dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We express our gratitude to our colleagues in the CERN accelerator departments for the excellent performance of the LHC. We thank the technical and administrative staff at the LHCb institutes. We acknowledge support from  CERN  and from the national agencies:  CAPES ,  CNPq ,  FAPERJ  and  FINEP (Brazil) ;  NSFC (China) ;  CNRS/IN2P3  (France);  BMBF ,  DFG  and  MPG (Germany) ;  INFN (Italy) ;  FOM  and  NWO  (The Netherlands);  MNiSW  and  NCN (Poland) ;  MEN/IFA (Romania) ;  MinES  and  FASO (Russia) ;  MinECo (Spain) ;  SNSF  and  SER (Switzerland) ;  NASU (Ukraine) ;  STFC  ( United Kingdom );  NSF (USA). We acknowledge the computing resources that are provided by  CERN ,  IN2P3 (France) ,  KIT  and  DESY (Germany) ,  INFN (Italy) ,  SURF  (The Netherlands),  PIC (Spain) ,.
Solid state magnetic and thermal properties The influence of the methyl substituents on the SCO of the 1,3bpp/Fe(II) complexes was first assessed through bulk magnetic susceptibility measurements. Data from polycrystalline samples of 2 and 3 were collected between 5 and 400 K in the warming and cooling modes under a constant magnetic field (see the ESI †) and were compared to these from polymorphs 1a and 1b. All the results are displayed in Fig. 5  in the form of χ M T vs. T plots (χ M is the molar paramagnetic susceptibility). At low temperature, all complexes are essentially diamagnetic, with χ M T values at 100 K ranging 0. 06 to 0. 17 cm 3 K mol -1. In all cases, an abrupt increase of χ M T occurs upon warming up to nearly constant values of 3. 01 (2), 3. 26 (1a) and 3. 4 cm 3 Kmol -1 (1b), while for 3 the product (2.
Single-crystal X-ray diffraction Data for 2 and 3 were collected on a Bruker APEXII QUAZAR diffractometer equipped with a microfocus multilayer monochromator with MoKα radiation (λ = 0. 71073 Å), at 100 and 298/300 K for both compounds. Data for 2b were collected at 100 K on Beamline 11. 3. 1 at the Advanced Light Source, on a Bruker D8 diffractometer equipped with a PHOTON 100 CCD detector and using silicon (111) monochromated synchrotron radiation (λ = 0. 7749 Å). Data reduction and absorption corrections were performed with SAINT and SADABS, respectively. 53 ll structures were solved by intrinsic phasing with SHELXT  54  and refined by full-matrix least-squares on F 2 with SHELXL-2014. 55 The structure of 2b was refined as a 2-component twin, using a twin law found through PLATON. 56 The structure was first solved in P 1 on HKLF4 data and then transformed to the monoclinic Cc with PLATON/ADDSYM.
Differential scanning calorimetry (DSC). These experiments were done with a Q1000 calorimeter from TA Instruments equipped with the LNCS accessory. Calibration of the temperature and enthalpy scales was achieved with a standard sample of In, using its melting transition (156. 6 °C, 3296 J mol -1 ). Mechanically crimped Al pans with an empty pan as a reference were used. All reported data were obtained at a scanning rate of 10 K min -1. Measurements on 2 were also done at scanning rates down to 0. 5 K min -1 to confirm that no hysteresis was present. For heat capacity, a synthetic sapphire was measured in the same temperature range. By comparison, an overall accuracy of 0. 2 K for the temperature and up to 10% for the heat capacity was estimated over the whole studied temperature range. Powder X-ray diffraction (PXRD).
Computational details All energy evaluations were performed on molecular geometries optimized in the HS and LS states using the Quantum Espresso package (QE),  57  the PBE + U functional with a Hubbard-like U parameter of 2. 65 eV on the "d" orbitals of iron, the D2 correction of Grimme,  58  and Vanderbilt pseudopotentials. 59 The molecules were introduced in a cubic cell of 60 Bohr 3 to isolate them from the virtual counterparts, which means that all calculations simulate gas-phase conditions. This has been done with the help of the Makov-Payne approximation to treat the charged unit cells. 60 The Hubbard term has been used to cure the incomplete cancellation of the electronic self-interaction in the PBE functional, which results in an unrealistic delocalization of orbitals. 61, 62 The value U = 2.
Acknowledgements The authors thank the  Generalitat de Catalunya  for the prize ICREA Academia 2008 and 2013, and acknowledge the  ERC  for the Starting Grant StG-2010-258060 (GA),  MINECO  for grants  MAT2014-53961-R (OR) ,  MAT2015-70868-ERC (OR ),  CTQ2012-32247  (GA) and CTQ2015-68370-P (GA, CBM, RD),  LabEx-Chemistry of Complex Systems  for the post-doctoral grant  ANR-10LABX-0026CSC  (SV), the regional  High-Performance Computing (HPC) center in Strasbourg for computational resources (SV)  and the  Avempace II Erasmus Mundus Action  2program for a PhD scholarship (MD). This research used resources of the  Advanced Light Source , which is a  DOE Office of Science User Facility  under contract no. DE-AC02-05CH11231.
Upon completion of the measurement at 50 µmol CO2 mol -1 , Ca was increased back to 400 ppm to check whether the original An could be restored. If this was achieved, Ca was increased stepwise to 600, 700, 1000, 1200, 1500 and 2000 ppm. Leaves were allowed to equilibrate for at least 5 minutes at each step before data logging. At the end of each A-Ci curve, the leaf area and mass enclosed in the chamber was measured with a leaf area meter portable laser. The specific leaf area (SLA) was determined as the ratio of the leaf area to leaf dry mass of individual leaves. To estimate the CO2-saturated rate of photosynthesis (Asat), CO2 response curves were fitted using a three components exponential function  (Watling & Press 2000)  according to the following equation (eqn. 1): where An is leaf net photosynthetic rate and x is Ci.
iForest -Biogeosciences and Forestry L s =1-A/ A o A n =a (1-e -bx )+c Photosynthetic carbon assimilation in Cork aok seedlings were also calculated. All ANOVA analyses were performed using the software package SigmaPlot ® (Systat Software Inc. , San Jose, CA, USA). Pearson's correlation analysis was done using XLSTAT v. 2014 (http:// www. xlstat. com) after data standardization.
Acknowledgments This work was supported by the  National Research Institute for Rural Engineering, Waters, and Forestry in Tunis, Tunisia. We wish to thank  Dr. Peter Streb  ( Université-Paris-Sud 11, Ecologie, Systematique et Evolution, UMR-CNRS 8079, Orsay, France ) for carefully reading the manuscript. We sincerely thank  Mr. Ahmed Al-Fatlawi  for his review of the English language of this manuscript.
One of the possible direction to improve autofluorescence bronchoscopy is using multiphoton excitation, because of its advantages such as deeper penetration depth, reduced photodamage, and lack of out-of-focus bleaching  [28] [29] [30]. This has fostered the development of multiphoton endoscopes with great potential in clinical research for tissue imaging  [31] [32] [33] [34] [35]. However, the development of endoscopy techniques is slowed down by the fact that it is almost impossible to perform an accurate autofluorescence study of human tissue within the lungs due to the laborious procedure involved. While in most cases tissue health state influence autofluorescence the exact difference of spectral parameters might vary significantly. This variation might be partly explained by heterogeneity of NADH and flavins autofluorescence caused by altered cellular metabolism in different patients as well as response to treatment, therefore one needs to establish a large database to determine the long-term outcome of patients undergoing autofluorescence bronchoscopy  20, 36.
Acknowledgements L. B. and V. K. acknowledge the financial support by  Swiss SEFRI  (project  C15. 0041 ). L. B. , V. K. and S. C. also acknowledge the financial support from the  French-Switzerland Interreg programme  (project  NANOFIMT ). L. B. and J. -P. W. acknowledge also the financial support for equipment from Swiss  NCCR MUST and Fondation Schmidheiny, Geneva. This study was performed in the context of the European  COST Action MP1302, Nanospectroscopy.
Next, we tested whether there are specific genes on chromosomes X, 8, and 12 that are more prone to inactivation regardless of the Xist transgene position along the chromosome. To this end, we evaluated each gene in our allele-specific RNA-seq data sets. We first calculated the averaged allele-specific expression ratio for each gene across all clones of each category. Second, we ranked all X-linked and autosomal genes according to their general degree of silencing upon doxycycline treatment. Finally, we divided chromosomes X, 8, and 12 ranked genes into three categories: (I) genes that are efficiently silenced, (II) genes that are partially affected and (III) not silenced genes (Fig. 5a-c ). Ranking genes in separated data sets for chromosomes X, 12, and 8 allows us to relate different silencing effects to genetic and epigenetic features along each of the three chromosomes, and independently of the generally more efficient inactivation of chromosome X compared to autosomes (Fig.
We performed sequencing of targeted locus amplification libraries on the Illumina MiSeq platform pooling ~20 libraries per V2 PE150 sequencing run. Reads were mapped using split-read aware alignment with BWA mapping software. Density plots. Available ChIP-seq data sets were retrieved from the Gene Expression Omnibus (GEO) database and mapped to reference genome mm10 as previously described  75  , i. e. , sequences with low complexity that are unlikely to map uniquely to the genome were removed from the described ChIP-seq data sets using prinseq-lite with the dust method with 7 as threshold. The remaining sequences with a Phred score < 70 were mapped to the mm10 reference genome using Bowtie v0. 12. 7, where a seed length of 36 was used in which we allowed a maximum of two mismatches. If a read had multiple alignments, only the best matching read was reported.
Duplicated reads were removed. ChIP-seq data sets with multiple replicates were merged. For the ChIP-seq density plots mapped reads were counted in bins of 200 bp in 8 kb centered on the TSSs of genes. Reads were normalized to RPKM. Genes were divided in categories and average RPKMs were plotted. Box plots. The positions of all LINE and SINE elements along the entire length of chromosomes X, 12, and 8 were obtained from the mm10 repeat masker table (UCSC genomic browser). LINE and SINE elements were counted in 1 Mb regions centered on the TSSs of genes. Genes were divided in categories and plotted in box plots. RNA sequencing. RNA samples were prepared with the Truseq RNA kit, sequenced according to the Illumina TruSeq v3 protocol on the HiSeq2000 with a single 43 bp read and 7 bp index. Allele-specific analysis was performed as previously described with minor modifications  33.
Mouse Cast/Ei and 129/Sv genomes were built from the Mouse Sanger database project (version 3) and Mouse mm10 reference genome. Raw sequencing reads were aligned to both genomes with the TopHat aligner (v2. 0. 6). RefSeq gene annotation from UCSC genome browser was used as the reference for known transcripts. For each sample, mapping results against both parental genomes were merged to keep the best alignment for each read. Only unique alignments were reported for downstream analysis. At each SNP site, the number of bases matching each genotype was counted to obtain the abundance of the 129 and Cast alleles (samtools mpileup v0. 1. 19). The allelic counts per gene were then estimated by summing up the number of 129-and Castspecific reads of all exonic SNPs within the gene. Genes containing a singlepolymorphic site were included in the analysis only when they show a coverage higher than eight reads, whereas for genes carrying multiple informative SNPs the coverage threshold was of five reads per polymorphic site.
Acknowledgements This work was supported by grants from the  Netherlands Organization for Scientific Research  ( NWO-VICI 865. 10. 003 ) and the  European Research Council  ( ERC 260587 ) to J. G. ; and by an  EMBO  short-term fellowship ( ASTF640-2014 ) to A. L. We are thankful to  Sarra Merzouk  for carefully reading the manuscript and  Aristea Magaraki  and  Federica Federici  for help with some of the experiments.
Elemental analysis was conducted using the EDAX Element EDS Analysis System and accompanying Element EDS Analysis Software Suite. DNA Preparation. Cross-sectional tissue samples were taken from multiple locations (anterior, middle, and posterior) along the gills of three adult specimens of Kuphus polythalamia (SI Appendix, Table  S3 ). Approximately 25 mg of tissue was excised from each section, rinsed thoroughly with filter-sterilized seawater, and homogenized in 4. 5 M guanidinium thiocyanate, 2% N-lauroylsarcosine (wt/vol), 50 mM EDTA, pH 8. 0, 25 mM Tris•HCl. Genomic DNA was extracted from each tissue homogenate using a QiaCube DNA extractor (Qiagen) and Qiagen DNeasy Blood and Tissue Kit followed by the Zymo DNA Clean and Concentrate Kit, according to the respective manufacturer's recommended protocols.
Phylogenetic Characterization of Bacteria. To establish the phylogenetic identity of bacterial isolates in culture, and uncultivated bacteria in gill tissue, genes encoding 16S rRNA (SSU), a multifunctional cellulase (celAB), and a rhodaneselike thiotransferase (sseA) were PCR amplified from genomic DNA extracts and sequenced using primers and PCR conditions described in SI Appendix, Table  S1. PCR products were purified using GenCatch PCR Purification Kit and sequenced using an ABI 3130xl Genetic Analyzer (Macrogen). Similarity to previously pub-lished sequences in GenBank (National Center for Biotechnology Information) was determined using BLASTn or BLASTp as appropriate. Phylogenetic analyses of 16S rRNA sequences was performed using programs implemented in Geneious, version 8. 1. 2. Sequences were aligned using MAFFT (version 7.
017) by using the auto algorithm. The aligned sequences were trimmed manually, resulting in a final aligned dataset of 1,172 nucleotide positions. Phylogenetic analysis was performed using MrBayes (version 3. 2. 6) using the GTR + I + Γ substitution model. Chain length was set to 2 million, subsampling every 2,000 generations, and discarding the first 20% of analytical results (burn-in). FISH. FISH was performed as in ref. 34. Briefly, all samples were fixed in 4% paraformaldehyde in filter-sterilized seawater at 4 °C overnight. Samples were transferred to 70% ethanol and stored at -20 °C. Fixed samples were embedded in paraffin and sectioned at 10-μm thickness. Sections were deparaffinized with a 5-min treatment in xylenes, followed by a 5-min treatment in ethanol, and then rinsed in ddH 2 O.
Slides were air-dried. Sections were hybridized with 5 ng/μL probe (final concentration) in hybridization buffer [35% formamide, 0. 9 M NaCl, 20 mM Tris•HCl (pH 7. 4), 0. 01% SDS] for 2 h at 46 °C. After hybridization, the slides were incubated at 48 °C in wash buffer [35% formamide, 0. 7 M NaCl, 20 mM Tris•HCl (pH 7. 4), 50 mM EDTA, 0. 01% SDS] for 20 min, rinsed with ddH 2 O, and air-dried. After drying, 30 μL of 500 mM Sytox Green was added and incubated for 15 min, and then washed with ddH 2 O. Slides were then mounted in a 4:1 Citifluor (Citifluor, Ltd. )/Vectashield (Vector Labs) mounting medium. Slides were visualized on a Zeiss AxioImager laser-scanning confocal microscope with LSM 5 Pascal, version 4. 0, imaging software, with imaging parameters held constant between specific and control probes.
doe. gov/. The raw reads were assembled using HGAP (version: 2. 0. 0) (35). The final draft assembly contained 1 contig in 1 scaffold, totaling 4. 8 Mbp. The input read coverage was 204×. Metagenome Sequencing and Assembly. Illumina libraries were prepared as ∼350-bp inserts and sequenced using an Illumina HiSeq 2000 sequencer with 125-bp paired-end runs at the Huntsman Cancer Institute's High-Throughput Genomics Center at the University of Utah. Illumina fastq reads were trimmed using Sickle  (36)  with the parameters (pe sanger -q 30 -l 125). The trimmed FASTQ files were converted to FASTA files and merged using the Perl script 'fq2fq' in IBDA_ud package  (37). Merged FASTA files were assembled using IDBA_ud with standard parameters in Futuregrid (https://portal. futuresystems. org/) or the Center for High Performance Computing at the University of Utah.
A single FASTA file containing all bacterial contigs from 2141T-like clusters from each metagenome sample was used in the synteny comparison. The identity distributions of the average nucleotide identity (ANI) between the genome of strain 2141T and the pooled metagenome sequences (SI Appendix, Fig. S4 ) was calculated by online tool (enve-omics. ce. gatech. edu/ani/) with the following parameters: minimum length, 700 bp; minimum identity, 70%; minimum alignments, 50; window size, 1,000 bp; step size, 200 bp. SNP Analysis. A blast database was produced from the merged FASTA file used in IDBA_ud assembly with the command "makeblastdb -input_type fasta -dbtype nucl -parse_seqids". A BLASTn search (-perc_identity 90 -max_target_seqs 100000000 -outfmt "6 qseqid sseqid pident length evalue qcovs qlen slen") was performed to find Illumina reads that are homologs of the gyrB gene sequence in the genome of sulfur-oxidizing strain 2141T.
Hits were defined as "length/slen > 0. 95"; the sequence heads of the hit reads were extracted using Samtool  (39, 40)  and were aligned to the reference gyraseB gene using the CLC genomics workbench (version 9. 0). The resulting alignment was equally split into 29 fragments (starting from the 85th base pair, 85 bp for each) by shell script (alignment_split. sh; for code, see Dataset S1). The alignment in each fragment were also removed by the shell script. SNP categories of the reads in each small alignment were retrieved by unambiguous assembly (Word Length = 4, Word Length = 4, Maximum Gaps Per Reads = 0, Maximum Mismatches = 0, Maximum Ambiguity = 1) using Geneious (R9). Cell and Tissue Preparation for RuBisCO Assays. Analyses on bacterial samples were performed on previously frozen cell pellets.
Acid-stable products were resuspended in 400 μL of water and 7 mL of scintillation fluid, and label incorporation was measured using a Beckman LS6500 scintillation counter. Counts were converted to total micromoles of C incorporated and normalized using the negative controls at the corresponding time point (SI Appendix, Table  S5 ). Protein Assay. The Thermo Scientific Pierce 660-nm Protein Assay was chosen to avoid interference from bicine and DTT present in the RAB. Sonicated extracts were assayed according to manufacturer's instructions and compared with an albumin standard curve. All samples fell within the range of the standard curve. Data Analysis. All data analysis was carried out in GraphPad Prism 6. For the activity assays, each triplicate was plotted versus time, and a line was fitted to the data (SI Appendix, Table  S5 ).
The mass spectrometry settings were as follows: capillary voltage, 2. 50 kV; source temperature, 150 °C; desolvation temperature, 600 °C; cone gas flow rate, 150 L/h; desolvation gas flow rate, 1200 L/h; dwell time, 17 ms. Data collection and analysis was performed using Waters MassLynx software. PNPO activity was calculated by subtracting the endogenous PLP measured at 0 min in the T0 DBS punch from the amount of PLP present after 30 min of incubation of the DBS with PNP substrate in the T30 DBS punch. The enzyme activity was calculated and reported as pmol PLP (3 mm DBS) -1 h -1. To make comparisons with published data, we made the assumption that a 3 mm DBS punch contains 3. 2 μL of blood,  23  and a conversion factor of 0. 3125 was used to convert this activity to pmol PLP μL blood -1 h -1.
The area under the curve (AUC) upon LC-MS/ MS elution was thus used to quantify pyridoxal levels. Statistical Analysis. All analyses were carried out using GraphPad Prism version 6. 05 for Windows (GraphPad Software, La Jolla, CA). Statistical analysis was performed using one-way ANOVA followed by Tukey's multiple comparisons test; ** = P < 0. 01; **** = P < 0. 0001.
Eighteen samples were collected  from subjects (age range 1 day-25 years) with known variants in the PNPO gene (Table  S-5 ). Three of these samples were from individuals homozygous for the PNPO variant p. R116Q. We were interested in looking at the effect of p. R116Q as it is predicted to affect FMN binding and binding of pyridox(am)ine 5′-phosphate oxidase monomers to form the dimeric form of the enzyme; however, previous in vitro studies have suggested that this variant has high residual activity and indeed it is present in the ExAC database with an allele frequency of 0. 0558, suggesting it could be a polymorphism. 33 We have concluded previously, 2 because of its higher incidence in B 6responsive epilepsy patients relative to the general population, that it contributes to the pathogenesis of epilepsy and that it may be a common mutation, perhaps responsible for the susceptibility locus for genetic generalized epilepsy on 17q21.
This will be a powerful tool for clinicians to help diagnose these patients. ■ ASSOCIATED CONTENT * S Supporting Information The Supporting Information is available free of charge on the ACS Publications website at DOI: 10. 1021/acs. analchem. 7b01358. Tables and figures showing experimental data collected during optimization of enzyme assay conditions as well as more detailed information on the PNPO-deficient subjects analyzed during method development (PDF).
■ ACKNOWLEDGMENTS We would like to thank  Dr. F. Feillet ,  Dr. O. Maier ,  Dr. N. Gayatri ,  Dr. M. Taylor ,  Dr. H. Mundy ,  Dr. E. Del Giudice ,  Dr. L. Delfiner ,  Dr. C. Freihuber ,  Dr. P. Bala ,  Dr. Livingston , and  Dr. I. Kern  for their involvement in the study and  Dr. E. S. Reid  for her technical help and support. M. P. W. , P. T. C. , and P. B. M. are supported by  Great Ormond Street Children's Charity (GOSHCC). This project was funded by GOSHCC. P. B. M. , P. T. C. , P. G. , and S. J. R. H. are supported by the  National Institute for Health Research Biomedical Research Centre at GOSH for Children NHS Foundation Trust and University College London. P. G. was supported by a  Wellcome Trust Senior Clinical Fellowship  ( WT095662MA ). We are indebted to the patients and their families for participating in this study.
, 2001) , as shown in Fig. 7. The unit cell of the structure giving quasi-diffraction (Fig. 7a ) is encased in one pair of {110} (basal plane) planes, one pair of {112} planes and one pair of {101} planes (prismatic planes). The only difference from the cubic structure of the phase is that the atoms on {110} between the basal planes are displaced in the h110i direction by an amount a/6 h110i , as indicated in Fig. 7 (a). For comparison, the ideal structure is plotted as dashed lines in the figure. Using this structure model, the diffraction patterns of all acquired zone axes were simulated, using the software package CrystalMaker. With six possible variants (there are six distinct {110} planes), all the observed diffraction spots corresponding to the quasidiffraction are reproduced and properly indexed.
Overnight attended polysomnography A standard PSG montage was used for each attended inlaboratory diagnostic evaluation and included electroen-cephalogram (EEG, F4, C4, O2), electrooculogram (EOG), chin electromyogram (EMG), leg EMG, electrocardiogram (ECG), breathing effort parameters, airflow parameters, oxygen saturation (SpO 2 , finger probe, Oximetry board Massimo), and body position, according to AASM recommendations. The data were anonymized and then manually scored. Sleep stages, arousals, and abnormal respiratory events were quantified according to AASM 2007 criteria. 17.