dataesr/scientific-paragraphs-categorization huggingface dataset:
Although the average atomic structure of FeSi does not exhibit any notable changes with temperature, anomalous phonon properties have been reported recently from Raman  12  and inelastic neutron-scattering measurements  17. The authors of those publications found a surprisingly strong softening of phonon energies with increasing temperature, which they related to the closing of the charge gap in FeSi. However, the information obtained was limited because of restrictions in the accessible range of temperature and wave vector of Raman measurements. Furthermore, most inelastic neutron-scattering data were obtained on powder samples, not allowing an investigation of the lifetimes of phonon modes, or their directional dependences in reciprocal space. We have performed inelastic neutron-scattering experiments on a high-quality single crystal of FeSi.
Acknowledgements We acknowledge valuable discussion with L. Pintschovius. S. K. and F. W. were supported by the young investigator group VH-NG-840 of the Helmholtz society. T. K. was supported by the  DFG  through  SFB/TRR80. We acknowledge support by  Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Karlsruhe Institute of Technology.
Acknowledgments AJOM was financed by a PhD Grant of the  FPI program  from the  Spanish Ministerio de Ciencia e Innovación ;  TCB 's PhD Grant belonged to the  FPU Program  of the same Ministry. AJOM and AGC were supported by Projects  CGL2010-20748-C02-01  and  CGL2013-48247-P  of the mentioned Ministry, and  RNM6433  of the  Consejería de Economía, Innovación y Ciencia of the Junta de Andalucía. The European COST Action TD0903 contributed via two  Short Term Scientific Missions  to AJOM in FM's lab in Dijon. We also want to thanks  Carmen Salas  from the  University of Malaga (Spain)  for providing Pteria hirundo's shells.
Understanding the modification of the graphene's electronic structure upon doping is crucial for enlarging its potential applications. We present a study of nitrogen-doped graphene samples on SiC(0001) combining angle-resolved photoelectron spectroscopy, scanning tunneling microscopy and spectroscopy and X-ray photoelectron spectroscopy (XPS). The comparison between tunneling and angle-resolved photoelectron spectra reveals the spatial inhomogeneity of the Dirac energy shift and that a phonon correction has to be applied to the tunneling measurements. XPS data demonstrate the dependence of the N 1s binding energy of graphitic nitrogen on the nitrogen concentration. The measure of the Dirac energy for different nitrogen concentrations reveals that the ratio usually computed between the excess charge brought by the dopants and the dopants' concentration depends on the latter.
This is well illustrated in Fig. 4b  where the blue curve on the graph is an EDC acquired on the most lightly-doped sample (c = 0. 08%) (computed as the angle-integration of the spectrum displayed above the graph, on the same energy scale) and the black curve is an average over tunneling spectra acquired at four different locations (at each location ten spectra were acquired) with four different tips, on the same sample, both on the same horizontal scale (the sample bias for the STS and the binding energy for the EDC). As mentioned above, the spatial inhomogeneities of the tunneling spectra are the smallest for this sample, making the comparison with ARPES data ideal. In a first approximation, the two curves of Fig. 4b  should both be (below the Fermi level E F ) proportional to the DOS of the doped graphene (which is linear in energy close to the Dirac point).
Conclusions In conclusion, we combined STM/STS with ARPES and XPS experiments to investigate the charge distribution and electron doping in nitrogen-doped graphene. STS allows us to reveal that the Dirac energy varies spatially at the nanometer scale. The comparison of STS with ARPES shows that the STS data have to be corrected by the phonon excitation energy. The combination of the three experimental techniques together with theoretical arguments allows us to draw a picture of the doping effect of nitrogen atoms. The additional electron of nitrogen is distributed in two ways, a localized state and a delocalized state, the latter being responsible for the Dirac energy shift. This distribution depends on the concentration: at high concentration, the nitrogen atoms are more oxidized and the Dirac energy shift per nitrogen atom is larger.
Acknowledgments F. J. thanks  Alexandre Felten  for assistance with the XPS measurements. J. G. is a research associate of F. R. S. -FNRS. V. R. thanks the  Institut Universitaire de France  for support. Y. T. thanks the  Labex SEAM program  No. ~ANR-11-LABX-086  for financial support in the framework of the Program No. ~ANR-11-IDEX-0005-02. E. H. C. acknowledges support from the  National Science Foundation  under Grant No. DMR-1401193. The research leading to these results has received funding from the  European Union Seventh Framework Programme  under grant agreement n o 604391 Graphene Flagship.
Acknowledgements Financial support from  Central Research Grants Scheme of Deakin University  and a Discovery grant of the  Australian Research Council  is acknowledged. The  Australian Research Council is also acknowledged for funding Deakin University's Magnetic Resonance Facility , JEOL JEM-2100F transmission electron microscope and combined FTIR/Raman microspectroscopic instrument through LIEF grants  LE110100141 ,  LE100100195  and  LE120100166. The authors thank  Timcal Ltd. for providing a sample of Super P Li™ carbon black and acknowledge the use of facilities in the Victorian Node of the  Australian National Fabrication Facility (ANFF).
Material analysis. To investigate the influence of DUV irradiation on sol-gel IGZO, several material analysis methods such as XPS, AFM, FTIR, and ellipsometry analyses are performed on sol-gel IGZO films with and without DUV laser irradiation. The reactions within the sol-gel matrix under photochemical and thermal annealing are investigated by XPS. To investigate the condensation reactions activated by photochemical and thermal processes, we first focus on the O 1 s components. The raw spectra and details of the deconvolution are given in Figure  S4. Basically, one can find on each samples, 4 main components that are attributed according to data from literature  24  : O of carboxylate and nitrate species (533. 4 eV), O of surface hydroxide (532. 2 eV), O near an oxygen vacancy or O of volume hydroxide in defects, with interaction (H bonding for example) (531.
XPS analysis was performed on a Gammadata Scienta (Uppsala, Sweden) SES 200-2 X-ray photoelectron spectrometer under ultra-high vacuum (P < 10 -9 mbar). The monochromatized AlKa source (1486. 6 eV) was operated at a power of 420 W (30 mA and 14 kV) and the spectra were acquired at a take-off angle (TOA) of 90° (angle between the sample surface and photoemission direction). During acquisition, the pass energy was set to 500 eV for wide scans and to 100 eV for high-resolution spectra. CASAXPS software (Casa Software Ltd, Teignmouth, UK, www. casaxps. com) was used for all peak fitting procedures and area of each components were modified according to classical Scofield sensitivity factors (Zr3d: 7. 04, C1s: 1. 00 and O1s: 2. 93). All components on high-resolution spectra were referenced according to the CH x component at 285.
Acknowledgements This work was supported by  CNRS-MoST France-Taiwan  collaboration project under contract number  103-2911-I-009-515 ,  104-2923-E-009 -001 -MY3 , and  ANR  program  PHOTOMOC  ( N° ANR-14-CE26-0039-01 ). The authors thank  Philippe Fioux  for running XPS experiments.
The thickness of Material A corresponding to a small force of 0. 01 N was found to be 4. 49 mm, which was considered the initial thickness of the material h 0. Water was added at the same level of the material to ensure the full imbibition of the material. Several types of tests were performed, where the sample was: • Compressed and immediately uncompressed with a certain velocity. • Compressed with different velocities and kept over time under a fixed strain. • Compressed in several steps with pauses of constant strain over time. The reproducibility of the results was checked by superposition of the stress-strain experimental data for the three samples of different diameters and the results were agreeable (maximum 6% relative error at any given strain). Loading (v=0. 3mm/s) Unloading (v=0.
Two separate sets of data were presented for tensions along x and y; because of the finite size of the polycrystalline models, the properties were not expected to be entirely isotropic. Stress-strain curves were then analyzed after the conversion of engineering strain into true strain to determine elastic and fracture properties. Obtaining these properties was essentially trivial. The only subtlety here was related to the determination of Young's modulus (Y) because of well-known nonlinearity at low strains due to both out-of-plane ripples at mechanical equilibrium  (19)  and the interatomic potential used  (36). In this work, Y was determined by fitting the stress-strain curves in the 3% strain interval showing the highest slope. In some cases, we observed that this linear domain takes place at large strains (up to 5 to 8%, as shown in fig.
Acknowledgments:  J. -M. L. acknowledges B. Coasne  for fruitful discussions. Funding: This work was supported by  Agence Nationale de la Recherche  through the  PyroMaN project  (contract  ANR-2010-BLAN-929 ) and by  Institut Carnot  " Materials and Systems Institute of Bordeaux. "J. -M. L. 's stay at the  Massachusetts Institute of Technology  was supported by the  French ICoME2 LabEx  (grant  ANR-11-LABX-0053 ). Part of the simulations was achieved using the computer facilities at  Mésocentre de Calcul Intensif Aquitain. Author contributions: J. -M. L. and G. L. V. designed the study. A. G. , B. F. , P. A. , and  J. -M. L. developed  and optimized the simulation codes. A. G. , B. F. , and J. -M. L. performed the simulations. A. G. , B. F. , G. L. V. , and J. -M. L. analyzed the results.
Acknowledgements Authors acknowledge the support from  EU   FP7  grants, GRENADA (246073) and FUNPROB (269169) and by the  Engineering and Physical Sciences Research Council  via an Industrial  CASE award for JDW (Award No   07001545 ). CB is supported by the  Lloyd's Register Foundation. The  Lloyd's Register Foundation  helps to protect life and property by supporting engineering-related education, public engagement and the application of research.
The interaction of the probe beam with this index profile produces a scattered field with sidebands at the modulation frequency. The scattered field is then detected through its beatnote with the probe field reflected at the glass sample interface, which plays the role of a local oscillator as in any heterodyne technique and is extracted by lock-in detection. The modulation frequency was set to 700 kHz for which high signal to noise ratios are obtained with ms integration times  20. The sample was mounted on a piezo-scanner stage that allowed scanning the sample to acquire 2D images. All data where acquired with integration times of 5 ms/pixel using a resolution of 100 nm/pixel. Figure  2a  shows examples of PhI images corresponding to fractions C1, C2, C3, C4 & C5 (CoMoCAT sample preparations).
We analyzed the PhI signals by an automated home-built matlab routine to identify each point-like signal and fit its distribution by a 2D Gaussian. The fit amplitude of each spot provides a measure of the absorption signal of each detected nanotube. As expected, a monotonic behavior spanning over one order of magnitude is observed with increasing signals for increasing fractions. We then measured the fraction length distributions using AFM. To this aim, a small amount of each fraction was spin-coated on a freshly cleaved mica surface. Successive washing steps using ethanol and pure-water flows were performed to remove surfactant from the surface. The samples were then naturally dried in air over night and then mounted on the AFM setup. AFM images were acquired in tapping mode in air as exemplified in Fig.
Acknowledgements We are grateful to  Jean-Paul Salvetat  ( CRPP ) for Fastscan AFM imaging tests and  Edakkattuparambil Sidharth Shibu  ( LP2N ) for thoughtful discussion. This work was supported by  CNRS ,  DGA ,  Agence Nationale de la Recherche  ( ANR-2010-BLAN-1527-01 & ANR-RPIB-004-03 ),  Conseil Régional d' Aquitaine  ( 2011-1603009 ), the  France-BioImaging national infrastructure  ( ANR-10-INBS-04-01 ) and  IdEx Bordeaux  ( ANR-10-IDEX-03-02 ).
Thus, determining how the meiotic toolkit has been conserved in different eukaryotic lineages requires comparison of representatives for which sex and meiosis can be directly observed. The T. pseudonana genome was included in a study assessing phylogenetic distribution of core meiotic proteins  [6] , however, as mentioned above, this species is currently considered asexual, and further datasets have become available for other species for which sexual reproduction can be controlled in the laboratory, such as members of the Pseudo-nitzschia genus  [37, 38]. With the aim to improve the definition of the meiosis toolkit for diatoms, we assembled an expanded list of meiotic genes for eukaryotes  [6, 9, 33]  and looked for the presence of homologs in five diatom genomes and in transcriptome sequence data.
Genes exclusive to meiosis Compared to other studies, our list of meiosis-specific genes (Tables  1  and 2 ) contained three more ZIP (Zipping up meiotic chromosomes protein) genes, ZIP2, ZIP3 and ZIP4  [64] , all reported to be required for the synaptonemal complex in budding yeast  [47, 64, 65]. Moreover, we list as meiosis-specific both SPO11-1 and SPO11-2, therefore the total number of meiosis-specific genes increases from 11  [9]  to 15 (Table  1 ). Of these 15 genes, five were detected in all the diatom genomes surveyed (Table  2 ). In the Seminavis robusta dataset, these five genes were all clearly upregulated during mating (Fig. 4 ), as was the one tested in Pseudo-nitzschia multistriata (SPO11-2, Fig. 5 ). The role of sex in the ecology and biogeochemical function of natural diatom populations has been challenging to investigate with classical methods as diatom sexual stages are difficult to recognize and preserve poorly  [15].
More broadly, the presented data refine our knowledge of patterns of evolutionary divergence of meiosis, a fundamental process ancestral to all extant eukaryotes. The SAR supergroup has undergone fundamental modifications to the meiosis process compared to other representatives of both the Diaphoretickes/bikont megaclade (Archaeplastida) and the Amorphea/unikont megaclade (Opisthokonts: animals and fungi). Features common among the SAR members are the absence of Mlh2 and Xrs2/Nbs1 in DNA damage sensing and the loss of components involved in canonical SC formation. Within the Stramenopiles there is also a general trend to lose canonical components in meiotic recombination, some of which have occurred in specific branches, and in some cases the meiosis-specific components may have been replaced by distant homologs with known mitotic functions.
Culture conditions and strains used Seminavis robusta strains were grown at 18 °C in a 12 L:12D h (light:dark) regime with cool white fluorescent lamps at approximately 80 μmol photons m -2 s -1. S. robusta strains 85A and 85B used in RNA-seq experiments are publicly available in the diatom culture collection of the Belgian Coordinated Collection of Micro-organisms (BCCM/DCG, http://bccm. belspo. be, accession numbers DCG 0105 and DCG 0107). Pseudo-nitzschia multistriata strains B936 (MT-), B937 (MT+), B938 (MT+) and B939 (MT-) were grown at 18 °C, under 100 μmol photons m -2 s -1 irradiance with 12 L:12D h (light:dark) photoperiod. Cultures were grown in Guillard F/2 medium  [111]  made with autoclaved filtered natural sea water collected from the North Sea (for S. robusta) or the Gulf of Naples (for P.
Database search for conserved meiotic genes in diatoms A list of conserved meiotic genes was taken from  [6]  and expanded with additional genes reported to be involved in meiosis. Meiotic protein sequences of Arabidopsis thaliana or Saccharomyces cerevisiae (Table  2 ) were used as query sequences for the homology searches. Keyword based searches in the NCBI protein database were made to retrieve the protein sequences. S. cerevisiae proteins were selected when no A. thaliana protein could be found for a given meiotic gene (Table  2 ). Meiotic protein homologs for four diatom species with publicly available genomes, including Thalassiosira pseudonana v3. 0, Phaeodactylum tricornutum v2. 0, Fragilariopsis cylindrus v1. 0 and Pseudonitzschia multiseries v1. 0, were retrieved by BLASTp searches from the Joint Genome Institute (JGI) database (http://genome.
jgi-psf. org/). In the case of Thalassiosira pseudonana and Phaeodactylum tricornutum genomes, "unmapped sequences" databases (http://genome. jgi. doe. gov/Thaps3_bd/Thaps3_bd. home. html and http://genome. jgi. doe. gov/Phatr2_bd/Phatr2_bd. home. html, respectively) were also searched since a significant portion of their genome sequence is maintained in these additional databases. The diatom homologs were first searched in filtered models and search was further extended to all models only if the respective homolog was not detected in filtered models. Meiotic gene homologs of P. multistriata were retrieved by tBLASTn searches in the v1. 4 genome assembly (Ferrante, in preparation). Sequences for the retrieved P. multistriata gene models are given in Additional file 7 and corresponding proteins are given in Additional file 8.
The search for the presence of meiotic genes was extended to the de novo transcriptome of S. robusta using tBLASTn searches. Sequences for the S. robusta transcripts are given in Additional file 9. The protein sequences of the resulting transcripts were predicted using Trapid  [112]  and then manually curated by mapping the transcripts to an in-house draft genome of S. robusta (Vandepoele, De Veylder & Vyverman, in preparation). The resulting protein sequences were blasted (BLASTp) against the Uniprot-Swissprot database to confirm their functional annotation. The resulting protein sequences are given in Additional file 10. We took into consideration only those sequences showing a BLAST e-value smaller or equal to 1e10 -4. The resulting dataset was further manually curated verifying the presence of at least one functional domain using the phmmer search against the UniProtKB sequences with an e-value cutoff of 1e10 -4 on the webserver HMMER (http://hmmer.
janelia. org/) [113]. For dubious cases, Interpro scan (http://www. ebi. ac. uk/interpro/) and CD-search (http://www. ncbi. nlm. nih. gov/Structure/cdd/ wrpsb. cgi?) were performed. A reciprocal blast was performed to confirm that each retrieved diatom sequence had the corresponding query sequence as top hit when searching against the A. thaliana (or S. cerevisiae) protein database. An alternative approach to verify absence of genes involved searches using HMMER. Protein sequences (covering major taxa from different eukaryotic groups) from the NCBI protein database were downloaded and aligned using the MUSCLE program  [114]. Further, HMM profiles were generated (Additional file 11) using default settings of the HMMBUILD command in the HMMER 3. 1b software and these HMM profiles for respective gene families were then used to search against the diatom protein databases (already mentioned above).
Phylogenetic analyses For the phylogenetic analysis of each gene, the corresponding protein sequences from representative taxa of plants, animals, fungi and protists were retrieved from NCBI (http://www. ncbi. nlm. nih. gov/protein/) and JGI with keyword searches and aligned using the sequence alignment software MUSCLE  [114]. Maximum likelihood analysis was performed using MEGA 6 (Molecular Evolutionary Genetics Analysis)  [115]  with appropriate substitution model suggested by the software, specified in the figure legends.
RNA-seq for S. robusta For the mitotic libraries, S. robusta strains 85A (MT+) and 85B (MT-) with an average cell size below the sexual size threshold (SST) were grown under abovementioned growth conditions and before sampling, the dark period was extended with 12 h to synchronize cells at the G1 phase  [116]. After illumination, synchronization was assessed by light microscopy. Pictures were taken using a digital camera connected to a Zeiss Axiovert 40 light microscope and the percentage of dividing cells (distinguished from interphase cells by the newly built cell wall between the two valve-appressed chloroplasts) was counted using cell counter plug-in of the ImageJ software. Cultures were harvested hourly from seven until ten hours post-illumination and cell pellets were frozen in liquid nitrogen and stored at -80 °C until RNA extraction.
pl script from the Trinity  [118]  software (release r2013_08_14) with the following parameters: -seqType fq -JM 240G -max_cov 30 -SS_lib_type RF -JELLY_CPU 24. Assembly was performed using Trinity on the trimmed, filtered and normalized reads with the following parameters: -seqType fq -JM 220G -inchworm_cpu 22 -bflyHeapSpaceInit 22G -bflyHeapSpaceMax 220G -bflyCalculateCPU -CPU 22 -SS_lib_type RF -min_kmer_cov 2 -jaccard_ clip. All reads were mapped to the assembled transcriptome using bowtie (version 1)  [119]  with the following parameters -p 20 -S -chunkmbs 10240 -t -maxins 500 -trim5 20 -trim3 20 -seedlen 20 -tryhard -a. Quantification of the mapping to obtain the number of raw reads mapping on each transcript in each condition was performed using the samtools view, sort, index and idxstats programs with default parameters  [120].
Protein, gene model or transcript IDs for the genes involved in meiosis analyzed in this study (Continued) Genes marked with a are genes that do not have known functions outside meiosis. Arabidopsis thaliana meiotic proteins were used as query sequence; whenever the specific query gene was not found/present in A. thaliana, Saccharomyces cerevisiae proteins were used (accession numbers in bold). Protein IDs are given for the diatom genomes available at the JGI portal, gene models IDs are given for the Pseudo-nitzschia multistriata genome and transcripts IDs for Seminavis robusta. Actual gene model IDs for P. multistriata include the prefix PSNMU-V1. 4_AUG-EV-PASAV3.
Acknowledgements S. P. has been supported by an  Open University  PhD fellowship from  Stazione Zoologica Anton Dohrn. The project was partially funded by the  Marie Curie   FP7-PEOPLE-2011-CIG 293887  (GyPSy) to MIF. The work conducted by the  U. S. Department of Energy Joint Genome Institute  is supported by the  Office of Science of the U. S. Department of Energy  under Contract No. DE-AC02-05CH11231. LDV and WV acknowledge support by grants of the  Research Foundation Flanders  ( G. 0288. 13 )and  Ghent University  ( BOF  project  GOA 01G01715 ). M. J. J. H. is a Postdoctoral Fellow of the  Research Foundation Flanders. The authors wish to thank  Maria Valeria Ruggiero  for her help with phylogenetic analyses,  Marco Borra  for his help with qPCR data analysis,  Valerie Devos ,  Dr. Jeroen Gillard  and  Dr.
Ex situ characterization X-ray Absorption Spectroscopy (XAS) data of the corresponding powder pellets were measured at the Swiss Norwegian Beamline (SNBL) BM01B at the European Synchrotron Research Facility (ESRF) from 8. 850 to 9. 800 keV in continuous scanning mode with two ion chambers, one before the sample and one after the sample. The powders were diluted in cellulose to optimize the edge-step and pressed into pellets. Powder X-ray diffraction (PXRD) patterns of synthesized powders were collected on an Empyrean powder diffractometer (PANalytical B. V. , The Netherlands), operating in reflection mode under constant irradiated area conditions with Cu Kα radiation (45 kV, 40 mA). Scanning electron microscopy (SEM) images were taken on a Magellan 400 FEG (FEI, USA) to show the shape and morphology of the nanoparticles.