dataesr/scientific-paragraphs-categorization huggingface dataset:
NGS-BASED MAPPING ANALYSIS Bulked genomic DNA of the [mut] segregative population was sequenced following the same procedure as described in section Specific knowledge and tool requirement prior to localisation of a mutant locus. The read sequences have been deposited into the European Nucleotide Archive (ENA), with the accession number PRJEB8207. Using discoSNP to identify SNPs among the short reads, we found 196,648 candidates. Among these, ≈56. 6% are either purine-purine (55745) or pyrimidine-pyrimidine (55524) substitutions. These proportions are similar to those observed by comparing the two parental strains, Ec32 and Ec568 (see above and Figure  6 ). This shows that the UV-induced mutagenesis did not result in a huge accumulation of C/T (hence G/A on the complementary strand) mutations spread throughout the genome.
These results are compared with earlier published physiological studies of amino acid and monocarboxylate transport in developing rodents. This comparison shows correlation of high expression of some transporters in the developing brain with higher amino acid transport activity reported previously. Data for divalent metal transporters are also considered. Immunohistochemistry of several transporters (e. g. , Slc16a10, a thyroid hormone transporter) gene products was carried out to confirm translational activity and to define cellular distribution of the proteins. Overall the results show that there is substantial expression of numerous influx transporters in the embryonic choroid plexus, many at higher levels than in the adult. This, together with immunohistochemical evidence and data from published physiological transport studies suggests that the choroid plexus in embryonic brain plays a major role in supplying the developing brain with essential nutrients.
Gene ontology descriptions for rat were downloaded from Biomart  (Hubbard et al. , 2009) , and genes with "transport" mentioned in their gene ontology description were selected. Genes of interest were then extracted from this list. For initial analysis genes with >100 sequence reads and age-related fold changes (FC) > 2. 0 (log 2 FC > 1. 0) were collated and are summarized in Tables  4-6,  and Supplementary   Tables S1-S3 ; this level of gene expression was taken as likely to be functionally significant. For identification of the presence of a particular gene a lower cut-off of 10 sequence reads was used; these are also included in Tables  4 5 6. Illumina RNA sequencing data have been deposited with the Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/) under accession code GSE44072.
Briefly, 10 µg of labeled cRNA was fragmented and denaturated in hybridization buffer, then hybridized on the chip for 16 h at 45 • C with constant mixing by rotation at 60 rpm in a Genechip hybridization oven 640 (Affymetrix). After hybridization, arrays were washed and stained with streptavidin-phycoerythrin (GeneChip R Hybridization Wash and Stain Kit) in a fluidic station 450 (Affymetrix) according to the manufacturer's instruction. The arrays were read with a confocal laser (Genechip scanner 3000, Affymetrix). CEL files summarizing the probe cell intensity data were generated using the Affymetrix GeneChip Command Console (AGCC) software 3. 0. Data were normalized with Affymetrix Expression Console software using MAS5 statistical algorithm. Data have been deposited into the Gene Expression Omnibus repository (http://www.
Amino Acid Transporters There were twice as many genes coding for amino acid transporters in the embryonic choroid plexus expressed at a FIGURE 2 | (A) Scatter plot comparing log2(FPKM), i. e. , fragment count per kilobase of exonic length per million reads mapped, for all transcripts detected by RNA sequencing of the rat lateral ventricular choroid plexus, averaged across replicates from embryonic day 15 (E15) and adult. Red points show transcripts with higher expression at E15 (greater than 2-fold) while blue points are those with higher expression in the adult. FPKM was estimated using a standard ArrayStar pipeline (http://www. dnastar. com/t-help-arraystar. aspx). There is a greater number of transcripts enriched in the embryo. (B) Parallel coordinate plot of change in average expression (log2(FPKM)) of SLC transporters in E15 and Adult lateral ventricular choroid plexus.
Divalent Metal Transporters It has been known for many years that zinc is important for normal brain development and for function in the adult  (Sandstead, 1985; Marger et al. , 2014; Tyszka-Czochara et al. , 2014). In the present study there were 4 zinc transporter genes that were expressed at a higher level in embryonic choroid plexus than in the adult in the fold range of 2. 5-44 (Table  6 ). In the adult there were more up-regulated zinc transporter genes (  6 ), but their expression level was generally much lower (2. 7-12 fold). Both of the major zinc transporter families (Slc30, ZnT, and Slc39, ZIP) are represented in our dataset. The members of the two families function in opposite directions, thus maintaining cellular zinc homeostasis. ZnT proteins of Slc30 genes efflux zinc whereas ZIP proteins function to increase zinc uptake when cellular zinc is depleted  (Marger et al.
A transcript was considered absent in the choroid plexus if no single copy of transcript was detected (while those with "below threshold" had raw count values below 10). A transcript was considered absent in the rat if no annotation was found in the online ensemble database (http://www. ensembl. org/Rattus_norvegicus). "strong immunoreactivity, uniform distribution-type, " "weak immunoreactivity, uniform distribution-type") and in 2 different patterns of immunoreactivity in adult plexus epithelial cells ("weak or lack of immunoreactivity, " "strong immunoreactivity"). Representative micrographs from the 5 different patterns of immunoreactivity are shown in Figure  4.
Discussion All but four of the 52 known families of SCL transporters were represented in the dataset from RNA sequencing of lateral ventricular choroid plexuses in the rat embryo (E15) and in the adult (Supplementary Table  S1 ). Of the 389 individual SCLs, 64% had transcript numbers above the threshold taken to indicate likely functional significance (>100 sequence reads). 81 of these were expressed 2 fold higher or more in the embryonic plexus compared to the adult, 107 were expressed higher in the adult and 62 were expressed at similar levels at the two ages. Some genes were identifiable with transcript counts of 10-100, but thought less likely to be of functional significance; they have nonetheless been included in Tables 4-6. The results for  microarray were generally consistent with those for RNA-Seq in their developmental profile.
Metal Transport Both of the major zinc transporter families (Slc30, ZnT and Slc39, ZIP) are represented in our two datasets. The members of the two families function in opposite directions, thus maintaining cellular zinc homeostasis. ZnT proteins of Slc30 gene efflux zinc whereas ZIP proteins function to increase zinc uptake when cellular zinc is depleted  (Marger et al. , 2014; Tepaamorndech et al. , 2014). In the context of transfer of zinc across the epithelial cells of the choroid plexus it may be that they operate in tandem. Support for this comes from the observation that SCL39A6 (LIV-1) has been immunolocalised to the apical membrane of the neonatal choroid plexus epithelial cells  (Chowanadisai et al. , 2005). None of the six Slc30 genes identified in this study (two high in the embryo, Slc30a2, Slc30a10, and four in the adult, Slc30a3-6, 2.
Limitations of Study There are several limitations in this study. One concerns the use of whole choroid plexus tissue. However, as discussed previously  (Liddelow et al. , 2013)  the epithelium is the predominant cell type, representing up to 90% of the plexus tissue  (Keep and Jones, 1990; Liddelow et al. , 2012). The absence of transcript for Cldn5 (a brain barrier cerebral endothelial-specific claudin family member) in the current RNA-Seq dataset suggests that any possible contamination is below detectable limits  (Liddelow et al. , 2013). The immunohistochemical evidence in that paper and in the current study for a range of protein products of the genes identified in the choroid plexus samples showed that these proteins were largely confined to the epithelial cells of the plexus. The analysis of large RNA sequencing databases is still quite new and relies on the accuracy of the annotations for each species studied.
The rat genome is well annotated and the number of unknown genes is very low, however, there is still the possibility that some transcripts were missed. The papers based on microarray studies of adult mouse choroid plexus  (Marques et al. , 2011 and Janssen et al. , 2013)  on adult human and mouse adult choroid plexus provide important additional data on gene expression in the choroid plexuses of other species. These together with that of  Liddelow et al. (2012)  a mouse microarray study and that of  Ek et al. (2015)  an RNA-Seq study in primate choroid plexus provide comprehensive datasets for interspecies comparison reviews; however, this is outside the scope of this research paper. We did not attempt to analyze all functional groups represented in the transcriptomic dataset. For example Slc16a10 showed strikingly high expression (Table  4 ) exclusively in the embryo; it has been included primarily because it is a monocarboxylate transporter (MCT10) although its little investigated putative function as a thyroid hormone transporter may well prove to be more functionally important.
Acknowledgments KD, MH and NRS are supported by the  National Health and Medical Research Council (Australia)  -Grants No. 567205  and  1049287. SL, KD,  NRS ,  NS  and J-FG-E were supported by the  European Union   Seventh Framework Program  ( FP7) Neurobid  consortium -Agreement No. HEALTH-F2-2009-241778 , J-FG-E is supported by  ANR-10-IBHU-0003 Cesame grant , SL was supported as a Neurological Fellow by the  American-Australian Association  and as an  NHMRC   CJ Martin Fellow.
We intended to study the prognostic determinants over time of a large series of breast cancer patients treated with neoadjuvant chemotherapy at Institut Curie. To accurately decipher the prognostic impact of clinical and pathological factors in this particular breast cancer treatment setting, we performed a prognostic analysis on the whole dataset after a stratification based on the follow-up length (5-year follow-up without distant recurrence). We first identified the clinical and pathological markers with a time-varying hazard, and they were evaluated to determine the most relevant statistical model, allowing us to perform a time function multivariate Cox model regression analysis.
MATERIALS AND METHODS We recorded the experience of neoadjuvant chemotherapy in breast cancer over time at Institute Curie, Paris. From 1981 to 1998, a consecutive series of 956 patients who received neoadjuvant chemotherapy were selected from our prospective Breast Cancer Database. The selection criteria included prior NAC for operable breast cancer, T2-T3-N0-N1 tumours. Eligibility criteria for NAC included age between 18 and 65 years, OMS status 0-1, granulocyte count X1500 ml À 1 , platelets X100 000 l À 1 , haemoglobin level X10 g dl À 1 and adequate liver, renal and cardiac functions. Patients with metastatic, locally advanced or inflammatory breast cancer were excluded, as well as patients with bilateral breast cancer, previous primary tumour and male breast cancer. Clinical, radiological and pathological data such as patient age, menopausal status, T stage, N stage, histological tumour grade, oestrogen receptor (ER), progesterone receptor (PR) and pathological response to NAC were collected through a retrospective review of medical and pathological records.
RESULTS Patient characteristics. A total of 956 patients were included in our study. Patients and tumour characteristics are shown in Table  1. The median age was 46 years. About 734 patients were premenopausal (77%). Median tumour size was 4. 5 cm (2-15). About 676 patients (70%) had a T2 tumour and 280 had a T3 tumour (29%). Lymph node involvement was found in 490 patients (44%). The vast majority of these tumours were infiltrating ductal carcinoma (88%), graded II or III (85%) and positivehormone receptors (72%). The time distribution of patients ´initial date of diagnosis was as follows: 177 patients (18%) were treated between  1986 and 1990, 450 (47%) between 1991 and 1995, and 329 (34%) between 1995 and 1998. Statistical significant differences between periods were found in clinical and pathological data at diagnosis.
MALDI-TOF protein analysis was carried out as previously described  [23]  using a Microflex spectrometer (Brüker Daltonics, Leipzig, Germany). Twelve individual colonies were deposited on a MTP 96 MALDI-TOF target plate (Brüker). The 12 spectra were imported into the MALDI BioTyper software (version 2. 0; Brüker) and analysed by standard pattern matching (with default parameter settings) against the main spectra of 6. 252 bacteria, including 199 spectra from 104 validly named Bacillus species used as reference data in the BioTyper database. A score enabled the presumptive identification and discrimination of the tested species from those in a database: a score of >2 with a validated species enabled the identification at the species level, and a score of <1. 7 did not enable any identification  [23].
No significant score was obtained for strain mt2, thus suggesting that our isolate was not a member of any known species. The obtained reference spectrum for B. rubiinfantis strain mt2 T (Fig. 4 ) was incremented in our database and compared to other members of the Bacillus genus. The observed differences are shown in gel view in Fig. 5. Growth conditions and genomic DNA preparation B. rubiinfantis sp. nov. , strain mt2 T (= CSUR P1141 = DSM 28615), was grown on 5% sheep's blood-enriched Columbia agar (bioMérieux) at 37°C in aerobic atmosphere. Bacteria grown on three petri dishes were collected and resuspended in 4 × 100 μL of Tris-EDTA (TE) buffer. Then 200 μL of this suspension was diluted in 1 ml TE buffer for lysis treatment that included a 30-minute incubation with 2. 5 μg/μL lysozyme at 37°C, followed by an overnight incubation with 20 μg/μL proteinase K at 37°C.
Genome annotation and genome analysis Open reading frames (ORFs) were predicted using Prodigal (http://prodigal. ornl. gov/) with default parameters, but the predicted ORFs were excluded if they spanned a sequencing gap region (contain N). The predicted bacterial protein sequences were searched against the Clusters of Orthologous Groups (COGs) using BLASTP (E-value 1e-03 , coverage 0. 7, identity 30%). If no match was found, it searched against the NR database using BLASTP with an E-value of 1e-03 , coverage 0. 7 and identity 30%, If the sequence lengths were smaller than 80 amino acids, we used an E-value of 1e-05. The tRNAScanSE tool  [24]  was used to find tRNA genes, whereas ribosomal RNAs were found by RNAmmer  [25]. Lipoprotein signal peptides and the number of transmembrane helices were predicted using Phobius  [26].
ORFans were identified if all the performed BLASTP did not give positive results (E value smaller than 1e-03 for ORFs with sequence size upper than 80 aa or E value smaller than 1e-05 for ORFs with sequence length smaller 80 aa). Such parameter thresholds have already been used in previous works to define ORFans. For the genomic comparison, we compared our type strain Bacillus rubiinfantis strain mt2 T to Bacillus bataviensis (GenBank accession number AJ542508. 1), Bacillus infantis (AY904032. 1), Bacillus endophyticus (AF295302. 1), Bacillus pseudomycoides (AF013121. 1), Bacillus thuringiensis (D16281. 1), Bacillus amyloliquefaciens (AB006920. 1), Bacillus mojavensis (AB021191. 1), Bacillus thermoamylovorans (L27478. 1) and Clostridium butyricum (AJ58420. 1). Genomes were automatically retrieved from the 16S RNA tree using Xegen software (Phylopattern)  [27].
Genome properties The genome of B. rubiinfantis strain mt2 T is 4 311 083 bp long with a 40. 0% G+C content (Fig. 6 ). Of the 4149 predicted genes, 4028 were protein-coding genes and 121 were RNAs. Out of these 121 rRNA genes, 11 are 16S rRNA genes, 9 are 23S rRNA, 11 are 5S rRNA and 90 predicted tRNA genes were identified in the genome. A total of 3026 genes (72. 93%) were assigned a putative function. Two hundred two genes were identified as ORFans (5. 04%). The remaining genes were annotated as hypothetical proteins. The properties and statistics of the genome are summarized in Tables  3  and 4. The distribution of genes into COGs functional categories is presented in Table  4. It was the 70th organism identified within the Bacillus genera. The genome's GenBank accession number is CCFE01000000 and consists of 12 scaffolds and 33 contigs.
Negative reactions are observed for lipase (C14), trypsin, nitrate reduction, alkaline phosphatase, β-glucuronidase, α-glucosidase, β-glucosidase, α-fucosidase, α-mannosidase and N-acetylβ-glucosaminidase. Cells are susceptible to vancomycin, rifampicin, doxycycline, erythromycin, amoxicillin, nitroflurantoin, ciprofloxacin, ceftriaxone, penicillin G, gentamicin and imipenem but resistant to trimethoprim/sulfamethoxazole and metronidazole. The G+C content of the genome is 40. 0%. The 16S rRNA gene sequence and whole-genome shotgun sequence of B. rubiinfantis strain mt2 T are deposited in GenBank under accession numbers LK021113 and CCFE01000000, respectively. The type strain mt2 T (= CSUR P1141 = DSM 28615) was isolated from the stool of a child living in Niamey, Niger, with kwashiorkor.
Pyrosequencing The structure of BCs was assessed by pyrosequencing on gene coding for 16S rRNA. Two primer sets were used to amplify different variable regions on the 16S rRNA fragment. The first primer set, namely 563F  [22]  and 907rM  [23] , was used to amplify V4 regions of the major part of bacterial 16S rRNA fragments (including cyanobacteria). This primer set was named Eub-Pr1 for Eubacteria primer-set. The second primer set, namely 895F  [24]  and 1492R  [25]  was used to amplify the V6-V8 region across the bacteria excluding chloroplast and cyanobacterial sequences of the 16S rRNA fragment. This primer set was named NC-Pr2 for Non-Cyanobacteria primer set. In silico analyses against SILVA SSU Ref 108 NR database  [26]  confirmed that most of the cyanobacterial 16S rDNA sequences were excluded by NC-Pr2 and that some non-cyanobacterial sequences could be omitted (data not shown).
Clustering, alignment and phylogenetic of 16S rRNA gene fragments A total of 180 876 reads (Eub-Pr1 primer set) and 276 806 reads (NC-Pr2 primer set) were obtained. The whole reads were analyzed with PANAM software: a tool for the Phylogenetic Analysis and Taxonomic Affiliation of SSU rRNA Amplicons (https://code. google. com/p/ panam-phylogenetic-annotation/)  [27]. All of these sequences were checked against the following quality criteria: (i) no Ns, (ii) quality score 23 according to the PANGEA process  [28] , (iii) a minimum sequence length of 200 bp and (iv) no sequencing error in the forward primer. The putative chimeras (UCHIME,  [29] ) and homopolymers  [30]  were detected. Secondly, the reads were de-multiplexed according to TAGx sequences in order to recover reads for each sample.
Subsequently, reads were clustered in OTU (Operational Taxonomic Unit) with UCLUST  [31]  at a cut-off of 98% similarity. Then the OTUs were processed with USEARCH to obtain experimental reads sorted into different phyletic groups. Ad hoc profile alignments (HMMER,  [32] ) were processed prior building of maximum-likelihood phylogenetic trees (FastTree,  [33] ). Based on these trees an accurate taxonomy was assessed for each OTU. The reads assigned to cyanobacteria where removed from the data. Thresholds for abundant OTUs were defined with an abundance of reads > 1% within a sample  [34]. In parallel, a BLAST analysis was performed on the representative sequences of abundant OTUs (> 1% in NC-Pr2 data) using the nucleotide collection nr/nt database. Sequences sharing at least a 98% sequence identity with the ones in GeneBank1 were selected in order to determine their representativeness in this database and the ecosystems they were retrieved from.
A Correspondence analysis using the "ade4TkGUI" package  [39]  was performed to explore the relationship between bacterial OTUs obtained for each primer set used. Using the "vegan" package, a Mantel-test was performed to compare the Bray-Curtis-transformed OTUs distribution matrices obtained with Eub-Pr1 to that obtained with NC-Pr2. Permutational Multivariate Analysis of Variance (PERMANOVA), carried out with the "vegan" package using Bray-Curtis distances matrices and 9999 permutations was used to analyze differences between BC at the OTUs level. Kruskal-Wallis tests were used with Bonferroni correction to compare the distribution of phylum/Class/Order between fraction and/or blooms.
Eubacterial versus Non-cyanobacterial primers set After cleaning, a total of 166 622 and 194 197 high quality reads were obtained for classical (Eub-Pr1) and Non-Cyanobacterial (NC-Pr2) primer sets respectively. As expected, the cyanobacterial reads dominated the Eub-Pr1 dataset with an average of 92% of the reads for the associated fraction and 32. 7% for the free-living fraction (Table  1 ). The cyanobacterial reads from the Eub-Pr1 data were used to analyse the proportion of cyanobacteria for both bloom (S2 Table ). The Microcystis reads and the Anabaena reads were the most abundant cyanobacteria for each bloom respectively (> 50% in the associated fractions). We also noted a less important presence of Limnothrix in the Microcystis bloom and Uncultured Nostocales in the Anabaena bloom. We also found some Uncultured cyanobacteria during both blooms In the NC-Pr2 dataset, cyanobacterial reads were less abundant with an average of 66.
2% in the associated fraction, and 18. 7% in the free-living one. Although NC-Pr2 was not fully selective against cyanobacterial 16S rDNA, this primer set decreased the proportion of cyanobacterial reads. After normalization (n = 786 due to the high proportion of cyanobacterial reads removed from Eub-Pr1 dataset) the same overall distribution was observed for both primer sets (Fig 1 ).
when BCs were compared at the OTU level (Mantel-test; Pearson r = 0. 97; p-value > 0. 001). A clear discrimination of BC was observed between bloom-forming genus (Anabaena versus Microcystis) (first axis) and between associated and free-living states (second axis) (PERMA-NOVA; p-value = 0. 01). Moreover, with both primers sets, BC distribution of Anabaena and Microcystis blooms were more distinct (PERMANOVA; p-value < 0. 001) than free-living and associated bacterial communities during each bloom (PERMANOVA; p-value < 0. 01) (Table  2 ). The estimated OTUs richness (Table  1 ) was higher in NC-Pr2 than Eub-Pr1 dataset (ANOVA; p-value < 0. 001; Table  3 ). In the same way, the expected richness and diversity indices values (S. Chao and ACE values, Shannon index) were also significantly higher (ANOVA; p-value < 0.
001; Table  3 ) with NC-Pr2 than with Eub-Pr1 dataset (Table  1 ). At the phylum level, all fractions were largely dominated by the Proteobacteria, followed by the Bacteroidetes (Fig 2 ), regardless of the primer set used. Similarly, the presence of Actinobacteria in the free-living fraction and their almost total absence in the associated fraction was observed for both primer sets. The only differences observed between the two primer sets were observed for rare phyla. In conclusion, both primer sets provided similar results but knowing that the NC-Pr2 primer set (i) allowed a deeper BC description by decreasing the proportion of cyanobacterial 16S rRNA sequences and (ii) did not reduce the richness and diversity in the bacterial communities, the following in depth analysis was performed on data obtained with the NC-Pr2 primers.