dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusion: In our experience, DSA ability to fix complement is evaluated similarly by c1q and c3d positivities and strongly correlate with DSA MFI values. O56 Introduction: Development of de novo donor-specific anti-HLA antibodies (DSA) is a crucial event after kidney transplantation. Time to onset of de novo DSA and their impact on graft outcome are highly variable. We studied clinical and histological phenotype of kidney transplant patients with de novo DSA. Method: This was a national multicenter cohort study using the ASTRE database and concerning 13 French centers. We included renal transplant patients with de novo DSA with or without degradation of renal function. Biopsies were performed at the time of DSA discovery. Results: We reported 96 cases. The median time to onset of DSA was 5.
Conclusion: These data provide novel insights into the characterization of B cell-mediated immune-regulation in tolerance in clinic and may constitute a useful therapeutic tool in solid organ transplantation and autoimmune diseases. O63 We conducted a comparative flow-cytometry analysis of circulating TFH (cTFH), defined by the markers CD3 + CD4 + CD45RA-CXCR5 + , in kidney transplanted patients with stable graft function. The patients were divided in 3 groups and were compared to healthy blood donors : (A) Naive patients (with absence of HLA sensitization before the transplantation) treated with CTLA4-Ig for 10 years (n = 6), (B) Naive patients treated with CNI for 10 years (n = 10) and (C) Sensitized patients (with presence of DSA with MFI <3000 before kidney transplantation) treated with CTLA4-Ig for 1 year (n = 8).
Data collected comprised clinical and biological features at the time of LT for recipients and their donors, assessing ACLF status according to ACLF/CANONIC criteria to categorize patients. A survival Classification and Regression Analysis (CART) algorithm was applied to build the prognostic model for 90-day mortality. Results: 1657 patients (41%) met the CANONIC criteria of ACLF with at least one organ failure (1: 20. 3%; 2: 12. 6%; 3 and more: 8. 4%). Overall 90-day mortality rate was 7. 6%, with corresponding rates of 5. 4%, 7. 2%, 10. 2% and 20. 1% in patients with 0, 1, 2, 3 and more organ failures, respectively. Decisiontree modelling identified 12 subgroups further classified in 4 increasing risk classes  (Figure) , highlighting the prognostic importance of respiratory failure and acute renal failure at the time of LT, as well as complex interactions between donor and recipient features.
Mass spectrometry analysis The liquid chromatography equipment coupled to mass spectrometry (LC/MS) system consisted of an UPLC chromatograph (ACQUITY UPLC from Waters) coupled to a quadrupole time-offlight mass spectrometer (Xevo G2-QTof-MS from Waters) (UPLC-QTof-MS). UPLC analyses were performed using an Acquity UPLC BEH C18 (1. 7 μm; 2. 1 Â 50 mm) column (Waters), and isocratic elution with 25 mM formic acid (pH ¼3. 2) at a flow rate of 0. 2 mL min À 1. The mass spectrometer was operated in the negative ion mode. Therefore the samples were injected into the chromatograph, the components were separated and then the mass spectra were registered for each peak of the corresponding chromatograms. In addition, mass chromatograms, i. e. representations of mass spectrometry data as chromatograms (the x-axis representing time and the y-axis signal intensity), were registered using different scan ranges.
Fluorescence measurements Steady-state and time-resolved fluorescence measurements were performed at room temperature using a single-photon-counting equipment FL3 TCSPC-SP (Horiba Jobin Yvon), described elsewhere  [47]. For a given solution, the decay curve was recorded at multiple emission wavelengths to construct the time-resolved emission spectra (TRES), 3D data set of counts versus time and versus wavelength. The Global Analysis of TRES, a fit calculation (up to 5 exponentials) performed globally on up to 100 separate decay curves, was carried out using the DAS6 Fluorescence Decay Analysis software.
Acknowledgements The present work was partially supported by  Consejo Nacional de Investigaciones Científicas y Técnicas  ( CONICET-Grant PIP 112-200901-00425 ),  Agencia de Promoción Científica y Tecnológica (ANPCyT- Grant  PICT-2012-0508 ),  Universidad Nacional de La Plata  ( UNLP-Grant   X712 ). The authors thank the  Centre National de la Recherche Scientifique (CNRS)  and  CONICET  for supporting their collaboration through a  Programme de Coopération Scientifique  ( CONICET-CNRS/PICS No. 05920 ). M. P. S. thanks  CONICET  for doctoral research fellowship. M. V. , C. L. and A. H. T. are research members of CONICET. P. V and E. O are research members of  CNRS. The authors also thank  Lionel Rechignat  of the  Service des Mesures Magnétiques du Laboratoire de Chimie de Coordination  ( LCC, CNRS, Toulouse, France ) and  Nathalie Martins-Froment of Service Commun de Spectrométrie de Masse  ( FR2599 ),  Université de Toulouse III  ( Paul Sabatier ) for their valuable help with the EPR and mass spectrometry measurements, respectively.
This paper presents a search for massive charged long-lived particles produced in pp collisions at √ s = 13 TeV at the LHC using the ATLAS experiment. The dataset used corresponds to an integrated luminosity of 3. 2 fb -1. Many extensions of the Standard Model predict the existence of massive charged long-lived particles, such as R-hadrons. These massive particles are expected to be produced with a velocity significantly below the speed of light, and therefore to have a specific ionization higher than any Standard Model particle of unit charge at high momenta. The Pixel subsystem of the ATLAS detector is used to measure the ionization energy loss of reconstructed charged particles and to search for such highly ionizing particles. The search presented here has much greater sensitivity than a similar search performed using the ATLAS detector in the √ s = 8 TeV dataset, thanks to the increase in expected signal cross-section due to the higher center-of-mass energy of collisions, to an upgraded detector with a new silicon layer close to the interaction point, and to analysis improvements.
In this paper, this information is used to search for LLPs using data collected at √ s = 13 TeV, extending in reach a study performed on data collected at √ s = 8 TeV  [16]. The increase in probability for highenergy parton-parton collisions significantly enhances the production cross-section of LLPs via the strong interaction. Together with this enhancement, the search sensitivity has been considerably extended thanks to the upgrades to the Pixel detector (see Section 2) and improvements to the analysis (see Section 6). Many strategies have been explored to find LLPs at the LHC. A search using the complete √ s = 8 TeV dataset recorded by the ATLAS detector  [17]  combined Pixel dE/dx information with time-of-flight measurements, made in both the calorimeters and the muon spectrometer, to search for LLPs that do not decay within the detector.
[35]. The distribution of the dE/dx versus momentum is shown in Figure  2  together with the fits to the pion, kaon and proton masses. The mass calculation performed through the dE/dx method is monitored by checking the stability of the proton mass measurement during the data taking. 2 : Two-dimensional distribution of dE/dx versus charge signed momentum (qp) for minimum-bias event tracks compatible with a primary vertex, which has the same data selection as in Ref. [34]. The distributions of the most probable value for the fitted probability density functions of pions, kaons and protons are superimposed. A mass estimate M is obtained by numerically solving the equation 1 for the unknown M. In simulated R-hadron events, the reconstructed mass is found to reproduce well the generated mass up to masses around 1800 GeV, and a residual 3% correction is applied to the reconstructed mass to improve the agreement.
This benchmark decay mode is chosen as it has the highest sensitivity among those studied in Ref. [16]. Heavier neutralino masses would give lower signal efficiencies, mainly because of the smaller missing transverse momentum available to trigger. The gluino lifetime (τ) is varied from 0. 4 ns to 50 ns. All simulated samples include a modeling of pileup, adding the expected number of minimum bias proton-proton interactions from the same (in-time pileup) and nearby (out-of-time pileup) bunch crossings. Simulated events are reconstructed using the software used for the collision data. Additional samples of gluinos are generated for all mass points using MG5_aMC@NLO  [49] , to get a more accurate description of radiative effects than Pythia 6 provides. The distribution of the transverse momentum of the gluino-gluino system simulated with Pythia 6 is then reweighted in such a way as to match that obtained in samples simulated with MG5_aMC@NLO.
Data Sample and Event Selection The data sample used for this search was collected while tracking detectors, calorimeters, muon chambers, and magnets were operating normally and corresponds to an integrated luminosity of 3. 2 fb -1 in 2015. The luminosity measurement was calibrated during dedicated beam-separation scans, using the same methodology as that described in Ref. [52]. The uncertainty in the luminosity measurement is 5%. Candidate events are selected by an E miss T trigger, formed from energy deposits in the calorimeter  [51] , with a threshold of 70 GeV. The event selection, described in detail below, was optimized relative to the √ s = 8 TeV search  [16]  to improve the sensitivity to events with R-hadrons relative to background events from SM processes. Major improvements include the addition of selections designed to reject tracks from hadrons and electrons, as well as changes to the isolation requirements, which now reject background events from overlapping tracks by identifying clusters in the Pixel or SCT detectors which are consistent with energy deposition from multiple particles.
The systematic uncertainties are calculated and used independently for each mass bin and signal lifetime. In the table, only the maximum uncertainty is quoted. The trigger and offline E miss T selections are sensitive to the modeling of ISR in the event, in particular for signal events that do not decay inside the detector volume. Half of the difference between the selection efficiency of the Pythia 6 samples and those reweighted with MG5_aMC@NLO is taken as an uncertainty due to radiative effects. The E miss T trigger modeling is studied in a sample of Z → µµ events and an uncertainty is assigned based on differences between efficiencies measured in data and in simulation. The uncertainty in the E miss T calibration comes primarily from uncertainties on the jet energy scale. A systematic uncertainty in the measurement of the Pixel ionization is evaluated by comparing the ionization of an inclusive sample of simulated and observed low-momentum tracks.
MSSR, Slovakia; ARRS and MIZŠ, Slovenia; DST/NRF, South Africa; MINECO, Spain; SRC and Wallenberg Foundation, Sweden; SERI, SNSF and Cantons of Bern and Geneva, Switzerland; MOST, Taiwan; TAEK, Turkey; STFC, United Kingdom; DOE and NSF, United States of America. In addition, individual groups and members have received support from BCKDF, the Canada Council, CANARIE, CRC, Compute Canada, FQRNT, and the Ontario Innovation Trust, Canada; EPLANET, ERC, FP7, Horizon 2020 and Marie Skłodowska-Curie Actions, European Union; Investissements d'Avenir Labex and Idex, ANR, Région Auvergne and Fondation Partager le Savoir, France; DFG and AvH Foundation, Germany; Herakleitos, Thales and Aristeia programmes co-financed by EU-ESF and the Greek NSRF; BSF, GIF and Minerva, Israel; BRF, Norway; the Royal Society and Leverhulme Trust, United Kingdom.
Acknowledgments We thank  CERN  for the very successful operation of the LHC, as well as the support staff from our institutions without whom ATLAS could not be operated efficiently. We acknowledge the support of  ANPCyT , Argentina; YerPhI, Armenia;  ARC, Australia ;  BMWFW  and  FWF , Austria; ANAS, Azerbaijan; SSTC, Belarus;  CNPq  and  FAPESP, Brazil ;  NSERC ,  NRC  and  CFI ,  Canada ; CERN; CONICYT, Chile; CAS,  MOST  and  NSFC, China ;  COLCIENCIAS, Colombia; MSMT CR, MPO CR  and  VSC CR, Czech Republic ;  DNRF  and  DNSRC, Denmark ;  IN2P3-CNRS ,  CEA-DSM/IRFU , France; GNSF, Georgia; BMBF,  HGF , and  MPG, Germany ;  GSRT, Greece; RGC, Hong Kong SAR, China ;  ISF, I-CORE  and  Benoziyo Center , Israel; INFN, Italy;  MEXT  and  JSPS, Japan ; CNRST, Morocco; FOM and  NWO, Netherlands ;  RCN, Norway ;  MNiSW  and  NCN , Poland; FCT, Portugal; MNE/IFA, Romania;  MES of Russia  and  NRC KI , Russian Federation; JINR; MESTD, Serbia;.
To screen the validity of the DFT and LDC results they are confronted with data from X-ray diffraction measurements. The effect of the strong phonon renormalization in ScV 2 Al 20 on thermodynamic observables is computed on grounds of the LDC derived inelastic response. To set the data in a general context of AV 2 Al 20 compounds and their physical properties we report in addition computer and experimental results of the binary V 2 Al 20 compound.
B. X-Ray diffraction and thermal conductivity Powder X-ray diffraction (XRD) measurements were made using CoKa radiation (l = 1. 789007 Å) applying the Guinier-Huber technique. Single crystal data for ScV 2 Al 20 and Al x V 2 Al 20 were collected on a Rigaku R-axis RAPID diffractometer (Mo K a , l = 0. 71073 Å). Crystallographic structure refinements and calculations were made using the WINCSD  51   The thermal conductivity k(T) (see Fig. 2 ) was determined simultaneously with electrical resistivity r(T) and the Seebeck coefficient S(T) using a commercial setup (option TTO, PPMS, Quantum Design). The lattice contribution to thermal conductivity, k l (T), was estimated by subtracting the conduction electron contribution k e from the total k(T). k e was estimated by the Wiedemann-Franz law with L 0 = 3(pk B /3e) 2 E 2.
Powdered specimen of the compounds of about 20 g each was measured at temperatures T between 2 and 300 K. We applied T E 100 and 300 K for all samples on IN6@ILL. On IN4@ILL ScV 2 Al 20 and LaV 2 Al 20 were measured at T E 2, 50, 100, 200 and 300 K whereas CeV 2 Al 20 was studied at 2, 70, 230 and 300 K. Precise T values are reported with the data hereafter. Standard procedures for data correction and conversion were utilized. Data are corrected for empty can scattering, for absorption, self-attenuation and frame overlap effects, for different detector efficiencies of the multidetector units, and for the energy dependent efficiency of the Helium-3 counters. Scattering lengths and absorption cross sections tabulated in the literature were exploited. 53 Their values are listed in Table  1. The dynamic structure factors S(o,T) were calculated as a scattering-angle averaged signal.
To allow a direct comparison of the computer generated response with experimental data we applied the PALD technique to compute the Q-resolved and orientationally averaged phonon form-factors of the compounds. 33, 36, 39, 40 A total of 10 5 Q-points in the wave vector range 0-10 Å À1 was exploited for the PALD response. Extracting the phase-space region monitored using the IN6@ILL and IN4@ILL instruments, accounting for the scattering lengths and cross sections of the compounds' constituents, and approximating the energy resolution of the spectrometers allow computing PALD-generated Q-averaged generalized density of states G 0 (o) in analogy to the measured G(o). To highlight the strong differences in the scattering properties of the compounds' constituents we report in Table  1  their scattering power.
We find an overall good match between the experimental and PALD data sets. In any of the measured G(o) pronounced low-energy peaks are identified giving evidence of the localization of the Sc, La and Ce dominated vibrations at low energies as discussed above. In particular for LaV 2 Al 20 and CeV 2 Al 20 the overall spectral distribution, the characteristic peaks and their relative intensities are well reproduced by the PALD. Note that the distinguished maximum at about 30 meV present only in G(o) of LaV 2 Al 20 and CeV 2 Al 20 corresponds to the characteristic maximum in Z Al(16c) (o) in these compounds. Despite the overall good approximation of the ScV 2 Al 20 INS response the match is less satisfactory for two reasons. Firstly, the pronounced low-energy peak dominated by Sc dynamics is shifted towards low energies in the PALD data.
This study is especially efficient regarding mass spectrometry analytical time. From the 534 validated N termini, 480 confirmed existing gene annotations, 41 highlighted erroneous start codon annotations, five revealed totally new mis-annotated genes; the mass spectrometry data also suggested the existence of multiple start sites for eight different genes, a result that challenges the current view of protein translation initiation. Finally, we identified several proteins for which classical genome homology-driven annotation was inconsistent, questioning the validity of automatic annotation pipelines and em-phasizing the need for complementary proteomic data. All data have been deposited to the ProteomeXchange with identifier PXD000337.
correct translational start site is essential for the genetic and biochemical analysis of a protein because errors can seriously impact subsequent biological studies. If the N terminus is not correctly identified, the protein will be considered in either a truncated or extended form, leading to errors in bioinformatic analyses (e. g. during the prediction of its molecular weight, isoelectric point, cellular localization) and major difficulties during its experimental characterization. For example, a truncated protein may be heterologously produced as an unfolded polypeptide recalcitrant to structure determination  (25). Moreover, N-terminal modifications, which are poorly documented in annotation databases, may occur  (26, 27). Unfortunately, the poor polypeptide sequence coverage obtained for the numerous low abundance proteins in current shotgun MS/MS proteomic studies implies that the overall detection of N-terminal peptides obtained in proteogenomic studies is relatively low.
The solvent gradient was performed as in the primary run, and N-terminal peptides were collected in the same 4 min intervals. The nine resulting fractions were dried, redissolved in 11 l of 0. 1% TFA, and 10 l were analyzed using nanoLC-MS/MS. NanoLC-MS/MS Analysis-NanoLC-MS/MS experiments were performed on an LTQ-Orbitrap XL hybrid mass spectrometer (Ther-moFisher) coupled to an UltiMate 3000 LC system (Dionex-LC Packings). The parameters for recording MS/MS spectra were as described previously  (21). Peptide mixtures were loaded and desalted on line in a reverse phase precolumn (Acclaim PepMap 100 C18, 5 m bead size, 100-Å pore size, 5 mm x 300 m) from LC Packings at a flow rate of 0. 3 l/min. The previously optimized gradient (21) was applied. Whole Genome Database Mining-Peak lists from the LC-MS/MS raw data were generated with the MASCOT DAEMON version 2.
3. 2 software (Matrix Science, Boston, MA) using the extract_msn. exe data import filter Xcalibut FT package (version 2. 0. 7) proposed by ThermoFisher, generated as previously described  (49). To compare and optimize the different steps of the protocol, MS/MS spectra were searched against a coding domain sequence (CDS) database comprising the 4129 polypeptides sequences annotated in the genome of R. denitrificans  (50) , totaling 1,288,451 amino acids with an average of 312 amino acids per polypeptide (NCBI download, 2010/02/17). The 22 most common keratin contaminants and the proteases used in this study were also included in the database. Searches for peptides were performed with Mascot using the following parameters: a mass tolerance of 5 ppm on the precursor ion and 0. 5 Da on the MS/MS, static modification of carboxamidomethylated Cys (ϩ57.
0215), and variable modifications of oxidized Met (ϩ15. 9949), N-terminal acetylation (ϩ42. 0106), and TMPP ϩ -Ac (C 29 H 35 O 10 P, ϩ572. 1811) or TNBS (C 6 H 2 O 6 N 3 , ϩ210. 9865) labels on the N termini or Lys lateral chains. The variable modification of TMPP ϩ -Ac-Met (C 34 H 44 N 1 O 11 P 1 S 1 , ϩ703. 2216 amu as calculated after taking into account the additional positive charge introduced by TMPP) on the N termini was also included; this modification, in combination with a semi-specific digestion requirement, allows the identification of translation initiation at non-AUG codons, such as when GTG codons, which normally code for valine residues, actually encode the initial methionine. Mascot will treat the resulting peptide as if the C terminus is specifically cleaved, but not the N terminus, which begins with a methione, contrary to the theoretically encoded valine.
Mis-cleavages were set at 3 for trypsin or chymotrypsin, and 2 for endoproteinase Glu-C. All peptides with a score above its peptide identity threshold set at p Ͻ 0. 01 with the CDS database and rank 1 were filtered by the IRMa 1. 28. 0 software  (51). At the proteogenomic stage of genome refinement of R. denitrificans OCh114, the MS/MS datasets were searched against an amino acid sequence database corresponding to a six-frame stop-to-stop translation of the genome sequence and that was restricted to open reading frames (ORFs) with at least 40 amino acids. This ORF database comprised 61,652 polypeptide sequences, totaling 6,201,552 amino acids with an average of 101 amino acids per polypeptide. The sequence of the proteases and the 22 most common keratin contaminants were also included in this database.
The maximum numbers of mis-cleavages were set as above. Fixed and variable modification searches were performed with the same parameters as described for the CDS database searches. Criteria for Extracting N-terminal Peptides-Each nanoLC-MS/MS experiment was analyzed first with specific protease cleavages and then in semi-specific mode to identify TMPP-derivatized peptides. All peptide matches with the ORF database were filtered with the IRMA 1. 28. 0 software with cutoff values at p Ͻ 0. 01. Redundant assignments to the same from the dual assignment strategy or multiple records by the mass spectrometer were reduced to a single event. Peptides having an acetylation or TMPP N-terminal label were extracted, and only non-redundant N-terminal most peptides corresponding to a possible start (ATG, GTG, and TTG codons) were conserved.
Further validation was applied as follows: peptide score, coding length to total ORF length ratio greater than 0. 45, similarities detected with other known proteins, and manual annotation of MS/MS spectra. In Silico Analysis of Protein Sequences-Prediction of secreted proteins was performed by analyzing proteins with evidence of multiple translational starts or incorrect annotations using the prediction tools SignalP 4. 0, SecretomeP 2. 0, and LipoP 1. 0 as described previously  (49). PSI-BLAST (http://blast. ncbi. nlm. nih. gov/blast) searches were performed using the NCBI non-redundant protein sequence database and default parameters. Proteomic Data Repository-The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral. proteomexchange.
To test the efficiency of this acetylation step, we analyzed an acetylated tryptic digest ("Ta" in Table  I ) and compared the results with those obtained with an equivalent non-acetylated sample ("Tb" in Table  I ). Both fractions were analyzed in a single nanoLC-MS/MS run, and MS/MS spectra were searched against the CDS database. A complete list of assigned peptides and proteins is given in supplemental Table  S1. No acetylated peptides were detected when the sample was not treated with sulfo-NHS-acetate ("Tb" in Table  I ), whereas the acetylated sample showed 73% protection of lysine residues ("Ta" in Table  I ). In the acetylated sample, 113 distinct N-terminal peptides matching annotated proteins were found, corresponding to 89 non-redundant polypeptides. Of these, 65 were detected with their N terminus labeled with TMPP; 23 were acetylated at the N terminus, and one was unmodified.