dataesr/scientific-paragraphs-categorization huggingface dataset:
In general, only ions of the charge state 2-5 were considered for fragment ion spectrum recording. We preformed LC-MS data analysis using proteome discoverer 2. 1 (Thermo Scientific). In brief, we imported all LC-MS runs as fractions ignoring MS peaks below 3 S/N. Subsequently, we matched MS2 spectra to the Toxoplasma gondi proteome (5811 GT1) using the SEQUEST HT search engine and the following settings: Enzyme specificity: semi-ArgC, Peptide mass tolerance: 10 ppm, Fragment mass tolerance: 0. 05 Da, Ion series: y-and b incl. neutral losses; Static modifications: Carbamidomethyl (C) and TMT6plex (K); Variable modifications: Oxidation (M), Acetylation or TMT6plex (peptide n-terminus), Met-loss (protein terminus). FDR was set to 1% by the target +decoy approach in conjunction with Percolator  (Ka ¨ll et al.
Parsing of datasets and interpretation Generally speaking, abundance ratios of <1 were interpreted as proteolytic processing due to active ASP3 in -ATc conditions, that is, higher abundance of the correctly processed (acetylated) N-terminal peptide. Conversely, ratios >1 may be either due to higher abundance of peptides representing unprocessed N-termini or accumulation of degradation products in +ATc conditions. However, for the purpose of identifying likely biologically relevant changes of +ATc/-ATc peptide ratios we calculated stringent cut-offs based on the distribution of log2 ratios in the normalized pre-TAILS dataset. Using an assumption-free empirical cumulative distribution function (ECDF) to determine the distribution of log2 ratios for R. XXXXR peptides, that is, all peptides generated by tryptic cleavage (pre-TAILS data) cut-off ratios at the 1% and 99% quantiles were calculated.
The calculated log2 values of À0. 4719 (0. 72) and 0. 919 (1. 89), respectively, predict 1% false-positives in the dataset. However, manual surveillance of the data indicated that a more stringent lower cut-off ratio of 0. 22 was more appropriate considering that ASP3 is virtually absent in +ATc conditions. Instead of the calculated upper cut-off (log2 0. 9119) we applied a slightly more stringent threshold of 2-fold higher abundance of peptides in +ATc conditions as secondary criterion for interpretation of the TAILS dataset in terms of ASP3 substrate specificity. In addition, we also considered more relaxed selection criteria with +ATc/-ATc ratio cut-off above or below 2-fold change on either side, i. e. ratios of <0. 5 and>2, respectively). The criteria for substrate selection and further pertinent analysis are described in Appendix 1.
Phylogenetic tree construction Sequences of Apicomplexan aspartyl proteases were procured from EuPathDB and aligned using MUSCLE sequence alignment software  (Edgar, 2004a (Edgar, , 2004b)). The resulting sequence alignment was manually curated utilizing BioEdit (http://www. mbio. ncsu. edu/bioedit/bioedit. html) to edit out uninformative alignment positions. Phylogeny tree was generating utilizing PhyML  (Guindon et al. , 2010)  on the curated MUSCLE alignment, using LG model of amino acids substitution with NNI topology search. Phylogeny. fr (Dereeper et al. , 2008)  platform was utilized for much of the above analysis. The EupathDB IDs of sequences used in the phylogenetic analysis were listed in Supplementary file 9, and the curated alignments shown in Supplementary file 10. TAILS. A highly abundant N-terminal peptide  [T].
EDDKSAASIVR. [G] (58-68) with a ratio of 0. 045 robustly predicts an ASP3-dependent cleavage site in this 204 aa protein at  [VETT | EDDK]. Here too, detection of an N-terminal peptide shifted by two amino acids (56-68) with a ~15 fold lower abundance likely represents a minor alternative cleavage site. In addition, four peptides with ratios >2 were detected, one of which is highly abundant in +ATc conditions and likely represents an immature N-terminus after cleavage of the signal peptide. Some ASP3 substrates may be revealed in the TAILS dataset only by peptides with ratios <0. 22 (0. 5). This is the case for MIC6 whose predicted ASP3 cleavage site [VQLS | ETPA] is represented by the abundant peptide [S]. ETPAACSSNPCGPEAAGTCKETNSGYICR. [C] with an +ATc/-ATc ratio of 0. 089 in the TAILS dataset.
No peptides with ratios >2 have been detected in this experiment. ASP3-dependent processing of MIC6 has been experimentally validated (Figure  3B ), as well as for the hypothetical protein TGGT1_273860 (TAILS3) (Figure  5A ), which presents a very similar profile in TAILS analysis. Conversely, ROP1 was only represented by peptides with +ATc/-ATc ratios >2 in the TAILS dataset. Nevertheless, in vitro cleavage experiments show ASP3-dependent processing producing a mature protein of ~55 kDa (Figure  4A ). Although two acetylated N-termini were detected in MS analysis, in this case, likely for technical reasons (e. g. flyability), the quantitative information was not sufficient to calculate peptide abundances. However, the high number of peptides (4 N-terminal, 5 internal) in the TAILS profile with ratios >2 is consistent with ROP1 being an ASP3 substrate.
Figure2. Global analysis of MS data and peptide ratios. (A) All measured spectra (65'900) minus those with low quality attributes leave 32'594 high quality spectra (9169 peptide groups) for the analysis. The graphical representation depicts proportions of N-terminal peptides in the pre-TAILS and TAILS datasets (blue pie charts) and corresponding N-acetyl modifications (ochre pie charts). N-termini in the TAILS fraction are enriched by >10 fold (69% vs 6%) over internal peptides (generated by trypsin cleavage). (B) Graphical representation of the 1529 proteins in the combined datasets. Of those 642 and 293 are unique to the pre-TAILS or the TAILS fractions, respectively. (C) Graphical depiction of data generated by calculating +ATc/-ATc peptide ratios revealing ASP3-dependent processing (for details see also Table supplement 1-4).
Acknowledgements We would like to thank  Valerie Polonais  for her contribution and initial investigation into aspartyl proteases in Toxoplasma gondii. This work was supported by  Carigest SA , the  Swiss National Science Foundation  ( FN3100A0-116722  to DS-F and  CRSII3_16002  to AH and DSF). DSF is an  HHMI senior international research scholar. BM is recipient of long-term EMBO fellowships. SKD was supported from the  Sir Jules Thorn Charitable Overseas Trust reg. , Schaan ( Dr. Karine Frenal ) and MalarX (SystemsX. ch).
Video 3. 3 Figure2. Global analysis of MS data and peptide ratios. (A) All measured spectra (65'900) minus those with low quality attributes leave 32'594 high quality spectra (9169 peptide groups) for the analysis. The graphical representation depicts proportions of N-terminal peptides in the pre-TAILS and TAILS datasets (blue pie charts) and corresponding N-acetyl modifications (ochre pie charts). N-termini in the TAILS fraction are enriched by >10 fold (69% vs 6%) over internal peptides (generated by trypsin cleavage). (B) Graphical representation of the 1529 proteins in the combined datasets. Of those 642 and 293 are unique to the pre-TAILS or the TAILS fractions, respectively. (C) Graphical depiction of data generated by calculating +ATc/-ATc peptide ratios revealing ASP3-dependent processing (for details see also Table supplement 1-4).
For instance, this would permit the direct determination of the quantum Fisher information  13  , a witness for genuinely multipartite entanglement and the detection of entanglement between subsystems of the complex spin cluster  15. Finally, the improvement in the flexibility and in the flux of the new generation of spectrometers, like those under development at the new European Spallation Source (https://europeanspallationsource. se), will further expand the possibilities of this kind of technique. ) were collected at a temperature of 150 K using a using Mo-K radiation on an Agilent Supernova, equipped with an Oxford Cryosystems Cobra nitrogen flow gas system. Data were measured and processed using CrysAlisPro suite of programs. More details on the crystal structure determination, crystal data and refinement parameters are reported in Supplementary Note 5 and Supplementary Table  1.
Methods Supplementary Data 1 contains the supplementary crystallographic data for this paper. An incident neutron wavelength of 7. 5 Å was selected to probe the excitations centred at 0. 24 and 0. 28 meV, with an energy resolution (full-width at half-maximum) of 22 meV at the elastic line. The magnetic field was applied along the y-vertical axis. Preliminary measurements were also performed on the high-resolution LET 44 spectrometer at ISIS neutron spallation source using an incident energy of 2. 5 meV (40 meV energy resolution), at a temperature of 1. 8 K and a field of 5 T. Data analysis and simulations. Measurements for different rotation angles were combined using the HORACE analysis suite  45. Corrections for attenuation as a function of rotation and scattering angle based on the slab-like geometry of the sample holder were performed using the formula given in ref.
Acknowledgements Very useful discussions with  M. L. Baker  and  F. Troiani  are gratefully acknowledged. E. G. , P. S. , G. A. and S. C. acknowledge financial support from the  FIRB  Project No. RBFR12RPD1  of the  Italian Ministry of Education and Research. G. T. , I. J. V. -Y. , G. F. S. W. and R. E. P. W. thank the  EPSRC(UK)  for support, including funding for an X-ray diffractometer (grant number  EP/K039547/1 ) and for the  CDT NowNANO , which supported G. F. S. W. We acknowledge the  Institute Laue-Langevin  for funding the PhD of S. A. and for instrument time. We thank the ILL technical staff, in particular  S. Turc  and  J. Halbwachs  for technical assistance during the experiment. We thank  John Crawford  and  Michael Hellier  from the ISIS technical support for designing and machining the sample holders for the INS experiments.
Data availability. Supplementary Data 1 has been deposited at the Cambridge Crystallographic Data Centre (deposition number: CCDC 1480868) can be obtained free of charge via www. ccdc. cam. ac. uk/conts/retrieving. html (or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB21EZ, UK; fax: ( þ 44)1223-336-033; or deposit@ccdc. cam. ac. uk). Raw data from the INS experiment were generated at the Insitut Laue-Langevin large-scale facility and are available at the ILL Data Portal with the identifier http://doi. ill. fr/10. 5291/ILL-DATA. 4-04-457. Derived data supporting the findings of this study are available from the corresponding author upon reasonable request.
2a-c ). Stabilisation of the E-dimer. We used a structure-based approach to identify pairs of residues at the dimer interface located such that their replacement by cysteine could potentially lead to formation of inter-subunit disulfide bonds and improve sE-dimer stability. We analysed the crystal structure of the DENV2 sE dimer (DENV2 sE in complex with EDE2 B7 Fab, PDB accession code 4UT6 (ref. 22)) with the MODIP server (http://caps. ncbs. res. in/iws/modip. html)  25  , which identified four pairs of amino acids facing each other across the dimer interface with C b -C b distances under 4. 5 Å. These were residues S255, A259, F108/T315 and L107/A313. S255 and A259 lying by the molecular two-fold axis, such that they face themselves in the dimer, and therefore only one mutation to cysteine is required to form a disulfide bond.
Structure of dimer DENV2 sE mutants/EDE2 A11 Fab complexes. To confirm that inter-subunit disulfide bond formation did not interfere with the overall conformation of the sE dimer, we carried out structural studies of the DENV2 sE mutants by X-ray crystallography. Because the mutants by themselves did not yield crystals of good enough quality, we tested crystallization in complex with EDE mAb fragments. We obtained crystals of both sE A259C and sE L107C/A313C in complex with Fab EDE2 A11 belonging to the orthorhombic space group P2 1 2 1 2. The crystals diffracted anisotropically to 3. 9 Å along the h and l axis and to only 7. 2 Å (A259C) or 6. 2 Å (L107C/A313C) along the long k axis. Given the limited resolution and anisotropy of the datasets we carefully selected the resolution cutoffs leading to the statistics shown in Table  1.
Both mutants crystallize with near identical unit cell parameters as the wild-type DENV2 sE-Fab EDE2 A11 complex (PDB accession code 4UTB,  22  ), but in a different orthorhombic space group (P2 1 2 1 2 for the mutants and of P2 1 2 1 2 1 for the wild type), resulting in a related but non-identical crystal packing. This lack of isomorphism precluded the calculation of an isomorphous difference map (Fo Mutant -Fo WildType ) with the 4UTB structure. We therefore determined the crystal structures of the mutants by molecular replacement using the 4UTB model as search. The resulting difference electron density maps, after one round of refinement, showed strong positive peaks mapping to the sites where the disulfide bonds were introduced (Supplementary Fig. 4a ). Refinement of the atomic models of the mutants was done at 3.
The abbreviation for anti-EDE2 mAbs 747(4)A11 and 747(4)B7 were A11 and B7, respectively  12. The abbreviation for anti-FLE mAb 749B12was B12 (ref. 12). sE direct ELISA. Purified DENV2 sE strain FGA02 (GenBank accession number KM087965. 1) (WT, A259C or L107C/A313C) and BSA were used as coating antigen and negative control antigen, respectively. NUNC immobilizer plates (436006) were coated with 50 ml of 10 mg ml À 1 protein and blocked with 3% BSA. Plates were then incubated with 50 ul of 1 mg ml À 1 of anti-FLE and anti-EDE mAbs supernatants followed by ALP-conjugated anti-human IgG. The activity was observed with PNPP and measured at 405 nm. Determination of the ability of anti-EDE mAb to stabilize the E-dimer. A MAXISORP immunoplate (442404; NUNC) was coated with 50 ul of 5 mg ml À 1 of human anti-FLE or anti-EDE mAbs.
The plate was then blocked with 3% BSA for an hour followed by incubation with serial dilutions of Strep-tagged recombinant envelope protein DENV2. The reaction was visualized by ALP-labelled Strep-Tactin and PNPP substrate. The reaction was stopped by adding NaOH and the absorbance was measured at 405 nm. Biochemical analyses. SEC-MALS was performed by loading B150 ug of DENV2 FGA02 A259C protein into Superdex 200 10/300 GL column (GE life sciences) and samples were run in Tris 50 mM, NaCl 500 mM (pH 8. 0) at a flow rate of 0. 4 ml min À 1. These samples passed through a Wyatt DAWN Heleos II EOS 18-angle laser photometer coupled to a Wyatt Optilab TrEX differential refractive index detector. Data were later analysed using Astra 6 software (Wyatt Technology Corp). Analysis of the complex of DENV2 FGA02 WT along with Fab C8 and Fab A11 were performed in similar manner by loading 150 mg of DENV2 FGA02, 300 mg of Fab C8, 300 mg of Fab A11 and for complex formation a mixture of 150 mg of DENV2 FGA02 with 300 mg of FabC8 and 150 mg of DENV2 FGA02 with 300 mg Fab A11.
Crystals were optimized with a robotized Matrix Maker and Mosquito setups on 400 nl sitting drops, or manually in 24-well plates using 2-3 ml hanging drops at 18 °C. The crystals of DENV2 sE A259C in complex with EDE2 A11 Fab were grown in 100 mM Hepes pH 7. 5, 19% PEG 6 K and 1. 5% (v/v) MPD. The crystals of the complex DENV2 sE L107C/A313C with EDE2 A11 Fab were obtained in 100 mM Tris pH 8. 5 and 20. 7% PEG 4 K. The crystals of A259C and L107C/A313C mutants were transfered in drops containg 67% of mother liquor with respectively 16% of glycerol and 16% of ethylene glycol as cryoprotectants, before being cryo-cooled in liquid nitrogen. X-ray diffraction data were collected at beam lines PROXIMA-2 at the SOLEIL synchrotron (St Aubin, France), and ID29 at the European Synchrotron Radiation Facility (Grenoble, France).
Only one crystal was used for each of the data sets. Diffraction data were processed using the XDS package and scaled with SCALA or AIMLESS  41  in conjunction with other programs of the CCP4 suite  42. The high resolution limits for each structure were determined using CC 1/2 -based cutoffs of 0. 30 (ref. 43). The structures were determined by molecular replacement with PHASER  44  using the search model DENV2 sE WT in complex with EDE2 A11 Fab (PDB 4UTB). Subsequently, careful model building with COOT  45  was done in 2Fo-Fc electron density map (Supplementary Fig. 6 ), alternating with cycles of crystallographic refinement with the programs Phenix. Refine  46  and/or BUSTER/TNT  47  , led to the final model. Refinement was constrained to respect non-crystallographic symmetry with TLS refinement  48  and target restraints using higher-resolution structures of DENV2 sE (from PDB 4UTA), scFv A11 (PDB 4UT7) and constant domains of Fab A11 (from PDB 4LLD).
Purified sE (WT, A259C or L107C/A313C from DENV2 FGA-02 or DENV4 1-0093 and WT, A257C, L107C/S311C from DENV3 H87) was mixed with liposomes and incubated for 10 min at RT before overnight incubation at 30 °C under acidic conditions. The mixture was separated by ultracentrifugation on an Optiprep (Proteogenix 1114542) continuous 0-30% gradient. Aliquots from top and bottom fractions were analysed by western blot using an anti-strep tag antibody. Data availability. Coordinates and structure factors amplitudes have been deposited in the Protein Data Bank under accession numbers 5N0A and 5N09 for DENV2 sE A259C and DENV2 sE L107C/A313C mutants in complex with EDE2 A11 Fab complexes, respectively. All other relevant data are available from the authors on request.
Acknowledgements We thank  Watchara Kasinrerk  and  Chunya Putthikhunt  for anti-dengue anti-DomIII mAb 2C8;  J. Freire  and  G. Bowler  for help and discussion; the staff at the crystallogenesis and chemogenomic & biological screening facilities at  Institut Pasteur ; the staff at beamlines  PX1  and  PX2  at  SOLEIL synchrotron (Saclay, France) , the staff at beamlines ID23-1, ID23-2, ID29 and IB30B at the  European Synchrotron Radiation Facility (Grenoble, France) ;  Fabrice Agou at Institut Pasteur  for the MALS system. We acknowledge support from the  European Commission   FP7 Programme  for the DEN- FREE  project under Grant Agreement number  282 378FP7  (F. A. R. , J. M. and G. R. S. ); the  'Integrative Biology of Emerging Infectious Diseases' Labex (Laboratoire d'Excellence)  grant number  ANR-10-LABX-62-IBEID  ( French Government's 'Investissements d'Avenir' program  ) (F.
e. as would be the case if it were a gravitar  (Palomba 2005; Knispel & Allen 2008) , and determining the equivalent strain expected at the Earth. 153 It can be calculated (see, e. g. Aasi et al. 2014 ) using h sd 0 = 5 2 GI zz | ḟrot | c 3 d 2 f rot 1/2 , (1) where f rot and ḟrot are the pulsar's frequency and first frequency derivative, I zz is the principal moment of inertia (for which we generally assume a canonical value of 10 38 kg m 2 ), and d is the pulsar's distance. In previous searches, this limit has been surpassed (i. e. a smaller limit on the strain amplitude has been obtained) for two pulsars: PSR J0534+2200 (the Crab pulsar;  Abbott et al. 2008)  and PSR J0835-4510 (the Vela pulsar;  Abadie et al. 2011). In this paper, we provide results from a search for gravitational waves from 200 known pulsars using data from the first observing run (O1) of Advanced LIGO (aLIGO).
For the LIGO Hanford Observatory (H1) and LIGO Livingston Observatory (L1), we used data starting on 2015 September 11 at 01:25:03 UTC and 18:29:03 UTC, respectively, and finishing on 2016 January 19 at 17:07:59 UTC at both sites. With duty factors of 60% 153 This is known to be a naïve limit. For several young pulsars where the braking index (see Section 4) is measured  (Lyne et al. 2015; Archibald et al. 2016) , we know that it is not consistent with pure gravitational wave emission, and other energy-loss mechanisms can be dominant. Effects of this on spin-down limit calculations are discussed in  Palomba (2000). Figures 9 and 10 of  Abdo et al. (2013)  also show that for pulsars observed as Fermi gamma-ray sources, a not insignificant proportion of their spindown luminosity is emitted through gamma-rays.
RESULTS For all pulsars, we quote 95% credible/confidence upper limits on the gravitational-wave amplitude h 0 set using coherently combined data from both H1 and L1. 158 We use this value to also set limits on the mass quadrupole moment Q 22 of the l = m = 2 mode of the star  (Owen 2005)  via Q 22 = h 0 c 4 d 16π 2 Gf 2 rot 15 8π. (4) In turn, this is related to the star's fiducial equatorial ellipticity ε through ε = Q 22 I zz 8π 15. (5) To calculate ε, we use the canonical moment of inertia of I zz = 10 38 kg m 2 (see, e. g. , Chapter 6 of  Condon & Ransom 2016). We also quote the ratio of our observed h 0 limits to the spin-down limits calculated using Equation 1. The distances used to calculate Q 22 and ε are (unless otherwise stated in Table  1  or 4) taken from v1. 54 of the ATNF pulsar catalog  (Manchester et al.
Future searches will also address gravitational-wave emission at not just twice the rotation frequency, but also at the rotation frequency (e. g. Pitkin et al. 2015) , further increasing the likelihood of a first detection of continuous gravitational waves. ∆φ(t) = (φ true (t)φ best-fit (t)). 165 hese combined processed datasets for each detector d are used to estimate the joint posterior probability distribution of the unknown source signal parameters, θ, using a Bayesian framework via p( θ|d, H S , I) = p(d| θ, H S , I)p( θ|H S , I) p(d|H S , I) , (A2) where p(d| θ, H S , I) is the likelihood of the data given the specific signal model (H S ) parameters, p( θ|H S , I) is the joint prior probability distribution of the parameters, and p(d|H S , I) is the evidence (marginal likelihood) of observing our data, given a signal of the type we defined.
Furthermore, the MCMC did not naturally produce a value for the evidence p(d|H S , I). To allow the calculation of p(d|H S , I) and, as a natural by-product, the joint parameter posterior probability distribution, we have adopted the nested sampling method  (Skilling 2006). In particular our analysis code  (Pitkin et al. (2012) ; M. Pitkin et al. 2017, in preparation)  uses the nested sampling implementation of  Veitch & Vecchio (2010)  as provided in the LALIinference library  (Veitch et al. 2015)  within the LIGO Algorithm Library (LAL) suite. 166 This implements more intelligent and efficient proposals than previously used. The code has been validated by extracting both software and hardware  (Biwer et al. 2016 ) signal injections into gravitational-wave detector data. Note. -Limits with constrained orientations (see Appendix B) are given in parentheses.
We collected information on the presence of cancer, but detailed information on activity of cancer is not available; however, based on data for cancer treatment (►Table 5), we can assume that the majority of patients had active cancer. Additionally, information relating to cancer stage was not collected, which may have impacted the outcomes and therapeutic decisions depending on the distribution of early-and late-stage cancers between the treatment groups. An implicit criterion for inclusion in the study was also life expectancy beyond around 3 months, as patients were required to have an indication for at least 12 weeks of anticoagulant treatment. Therefore, this also impacted mortality outcomes as patients with shorter life expectancies were excluded. This was consistent with what was done in the EINSTEIN DVT study.