dataesr/scientific-paragraphs-categorization huggingface dataset:
The fluorescence was measured at each cycle at 72 and 83 °C. The 2 Ϫ⌬⌬ C T method was used to analyze the database on the fluorescence at 83 °C  (42). Melting curves were performed after the PCR to assess the presence of a unique final product. RNA-seq-RNAs were sequenced by Illumina on a GAIIx system for estimating transcript abundance. The reads were aligned using Bowtie  (43)  in single-end mode and with a maximum tolerance of three mismatches to the Au10. 2 transcript sequences (see the Phytozome Web site), corresponding to the version 4. 0 assembly of the Chlamydomonas genome. Expression estimates were obtained for each individual run in units of reads per kilobase of mappable transcript length per million mapped reads (RPKM; see Ref. 44 ) after normalization by the number of aligned reads and transcript mappable length.
The transcript coverage across the genome was visualized on a local installation of the UCSC browser. Differential expression analysis was performed in R with the DESeq package  (45) , and p values were adjusted to control for false discovery rate with the Benjamini-Hochberg method  (46). Sequence files are publicly available in the NCBI Gene Expression Omnibus (accession numbers GSE25622 and GSE41096). Protein Isolation for Immunoblot Analysis-Chlamydomonas cultures were collected by centrifugation (1000 ϫ g, 5 min) and washed twice with 10 mM sodium phosphate, pH 7. 0. The total protein fraction was further subfractionated into soluble and membrane components as described by Howe and Mer-chant  (47). Protein concentration of soluble fractions was determined using the Pierce BCA protein assay kit following the manufacturer's instructions.
Approximately 30 g of protein (per lane) was separated by gel electrophoresis on 4 -12% NuPage BisTris gels (Invitrogen) and visualized by staining with Coomassie Blue (Bio-Rad). Gel lanes were divided into ϳ3-mm bands, and individual bands were subjected to in-gel trypsin digestion (sequencing grade modified trypsin; Promega). Digested peptides were extracted into a 50:50 water/ acetonitrile solution containing 2. 5% formic acid and lyophilized. Peptides were then resuspended into a 25 fmol/l bovine serum albumin (BSA) digest and quantification standard (Waters). LC-MS E was performed using a nanoAcquity UPLC (Waters) system coupled to a quadrupole time-of-flight mass spectrometer (Waters Xevo QTOF). Protein Lynx Global Server (PLGS version 2. 4; Waters) was used to process the LC-MS raw data and determine protein identification and quantification.
The quantification of protein levels was achieved via the addition of an internal protein standard (BSA trypsin digest standard) to which the data set was normalized. Our criteria were that the difference in protein abundance between growth conditions must be statistically significant (p Ͻ 0. 05 by Student's t test) and at least 2-fold or greater in magnitude in order to define a change in protein abundance  (48). Stoichiometric Measurements of Cytochrome/P 700 and Photosystem I (PSI)/PSII-Spectroscopic measurements were performed using a JTS-10 spectrophotometer (Biologic, Claix, France). Light-induced absorption changes were measured as absorption of flashed light at discrete times. Changes in the amount of functional photosynthetic complexes were evaluated measuring the electrochromic shift spectral change, a shift in the pigment absorption bands that is linearly correlated to the number of light-induced charge separations within the reaction centers.
5 M Zn-EDTA. Cells were collected from all cultures at mid-exponential phase. RNA was prepared and validated for physiology by RT-PCR for sentinel gene expression and analyzed by sequencing of cDNA libraries on the Illumina platform. The reads were aligned to the Augustus 10. 2 gene models on the version 4 assembly of the Chlamydomonas genome and were analyzed to quantify abundance of transcripts as described previously. Using a cut-off of 4-fold change and a p value of Ͻ0. 05, we identified 533 genes that showed increased transcript abundance and 119 genes that showed decreased transcript abundance in zinc-limiting conditions relative to zinc-replete conditions (supplemental Data Set 1). Total transcript abundance for the ZRT genes dramatically increased in zinc-limited conditions relative to zinc-replete conditions (Fig.
Acknowledgments-We thank Rey Martin, Kara Velez and Esperanza del Rio for assistance during the early phases of the project; Joan Valentine at UCLA for use of the ICP-MS for metal measurements; Dr. James V. Moroney  for providing antibodies to Cah1 and  Cah4 ;  Dr. Martin Spalding  for providing an additional antibody for Cah1; and  Dr. Joanna Porankiewicz  for providing an antibody to Cah3.
* This work was supported, in whole or in part, by  National Institutes of Health  Grant  GM42143  (to S. M. ) for work on the zinc-deficiency transcriptome. The proteomic analyses and expression of proteins for use as antigens were supported by the  Institute of Genomics and Proteomics at UCLA  (funded by the  Office of Science (Biological and Environmental Research) ,  United States Department of Energy , through Cooperative Agreement  DE-FC02-02ER63421 ). □ S This article contains supplemental Fig. S1 and Data Sets 1-3. 1 Supported in part by  National Institutes of Health Ruth L. Kirschstein National Research Service  Award  F32GM083562  and a Chateaubriand Fellowship for collaborative experiments with G. F. and F. A. W. 2 Supported in part by  National Institutes of Health Ruth L. Kirschstein National Research Service  Award  T32 GM07185  for the  UCLA predoctoral Cellular  and  Molecular Biology Training Program.
Dynamic Light Scattering. Dynamic light scattering (DLS) measurements were performed with a Brookhaven 90 Plus Nanoparticle Size Distribution Analyzer (scattering angle 90 ∘ , wavelength 659 nm, power 15 mW; Brookhaven Instruments Ltd, Redditch, UK). Correlation functions were analyzed using the Clementine package (maximum entropy method) for Igor Pro 6. 02A (WaveMetrics, Portland, OR, USA). is resulted in intensity-weighted distribution functions versus decay times. By converting the decay times with instrument parameters and physical parameters to hydrodynamic diameters, an intensity-weighted size distribution is obtained. A log-normal �t was applied to each population, resulting in the intensity-weighted average hydrodynamic diameter of the population. Mass-and number-weighted distributions were estimated using the Rayleigh scattering approximation and a correction factor for the form factor of spherical particles.
Acknowledgments We thank the paediatricians who willingly participated in this survey. We also thank  Mrs Barbara Heude  for intellectual input in the manuscript. Members of European  Confederation of Primary Care Paediatricians (ECPCP) research group : Marie-Noe ¨lle Robberecht-Riquet MD  (France) 1,2 ;  Marilena Moretto MD  ( Belgium )  6  ;  Gilbert Danjou MD  (France);  Elke Ja ¨ger Roman MD  and  Gottfried Huss MD  (Germany) 5 ;  Gabriella Pall MD  and  Peter Altornaj MD  (Hungary) 4 ;  Arieh Bahir MD  (Israel);  Laura Reali MD  (Italy) 3 ;  Janina Lajauskaite MD  and  Arunas Valiulis PhD  (Lithuania);  Emile Tockert MD  and  Sigurlaug Agustsson MD  (Luxemburg) 8 ;  Monica Olivar MD  (Portugal);  Ajda Cimperman MD ,  Andreja Borinc MD  and  Margareta Seher-Zupanc  ˇic ˇMD (Slovenia) 7 ;  Concha Sanchez Pina MD ,  Luis Martin A ´lvarez MD ,  Arantxa Garmendia MD  and  A ´ngel Carrasco Sanz MD (Spain) ;  Mario Schuhmacher MD  and  Francoise Bovet Boone MD (Switzerland) ;  Kvetoslava PrcuchovaMD (Slovakia) ;  Bjo ¨rn Wettergren MD (Sweden) ,  Charalampos Hadjigeorgiou MD  (Cyprus).
cDNA synthesis and qPCR First strand cDNA was synthesized from adult worm total RNA. RNA was extracted from worms using TRIzolH (Invitrogen) according to the manufacturer's instructions. cDNA was synthesized using the iScript cDNA synthesis kit (Bio-Rad) using 1 mg of total RNA. For quantitative PCR experiments, 1 mg of cDNA was used with the SsoFast TM EvaGreenH Supermix in an ABI PRISM 7900 sequence detection system (Applied Biosystems). qPCR primers were designed for SmPCS SmGST26, SmGST28, SmcGT and SmcCGL and for the housekeeping gene b-tubulin using PrimerQuest (IDT) (Table  1 ). Fold differences were calculated using the 2 2DDCt method  [30].
Gene Accession number Primer Sequence  were ionized by electrospray at 2. 5 kV and introduced into the mass spectrometer. Ions were scanned in the range m/z 100-1500 for acquiring MS spectra. Selected masses were fragmented by collision induced dissociation with energies between 10 and 60 V. c-CGS Smp_013860 c-GCS F 59ACGATCAGCTAGCAACAATGTGCC39 c-GCS R 59AACGGCAGTCCCAATCCAGTAAGT39 b-tubulin Smp_078040 b-tubulin F 59TGCCTCGTGCTATTCTGGTTGACT39 b-tubulin R 59AATTATCTGGCCGGAACAACTGCC39 GST26 Smp_102070 GST26 F 59AGGCCTTGTACAACCAACTCGTCT39 GST26 R 59ACATCGCCGTCATTGCGATCATAC39 GST28 Smp_054160 GST28 F 59ATGACTCTTGTGGCAGCTGGTGTA39 GST28 R 59ATCGTCCGCCTGGAATAGTTGGTT39 c-GT Smp_089100 c-GT F 59GGTGCTGTTGCAGTTGACGATGAT39 c-GT R 59CCATCGCATCAACAGCATTCCCTT39 PCS Smp_072740 PCS F 59TTGACGTGGTTGACTTCTGACGGT39 PCS R 59GTGAAAGGGCAATCATCAGTGGGT39 TGR Smp_048430 TGR F 59ACCTTTAGAATGGACCGTCGCTCA39 TGR R 59ACCCAGTACACGCATGTTGTCAGA39 Smp = Schistosoma mansoni The acquired data was analyzed with the Waters MassLynx 4.
Recombinant SmPCS synthesizes phytochelatins Three different forms of the S. mansoni PCS protein were produced in E. coli: the full length protein (PCS 1-591 ), the N-truncated protein (PCS 66-591 ) and the C-truncated protein (PCS 66-300 ) (Figure  1 ). All three purified, six-His-tagged recombinant proteins were successfully expressed and purified to homogeneity at 1 mg/L culture and formed homodimers as determined by size exclusion chromatography (data not shown). Recombinant PCS 1-591 , corresponding to the unprocessed, mitochondrial form of the protein  [11] , was enzymatically inactive for the production of phytochelatins. This suggests that the presence of the predicted mitochondrial signal peptide in the protein when expressed in E. coli may prevent correct protein folding. Recombinant SmPCS 66-591 , corresponding to the cytoplasmic form of the protein, was found to be active in phytochelatin synthesis (Figure  2 ).
4B  and 4C , respectively). Using extracted ions chromatogram we could measure the respective amount of GS-bimane and c-Glu-Cys-S-bimane that are co-eluted by LC-MS. We found that SmPCS 66-300 and SmPCS 66-591 activity for c-Glu-Cys-S-bimane synthesis was 109. 665. 3 and 11. 76 4. 2 mmol min 21 mg 21 respectively. This suggests that the Nterminal domain of the enzyme alone is more efficient in the catalytic cleavage of GS-conjugates than the full length enzyme. Production of the hydrolyzed products was detected in the presence and in the absence of added metals but no cleavage occurred in the absence of the reducing agent b-Me (data not shown). Similar results were obtained with GS-EA (data not shown).
27%. The upper electrode buffer was Tris 50 mM, taurine 200 mM, SDS 0. 1%. The lower electrode buffer was Tris 50 mM, glycine 200 mM, SDS 0. 1%. The gels were run at 25 V for 1 h and then 12. 5 W per gel until the dye front reached the bottom of the gel. Detection was carried out with fast silver staining  (47). Image Analysis-The gels were scanned after silver staining on a flatbed scanner (Epson Perfection V750), using a 16-bit grayscale image acquisition. The gel images were then analyzed using the Delta 2D software (v 3. 6). Four gels coming from four independent cultures were used for each experimental group. Spots that were never expressed above 100 ppm of the total spots were first filtered out. Then, significantly varying spots were selected on the basis of their Student t test p value between the treated and the control groups.
Fragmentation was performed using argon as the collision gas. Mass data collected during analysis were processed and converted into. pkl files using ProteinLynx Global Server 2. 3 (Waters Corporation, Milford, MA). A normal background subtraction type was used for both MS and MS/MS with a 5% threshold and polynomial correction of order 5. Smoothing was performed on MS/MS spectra (Savitsky-Golay, two iterations, window of three channels). De-isotoping was applied for both MS (medium de-isotoping) and MS/MS (fast de-isotoping). The nano-LC-IT-MS system was composed of an Agilent 1200 series nanoLC-Chip system (Agilent Technologies, Palo Alto, CA) coupled to an amaZon ion trap (Bruker Daltonics GmbH, Bremen, Germany). The system was fully controlled by HyStar 3. 2 and trap-Control 7. 0 (Bruker Daltonics, Bremen, Germany).
The mass range was 250 -1500 m/z. The ion charge control was 200,000, and the maximum accumulation time was 200 ms. A total of two scans were averaged to obtain an MS spectrum, and the rolling average was 1. The six most abundant precursor ions with an isolation width of 4 m/z were selected on each MS spectrum for further isolation and fragmentation. The MS/MS scanning was performed in the ultrascan mode at a scan rate of 32,500 m/z per second. The mass range was 100 -2000 m/z. The ion charge control was 300,000. A total of two scans were averaged to obtain an MS/MS spectrum. Mass data collected during analysis were processed and converted into. mgf files using DataAnalysis 4. 0 (Bruker Daltonics GmbH, Bremen, Germany). A maximum of 1700 compounds were detected with an intensity threshold of 150,000.
A charge deconvolution was applied on the MS full scan and the MS/MS spectra with abundance cutoffs of 5 and 2%, respectively, and with maximum charge states of 3 and 2, respectively. For protein identification, the MS/MS data were interpreted using a local Mascot server with the MASCOT 2. 4. 0 algorithm (Matrix Science, London, UK) against UniProtKB/SwissProt (version 2012 08, 537,505 sequences). The research was carried out in all species. A maximum of one trypsin missed cleavage was allowed. Spectra from QTOF were searched with a mass tolerance of 15 ppm for MS and 0. 05 Da for MS/MS data, and spectra from the ion trap were searched with a mass tolerance of 0. 3 Da in MS and MS/MS modes. Carbamidomethylation of cysteine residues and oxidation of methionine residues were specified as variable modifications.
We could, however, rule out FIG. 7. Analysis of the phagocytic capacity. This figure shows the determination of the phagocytic properties of the cells through the ingestion of fluorescent beads and analysis with a FACScalibur cell sorter. Top panel: distribution of the fluorescence of the cells, showing the negative cells (control at 4 °C) and the positive cells (control at 37 °C), as well as the raw data obtained for cells treated with copper oxide nanoparticles for 24 h prior to treatment with the fluorescent beads. Middle panels: variation of the phagocytic capacity of the cells under different conditions, expressed as a percentage of the control cells. Three independent experiments were conducted. A, results obtained with RAW264 cells. B, results obtained with primary macrophages derived from bone marrow (one experiment only for copper nanoparticles).
70/0. 23 1. 03/0. 72 1. 02/0. 73 7 64 Peroxiredoxin-3 P20108 28,109 1. 41/0. 10 1. 30/0. 22 1. 13/0. 12 0. 976/0. 73 6 65 Ferritin light chain 1 P29391 20,785 1. 29/0. 09 1. 31/0. 25 1. 62/0. 025 1. 18/0. 05 9 66 Eukaryotic initiation factor 4A-III P38919 46,824 1. 046/0. 75 1. 13/0. 38 0. 97/0. 88 0. 933/0. 55 20 67 Elongation factor 1-gamma Q9D8N0 50,043 1. 004/0. 98 0. 952/0. 73 1. 0/0. 99 0. 964/0. 65 16 Note: The accession numbers are those of the SwissProt Database.
Acknowledgements The authors are grateful to  Dominique Dozias  and the experimental installations of  INRA  ( SEA Le Pin au Haras-61310 Exmes ) and the abattoir of  INRA (UERT-Clermont-Ferrand/Theix)  for the management of experiments. We sincerely thank  Didier Micol  for his implication in the management of the research programme. They thank  Isabelle Cassar-Malek  for helpful discussions. They also thank  Genevieve Gentes ,  Christiane Legay  and  Agnes Thomas  for her excellent technical support, as well as  Sebastien Bes  for his technical advice.
Individual daily micronutrient intakes were estimated from nationally representative food consumption surveys in combination with the specific national food composition databases for the participating countries. Information on dietary supplement use was included for most countries (except Belgium, Spain and the Dutch 1997-1998 survey). For most surveys, information on supplement intake was collected within the dietary assessment method and the reference period was the same as for the dietary assessment. Exceptions were Denmark (separate questions referring to usual intake), German adults and France (both referring to 12 months). There were also some differences in the level of detail on the consumption of dietary supplements. Almost all countries collected information on brand names and doses of consumed supplements, with the exception of Denmark and Poland, which asked for type and doses of supplements.
National or study-specific supplement composition databases were used to calculate vitamin and mineral intake from dietary supplements as amounts per d. Composition information in these databases was obtained from the packaging, websites or manufacturers. Denmark used generic supplement information, where nutrient content was calculated from household purchase data. An adjustment for withinperson variation in supplement intake was performed for the Netherlands with a first add then shrink approach, where intake from supplements is added to intake from foods and then corrected for within-person variation with the method described later. In France, a first shrink than add approach was used, where usual nutrient intake from foods was estimated per individual with the method described later and then the individual mean supplement intake of the past 12 months (considered as a long-term intake) was added to obtain total usual nutrient intake.
BMR were estimated using the equations proposed by Schofield  (22). Persons with a ratio value below 1•0 were considered to be low energy reporters in the following referred to as under-reporters. The percentages of under-reporters are presented for each subgroup, for all countries except Poland and the UK. Analyses were additionally performed while excluding under-reporters for Belgium, Denmark, France, Germany and Spain to evaluate the impact on the results (data not presented).
Low intakes of micronutrients in Europe 757 Intakes were calculated for the base diet, namely from food, including the contributions of mandatory fortified foods, and also the base diet plus dietary supplements. Mandatory fortification was included in the definition of base diet because in most countries this fortification is either required by statute or officially encouraged in order to maintain availability of the specific nutrients. The contribution from voluntary fortified foods was explicitly assessed for children and adolescents in Germany, young adults and young children in The Netherlands or for particular foods for which fortification information was available in the food composition databases in Denmark, Spain and the UK. Base diet values include any contributions from voluntary fortification in countries where this is normal.
For women aged over 60 years, mean intake was lowest in Germany (98 mg/d) and highest in Denmark (164 mg/d). The highest proportion of intake below the LRNI was in Poland (17 %). The proportions of intakes below the EAR were highest in Germany (61 %) and lowest in Denmark (13 %). For men aged over 60 years, the highest proportion of intakes below the LRNI was seen in Germany (10 %) and the lowest in the UK (0 %). Similarly, the proportion of intakes below the EAR was highest in Germany (47 %) and the lowest in the UK (3•6 %). Where data on supplements were included, there was no substantial change in mean intake and in the proportions of intakes below the LRNI and EAR, except in Denmark. Iodine intake -under-reporting. Excluding the underreporters increased the mean intake for French adults by 8 %, but only slightly in other countries.
A recent investigation in the USA of the contributions from food, supplements and fortified foods to intakes in the National Health and Nutrition Examination Survey is the most comprehensive analysis to date  (44). Investigating the impact of fortification is a difficult task, and only few data in our project could be obtained, as most food composition databases in Europe do not differentiate voluntary from mandatory fortification or the contribution from fortification to the total content of micronutrients in food products. This remains an area worthy of further investigation. European countries vary considerably in their fortification practices, both voluntary and mandatory, and the impact of these may vary with the degree of wealth or social structure and may affect particular subgroups of the population more than others.
For example, 24 h recall can be conducted in a short period of time with little detail or can take an extended period with multiple passes through the preceding day to obtain as complete a record as possible. Furthermore, 24 h recalls can be repeated, giving greater precision to estimates; in the two studies mentioned earlier, Belgium used two computerised recalls, the UK administered four interviews and the diary methods varied as well. The main methods used in the surveys reported in this compilation were also carried out differently, and some used different methods for adults v. children. The surveys also varied in terms of recruitment methods, individual and household representativeness, numbers of subjects per household and weighting factors used. Another important factor in determining intakes consistently is in the alignment of food composition databases.
There is a need for composition data to be collected and presented in a standardised way to enable comparison between countries and across Europe. One nutrient where methods were different was folate. Some countries account for the greater bioavailability of synthetic folic acid as added to foods or as supplements, while other countries do not. This difference in methods could not be harmonised completely for this project, and since the majority of folate is food folate, and the included countries do not have a mandatory folic acid fortification, all countries were considered together. The problem of uniformity in food composition databases has been addressed by several European projects, most recently by the European Food Information Resource project, which developed draft standards for food data.
Similarly, the proportion of individuals from all age groups below the LRNI was very low for all countries except for Poland. For Cu, the proportions of intakes below the EAR and the LRNI were low in all age groups. For both Ca and Cu with low proportions below the LRNI, under-reporting had little impact on results. There were concerns about iodine, where the proportion of children with intakes below the EAR was high in several countries, and for older adults in France and Germany, with 40 -60 % below the EAR. Intakes below the LRNI ranged from 1 to 15 %, the highest proportion being in Polish women aged 18 -60 years at 18 %. About 20 % of those aged 4 -10 years and more than 10 % of those aged 11 -17 years in Poland had intakes below the LRNI. In many countries, voluntary iodine fortification of salt is a common practice, but the contributions of iodine from this source are not reflected in the national food composition databases, except in Denmark.