dataesr/scientific-paragraphs-categorization huggingface dataset:
Mass spectrometry identification of phosphorylation NP from egg grown influenza A/PR/8/34 virus was cut out from a Coomassie-stained 1D SDS-PAGE gel and digested with Trypsin (Roche Applied Science). The digest was analyzed by LC-ESI-MS/MS with an Ion trap MS HCT ultra PTM Discovery System (Bruker Daltonics, Bremen, Germany) coupled with a Nano-LC 2D HPLC system (Eksigent, Dublin, CA, USA). A CapRod monolithic C18 column (100 mm615 cm, Merck, Darmstadt, Germany) was used to separate the peptides. The gradient was 10-70% ACN within 20 min at 300 nl/min flow rate. The top two precursor ions were selected over m/z range from 400 to 1200 for fragmentation. Fragmentation was performed subsequently for 60 ms over 300 to 2000 m/z. The raw data were processed with DataAnalysis (Version 3. 1, Bruker, Bremen Germany).
The extracted MS/MS data were submitted to MASCOT (version 2. 103, Matrix Science, London, UK) in-house server via Biotools (version3. 0, Brucker, Bremen, Germany). Proteins were identified by searching the peptide lists against SwissProt. The following parameters were used: Taxonomy: Viruses; Enzyme: trypsin; Max Missed Cleavages: 2; Variable modifications: oxidation (M); carbamidomethyl (C); phospho (ST), phospho(Y); Peptide Mass Tolerance: 60. 5 Da: Fragment Mass Tolerance: 60. 5 Da.
This work was funded in part by the  French Agency for Research (ANR)  ( FLUNUCLEOVIR  Nu  ANR 2010 Blan 1307 01 ), the  European Commission  under grant agreement  no259751  ( Flupharm  project: New drugs targeting influenza virus polymerase,  11/2010-05/2014 ), a grant from the  French A(H1N1) research program , coordinated by the  Institut de Microbiologie et Maladies Infectieuses (INSERM, France)  and by  Lyon Biopole. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Case Ascertainment and Control Selection Cancers are reported by participants in annual (PHS) or biennial (HFPS and NHS) follow-up questionnaires. Medical records and pathology reports were obtained from hospitals after permission was received from subjects or for deceased cases identified through the National Death Index (NDI) or other sources from next-of-kin. Deaths are usually reported by family members or by the postal service in response to mailed questionnaires. In addition, the NDI was searched biennially for non-respondents, and this method has been shown to have a sensitivity of 98%  [24]. Approximately 88% of potential case subjects (self-reported or deceased cases with glioma) were subsequently confirmed with medical, pathology, cancer registry data or death certificate. For the present analysis, we included cases with any type of glioma brain tumor: astrocytoma, glioblastoma, oligodendroglioma, ependymoma, and mixed glioma subtypes.
Candidate Gene and SNP Selection DNA extractions were completed at the Channing Laboratory (Boston, MA) and shipped to Imperial College in London where a custom Illumina assay chip (Illumina, Inc. , San Diego, CA) was designed to amplify 384 SNPs distributed among approximately 40 genes. Most of the genes included in the assay were chosen because they have either been associated with allergy and atopy. In addition to the allergy genes, we included SNPs on 9 genes in the complement pathway (total 85 SNPs)  [6] ; gene (number of SNPs tested): C1QA (4), C1QB (7), C1QC (3), C2 (2), C3 (23), C5 (23), C5AR1 (3), CFB  (10) , and MBL2  (7). Three additional functional SNPs in MBL2 were selected and tested post-hoc (see below). For each gene, we chose a partially redundant set of haplotype tagging SNPs, using the HapMap data phaseIII/Rel #2 for the CEU population.
Genotyping and Quality Control DNA was obtained from all patients, and DNA concentrations were checked using Quant-iT TM PicoGreenH dsDNA reagent (Invitrogen, Carlsbad, CA) and normalized to 50 ng/ml before genotyping. A total of 250 ng DNA was used for the Illumina GoldenGate Assay (Illumina, Inc. , San Diego, CA), which was performed according to the manufacturer's standard three-day protocol. Each genotyping plate was prepared with both cases and controls to avoid plate-specific bias. Illumina clustering was performed on the raw data using Illumina's Genome Studio software version 2009. 1. All 384 SNPs were also manually inspected to make sure the clusters were correctly called after sorting via a statistical score called Gentrain. This score varies from 1 to 0 and is based on the shape of the clusters and their relative distance to each other.
A custom assay by design was ordered for SNP rs11003125 (Forward Primer Sequence: GGAGTTTGCTTCCCCTTGGT, Reverse Primer Sequence: GGGCCAACGTAGTAAGAAATTTCCA, Reporter 1 Dye: VIC, Reporter 1 Sequence: CAAGCCTGTGTAAAAC, Reporter 2 Dye: FAM, Reporter 2 sequence: CAAGCCTGTC-TAAAAC). Unfortunately, 3 of the 5 SNPs that have known impact on MBL2 serum levels have rare alleles with MAF,0. 05; data for two of the SNPs (rs1800451 and rs5030737) were monomorphic and could not be included in the data analyses. Deviations of the observed genotype frequencies from the Hardy-Weinberg equilibrium (HWE) were evaluated and all three SNPs (rs1800450, rs7096206 and rs11003125) were in HWE (p. 0. 05). Genotyping success rate for rs1800450 was 83%, rs7096206 was 97% and rs11003125 was 84%. A total of 8 replicates were used for internal quality control assessment and showed.
Statistical Analyses Departures from Hardy-Weinberg equilibrium for each SNP were determined using a x 2 test. We used unconditional logistic regression analyses to estimate odd ratios (OR) and corresponding 95% confidence intervals (95% CI) for individual SNPs and risk of glioma, controlling for age and cohort (conditional models resulted in similar OR estimates). Associations were evaluated using codominant models unless the minor allele frequency was less than 0. 05 in controls (in which case the dominant model was used). Test for trends were estimated using the Cochran-Armitage test. Haplotype analyses were constructed for MBL2 using 10 SNPs in two blocks previously identified using HapMap and including the SNPs that were identified from the literature post-hoc. The haplotype-specific odds ratios were estimated from genotype data on unrelated cases and controls using unconditional logistic regression.
Amongst the SIV that we observed to be resistant to TRIMCyp restriction, were SIVcol and, interestingly, SIVmon and SIVmus-1 which are closely related to SIVgsn (Figure  4B ). The CypA binding loop of lentiviral CA is the proline-rich sequence comprised between helices 4 and 5 on HIV-1 CA  [69]. By using the CA crystal structure of HIV-1 bound to human CypA (PDB: 1M9C) (Figure  5A ) and the raptorX server  [70] , we superimposed the predicted structure of the CA from SIVmnd1 (Figure  5B ), those of the three SIV of the SIVgsn lineage (Figure  5C ) and that of SIVcol (Figure  5D ). We found that the CypA-binding loop of SIVmnd1 superimposed closely with that of HIV-1 while the SIVcol loop, which is shorter, does not (Figure  5B  and D ). Interestingly, as shown in Figure  5C , within the SIVgsn lineage, the change of A (CA SIVgsn) to Q (CA SIVmon and SIVmus-1) introduced a subtle conformational change, that significantly altered the direct contact with the hydrophobic pocket of CypA, even if the target proline ′90′ remained present in the middle of the loop.
siRNA transfection Sequences of siRNA were as follows: 5′ -GGCAGCUCUA CCAAAUGUtt -3′ for the Nup153 (position 2593-2615) (NM_005124)  [96] ; 5′-GGCUCCAAAGAGCGGAUUUtt-3′ from Saitoh et al. [97] , 5′-GCGCGAAAUUGUUUCGU-Utt-3′ (position 3719 to 3738) and 5′-GCA-AAC-CAC-GUU-AUU-ACU-Att-3′ (position 8704 to 9723) for Nup358/RanBP2 (accession number NM_006267. 4). HEK-293T cells were transfected with 300 pmoles of each specific RNA duplex using Oligofectamine (Invitrogen) according to the manufacturer's instructions. A siRNA directed against firefly luciferase was used as control. Forty-eight hours after transfection, cells were trypsinized, plated in 96-well plates, infected with GFP reporter viruses and analyzed by flow cytometry 2 days later. In some experiments, a combination of multiple siRNAs was used (total of 300 pmol).
Computational structure predictions The computer modeling of N-terminal CA structure from the SIVgsn lineage, SIVmnd1 and SIVcol was performed with the raptorX server http://raptorx. uchicago. edu) [70] , using the experimental CA crystal structure of HIV-1 bound to human CypA (PDB: 1M9C; http://www. rcsb. org/pdb/explore. do?structureId=1m9c) as a structural template. The multiple sequence alignments of the target and template sequences were performed using ClustalX  [98]. The predicted CA structures were visualized using the PyMOL 1. 4. 1 Linux version (http://pymol. org/citing).
Acknowledgements We are grateful to  Pierre Roques  for the SIVmnd-1 isolate DNA,  Dr Didier Negre  for the pAd-SIV4 and GAE-SFFV-GFP-WPRE plasmids and  Dr Greg Towers  for the Mafa- TRIMCyp and Mamu-TRIMCyp plasmids. pMIG-TRIMCyp plasmid  ( David Sayah  and  Jeremy Luban ) and pLPCX-TRIM5arh plasmid ( Joseph Sodroski  and  Matt Stremlau ) were obtained via the  NIH AIDS Research and Reference Reagent Program, Division of AIDS, NIAID ,  NIH. This work was supported in part by grants from the  French AIDS National Research Agency (ANRS , to V. C and J. L. B), the  French National Research Agency (ANR)  to J. L. B, the  Japanese Health Science Foundation (JHSF , to  M. S, M. Miyazawa  principal investigator), the  Foundation for Medical Research (FRM , to M. S. ) and the  Portuguese Foundation for Science and Technology (FCT)  with a co-financing from the  European Social Fund  (fellowship # SFRH/ BD /45053/2008 ).
Recipient mice were subsequently injected with PBS, G-CSF, or plerixafor s. c. , followed by imaging for up to 2 h (n = 5 per group). (b, Bottom) A representative snapshot of the skull BM 4 h after cell transfer. GFP + cells (green) were predominantly present in the BM cavity outside the sinusoids (labeled with TRITC dextran; red). Bar = 200 µm. (c) Mean instantaneous velocities of transferred GFP + neutrophils in mice treated with G-CSF or plerixafor. Each graph shows a dataset from a representative mouse. (d) Mean GFP + neutrophils egressed from the skull BM after PBS, G-CSF, or plerixafor treatment (n = 5 per treatment group). All data are shown as mean ± SEM. One-way ANOVA analysis was performed. (e) The frequency distribution of neutrophils egressed from the BM into the sinusoidal circulation at various time points after G-CSF or plerixafor injection.
e). Consistent with previous studies  (Lien et al. , 1987; Doyle et al. , 1997; Kreisel et al. , 2010; Looney et al. , 2011) , we observed a large number of marginated neutrophils within the pulmonary circulation under resting conditions. Administration of plerixafor triggered a reduction in the number of marginated neutrophils in the lungs within 2 h (Fig. 8 e ). In contrast, the effects of G-CSF on marginated neutrophil numbers were negligible within this time frame, consistent with the neutrophil release data (Fig. 8  c and Video 8). As it is technically challenging to preserve the lungs under physiological conditions, each imaging field was imaged for neutrophils. Collectively, this set of data demonstrates that the CXCR4 mutant neutrophils respond similarly to wild-type neutrophils during plerixafor treatment by increasing their retention in blood while preventing neutrophils from trafficking back to the BM.
8 a ). This approach allowed us to perform differential counts of neutrophils in arterial blood (exiting the lung) and venous blood (entering the lung) while avoiding the potential influence of interposing organs on neutrophil numbers. To validate our tandem sampling method, we used epinephrine as a positive control, which is known to  Mice were pretreated for 90 min with PBS, G-CSF, or plerixafor s. c. , followed by imaging using spinning-disk confocal microscopy. Five different fields from each lung were imaged for 5 min each. (e, Bottom) Quantification of neutrophils adhering to the pulmonary capillaries over the 5-min observation period in PBS-, G-CSF-, and plerixafor-treated mice (n = 6 per group). Each symbol corresponds to data obtained from an individual mouse and the bars represent the mean number of adherent neutrophils in each treatment group.
Image analysis. Images were transformed into time series movies and analyzed using IMARIS image analysis software (Bitplane). Tracking of cell motility in three dimensions was performed in a semiautomated manner as described previously  (Ng et al. , 2008 (Ng et al. , , 2011)). The mean/median and instantaneous migration velocities were typically obtained from 121 consecutive frames of video. To quantitate the endogenous neutrophil egress, the relative GFP fluorescence intensity was determined in specified regions of the marrow space using the surface function in surpass mode in IMARIS. For the analysis of experimental model 1 (neutrophil egress), the number of transmigrated GFP + cells was quantified manually. increased circulating neutrophils with plerixafor treatment appears to be largely dependent on their decreased BM homing.
Data acquisition and analysis were performed using Volocity software (Perkin Elmer). Intravital multiphoton imaging of skeletal muscle. The tibial anterior muscle was surgically prepared for imaging the skeletal muscle. LysM-GFP mice were anaesthetized with a cocktail of 150 mg/kg ketamine and 10 mg/kg xylazine. The left jugular vein was cannulated to allow the administration of 50 µg Evan's blue (Sigma-Aldrich) in 50 µl saline to label blood vessels in vivo. The mouse was subsequently immobilized on a custom-made stage and a heat pad was used to maintain the body temperature. To expose the skeletal muscle for imaging, a small area of skin was removed and loose dermal connective tissue was cleared to allow better visualization of the intact skeletal muscle vasculature. The exposed area was superfused with sterile PBS and sealed with a coverslip, with additional heating provided for the exposed muscle at 37°C.
Cells were stained with DAPI (Invitrogen) to assess cell viability and CountBright absolute counting beads (Invitrogen) were added before acquisition to enable calculation of absolute cell numbers. All samples were acquired using a FACSCanto II flow cytometer (BD) equipped with FACSDiva software. Data analysis was performed using FlowJo software (Tree Star). Assessment of circulating neutrophils at different sites of blood collection. Mice were anaesthetized with a cocktail of 150 mg/kg ketamine and 10 mg/kg xylazine and placed on a heating pad at 37°C. The right carotid artery was cannulated using a previously described method  (Duyverman et al. , 2012). In brief, a midline incision was made on the neck and the glands were separated sideways to expose the trachea before the surrounding tissues were cleared to expose the underlying carotid artery.
Each symbol corresponds to an individual tracked neutrophil and the bars indicate the mean velocity during resting, 25 min and 50 min post-G-CSF injection. (d) Snapshots of neutrophils in BM during resting state (left) and after plerixafor treatment (5 mg/kg s. c. ; right). White lines indicate the tracks of neutrophils over the 1-h tracking period after plerixafor injection (vasculature labeled with TRITC dextran, red). Bars, 40 µm. (e) Relative GFP fluorescence intensity in the skull BM parenchymal region in LysM-GFP mice treated with G-CSF or plerixafor over time (representative of three independent experiments). (f) Mean instantaneous velocity of migrating monocytes in the BM of CX 3 CR1-GFP mouse after G-CSF treatment. Graph shows a representative dataset from three independent experiments.
The arrow indicates the time point whereby G-CSF was administered s. c. (g, Top) Mean instantaneous velocity of migrating GFP + neutrophils in skull BM in a LysM-GFP mouse at resting state and after plerixafor treatment (data from three independent experiments). (g, Middle) The mean migratory velocities of neutrophils at different time points after plerixafor injection (30-min tracking period, n = 3 per group). (g, Bottom) The relative frequency distribution of neutrophil velocities (dataset from a representative mouse). Each symbol corresponds to an individual tracked neutrophil and the bars indicate the mean velocity of the whole population. A Student's two-tailed unpaired t test was performed. Numbers above the frequency distributions indicate the median velocity of the population. PI = post-injection, n.
Each graph shows a dataset from a representative mouse. (d) Mean GFP + neutrophils egressed from the skull BM after PBS, G-CSF, or plerixafor treatment (n = 5 per treatment group). All data are shown as mean ± SEM. One-way ANOVA analysis was performed. (e) The frequency distribution of neutrophils egressed from the BM into the sinusoidal circulation at various time points after G-CSF or plerixafor injection. Analysis was performed on data pooled from five mice per treatment group. See also Videos 3-5. (f) The number of circulating GFP + neutrophils before and after G-CSF (left) or plerixafor (right) treatment (n = 4 per group per time point). Each line corresponds to a single mouse and shows the number of circulating neutrophils at resting state and 2 h after G-CSF or plerixafor treatment.
(d, Right) Confocal images of lung sections from CXCL12-GFP demonstrating GFP expression in subpleural area (apical; left) and secondary bronchiole (middle, right). Images are representative of three independent experiments. Bars, 25 µm. C: capillary; Al: Alveoli; Br: Bronchiole; Bv: blood vessel. (e, Top) The experimental procedure for intravital imaging of the lung. Mice were pretreated for 90 min with PBS, G-CSF, or plerixafor s. c. , followed by imaging using spinning-disk confocal microscopy. Five different fields from each lung were imaged for 5 min each. (e, Bottom) Quantification of neutrophils adhering to the pulmonary capillaries over the 5-min observation period in PBS-, G-CSF-, and plerixafor-treated mice (n = 6 per group). Each symbol corresponds to data obtained from an individual mouse and the bars represent the mean number of adherent neutrophils in each treatment group.
The response of CTgEZ. 4 T cells was mildly decreased (GRA6 II -K), severely disrupted (GRA6 II -L) or totally abrogated (GRA6 II -P, GRA6 II -HY10, GRA6 II -GFP) (Fig. 5A ). These data suggest that the Cterminal location determines optimal processing and presentation of the HF10 peptide when the precursor protein is expressed ectopically by the antigen-presenting cell. To assess the impact of HF10 position in T. gondii, we used CEP parasites expressing longer versions of GRA6 II , extended either by a leucine (GRA6 II -L) or by the HA tag (GRA6 II -HA). First, we verified that transgene levels were comparable by Western blot (Fig. 5B ). To investigate whether these additional C-terminal residues might perturb GRA6 transport, we took advantage of the HA tag and evaluated the subcellular distribution of transgenic GRA6-HA, as compared to total GRA6.
A recent study interrogating the Immune Epitope Database (www. iedb. org) for a positional bias of viral epitopes reported that epitopes from both ends of a protein tended to be underrepresented  [49]. An indirect way to assess the general relevance of the C-terminal position would be to transfer subdominant epitopes to the C-terminus of their respective antigens (e. g. GRA4, ROP7) and evaluate the impact on CD8 responses. Future studies, not only with T. gondii but also with other intracellular parasites, should shed light on the general relevance of this position. During T. gondii infection in vivo, two scenarios of MHC I presentation could co-exist. On the one hand, phagocytosed parasite material may be processed by bystander cells present in the vicinity of infected cells  [50]. On the other hand, parasite proteins may be directly presented by actively infected cells  [51].
Ten minutes prior to imaging, mice were injected intraperitoneally with 200 mL of 15. 4 mg/mL D-Luciferin in PBS and anesthetized using 2% isoflurane. Dorsal and ventral images were acquired for 5 minutes and luminescence (photons/s/cm 2 /sr, total flux expressed as photons/s) was quantified using IgorPro Image Analysis Software (Caliper).
Acknowledgments  J. Boothroyd ,  J. D. Dunn ,  T. Hansen ,  D. Raulet ,  J. Saeij ,  L. D. Sibley ,  R. Vance  for reagents, NIH tetramer core facility for the tetramers,  C. Mercier , M. -F. Delauw for reagents and helpful discussions,  J. Lopez  and the  Blanchard team  for technical help and discussions,  C. Bonnart ,  D. Dunia ,  R. Lesourne  for critical reading of the manuscript.
Data collection Patients completed the ABCD quality of life questionnaire before the first injection and then 2 months after the last session of injections and, if applicable, 12 to 18 months after the last session of injections. Concomitantly, the Overall Treatment Effect (OTE) scale was completed by patients 2 months after the last session of injections and 12 to 18 months after the last session of injections, if applicable*. Comparison of ABCD and OTE scores allowed calculation of the minimal important difference in overall ABCD quality of life score. *As it was an observational study the 12/18 months evaluation took place only if the patient returned to a visit during this period in the setting of usual management An expert committee (2 dermatologists, 1 plastic surgeon) graded photographs for lipoatrophy presence before the 1 st injection, 2 months after the last session of injections and, if applicable, 12 to 18 months after the last session of injections.
Safety was evaluated using side effect or adverse event data obtained from the Case Report Forms (CRF). The Assessment of Body Change and Distress (ABCD) questionnaire  [14]  consist of three parts. Lipodystrophy: Six items concern the presence/absence of lipodystrophy in 6 areas of the body. The score is calculated by adding up the total number of responses (0 or 1) to the 6 items (0= no area affected 6 = 6 areas affected). Satisfaction: One 5-point item investigates overall satisfaction with body appearance (from 1 = very dissatisfied to 5 = very satisfied). Quality of life: 21 items spread across four dimensions evaluate the impact of lipodystrophy on the patient's life; Dimension A: Control and adjustment to the illness, satisfaction with body appearance (9 items); Dimension B: Psychological, social and relational impact (7 items); Dimension C: Fear of the future (3 items); Dimension D: Impact of treatment (2 items).
Statistical methods Statistical analyses were performed with SAS software, version 8. 2  [19]. Data were described in terms of sample size, mean, standard error, percentage by modality, response, and number of missing data, pre-(time 1) and post-treatment (time 2: 2 months; time 3: 12-18 months). Evaluation of quality of life was performed based on a score calculated according to recommendations of the ABCD questionnaire. Wilcoxon t-tests were used to determine the significance of within-group changes over time in QoL component scores between the inclusion or pretreatment visit (time 1) and post-treatment visits (time 2, time 3). Determination of the minimal important difference in quality of life was derived from calculation of the pre-treatment (time 1) and post-treatment (time 2, time 3) change in QoL score that corresponded with an OTE rating  [2, 3]  of a condition 'a little improved' or 'somewhat improved'.