dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical Analysis Results are expressed as mean ± standard error of the mean (mean ± SEM). Statistical analyses were performed with StatView 5. 0 software. For reference memory, data were analyzed by a one-way ANOVA or repeated measures ANOVA (for learning phase) followed by a Fischer PLSD post hoc test and a Student's t-test to compare with chance level. For working memory data were analyzed by a two-way (group × trial) ANOVA followed by a paired Student's t-test to compare trials within groups. P values < 0. 05 were considered to be statistically significant.
However, to our knowledge, the present study is the first one that demonstrates a combined effect of n-3 LC-PUFAs and vitamin A supplemented diet on AKT in the hippocampus. Furthermore, the two vitamin A supplemented groups exhibited CAMKII and ERK1/2 mRNA and protein levels similar to those measured in the adult control group. According to the involvement of these kinases in learning and memory, it could be hypothesized that their maintenance during aging could participate to the beneficial effect of vitamin A on the reference memory in middle-aged rats  (Giese and Mizuno, 2013). As previously shown for CAMKII, the transcriptional regulation of these kinases could be mediated by retinoids  (Chen and Kelly, 1996). Since this is the first study investigating the effects of a combined EPA/DHA and vitamin A supplementation, no experimental data could yet explain this additive effect.
This region has been shown to be involved in the integration of SelT in the endoplasmic reticulum (ER) membranes  (23). Therefore, we presumed that this hydrophobic region might hamper the production of SelT in Escherichia coli since recombinant SelW, which lacks this segment, has previously been generated in this heterologous system  (1). We thus engineered the SelT protein without this domain, which could indeed be readily purified at high yield from bacterial extracts (Fig. 1B ). We then tested its putative activity as a GPx or a TrxR, which represent two major types of selenoprotein activities due to a CXXU domain  (19). In contrast to purified bovine erythrocyte GPx used as a positive control, recombinant SelT did not display a GPx activity assayed using Cayman's GPx assay (data not shown).
2% -9. 4% vs. 85. 7% -1. 7%, mean -SEM relative to control) (Fig. 3D, E ), which was associated with higher ROS levels (260. 7% -12. 1% vs. 130. 0% -6. 1%, mean -SEM relative to control) (Fig. 3F ). Finally, we analyzed phosphorylated TH (phosphoTH) at Ser31 as a readout of the active enzyme to determine the impact of SelT on TH activity. Silencing of SelT expression provoked a reduction in phosphoTH levels in control and MPP + -treated SH-SY5Y, suggesting that SelT is required for optimal TH activity in dopaminergic neurons in basal condition and under oxidative insult. Together, these data demonstrate that SelT protects SH-SY5Y cells and the dopamine-producing enzyme, TH, against excess ROS levels through its Seccontaining, thioredoxin-like catalytic domain.
8E, F ). Finally, the effect of rotenone administration on phosphoTH and dopamine levels was also more pronounced in Nes-Cre/SelT fl/fl mice (Fig. 8F, H, I ). Together with the data obtained with MPTP, these results emphasize the higher vulnerability of SelT-deficient mice in conditions of neurotoxicity and the importance of SelT for the survival of dopaminergic neurons and normal dopamine production. SelT is dramatically increased in the caudate putamen of postmortem PD patients Because SelT expression was induced in the nigrostriatal pathway of animal models of PD, we asked whether this increase could also be observed in patients with the disease. We have therefore screened by quantitative PCR the expression of SelT in different human brain samples, including the caudate putamen (CPu) from control subjects and PD patients.
Immunostaining was visualized using Alexa Fluor 488 or 594-conjugated secondary antibodies diluted 1:200 (Invitrogen). Counterstaining with 1 lg/ml 4,6diamino-2-phenylindole (DAPI; Sigma-Aldrich) in PBS for 1 min was performed before mounting the slides with PBS/ glycerol 50/50. Samples were analyzed with a Leica SP2 confocal laser scanning microscope (DMRAX-UV) equipped with the Acousto-Optical Beam Splitter system (Leica Microsystems). For immunocytochemistry, cultured cells were fixed with 2% instead of 4% PFA; all other procedures were the same. Quantification of fluorescence signals was performed using the ImageJ software. When human samples were used, frozen sections were first postfixed in 4% PFA for 20 min and then incubated for 1 h at room temperature with polyclonal rabbit antibodies directed against SelT or TH diluted 1:200.
Statistics In the experiments with mice, matched controls from the same litters were used. Results are expressed as mean -SEM and represent data from a minimum of three independent experiments. Statistical analysis of the data was performed with GraphPad Prism 6 software. Statistical significance of difference between groups was determined by the two-tailed unpaired Student's t-test or the Mann-Whitney U-test. For Kaplan-Meier curves, statistical comparisons between groups were made using the log-rank Mantel-Cox test.
Acknowledgments This work was supported by the  Institut National de la Santeet de la Recherche Medicale (INSERM , grant number  U982 );  Normandy University, University of Rouen ; the  Regional Council of Normandy ; the  European Community Interreg IV Program  (grants  PeReNE  and  TC2N ); the  GDRI Neuro  and the  FP7 Neuromed program  (Scholarships to L. B. ); and the  Ministere de l'Education Nationale et de la Recherche (Scholarship  to M. C. ). Images were acquired in PRIMACEN, the  Cell Imaging Platform of Normandy. The authors thank  Christine Bucharles  and  Celine Duparc  for helpful discussions and technical assistance.
Of note, we also observed that the lysosomes in pure infected CA cultures appeared to be slightly smaller than those in the mixed cultures. Upon quantification of lysosomal size in astrocytes from mixed versus pure infected cultures using ICY software  24  , we noted that the median lysosome size was significantly increased in mixed cultures (Supplementary Fig. S1 ). One possible explanation is that astrocytes within the mixed culture phagocytose portions of infected dying neurons or larger external aggregates and the large lysosomes we see might be phagolysosomes resulting from the phagocytic clearance of PrP Sc aggregates. PrP Sc aggregates transfer between astrocytes and neuronal cells. The above results show that propagation of PrP Sc could occur in both mixed CGN cultures and astrocyte cultures upon the exogenous application of a PrP Sc source.
To discriminate PrP Sc aggregate signal from PrP C , after guanidium denaturation to reveal PrP Sc epitopes, we first acquired images of uninfected controls at a detector gain and laser intensity setting to minimize the PrP C signal, then imaged the 22L-infected cultures at exactly the same acquisition parameter settings for the PrP channel. This constitutes an acquisition-level threshold for PrP Sc signal. Post-acquisition image analysis was performed using ICY software  24. A fluorescence intensity threshold was always applied to the control images to reduce PrP signal intensity to black, then the same intensity cut-off was applied to the corresponding infected images and the fluorescent objects that remain are considered as aggregated PrP Sc. These objects can also be detected using the automated Spot Detector plugin on the software, using the same sensitivity thresholds for the control and 22L culture images.
Z-stack images were acquired using a Zeiss LSM700 confocal microscope with a 63x oil plan apochromat objective (NA 1. 4) to eliminate chromatic aberration. Acquisition parameters were close to Nyquist sampling limits, in order to perform image deconvolution. Deconvolution was performed to reduce the point spread function and improve resolution using Huygens Essential software (Scientific Volume Imaging). Colocalization analysis was performed on deconvolved images using the objects-based colocalization plugin in the image analysis software ICY with object sizes set to 3-7 pixels and with an intensity threshold for PrP C signal. Co-culture transfer experiments. Transfer experiments were carried out using a simple Infected Donor-to-Acceptor co-culture system that was adapted to use either astrocytes or neuronal cells interchangeably as donors or acceptors.
Acknowledgements The authors thank  Dr. Yuan-ju Wu  and  Dr. Elise Delage  for critical comments on the manuscript. G. S. V. is a recipient of fellowships from the  Fondation Recherche Médicale  and the  Bourse Pasteur-Roux, Institut Pasteur. A. A. is supported by a  Ph. D fellowship  from the  Ministère de l'Enseignement Supérieur et de la Recherche. S. Z. is supported by a PhD fellowship from the  Chinese Scholarship Council. This work is supported by research grants from the  MI CARNOT ICSA/PMI ,  Agence Nationale de la Recherche  ( ANR-14-JPCD-0002-01 ) and  Equipe FRM (Fondation Recherche Médicale)   2014  ( DEQ20140329557 ) to C. Z.
Methods Additional methods are described in SI Methods. DraNramp Microscale Thermophoresis Binding Assay. Purified strep-tagged fluorescently labeled DraNramps were diluted to 100 nM in 150 mM NaCl, 10 mM Hepes, pH 7. 5, and 0. 03% β-dodecylmaltoside (β-DDM), mixed 1:1 with 14 serially diluted CdCl 2 solutions, and loaded into Premium Coated capillaries (NanoTemper Technologies). Thermophoresis data were obtained with a NanoTemper Monolith NT. 115 at 70% light-emitting diode, 80% microscale thermophoresis (MST) power and 30-s MST time, and analyzed using GraphPad prism. 10 μL 100 mM EDTA (20 μL 200 mM EDTA when Ca 2+ or Mg 2+ was included) was added. Cells were pelleted and washed three times before precipitating the metal with 1% (NH 4 ) 2 S. Scanned images of the resulting pellets were converted to black and white, and pellet darkness was determined using ImageJ64 (NIH).
ACKNOWLEDGMENTS. We thank  Ming-Feng Tsai ,  Chris Miller , and  Ute Hellmich  for assistance with developing the liposome assay;  Ali Raja ,  Gunes Bozkurt , and  Hao Wu  for assistance with the microscale thermophoresis system;  Jack Nicoludis  and members of the R. G. laboratory for discussions;  Mathieu Cellier  for providing several bacterial Nramp clones; and  Raimund Dutzler  for sharing the ScaNramp coordinates before release and providing the ScaNramp gene. The work was funded in part by a  Basil O'Connor Starter Scholar research award  from the  March of Dimes Foundation  (to R. G. ),  NIH  Grant  9P41GM104601  (to K. S. ), and a  Beckman Postdoctoral Fellowship  (to A. S. ). We gladly acknowledge supercomputer time from the  Texas Advanced Computing Center via Extreme Science and Engineering Discovery Environment Grant National Science Foundation  ( NSF)-MCA93S028.
Aim: We explored the prevalence and management of iron deficiency and anemia among pregnant women in France. Patients & methods: In this prospective, observational, multicenter registry study, randomly selected investigators (gynecologists/obstetricians/midwives registered in the CEGEDIM ® database) assessed pregnant women presenting for a consultation. Participants completed a questionnaire at study inclusion. Results: A total of 1506 patients were enrolled by 95 investigators. Overall, investigators estimated a moderate or significant risk of iron deficiency in almost 60% of women. The overall prevalence of anemia (15. 8%) increased with longer pregnancy duration. Medication (mainly iron-based) was prescribed to 57. 3% of patients. Conclusion: In French clinical practice, the estimated risk of iron deficiency and prevalence of anemia during pregnancy align with expectations and are managed according to national/international recommendations.
Patients & methods PRECAM was a prospective, observational study conducted at 95 centers in France between March 2013 and June 2014. Study investigators (gynecologists/ obstetricians and midwives) were asked to include the first 15 pregnant women who presented for a consultation. The randomly selected investigator sample consisted of physicians/midwives registered in the CEGEDIM ® (CEntre de GEstion, de Documentation, d'Informatique et de Marketing) database  [18]. CEGEDIM, a global technology and services company specializing in the healthcare field, supplies services, technological tools, specialized software, data flow management services and databases, to healthcare industries, life sciences c ompanies, healthcare professionals and insurance companies. At study inclusion, each patient who agreed to participate in the study received a questionnaire consisting of one section to be completed by the clinician and a second section to be completed by the patient (selfassessment).
Data collected on the patient questionnaire included age, gestation week, laboratory values (e. g. , Hb, ferritin), type and reason for the prescription of medication and/or lifestyle/dietary advice. The duration of pregnancy was defined, in gestation weeks, as <16 weeks (first trimester of pregnancy), ≥16 and ≤28 weeks (second trimester) and >28 weeks (third trimester). Anemia was defined as Hb <11 g/dl (in the first and third trimesters) or <10. 5 g/dl (second trimester)  [19, 20]. Iron deficiency was defined as serum ferritin <15 μg/l. The study was strictly anonymous; there was no possible link between the patients' or clinicians' identities through the questionnaire. Additionally, the study was strictly noninterventional and care was never modified as a result of patient participation.
Results One thousand five hundred and six patients were enrolled by 95 investigators (55% male, 99% gynecologists, 17. 4% hospital-based from across France); data were analyzed for 1478 patients. A total of 28 patients were removed from the analysis because they were receiving folic acid alone during the first trimester of pregnancy, for the prevention of neural tube defects and therefore deemed to be outside the scope of assessing the prevention/treatment of iron deficiency. The mean age of the study population was 29. 9 ± 5. 1 (range: 15-45) years. 31. 9, 43. 6 and 24. 5% of Iron deficiency during pregnancy in France Research Article women were in the first, second and third trimesters of pr egnancy, respectively.
Prevalence of anemia Overall, data regarding Hb levels were available for the majority (88. 8%) of all pregnant women (80. 2, 89. 7 and 97. 4% at the first, second and third trimesters, respectively) and 15. 8% of these women were determined to have anemia. The prevalence of anemia increased with increased pregnancy duration (8. 8, 13. 7 and 26. 0% at the first, second and third trimesters, respectively). A total of 2. 9, 17. 3 and 56. 4% of pregnant women who were estimated by their physician to have no, moderate or significant risk of iron deficiency, respectively, had anemia. Medication (any, 98. 5%) and/or lifestyle/dietary advice (90. 2%) was prescribed to the vast majority of anemic women. Interestingly, nonanemic women were also prescribed lifestyle/dietary advice (78. 4%). More than three-quarters of the nonanemic women were in the second (48.
Discussion It is well documented that the prevalence of iron deficiency and anemia is particularly elevated in pregnant women. Based on historical data (published between 1985 and 1998), the prevalence of iron deficiency anemia in pregnant women in Europe ranged from 6 to 30%  [4]. The current study (PRECAM) provides a real-life clinical view, from the perspective of gynecologists and midwives in France, of the estimated risk of iron deficiency among pregnant women and explores reasons for the prescription of medications for the management of iron deficiency and anemia. Many pregnant women in the current study were estimated, by their gynecologist or midwife, to have a moderate or significant risk of iron deficiency throughout the course of their pregnancy. Given the known increased need for iron during pregnancy, resulting from the increased total cell volume, the needs of the fetus and placenta  [10] , these observations were in line with medical expectations.
Our data demonstrate that, in the event of an estimated elevated risk of iron deficiency, the choice of iron treatment was most often an oral ferrous sulfatebased product. Our analysis showed that, out of the women receiving iron/folic acid combinations, the highest proportion received them during the earlier stages of pregnancy but, with increasing duration of pregnancy, the proportion of women receiving combination therapy reduced and a greater proportion of women received iron alone. These observations are in line with current French recommendations for the management of iron deficiency [21]. The lack of ferritin and Hb levels in some patients is a limitation of the current study. Indeed, ferritin levels were only measured in 605 of 1300 patients because data were unavailable for the remainder.
However, one of the objectives of this trial was to evaluate the practices of French obstetricians, for example, in identifying the reasons for the prescription of medications for iron deficiency and anemia. Determination of serum ferritin is not yet usual practice in developed countries such as France. The future study cohort following this trial will estimate the iron status of anemic pregnant women. In addition, severity thresholds for the risk of iron deficiency were left free to be chosen by individual physicians. The results of this study demonstrate that the thresholds identified by physicians vary from one physician to another. When interpreting the results from PRECAM, one must bear in mind that this is a descriptive observational study, and the outcomes presented relate to the period of data collection.
The cDNA libraries were subsequently enriched by PCR amplification. The resulting cDNA libraries were subjected to sequencing on a single lane of an Illumina HiSeq 2000 machine. RNA-seq and data collection was done following the protocol of Mortazavi et al. 18. The length of the cDNA library was maintained from 250 to 300 bp with a 5′ -adapter of 20 bp and a 3′ -adapter of 33 bp at both ends. Eventually, the fragment length range of the cDNA was 200 to 250 bp. To quantify gene expression levels, 75-mers sequences were aligned to the genomic sequence annotated in TAIR10 using the BLAT program  19  and RPKM (Reads Per Kbp per Million reads) values were computed using the RACKJ (Read Analysis & Comparison Kit in Java, http://rackj. sourceforge. net/) software.
Bioinformatics. Gene clustering was performed using the MACCU software package (http://maccu. sourceforge. net/) to build co-expression clusters based on pairwise co-expression relationships of genes with Pearson coefficients greater than or equal to 0. 75. In order to capture the co-expression relationships specifically in roots, Pearson coefficients were computed based on robust multi-array averaged array data derived from publically available root-specific experiments downloaded from NASCArrays (http://affymetrix. arabidopsis. info/). Visualization of the networks was performed with the Cytoscape software version 3 (http://www. cytoscape. org/). qRT-PCR. Shoot and root samples (pooled from 10-20 seedlings from three independently grown batches of plants) were collected from 14-day-old seedlings and frozen immediately in liquid nitrogen.
HCD collision energy was set to 30% NCE. HCD-generated ions were detected in the Orbitrap at resolution 17,500. Database search. Two search algorithms, Mascot (version 2. 4, Matrix Science) and SEQUEST, which is integrated in Proteome Discoverer software (version 1. 4, Thermo Scientific), were used to simultaneously identify and quantify proteins. Searches were made against the Arabidopsis protein database (TAIR10 20110103, 27416 sequences; ftp://ftp. arabidopsis. org/home/tair/Sequences/blast_datasets/TAIR10_blastsets/ TAIR10 pep 20110103 representative gene model) concatenated with a decoy database containing the reversed sequences of the original database. The protein sequences in the database were searched with trypsin digestion at both ends and two missed cleavages allowed, fixed modifications of carbamidomethylation at Cys, iTRAQ 4plex at N-terminus and Lys, variable modifications of oxidation at Met and iTRAQ 4plex at Tyr; peptide tolerance was set to 10 ppm, and MS/MS tolerance was set to 0.
05 Da. iTRAQ 4plex was chosen for quantification during the search simultaneously. The search results were passed through additional filters, peptide confidence more than 95% (P < 0. 05), before exporting the data. For protein quantitation, only unique peptides were used to quantify proteins. These filters resulted in a false discovery rate of less than 5% after decoy database searches were performed. For each of the three biological repeats, spectra were combined into one file and searched. Annotated spectra of proteins and peptides identified in roots and leaves (available at ProteomeXchange Consortium; http://www. ebi. ac. uk/pride; dataset identifier PXD003309).
A lock mass calibration of sulfadimethoxin at a concentration of 0. 05 mg/L in water:methanol (50:50, v/v) was introduced by HPLC pump (LC-10ATVP, Shimadzu, Japan) and split the 60 μ L/min to lock spray interface. The MS range acquired was 50-1200 m/z with 0. 2 sec/scan in the centroid mode. For data analysis, the acquired mass data were imported to Markerlynx (Waters) within the Masslynx software (version 4. 1) for peak detection and alignment. The retention time and m/z data for each peak were determined by the software. All data were normalized to the summed total ion intensity per chromatogram.
2 ). To exclude noisy genes that are likely of minor importance for the processes under study, we defined biologically relevant expression based on data distribution. Only transcripts with a RPKM value larger than the square root of the median of the distribution of the RPKM values of all detected genes (√10. 95 = 3. 31) were considered for further analysis. Applying this filter yielded a subset of 17,185 genes that were defined as robustly expressed. A subset of 5,173 genes was consistently detected but at low expression levels and was not further considered here (Fig. 2c ). To gain a comprehensive picture of the Mn deficiency responses, we complemented the catalog of expressed transcripts with a proteomic survey using the iTRAQ methodology. iTRAQ-labeled peptides were analyzed by liquid chromatography in combination with tandem mass spectroscopy on a Q Exactive hybrid quadrupole-Orbitrap mass spectrometer, using the Mascot and SEQUEST search algorithms to identify the proteins.
Functional information from differentially expressed genes can be inferred from the analysis of relationships of these genes ('guilt by association'). To include the information of proteins that accumulate differentially upon Mn deficiency, a chimeric co-expression network was constructed from DE transcripts and DE proteins by using the MACCU software and publically available microarray experiments as a database  26, 27. Only DE genes that were co-expressed with a Pearson correlation coefficient greater than 0. 75 were included in the network. This chimeric co-expression network comprises 366 DE transcripts and 129 DE proteins (with 33 of them regulated at both levels), which could be divided into several modules comprising transcripts/proteins of putatively related functions (Supplemental Table  S3 , Supplemental Fig.