), young trophozoites (YT), trophozoites (T), and schizonts (S) (Figure  2A-B-C ). Automatic analysis was also performed using FlowJo® software (Figure  2D ). Uninfected RBCs were detected in the lower left corner of the cytogram (less than ten as fluorescence intenity for the two dyes).
Cytometry analysis of inhibition of maturation This study compared HE/TO labelling with standard [ 3 H]-hypoxanthine test on both cultured strains and fields isolates for the determination of effect of chloroquine. As the two methods do not consider the same biological events in the parasite, concentration inhibiting 50% of the parasites were compared and not individual data obtained for each drug concentration. Seven independent experiments were done for cultured strains (Figure  3B ). Mean IC 50 ranged from 55. 7 and 133. 7 nM and from 93 to 230 nM for Palo Alto and 3D7 strains, respectively. Correlation between the two techniques was 96 and 99% for PA and 3D7 strains, respectively. In the same line, 26 field isolates were analysed but due to lake of maturation of the parasites, four isolates were excluded from analysis.
Acknowledgements This work and  ML Varela  were supported by the following programmes: the  Institute Pasteur Transverse Research Programs  (PTR No. 141 ), by the  "Fonds dédiés pour les maladies parasitaires", and "Fond de Solidarité Prioritaire (FSP-RAI )" from the  French Minister  of foreign affairs. We thank the  'malaria unit' of Institut Pasteur de Madagascar and Dispensaire St Martin in Dakar for supplying field isolates of Plasmodium  falciparum.
The jet fragmentation function of inclusive jets with transverse momentum p T above 100 GeV/c in PbPb collisions has been measured using reconstructed charged particles with p T above 1 GeV/c in a cone of radius 0. 3 around the jet axis. A data sample of PbPb collisions collected in 2011 at a nucleon-nucleon center-of-mass energy of √ s NN = 2. 76 TeV corresponding to an integrated luminosity of 150 µb -1 is used. The results for PbPb collisions as a function of collision centrality and jet transverse momentum are compared to reference distributions based on pp data collected at the same center-of-mass energy in 2013, with an integrated luminosity of 5. 3 pb -1. A centrality-dependent modification of the fragmentation function is found. For the most central collisions, a significant enhancement is observed in the PbPb/pp fragmentation function ratio for charged particles with p T less than 3 GeV/c.
Monte Carlo simulations In this analysis, Monte Carlo (MC) simulations have been used primarily for evaluation of reconstruction performance, particularly in determination of tracking efficiency, and jet energy response and resolution. These studies mostly used QCD jet events simulated by the PYTHIA MC generator  [24]  (version 6. 423, tune Z2)  [25]. These simulated PYTHIA events are propagated through the CMS detector using the GEANT4 package  [26]  to simulate the detector response. In order to account for the effect of the PbPb underlying event, the PYTHIA events are embedded into fully simulated PbPb events, generated by the HYDJET event generator  [27]  (version 1. 8) which has been tuned to describe the centrality dependence of the hadron multiplicity, p T spectra, and elliptic flow in minimum bias PbPb data.
Proton-proton reference data In order to quantify any medium-related effects, the results are compared to reference distributions using the high statistics jet data in pp collisions collected in 2013 at √ s NN = 2. 76 TeV corresponding to an integrated luminosity of 5. 3 ± 0. 2 pb -1. For a direct comparison between pp and PbPb collisions, the jet momentum resolution deterioration in PbPb events has to be taken into account. For this purpose, the reconstructed p T of every jet in the pp data is smeared using a Gaussian distribution based on the quadratic difference of the jet momentum resolution in PbPb and pp data. The jet momentum resolutions are derived from the PbPb and pp MC simulations described in Section 4. In order to keep the jet kinematic constraints consistent, a reweighting factor, derived based on the ratio of the PbPb and the smeared pp jet p T spectra, is applied to each pp jet.
Systematic uncertainties Systematic uncertainties are primarily due to the tracking efficiency estimation, jet reconstruction, subtraction of the underlying background, and differences between MC simulations and data. One systematic uncertainty arising from the tracking efficiency and rate of reconstructing misidentified (fake) tracks is estimated using the Monte Carlo simulations. This uncertainty is based on the comparison of the fragmentation function obtained by corrected, reconstructed tracks with those obtained using the generator-level particles. In both cases, the same (i. e. matched) reconstructed and generated jets are used. An additional 10% tracking efficiency uncertainty is assigned to account for the effects found in a study of the charge composition of reconstructed jets. Specifically, the observed charged fraction of a jet (as determined using the PF objects within the jet) decreases with in the more central collisions with a 10% difference between central and peripheral heavy-ion data (the latter being very similar to pp data and the MC results).
The difference in charge fraction between central and peripheral MC events is less than 2%. It is possible that this change is due to physics. However, to be conservative, a value of 10% is used as an estimate of a possible tracking inefficiency in high multiplicity PbPb events that is possibly not reproduced by PYTHIA+HYDJET. The estimated uncertainty ranges from 0 for peripheral events to 10% for the most central events. The fragmentation function is also sensitive to uncertainties in the jet reconstruction in two aspects: the smearing of jet energy due to resolution and the overall energy scale. In order to estimate the effects of the jet energy resolution, a fragmentation function is constructed from the same PbPb data but with the jet energy artificially modified by smearing with the additional jet energy resolution due to the underlying event.
Comparison of the fragmentation function with and without modified jet energies is used to estimate the impact of these underlying event fluctuations. The full difference found between the two fragmentation functions is assigned as a systematic uncertainty. The uncertainty due to the jet energy scale is estimated by varying the energy of jets in the PbPb data by 5%. This factor is determined using a quadratic sum of the following three contributions. The uncertainty in the jet energy scale in pp data was found to be 2-3%  [35]. Comparing jet energies in reconstructed PYTHIA+HYDJET events to the generator-level values showed a variation of about 1%. As will be shown in Section 8, the observed modification in the PbPb fragmentation function is largely characterized by an excess of particles with p T < 3 GeV/c ( p T = 1.
Results Figure  1  shows the fragmentation function reconstructed in PbPb data and pp reference for 100 < p jet T < 300 GeV/c and tracks with p T above 1 GeV/c within a radius of 0. 3 relative to the corresponding jet axis. For the PbPb fragmentation function, the contribution from the underlying event is subtracted using the η reflection method. For the pp reference data, the corresponding jet distribution is first smeared with the additional PbPb jet resolution due to the underlying event, and then re-weighted to match the jet p T distribution in PbPb data. Figures  2 3 4 show the same fragmentation function differentially in jet p T , for 100 < p jet T < 120 GeV/c, 120 < p jet T < 150 GeV/c, and 150 < p jet T < 300 GeV/c, respectively. In the higher statistics Figure  1 , we retained the same 50-70% and 70-100% centrality binning from  [19].
Freshwater Microalgae Cultures of three microalgal species in exponential growth phase were exposed to the test mixtures and the effects on growth rate and photosynthesis (for freshwater algae only) were assessed. SC at equivalent dilutions as the reference mixtures was tested in parallel. The tests were conducted with three replicates for each treatment. Sigmoidal curves were fitted to the data with GraphPad Prism 5 Software (La Jolla, CA, USA). The EC 50 and EC 10 values were calculated from the fit. Pseudokirchneriella subcapitata cultures with a cell density of 2 × 10 5 cells/ml were exposed to samples in 96-well plates according to  Escher et al. (2008). The two mixtures were tested at concentrations ranging from 0. 03× to 100×EQS for Mix14 and from 0. 8× to 100×EQS for Mix19. Diuron was used as a reference compound and the data expressed as diuron-equivalent concentration (DEQ), by multiplying the relative potencies of the photosystem II (PSII) inhibitors diuron, atrazine, isoproturon, and simazine with their known concentration in the mixture  (Vermeirssen et al.
Daphnia Magna Acute Immobilization test The test followed the ISO 6341 (2012) standard method. Five newly hatched neonates (age Ͻ24 h) were placed in glass beakers (100 ml) and exposed to the mixtures in the dark at 18-22 • C. Four replicates were made per treatment (i. e. , 20 animals per treatment and 20-40 animals in the control group). The number of immobile animals was counted after 24 and 48 h. Potassium dichromate was used as a reference compound, with an EC 50 of 1. 8 mg/l (95% CI, 1. 7-1. 9 mg/l), fulfilling the validity criteria in the ISO standard of an EC 50 between 0. 9 and 2. 4 mg/L22. The concentration-response relationships were calculated with the ToxCalc software (Ver 5. 0) (Tidepool) with maximum likelihood logit regression.
D. Magna Reproduction Test The test followed the  OECD Test No. 211 (2012)  and the ISO 10706 (2001) guidelines, with newly hatched daphnids placed separately in glass beakers. Exposure to the mixtures, control, and solvent occurred at 21 ± 1 • C and photoperiod 16/8-h light/dark (10 animals per condition). During 21 days of exposure, the survival and the reproduction were monitored. Exposure mixtures were changed three times a week and daphnids were fed with green algae (Pseudokirchneriella, Chlorella, and Scenedesmus spp. ). Offspring produced by parent animals were counted and removed. Survival of parent animals and the number of live offspring were evaluated and expressed as a percentage of control. Mean, standard deviation, and the number of replicates were used for statistical evaluation using GraphPad QuickCalc on-line software, and statistical significance of differences between control and exposure mixtures was tested by unpaired t-test.
FET Test The FET test was conducted according to the OECD TG. 236 (  2013 ) and the ISO 15088 (2008) guidelines with zebrafish (Danio rerio) embryos. Fertilized eggs were exposed to the mixtures under static conditions for 5 days: 10 embryos per 40-ml media and three replicates per treatment in two independent experiments. Embryos were monitored daily for mortality, the number of hatched embryos, type of deformities (head, tail deformities, absence of gas bladder) and the number of defected embryos, underdeveloped embryos and length. Statistical evaluation of the data was done by ANOVA followed by Dunnett and Fisher LSD post hoc test (for data in individual experimental runs). Homogeneity of variance and normality were tested by Levene and Shapiro-Wilk tests, respectively. Nonparametric Kruskal-Wallis test was used for data without normal distribution and a Chi-square test was used for testing differences in frequencies.