dataesr/scientific-paragraphs-categorization huggingface dataset:
6 ml each. These fractions were then analyzed using nanoLC-MS/MS. Data from the four runs ("T1" in Table  I ) resulted in the identification of 3449 different peptides (Table I and supplemental Table  S1 ). Of these, 325 were N-terminal peptides. As expected, increasing the number of spectra acquired in this experiment compared with our previous analysis ("Ta" in Table  I ) led to a higher number of peptides identified. We then modified the same four fractions with TNBS and subjected them to diagonal reverse-phase chromatography. The four resulting fractions were then analyzed by nanoLC-MS/MS. This dataset ("T2" in Table  I ) yielded less than half of the total identifications from Data "T1" (1559) but a higher number of N-terminal peptides (386). After the first chromatography step, 9% of identified peptides corresponded to N termini, whereas after the second chromatography step, they increased to 25%, showing a clear enrichment of these specific peptides.
Only 25 TNBS-labeled peptides were found in these four fractions ("T2" in Table  I ) and none corresponded to the N terminus of a protein. As expected, fractions eluting with a delay contained a higher ratio of TNBS-labeled internal peptides (data not shown). A total of 291 unique proteins were detected through their N-terminal peptides, compared with 230 found without the intermediate COFRADIC step. Therefore, this method is efficient at enriching N-terminal peptides. Spectral Assignment Using the CDS and Six-frame ORF Databases-Using nanoLC-MS/MS, we analyzed all the CO-FRADIC fractions from the tryptic digest, generating 93,545 MS/MS spectra (supplemental Table  S2 ). After merging the search results and removing the peptides assigned to ambiguous loci, contaminants, and protease autolysis, 61,849 MS/MS spectra assigned to tryptic or semi-tryptic peptides remained.
These peptides correspond to 1556 potential Nterminal sequences with the conventional translational start codons ATG, GTG, and TTG (supplemental Table  S3 ). MS/MS data acquired from chymotrypsin and endoproteinase Glu-C digests were processed as for the tryptic digest, allowing 3 and 2 mis-cleavages, respectively. After processing, samples from these two enzymes yielded an additional 24,052 unique MS/MS spectra. In total, 2603 peptides beginning with the possible start codons ATG, GTG, or TTG (supplemental Table  S3 ) were found, corresponding to 840 non-redundant proteins. From the whole peptide pool, the vast majority (1556) arose from trypsin, with 473 and 574 generated by chymotrypsin and endoproteinase Glu-C, respectively. The false discovery rate for peptide assignment, estimated using the same search strategy with a decoy database, was less than 1% with both CDS and six-frame ORF databases.
Decoy databases were constructed using the "decoy" function in the Mascot Daemon and consisted of reversed amino acid sequences from the target databases. Validation of TMPP-labeled N-terminal Peptides-For automatic validation of N-terminal start sites we took advantage of data redundancy arising from differences in terms of miscleavages, methionine oxidation, different proteolytic enzymes (i. e. trypsin, chymotrypsin, and endoproteinase Glu-C), and partial removal of the initial methionine. Chymotrypsin specifically hydrolyzes peptide bonds at the C termini of tyrosine, phenylalanine, and tryptophan; leucine, methionine, alanine, aspartic acid, and glutamic acid are cleaved at a FIG. 1. Strategy applied for N termini enrichment. Proteins are first labeled with TMPP on their N terminus before reduction and alkylation of cysteines.
The false discovery rate for N-terminal peptide assignment was estimated to be less than 1% using the same approach and the ORF target-decoy database. Most of the detected proteins (66%) were identified from their N-terminal initiation peptides recorded with only one protease, whereas 25 and 9% of the proteins were detected with a combination of two or all three proteases, respectively. Of those detected with at least two proteases, more proteins are identified with the combination of trypsin and endoproteinase Glu-C (70 proteins), than with trypsin and chymotrypsin (45 proteins) or endoproteinase Glu-C and chymotrypsin (eight proteins). Protease mis-cleavages allowed the corroboration of sequences pointing at the same N-terminal initiation, more so even than parallel proteolysis with different enzymes.
The coordinates of these genes do not overlap with those of previously annotated genes, potential promoters and Shine-Dalgarno sequences exist upstream of each coding sequence, and the corresponding peptides could not be assigned to any other gene. The ORF located at the position 331,094 -330,567 on the chromosome was validated with two different peptides obtained during the semitrypsin and semi-endoproteinase Glu-C analysis; an annotated spectrum from the semi-triptic peptide, as well as the predicted sequence of the entire gene and corresponding product, is shown in Fig. 6. This orphan CDS has no homologs in the NCBI database and thus no function could be assigned. The novel gene at locus 338,913-339,212 on the chromosome was observed with two translation start sites, both of which were detected by two different TMPP-labeled peptides (supplemental Table  S5 ).
* This work was supported by the  Commissariat al'Energie Atomique et aux Energies Alternatives , and the  Region Languedoc-Roussillon (label Ͻ Ͻ Chercheur d'Avenir ConfirmeϾ Ͼ 2010 ). CB gratefully acknowledges the  Commissariat al'Energie Atomique et aux Energies Alternatives  and the  Region Languedoc-Roussillon  for their support. JAC-O acknowledges the  Ramon Areces foundation  and  FP7 Marie Curie Actions  for financial support.
This contribution focuses on two aspects of our work, which relate to refractory residue analysis formed from UV irradiation of ice analogues, the RAHIIA project, and for the other, a new project that will be developed during 2013 and aims to analyse volatile organic compounds coming from the heating of such analogues, the VAHIIA project (ANR-12-JS08-0001-01 2013-2016). Understanding the formation of refractory residues, commonly called "Yellow Stuff" is an important step to establish what kind of organic matter could be available within interplanetary objects such as comets or asteroids, and therefore available for the development of a prebiotic chemistry on the surface of terrestrial planets. We present here the first results obtained by high resolution mass spectrometry (LTQ-Orbitrap) of these residues.
EXPERIMENTAL PROCEDURES General-Chemical reagents were purchased from Sigma Aldrich and used as received unless otherwise stated. Protein purity was assessed by gel electrophoresis by loading samples on PhastGel TM ; Gradient 10 -15 precast gels (GE Healthcare) with Precision Plus Protein TM standards (Bio-Rad). Migration was achieved on a PhastSystem Separation and Control apparatus (Pharmacia). Protein concentrations were determined with the Bio-Rad Protein Assay, using bovine serum albumin as a standard. In vivo quantification of NrdI in cell paste was performed by densitometry measurements from SDS page gels run on whole cell lysis material, using purified B. anthracis NrdI as internal standard. Images were recorded on a Molecular Imager ChemiDoc TM XRSϩ system and calculations performed using the Imagelab TM software from Bio-Rad.
These drastic changes in the spectra of the B. anthracis Mn-NrdF radical are in contrast to the temperature behavior of the tyrosyl radical in B. anthracis Fe-NrdF. The latter does not display any change in line shape in the temperature region 10 to 136 K (data not shown) indicative of a rather weak interaction with the assumed antiferromagnetically coupled diiron site. The relaxation properties of the split-tyrosyl radical were evaluated from microwave saturation studies in the temperature range 6. 7 to 77 K. The relaxation characteristic P 1/2 was calculated both in the absence and the presence of NrdI with no significant difference. As mentioned above the radical does not saturate at all at 77K and even at 40K the available microwave power was not enough to determine a P 1/2 value, again manifesting a strong interaction with the dimanganese site.
Cytotoxicity Studies The synthesized complexes were subjected to preliminary cell viability and proliferation assays. In particular, the cytotoxic behaviour was studied in A549 adenocarcinomic human alveolar basal epithelial and MCF7 human breast adenocarcinomic cancer cell lines by MTT and BrdU assays, to investigate the potential effects of platinum complexes on cell viability and proliferation, respectively. The incubation of A549 cells with 8a,b and 10a,b (50, 100 and 200 µM) for 72 h caused a concentration-dependent reduction of cell survival (Figure  3 , panel A) as well as an inhibition of cell proliferation at the higher concentrations (Figure  3 , panel B) compared to untreated cells. Indeed, comparable results were obtained when the cell number was directly determined by cell counting (data not shown).
8 × 150 mm), eluted with a linear gradient of CH 3 CN in 0. 1 M triethylammonium bicarbonate (TEAB) buffer (System A: from 0% to 50% in 90 min, flow 1. 3 mL/min, or System B: from 0% to 100% in 90 min, flow 1. 3 mL/min). Human alveolar basal carcinoma epithelial cells (A549) and human breast cancer cells (MCF7) were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% Foetal bovine serum (FBS), 100 U/mL penicillin and 100 U/mL streptomycin at 37 °C under 5% CO 2. The cell lines were all from the ATCC catalogue. All media and supplements for cell culture were purchased from Gibco-Invitrogen (GE Healthcare). N 6 -(6-Aminohexyl)adenosine  (5). Compound 5 (326 mg) was obtained by reaction of 4 (297 mg, 01. 04 mmol) in accordance to the procedure by Schammells et al. [37]. Spectroscopic data and yields were in agreement with those reported by the authors.
Scheme 1. Synthesis of metallosupramolecular cages of type [M 2 (L) 4 ][X] 4. O Me N N 2 MX 2 Solvent S 4 O Me N N O Me N N M M O Me N N O Me N N M = Pd, X = NO 3 , L 1 , S = DMSO M = Pd, X = OTf, L 1 , S = CH 3 CN M = Pt , X = OTf, L 1 , S = CH 3 CN M = Pd, X = OTf, L 2 , S = CH 3 CN 4 X - 4 1a 1b 2 3 69 % 67 % 84% 90% R R R R R L 1 , R = H L 2 , R =NH 2 Moreover, these molecular capsules appeared to be stable both in the solid state and in solution the integrity of the cages is maintained. For example, the electrospray mass spectrum of [Pd 2 (L 1 ) 4 ][OTf] 4 (1b) clearly indicates the formation of PdL 4  species in association with varying numbers of triflate counterions (Figure  1 ). The 1 H NMR spectrum of [M 2 L 4 ][X] 4 cages were recorded either in DMSO-d 6 or CD 3 CN. Upon cage formation with Pd(II) or Pt(II) salts, the spectroscopic data were consistent with the higher symmetry of the assemblies.
General Information and Materials All solvents used were reagent grade or better. Commercially available reagents were used as received. L 1 , L 2 and Pd(CH 3 CN) 4 OTf 2 were prepared according to published methods 41,43. All experimental manipulations were carried out under argon using Schlenk techniques. IR spectra were recorded on a Bruker Tensor 27 (Bruker Corp. , Rheinstetten, Germany) equipped with a Harrick ATR. Elemental analyses were performed by the microanalytical laboratory of Institut de Chimie des Substances Naturelles, Gif-sur Yvette. Positive ESI mass spectra were obtained using a triple quadrupole mass spectrometer (Quattro II Micromass, Waters, UK). Automatic data acquisition was processed using the software Masslynx V4. 0. NMR experiments were carried out on a Bruker Avance II 300 MHz or Bruker Avance III HD 400 MHz spectrometer operating at 300 K with chemical shifts references to residual solvent peaks.
X-Ray Crystal Structure Determination of Metallocage (1b) X-ray crystal structure determination of metallocage (1b): Data was collected on a Bruker Kappa-APEXII. Unit-cell parameters determination, data collection strategy and integration were carried out with the Bruker APEX2 suite of programs. Multi-scan absorption correction was applied  [44]. The structure was solved using SIR92  [45]  and refined anisotropically by full-matrix least-squares methods using SHELXL-2013  [46]. Crystallographic data (excluding structure factors) for this structure was deposited at the Cambridge Crystallographic Data Centre with the number CCDC 972857. This data can be obtained, free of charge, from the Cambridge Crystallographic Data Centre via www. ccdc. cam. ac. uk. Crystal data for (1b).
Measurement of E. coli type 1 fimbriae-mediated yeast agglutination. We assessed the capacity of type 1 fimbriae to agglutinate yeast cells following a protocol previously described. 28  from Sigma-Aldrich (Sigma Aldrich, Saint-Quentin Fallavier, France) and used as received. PEG-acetal linkers were purchased from Hermann Gruber group (Institute of Biophysics, University of Linz, Austria). AFM-tips were functionalized with mannosamine using a procedure previously described  12, 29  for the detection and stretching of type Biological replicates from independent bacterial growth culture, and performed at pH 7 for the 6 pulling rates were close to the triplicates with less than 10% deviation (data not shown). The uncertainties given in this work were calculated from the technical triplicates only.
In particular, we evidenced an optimum of yeast agglutination in the pH range 5 to 7, in line with the maximum detected by AFM for the binding force between FimH and mannose at neutral pH under moderate applied pulling rate. Moreover, electrokinetic measurements Tables  Table  1. Values for the rupture forces corresponding to the main modes of the statistical distribution given in Figure  2c. Corresponding conformational parameters (persistence and contour lengths, l p and L c , respectively) as derived from WLC model (eq 1). Data were extracted from a 5 m 5 m Force Volume Image (FVI) consisting of 1024 force curves recorded on several bacteria at pH 7 and for a pulling rate of 2 µm/s. Yeast agglutination assay for E2146 performed over the pH range 3 to 9. The strain E2152 is deleted for type 1 fimbriae fim operon and it thus does not agglutinate yeast cells.
Crystal data Cd 4 As 2 Br 3 M r = 839. 17 (Bruker, 2006) ; data reduction: SAINT; program(s) used to solve structure: SIR97  (Altomare et al. , 1999) ; program(s) used to refine structure: SHELXL97  (Sheldrick, 2008) ; molecular graphics: DIAMOND  (Brandenburg & Putz, 1999) ; software used to prepare material for publication: WinGX (Farrugia, 2012) and CRYSCAL  (Roisnel, 2013). Supporting information for this paper is available from the IUCr electronic archives (Reference: VN2080).
Refinement La structure a été déterminée par isotypie aux halogénopnictures de cadmium et de mercure de formule générale M 4 A 2 X 3 (M = Cd, Hg; A = P, As, Sb; X = Cl, Br, I). En fin d'affinement, la carte de densité électronique obtenue est: ρ max = 1. 932 e Å -3 (localisée à 0. 61 Å de C d1) et ρ min = -1. 571 e Å -3 (localisée à 1. 16 Å de Br1). program(s) used to solve structure: SIR97  (Altomare et al. , 1999) ; program(s) used to refine structure: SHELXL97  (Sheldrick, 2008) ; molecular graphics: DIAMOND  (Brandenburg & Putz, 1999) ; software used to prepare material for publication: WinGX (Farrugia, 2012) and CRYSCAL  (Roisnel, 2013). Environnement tétraèdrique distordu des atomes de As, avec un déplacement des ellipsoīdes à 95% de probabilité.
Since the 1980s it has been possible to probe crystallized matter, thanks to X-ray or neutron scattering techniques, to obtain an accurate charge density or spin distribution at the atomic scale. Despite the description of the same physical quantity (electron density) and tremendous development of sources, detectors, data treatment software etc. , these different techniques evolved separately with one model per experiment. However, a breakthrough was recently made by the development of a common model in order to combine information coming from all these different experiments. Here we report the first experimental determination of spin-resolved electron density obtained by a combined treatment of X-ray, neutron and polarized neutron diffraction data. These experimental spin up and spin down densities compare very well with density functional theory (DFT) calculations and also confirm a theoretical prediction made in 1985 which claims that majority spin electrons should have a more contracted distribution around the nucleus than minority spin electrons.
The best suited values for extension/contraction f i ; 0 i g and valence and multipole population fP ðvalÞ i ; P i;';mAE g parameters are determined to match experimental data fF XRD ðQÞg. This particular model for charge density has encountered such tremendous success since the 1980s that high-resolution XRD is now frequently employed to analyze chemical bonds and more generally the charge redistribution due to molecule or crystal formation. This experimental approach to electron probability distribution has become extensively used and was developed to calibrate advanced quantum chemistry computations. Such a landmark is of course essential, especially if the aim is to extend the theoretical modelling to a set of systems which cannot yet be studied experimentally  (Gatti & Macchi, 2012).
Polarized neutrons for unpaired electron probability distribution As a consequence of this success, the quest for a deeper understanding of mechanisms responsible for spin magnetism has led to the use of the same approach to reconstruct electron magnetization distribution in crystals from polarized neutron diffraction (PND) data. While XRD and non-polarized neutron diffraction data consist of integrated intensities of Bragg reflections, PND measures 'flipping ratios' (hereafter denoted F PND ðQÞ). They are defined as the ratio between the diffracted intensities for spin up and spin down incident neutrons. This technique thus aims to identify regions of the crystal unit cell where an electron spin majority exists and how it is distributed. PND gives access to the magnetization density that is the sum of the pure spin density and the orbital contribution  (Schweizer, 2006).
In a PND data collection, the explored reciprocal space domain is generally more limited than its XRD counterpart because of the restricted access to neutron beam time and the available range of experimental geometries (the sample is submitted to a strong magnetic field, typically 5 T). Thus, PND is often limited to the domain of Q for which a significant magnetic contribution is expected, i. e. Q max is 0. 5 A ˚À1 for 3d transition metals. Moreover, as opposed to structural data collections which concern all the existing reflections in a given domain of Q, PND measurements are performed only for the strong nuclear reflections for which good experimental accuracies may be achieved for the flipping ratios. Therefore, only $ 10% of all reflections in a given reciprocal domain are measured by PND.
The combination challenge in determining a spinresolved electron density distribution From the above considerations it is quite clear that XRD and PND consider electron distributions from different and complementary perspectives. XRD enables the reconstruction of the total electron distribution, r ð Þ, while PND provides information which yields the spin density, s r ð Þ. The two quantities can therefore be expressed in terms of spin-resolved electron densities, " r ð Þ and # ðrÞ, respectively, representing spin up and spin down only electron density distributions r ð Þ ¼ " r ð Þ þ # ðrÞ ð 2Þ s r ð Þ ¼ " r ð Þ À # ðrÞ: ð3Þ It is therefore obvious that a combined analysis of accurate high-resolution X-ray and polarized neutron diffraction data should yield unprecedented access to spin-resolved electron densities for crystals with significant magnetic properties.
In our approach it was found that a satisfying result was reached when the following quantity was considered for minimization  (Gillet et al. , 2001; Bell et al. , 1996) : L ¼ N XRD log X N XRD i¼1 jF model XRD ðQ i Þ À F expt XRD ðQ i Þj 2 2 i " # þ N PND log X N PND j¼1 jF model PND ðQ j Þ À F expt PND ðQ j Þj 2 2 j " # ; ð5Þ where N XRD and N PND are the number of data points in each set and represents the estimated standard deviation for each data point. A more detailed description of the joint refinement methodology is given in  Deutsch et al. (2012).
This was followed by the incubation of coverslips with LR White in ethanol-free conditions for 1 h. The cells were then embedded at 4 °C with LR White and accelerator mixture (London Resin Company Ltd), and incubated for 15 min. Later, they were incubated for 90 min at 60 °C, and cooled down to room temperature. 200-nm-sections were cut from the resulting blocks using an EM UC6 ultramicrotome from Leica Microsystems. Fluorescence imaging. Fluorescence images were acquired using a Leica TCS SP5 STED confocal microscope (Leica Microsystems) equipped with a 100 Â 1. 4N. A. HCX PL APO CS oil objective (Leica) and the Leica Application Suite Advanced Fluorescence software. In STED mode, the excitation of Atto647N was performed using a pulsed diode laser (Leica Microsystems) at 635 nm, and depletion was achieved by means of a Spectra-Physics Mai Tai tunable laser (pulsed at 80 MHz; Titanium Sapphire, Newport Spectra-Physics) at 750 nm, with an output power of 1.
These ions were then mass separated and detected by using a double focalization mass spectrometer equipped with seven miniature electron multipliers (Hamamatsu). The mass resolving power was adjusted to suppress interferences at all masses (allowing the optimal separation of 12 C 15 N À from interfering ions like 13 C 14 N À ). Primary ion beam current was 0. 5 to 1 pA, scanning parameters were 512 Â 512 pixels for areas of 3. 2 to 12. 9 mm with a dwell time of 500 ms per pixel. All figures represent data from single plane without accumulation. Image processing. For Figs 1, 3 and 4, the fluorescence images were rotated and aligned to the SIMS images. A background subtraction was performed for the  15  N/ 14 N ratio images, for display purposes. All line scans and spot size measurements were performed using custom-written routines in MATLAB (The Mathworks Inc).
Only horizontal line scans were used; several lines were averaged, to increase the signal-to-noise ratio (three lines for Fig. 1a  and Supplementary Fig. 1 ; 5 lines for Supplementary Figs  3b  and 5b ; three lines for all other  14  N images, and seven lines for all other  15  N images, unless otherwise noted in the figure legends). Fluorescence images were deconvolved (applying classical maximum likelihood estimation algorithm) with the aid of Huygens Essential software (Scientific Volume Imaging), using the inbuilt routines designed specifically for confocal and STED images. For identifying individual protein clusters in Fig. 3 , we first selected a region of interest centred on the synapse (indicated by an arrowhead in Fig. 3a ). The region was then filtered using a median filter (2 Â 2 pixels), to remove noise.
Acknowledgements We thank  Dr U. Ehrke  ( Cameca, Unterschleissheim, Germany ) for valuable comments on the data and on the manuscript. We thank  C. Scha  ¨fer for technical assistance. We thank  B. Rizzoli  for proofreading the manuscript. The SIMS instrument was funded by the  German Federal Ministry of Education and Research (BMBF) , grant identifier  03F0626A. S. K. S. was supported by a  Boehringer Ingelheim Fonds PhD Fellowship. The work was supported by grants to S. O. R. from the  German Research Foundation  (DFG, grant identifiers  RI 1967/2-1 ,  RI 1967/3-1  and the  Collaborative Research Center 889 'Cellular Mechanisms of Sensory Processing' ,  SFB 899 ).