dataesr/scientific-paragraphs-categorization huggingface dataset:
5 μl reservoir solution. Large dagger-shaped crystals were obtained after 5 days. The best crystals grew in mother liquor containing 0. 2 M sodium formate, 14% PEG 3350 and 0. 1 M bis-Tris pH 6. 5. 15% glycerol was added to cryo-protect. Data collection and structure determination. Data for both NS1-ED/TRIM25-CC and NS1-FL (R83A/K41/W187A)/TRIM25-CC crystals were collected on beamline IO4 (λ = 0. 9795 Å) at the Diamond Light Source (Oxford, UK) and processed using XDS  53  and autoPROC  54  , respectively. Both structures were solved by molecular replacement (MR) using 3O9T as a search molecule for NS1-ED, 1AIL for NS1-RBD and 4LTB for TRIM25-CC in Phaser  55. For the NS1-ED/ TRIM25-CC structure, we first identified the MR solution for TRIM25-CC, which was fixed as a partial solution in order to locate NS1-ED.
The solution for the three copies of TRIM25-CC and three copies of NS1-ED in the asymmetric unit was unambiguously identified with a translational function Z-score (TFZ) of 19. 8. For the NS1-FL (R38A/K41A/W187A)/TRIM25-CC structure, we first identified the partial molecular replacement solution containing two complexes of NS1-ED/ TRIM25-CC in the asymmetric unit (TFZ = 16. 5). Subsequently, this solution was fixed and two out of four molecules of NS1-RBD were located with a TFZ score of 18. 6. Models were iteratively improved by manual building in Coot and refined using REFMAC5 and Phenix  56, 57. All structural figures were prepared in PyMOL. Protein interfaces were calculated using PISA  58. Coordinates and structure factors were deposited in the Protein Data Bank under accession codes 5NT1 and 5NT2.
For phasing of the human TRIM25 PRYSRPY domain, a crystal grown under native conditions was transferred into the reservoir solution supplemented with 2 mM ethyl-mercuric chloride and soaked for 8 h before cryo-protection and freezing. Diffraction measurements were made at the ESRF on beamlines ID23-2 (native) and ID14-EH4 (Hg derivative) and processed with XDS  53. The structure was solved by single isomorphous replacement with anomalous scattering. Six mercury sites were found and refined with SHARP  59. The resultant map was improved by threefold non-crystallographic averaging and an initial model was built by ARP/WARP  60. Subsequent refinement was done with REFMAC  57. Data collection and refinement statistics are listed in Supplementary Table  1. Data of human TRIM25 CC-PRYSPRY crystals were collected on ESRF beamline ID29, which was able to nicely resolve the diffraction spots along the very long c*-axis (1/827 Å -1 ), and processed with XDS  53.
The structure was solved by molecular replacement using PHASER  55  and the known structure of the hTRIM25 coiled-coil (PDB:4LTB)  21  and the hTRIM25 PRYSPRY domain described here. Refinement was performed with REFMAC  57  and BUSTER. Data collection and refinement statistics are listed in Table  1. An example of the map-sharpened electron density is in Supplementary Figure  4A. There are one and a half coiled-coil dimers in the asymmetric unit with a crystallographic twofold completing the second dimer and the molecules form a three-dimensional network throughout the crystal (Supplementary Figure  4B ). Small-angle X-ray scattering data collection and analysis. Small-angle X-ray scattering (SAXS) measurements were carried out at the BM29 beamline at the ESRF, Grenoble  61. The CC-PRYSPRY sample was measured in NMR buffer (20 mM Na 2 HPO 4 pH 6.
5, 150 mM NaCl, 2 mM DTT) at four different concentrations ranging between 1. 0 and 20 mg/ml at 300 K. Ten frames with 1 s exposure time per frame were recorded for each sample and buffer using an X-ray wavelength of 0. 992 Å. Measurements were performed in flow mode, by pushing the sample through a capillary at constant flowrate to minimise radiation damage. Frames showing radiation were removed before data analysis. For SAXS data collection and processing, the dedicated beamline software BsxCuBE was used in an automated fashion. The one-dimensional scattering intensities of samples and buffers were expressed as a function of the modulus of the scattering vector Q = (4π/λ)sin θ with 2θ being the scattering angle and λ the X-ray wavelength. Buffer intensities were subtracted from samples using the software PRIMUS  62.
In a first calculation of 5000 structures, the interface between the CC and PRYSPRY domain was kept rigid but the linker was allowed to move freely. During the second calculation only one PRYSPRY domain was fixed to the CC domain, whereas the other and the linker were allowed to move freely. The third calculation allowed free movement of both PRYSPRY domains including the linker. Each pool of 5000 structures was fitted against SAXS data using CRYSOL  67. NMR data collection and analysis. NMR spectra were acquired at 298 K on a Bruker Avance III NMR spectrometer equipped with a cryogenic triple resonance gradient probe head at a magnetic field strength corresponding to a proton Larmor frequency of 800 MHz. Samples were measured at concentrations ranging between 0. 1 and 0. 5 mM in 20 mM Na 2 HPO 4 , 150 mM NaCl, 0.
5 mM TCEP at pH 6. 5. All spectra were processed with NMRPipe 68 and analysed using Sparky  69  , CCPNMR  70  and CARA (http://cara. nmr. ch). For backbone resonance assignments of the PRYSPRY domain, HNCACB, CBCA(CO)NH and HNCA spectra were recorded. Backbone resonance assignment was obtained to a completion of 95% (175 out of 184 HN-N resonances). Backbone resonance assignments of the Y463S/Y476S double mutant was possible by tracing the peak shifts. Ambiguous peak positions were left out of the analysis. Peak intensities for NMR titrations were calculated in SPARKY by keeping the linewidth constant during fitting and manually corrected for dilution during the titration. Data availability. Atomic coordinates and structure factors have been deposited in the Protein Data Bank under accession codes 5TN1 for the TRIM25-CC/NS1-ED complex, 5NT2 for the TRIM25-CC/NS1-FL complex, 6FLM for the TRIM25 PRYSPRY domain and 6FLN for the TRIM25 CC-PRYSPRY fragment.
Acknowledgements We thank the  Crick Structural Biology and Proteomics Science Technology Platforms  for expert technical support, especially  Phil Walker ,  Andy Purkiss  and  Evangelos Christodoulou ; the  Diamond Light Source, Oxford  for synchrotron access;  Ian Taylor  for help with SEC-MALLS experiments; the tutors of the December 2016 DLS/CCP4 Workshop for expert advice;  Luigi Martino  and all other members of the KR group and  Rodolfo Ciuffa ,  ETH Zürich  for helpful discussions, and  Steve Smerdon  and  Ian Taylor  for comments on the manuscript. We thank  Sandra Augsten  for sample preparation and  Bernd Simon  for structural modelling. We thank the  EMBL Grenoble Eukaryotic Expression Facility (EEF)  for insect cell culture and HTX Facility for crystallisation. We thank the  European Synchrotron Radiation Facility  for access to its beamlines for the work on TRIM25 PRYSPRY and CC-PRYSRY domains,  Jan Kadlec  for help in solving the PRYSPRY structure,  Bernd Simon  for help in analysing SAXS data and  Sandra Anett Augsten  for technical help.
CT scan analyses CT scans were computed to obtain 5-mm-thick contiguous sections (Advance Workstation, General Electrics Healthcare). Qualitative assessment of lung aeration, was obtained using the UCLA color-coding table (http:// osirixfoundation. com/, OsiriX, Switzerland) and digital post-processing to convert purple into white pixels (http://gimp. org, GNU Image Manipulation Program, Version 2. 8. 20). Quantitative assessment was performed using dedicated software (Maluna 3. 17, University Hospital of Göttingen, Germany). Regions of interest were drawn manually including only lung parenchyma and excluding large vessels and bronchi. Lung gas content, lung weight and aeration distribution were measured as previously reported  [23]. Lung tissue aeration was divided into four compartments according to their Hounsfield Units (HU): hyperinflated (densities from -1000 to -900 HU), normally aerated (-900 to -500 HU), poorly aerated (-500 to -100 HU) and nonaerated tissue (-100 to 100 HU).
Statistical analysis Categorical data were expressed as numbers and percentages, and quantitative data as mean (SD) or median (IQR). Distribution normality was tested using the Shapiro-Wilk test. Continuous variables analyses were performed using Student's t test or the non-parametric Mann-Whitney U test. Changes in arterial blood gases and hemodynamic data were analyzed by longitudinal analysis using mixed models to take into account between-subject and within-subject variability (with patient as random effect). Spearman's rank correlation coefficient was calculated to assess the relationship between HFPV-induced hyperinflation and CMV volumes, and animal pulmonary pressures monitoring. Monitored and measured pressure was compared by Bland and Altman analysis for multiple measurements. P < 0.
RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of rsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.
Bacterial strains, plasmids and growth conditions This study was performed using HG003, a model strain for S. aureus regulation  (23) , and constructed derivatives (Supplementary Table  S1 ). For HG003 gene description, the NCTC8325 nomenclature retrieved from Genbank file CP00025. 1 was used. Engineered plasmids were constructed in Escherichia coli DH5␣, transferred to RN4220 (a strain transformable by exogenous DNA) and subsequently to HG003. Chromosomal gene modifications (deletions and point mutations) were performed using pMAD2 derivatives as described  (24). Conditional gene expression was obtained by cloning genes under the xyl/tetO promoter in pRMC2  (25). Translational regulations were studied by gene fusions with untranslated transcriptional regions (UTRs) + the first codons cloned downstream the rpoB promoter as reported (26) using pTCV-PrpoB-lac (Supplementary Table  S2 ), a pTCV-lac derivative  (27).
2, 9. 8 and 12. 8, and late stationary phase (24 h), (ii) seven samples grown under stress conditions (cold shock, heat shock, oxygen limitation, alkaline stress, peroxide stress, disulfide stress, irondepletion) and (iii) one sample from colonies on BHI-agar plates. The complete description of the 16-condition RNA pool is available in the GEO database (GEO accession number: GSE104971)  (10). Twenty g of each of the 16 total RNA extracts were pooled to obtain the combined RNA extract sample used for the procedure. Hybrid-trap-seq experiments were then carried out as follows: MasterBeads precoated with streptavidin (Ademtech, Pessac-France) were equilibrated in binding buffer (20 mM Tris-HCl, 0. 5 M NaCl pH 8) and incubated 10 min at 20 • C with 100 pmol of biotinylated sRNA. Unbound sRNAs were removed by magnetic separation, and then sRNA-bound streptavidin beads were washed twice with binding buffer.
Read mapping and differential expression analysis Quality control of all transcriptome samples using FastQC (v0. 10. 1) confirmed that the reads could be directly used for the mapping step. Reads were aligned to the S. aureus NCTC8325 chromosome sequence (CP000253. 1) using bowtie2 mapper (v2. 1. 0) and default values  (33). Log-read coverage profiles were computed using in-house shell scripts as described  (32)  and visualized in the Artemis viewer  (34). Uniquely mapped read counts per gene were calculated for each dataset with feature Counts (1. 5. 0-p1, with options specifying paired-end and stranded library) (35) using the list of CDS retrieved from Refseq CP000253. 1. The list of CDSs differentially expressed between two conditions (i. e. rsaE mutant versus wild-type strain; induced versus non-induced RsaE expression) was supplied by SARTools v1.
Read counts per gene were then calculated with HTSeq-count (http:// htseq. readthedocs. io/). Raw read counts of the four datasets (namely, RsaE, RsaA, RsaH and RNAIII used as bait) were normalized using DESeq and fold changes were computed from normalized read counts of RsaE-bait dataset to normalized read counts of control datasets (i. e. the three other sRNA datasets). Genes considered as putative sRNA targets displayed fold changes ≥10.
Computational analysis of RNA-RNA hybrids Target RNA-sRNA interactions were predicted using the IntaRNA package  (38) ; scoring is based on hybridization free energy and accessibility of the interaction sites in both RNA molecules (IntaRNA V 2. 1. 0 through the web interface at http://rna. informatik. uni-freiburg. de with default parameters). For Figure  2 , complete sRNA sequences were used as input, and each putative target comprised the region from the transcriptional start site (TSS) to 150 nucleotides past the start codon. When possible, TSSs were defined from sequencing of the 16-condition RNA pool as described  (32). Coordinates of relevant transcripts are provided (Supplementary Table  S4 ). We searched for consensus motifs in the twelve putative target sequences and rsaE (in antisense) using the MEME suite V.
Quantitative reverse transcriptase PCR and northern blots qRT-PCR experiments were performed on a subset of putative targets selected among the most enriched mRNAs of RsaE Hybrid-trap-seq set. Experiments were performed on biological triplicates and data were analyzed as described; the geometric mean of 4 genes (recA, gyrA, glyA and ftsZ) was used to normalize the samples  (40). All Northern blots were performed as described in duplicates  (41) (42) (43). Samples were separated by either PAGE or agarose gels and probed with 32 P-labeled PCR probes using the Megaprime DNA labeling system (GE Healthcare) (for primer used, see Supplementary Table  S3 ).
The modified protocol is called Hybrid-trap-seq (Supplementary Figure  S1 ). Total HG003 RNAs were extracted from 16 growth conditions and pooled together. Hybrid-trap-seq experiments were run in parallel with four baits: RsaE, and three other sRNAs, RNAIII, RsaA and RsaH. The background noise due to nonspecific RNA binding was filtered out from the RsaE Hybrid-trap-seq dataset by a differential analysis using the three other sRNA datasets. This procedure identified eleven mRNAs and one sRNA that accumulated more reads (>10fold difference) with the RsaE trap than with the three other sRNAs used as baits (Figure  1  and Supplementary Table  S2 ).
ACKNOWLEDGEMENTS We thank  Tim Foster  and  Friedrich G ötz  for providing plasmids and strains. We thank  Sandy Gruss ,  Steven Carson  and  Vinai Thomas  for critical reading of the manuscript. We thank  Sandy Gruss ,  David Halpern ,  Elise Borezée-Durant  and  Hoega Arden  for helpful discussions and warm support. Lastly, we thank  Valerie Shostrom  for statistical analyses. This work has benefited from the facilities and expertise of the high throughput-sequencing platform of IMAGIF (http://www. i2bc. paris-saclay. fr) and of the  INRA MIGALE bioinformatics platform  (http://migale. jouy. inra. fr)for computational resources.
FUNDING Agence Nationale pour la Recherche  [ ANR-2012-BLAN-1602  ( Duplex-Omics );  ANR-15-CE12-0003  (sRNA-Fit)];  Fondation pour la Recherche Médicale  [DBF20160635724];  National Institutes of Health  [ NIH/NIAID P01AI083211 ]. Funding for open access charge:  Agence Nationale pour la Recherche  [ ANR-15-CE12-0003 ].
75) in both transcriptome comparisons. ** Fold change expression of HG003 rsaE relative to wild-type. *** Fold change expression of HG003 rsaE pRMC2RsaE induced relative to not induced. Fold changes and adjusted P-values are available in the GEO database (GEO accession number GSE106457: GSE106456 Supplemental table 1. txt for the ' rsaE relative to wild-type' comparison; GSE106456 Supplemental table 2. txt for the ' rsaE pRMC2RsaE induced relative to not induced' comparison).
Among sites hypomethylated in patients 44% were CpG islands and among hypermethylated sites 25% represented CpG islands. Thirty-four percent CpG sites were isolated ("open sea"  13  ) and 31% of hypermethylated sites were in "open sea" regions. The percentages of hypomethylated CpG sites in "shelves" (2-4 kb from CpG island) was 6%, and that in "shores" (up to 2 kb from a CpG island  13  ) was 17%. The corresponding percentages for hypermethylated sites are 8 and 36% (Fig. 1d ). Chromosomal location of differentially methylated genes. Figure  2  depicts the 375 genes with significant methylation differences between patients and controls and highlights the ten genes with differences ≥ 5% (see also Supplementary Data 2). Eight of these genes are hyper-and two are hypomethylated. In order to check validity of the BeadChip-based primary results we analyzed the methylation status at selected loci by pyrosequencing of bisulfite-converted DNA of the same samples.
strNPCs overexpressing either 3R-or 4R-Tau were co-transfected with siRNAs directed against either DLX1 or DLX1AS. As shown in Fig. 5d , siRNA-mediated knock-down of DLX1 decreased cellular viability, in particular of cells overexpressing 4R-Tau. Conversely, knock-down of DLX1AS significantly increased survival of strNPCs (Fig. 5d ). Functional analysis of differentially methylated genes. We performed in silico functional analyses of 375 different annotated genes that are represented by 451 (out of a total of 717) differentially methylated CpG sites on the Illumina 450 kb chip (Supplementary Data 2). Applying the Pathway Studio software and Fisher´s exact test we searched for enrichment of the Gene Ontology (GO) category "biological process" (Supplementary Data 4). P-values were corrected for multiple testing according to  Benjamini and Hochberg  14.
(2) Tau phosphorylation via GABA(A) receptors: DLX1, DLX2, and GABA(A) receptors (encoded by the differentially methylated genes GABRA5, GABRB3, and GABRD) are members of the GABAergic interneuron-related network in humans  33. Within this network DLX1/DLX2 regulate GABA synthesis  24. Expression changes of DLX1/DLX2 can alter activation of GABA(A). GABA(A) receptors in turn play an important role in Tau phosphorylation  34. This observation is consistent with the notion that Tau may be affected via DLX1/DLX2 -GABA(A) in PSP. Interestingly, we also detected two specific DLX1-binding sites in the MAPT promoter. One is located 1972-bp upstream of the TSS. The previously not described DLX1-binding motif (CAT-AATTAAAAT) was detected using the DiAlign TF program (Genomatix)  35  by utilizing an optimized matrix similarity.
Methods Brain tissue. The use of human brain tissue for this project was approved by the ethics committees of the University of Giessen and of the Technical University of Munich. Brain samples were from patients who had given informed consent before death. For the epigenome-wide DNA methylation analysis, postmortem prefrontal lobe tissue of PSP patients (N = 94, 72 ± 5. 3 years of age, N = 54 (57%) male) and controls without neurological or psychiatric diseases (N = 71, 76 ± 7. 9 years of age, N = 46 (67%) male) was obtained from the CurePSP brain bank, Mayo Clinic, Jacksonville, Florida and the Victorian Brain Bank, Carlton, Australia. Detailed information on clinical and neuropathological findings is given in Supplementary Data 1. Of the PSP patients, 83 were homozygous and 11 were heterozygous for allele H1 of MAPT, none were homozygous for the H2 allele.
Nucleic acids and PCR. DNA and RNA were extracted from tissue samples by standard procedures. DNA was prepared using the tissue extraction kit from Qiagen (Hilden, Germany) and RNA was extracted using the RNeasy Lipid Tissue-Kit (Qiagen). Genomic DNA was bisulfite-converted using the EpiTect Bisulfite Kit (Qiagen). For RT-qPCR, total RNA was converted into cDNA using the QuantiTec-Reverse-Transcription kit (Qiagen). For investigation of the brain tissue samples, all primers used for standard PCR and RT-qPCR were designed using OLIGO Primer analysis software (Vers. 6. 41; Molecular Biology Insights, Inc. , Colorado Springs, CO, USA). Primers used for qPCR are given in Supplementary Table  1. Fluorescence data were compiled using the CFX384 qPCR system from Bio-Rad (Hercules, CA, USA). Housekeeping genes EIF4A2 and CYC1 were co-analyzed for normalization of RNA content in each brain sample  53.
Quantification of expression differences (fold-expression) was calculated using the REST-Software-Package-2009 as described elsewhere  54. Expression of the housekeeping genes B2M, EIF4A2, and CYC1 was analyzed for normalization in cell culture experiments with SH-EP und Ntera2 cells. Stability values, i. e. , coefficient of variation (CV-value) and gene stability value (M-value) for each housekeeping gene were < 0. 25 for CV-and < 0. 5 for the M-value. Fold expression was calculated with the integrated qBase module of the Bio-Rad CFX Manager 3. 1 (3. 1. 1517. 0823) software. Significance of expression changes was evaluated by unpaired two-tailed Student´s t-test. We have used DNAse treated total-RNA in all RT-qPCR experiments. This excluded co-amplification of DNA that might have contaminated RNA preparations.
Exclusion of DNA co-amplification was particularly important for analysis of exon1-derived RNA of DLX1AS. Exon1 RNA of DLX1AS was analyzed since this exon was present in all alternative transcripts. RT-qPCR analyses were performed on RNAs extracted from strNPCs using SYBR Green Select qPCR Supermix (#4472954, Life Technologies, Carlsbad, USA), 5 ng cDNA synthesized from total RNA, 0. 2 μM forward and reverse primers (primer sequences are given in Supplementary Table  1 ). qPCR analysis was performed on a Step One Plus instrument (Thermofisher Scientific, Carlsbad, USA). Initial incubation at 50 °C for 2 min and an additional 2 min at 95 °C was followed by 40 cycles of 15 s at 95 °C and 60 s at 60 °C. Threshold cycle (CT) values were set within the exponential phase of the PCR. Data were normalized to five housekeeping genes: TBP, GPBP1, PPIA, PSMC1, UBQLN2 and the comparative normalized relative quantity (CNRQ) was used to calculate fold expression (qBase®, Biogazelle, Belgium).
Gene regulation was statistically evaluated by twotailed Student's t-test on the assumption of equal variances. Array analysis. The Infinium 450k array of Illumina Inc. (San Diego, CA) was used for methylation analysis. This array analyzes more than 485,000 CpG sites distributed over the entire genome. Two-hundred nanograms of bisulfite-converted DNA were hybridized to the arrays according to the manufacturer´s instructions. In order to exclude batch effects, we alternated hybridization of PSP and control samples. Arrays were scanned on an Illumina iScan platform at the Life & Brain Center (Bonn/Germany). Array data were evaluated, preprocessed and normalized using the ChAMP pipeline (V. 2. 8. 1)  55, 56  with minor modifications. Specifically, raw array data were uploaded to the ChAMP pipeline using the minfi option  57.
Relative proportions of neuronal and non-neuronal cells in each sample were estimated based on the raw data applying the compositeCellType = "DLPFC" option of estimateCellCounts function of the R Bioconductor minfi package  58. Probes with less than three measured beads or a detection P-value > 0. 01 as well as probes interrogating CpGs that fall on or near to a SNP were removed based on recommendations by Zhou et al. 59. Similarly, probes aligning to multiple locations as defined by Nordlund et al. 60  were removed from the analysis. All samples had more than 99. 3% of valid probes, therefore, no samples were removed from the analysis based on the quality of the data. The sex of each sample was verified using an in-house R script based on the DNA methylation profile of the X and Y chromosomes.