dataesr/scientific-paragraphs-categorization huggingface dataset:
Expression of co-stimulatory molecules Both monocyte-derived DCs and macrophages treated with soluble EBOV GPs for 48 hours were washed in cold PBS supplemented with 2% fetal bovine serum and pre-blocked at 4uC for 30 min in FACS buffer. Cell-surface staining was performed using the following antibodies: FITC-conjugated anti-CD80, PEconjugated anti-CD40 (Beckman Coulter) and APC-conjugated anti-CD83, Peridinin Chlorophyll Protein Complex Vio 700 (PerCP-Vio700)-conjugated anti-CD86 (Miltenyi Biotec). After incubation with antibodies for 1 hour at 4uC, cells were washed with PBS, fixed with 1% PFA solution and analyzed using a Becton Dickinson LSRII flow cytometer (BD) and FlowJo software. A minimum of 10000 events were collected and analyzed for each sample. The statistical significance of the differences in median fluorescence intensity (MFI) values for each donor were evaluated by paired-sample t test and GraphPad Prism 6 software (GraphPad Software, La Jolla California, USA).
(C) DCs and MØ were incubated with serum containing 150 ng/ ml of MBL-containing sera (MBL + ), MBL-deficient sera (MBL 2 ) or culture media alone before washing and incubation with shed GP (as above). (A, B and C) Shed GP binding to cells was analyzed by flow cytometry and shown as raw MFI data for at least three independent blood donors. Statistically significant differences compared to HS are shown as follows: * -p,0. 05 and ** -p,0. 01; n. s. -not significant. (EPS) Figure  S4  EBOV shed GP containing sera does not activate DCs and MØ. Human monocyte-derived dendritic cells (DCs) and monocyte-derived macrophages (MØ) were incubated with either shed GP as above (HS+0%) or with shed GP in the presence of 5% bovine sera (HS+5%). As control, the cells were incubated with LPS or concentrated culture supernatants from GFP expressing cells (Mock).
Statistically significant differences (paired-sample t test) compared to HS+0% are shown as follows: * -p,0. 05. (EPS) Figure  S5  Quantitative data and statistical analysis of data presented in Figure  5. Shed GP induces the phenotypic maturation of DCs and MØ. 5610 5 of DCs (A) and macrophages (B) were incubated with concentrated culture supernatants. The cells were harvested at 48 h post-incubation and expression of CD80, CD86, CD40 and CD83 was analyzed by flow cytometry. Shed GP binding to cells was analyzed by flow cytometry and shown as raw MFI data for at least three independent blood donors. Statistically significant differences compared to HS are shown as follows: * -p,0. 05 and ** -p,0. 01; *** -p,0. 001. (EPS).
Serial dilutions of sera collected at day 6 post-infection (5 ml, dilutions 1/4, 1/8, 1/16 & 1/32, lanes 2-5), supernatant from EBOVinfected Vero E6 cells (20 ml, EBOV Vero, lane 1) and a sample of concentrated recombinant shed GP (5 ml, HS, lane 6) were analyzed by Western blot using anti-GP2 antibodies. Estimation of shed GP amounts in the sera of animals in comparison with shed GP from GP-HS expressing cells was performed using ImageQuantTL software (GE Lifesciences). Sera of animals contained approximately 85 times higher amounts of shed GP than those used in experiments with immune cells. (D). Samples of sera collected at different intervals post infection from Mock (day 3 p. i. ) -and EBOV-infected guinea pigs(animal numbers 192, 193, 195 & 196)  as indicated, were analyzed by Western blot using anti-GP2 antibodies.
Shed GP binding to cells was analyzed by flow cytometry. (C) DCs and MØ were incubated with serum containing 150 ng/ml of MBLcontaining sera (MBL + ), MBL-deficient sera (MBL 2 ) or culture media alone before washing and incubation with shed GP (as above). Filled histograms represent staining with an isotype control antibody. Data shown are representative of three independent experiments with at least three different donors. For quantitative data and statistics see figureS3. doi:10. 1371/journal. ppat. 1004509. g002.
This work was supported by the  European Union   FP7  project  ANTIGONE  ( 278976 ),  Agence Nationale de la Recherche  ( ANR-07-MIME-006-01 ),  Fondation pour la Recherche Medicale  ( DMI20091117323 ), the  Direction Generale de l'Armement (DGA)  and  « La Caixa » Fondation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Locomotive dyskinesia displayed as contralateral rotations were scored separately. The severity of each AIM subtype was scored from 0 to 4 (0: no abnormal behaviors detected, 1: occasional AIMs, i. e. present less than 50% of the time; 2: frequent AIMs, i. e. present more than 50% of the time; 3: continuous AIMs, but interrupted by sensory stimuli and 4: continuous AIMs, not interrupted by sensory stimuli). Half-points were used when the behavior of the animal were clearly in between the two defined points. The data are calculated as time-integrated total scores and represented by sum of the orolingual, limb and axial subtypes. To evaluate the effect of the 5HT receptor agonists on L-DOPA induced dyskinesia, selective 5-HT1A agonist, 8-OH-DPAT ((6)-8-hydroxy-2-dipropylaminotetralin hydrobromide; TOCRIS, Sweden), and the 5-HT1B agonist, CP-94253 (TOCRIS, Sweden) were injected subcutaneously 5 min before L-DOPA.
PET data analysis Dynamic emission scans were acquired in list-mode format over 120 min. The data files were displayed as 3D sinograms with a maximum ring difference of 47 and a span of 3. The acquired data were then sorted into 31 time-frames [1*15 s, 5*30 s, 1*45 s, 6*1 min, 1*1. 5 min, 4*2 min, 1*3. 5 min, 5*5 min, 1*7. 5 min, 6*10 min]. Finally, each emission sinogram was normalized, corrected for attenuation and radioactivity decay, and reconstructed using Fourier rebinning and 2-dimensional orderedsubsets expectation maximization (16 subsets, 4 iterations). Time frames collected were summed to create an integrated image. In order to define volumes of interest (VOIs) using anatomical landmarks, rats underwent as well a T2-weighted MR imaging that was used for PET/MRI co-registration. To this aim, rats were placed on a 7 Tesla MR system (Varian-Agilent Technologies, USA) equipped with a gradient coil reaching 600 mT/m (120 ms rise time), a radiofrequency birdcage 1H coil for transmission, and a 4-channel surface receive coil and T2weighted images were acquired over a total acquisition time of 9 minutes.
PET/MRI co-registration was then performed using the in-house image processing software Anatomist (http://www. brainvisa. info). Striatal VOI were delineated using the microPET Data analysis software ASIPro (ASIPro VM, Siemens) and ROI drawn over 13 to 15 continuous planes. To measure in vivo the fraction of [ 18 F]fallypride non-specific binding, a 10-voxel-diameter spherical region of interest (voxel size of 0. 47; 0. 47; 0. 796 mm) was drawn over the cerebellum, in a region devoid of D2R. The mean activity concentration values in all VOIs (left and right striata, cerebellum) were then calculated and plotted over time yielding regional time-activity curves. These curves were then normalized to the injected dose and body weight and expressed as standardized uptake values (SUVs). Kinetic modelling analysis was performed using the PMOD software package (version 2.
After waiting for additional three time bins, 12 mg/kg L-DOPA (plus 10 mg/kg benserazide hydrochloride) was injected systemically. A second challenge with KCl was then applied during the 6 th time bin (62. 5-80 min after L-DOPA administration) and data analyzed for four consecutive sampling intervals as described above. OMD Protocol 2. Extracellular DA levels under physiological conditions. For this purpose, we designed an OMD protocol in freely moving rats where we first obtained measurements in baseline and then injected these animals with 12 mg/kg L-DOPA (plus 10 mg/kg benserazide hydrochloride)which lead to peak dose dyskinesia that lasted for about 2 hoursand continued sampling the extracellular DA levels during this time without any other intervention or drug treatment. OMD Protocol 3.
Next day, the plates were punched using a MultiScreen Punch Kit (Millipore) in order to isolate the tissue bound membranes, which were then collected individually in scintillation vials. The vials were instantly filled with LSC cocktail (Ultima Gold, PerkinElmer). Fourty-eight hours later, the radioactive decay was determined in each vial using a liquid scintillation counter (Beckman LS 6500). Data obtained in the wells treated with the cold compounds was used to measure the non-specific binding under each condition, while the corresponding wells without the unlabeled compound gave the total binding.
Stereological analysis The numbers of TH-and 5HT-immunoreactive cell numbers in the striatum were estimated using an unbiased stereological quantification method by employing the optical fractionator principle  [27]. All quantifications were done after blinding the identity of the sections by a coding system. The borders for the region of interest was defined by using a 4x objective, whereas the actual counting was performed using a 60x Plan-Apo oil objective (Numerical aperture = 1. 4) on a Nikon 80i microscope equipped with an X-Y motorized stage, a Z-axis motor and a high-precision linear encoder (Heidenhein). All three axes and the input from the digital camera that were controlled by a Computer Assisted Toolbox Software (New CAST) module in VIS software (Visiopharm A/S, Denmark), which carries out the procedure with a random start and systematic sampling routine.
Image analysis The numbers of FosB/dFosB immunoreactive cells in the striatum were analyzed on images captured using a 10x Plan-Fluor objective on a Nikon BXA microscope equipped with a Olympus DX72 camera using cellSens standard 1. 5 software (Olympus Corporation). The images were captured from the striatal level corresponding to AP +1. 20 relative to bregma according to the rat brain atlas of Paxinos and Watson  [29]. The quantification was carried out using TIFF formatted images analyzed by using the ImageJ software (Version 1. 42i, NIH). After background subtraction, the total numbers of profiles specifically labeled with FosB/ dFosB were counted using the particle analysis tool. The density of immunopositive FosB/dFosB profiles was expressed as number of immunoreactive cellular profiles per mm 2.
Statistical analysis The statistical analysis pertaining to the behavioral, histological microdialysis and imaging data were conducted using the SPSS statistical package for Mac version 19 (SPSS Inc. , Chicago). Initial analysis was conducted using two-way ANOVA and the general linear model. When ANOVA gave significant effects this was followed by pairwise comparisons adjusted using Bonferroni correction. Estimation of the maximum binding (Bmax) and the binding affinity (Kd) of the D1 and D2 ligands in the in vitro receptor binding assays were analysed using generalized nonlinear least squares using [the gnls function in] the nlme 3. 1-106  [30]  package in R software, version 2. 15. 2  [31]. The model was Bound~(1{Type) Ã alpha i Ã Conc7(beta izConc) zgamma i Ã Conczepsilon Where Bound is the concentration of chemically bound ligand after adding Conc to the sample.
Type is an indicator being zero if only Hot ligand is added and 1 if Cold and Hot ligand is added. Alpha_i is the asymptotical maximum of bound ligand for treatment i (i = 1,…,4), beta_i is the half-saturation constant for treatment i, and gamma_i is the unspecific non-saturable binding in treatment i. Epsilon is normally distributed with variance propor-tional to a power function fitted value in order to obtain homoscedasticity. Comparisons of estimates between groups were adjusted for multiple comparisons using the package multcomp v 1. 2-15  [32].
7 ). Under baseline conditions (i. e. , in the absence of L-DOPA), animals with unilateral 6OHDA lesions showed increased Figure  6. Assessment of changes in extracellular DA levels following L-DOPA injection. Animals were subjected to on-line microdialysis measurements either under baseline conditions, or following a systemic injection of 12 mg/kg L-DOPA without any perturbation of the release sites using release-inducing drugs. Time course data is shown in A, while quantification of the two phases (4 time bins in each case) is given in panel B (Two-way ANOVA, F (7,27) = 12. 15, p,0. 001; followed by pairwise comparison adjusted using Bonferroni, p,0. 0071). Panel C illustrates the dyskinesia rating scores obtained during the OMD experiment as the animals were sampled in awake and freely moving state.
The imaging data was quantified using Logan plots to determine the binding potential in the striatal tissue (D; two-way ANOVA F (5,55) = 6. 70, p,0. 001; followed by pairwise comparison adjusted using Bonferroni, p,0. 008). L-DOPA injection did not result in any change in the binding potential (E; two-way ANOVA F (5,55) = 3. 15, p = 0. 15). In vitro receptor binding assay was performed for D2R (F,H) and D1R (G,I) and analyzed using a generalized non-linear model. In panel F and H, post-hoc comparisons between B and LD in the D2R in the intact brain is p,0. 001 for K d and ,0. 002 for B max , respectively and posthoc comparisons between LD injected intact and lesioned brains is p,0. 001 for K d and ,0. 003 for B max , respectively. L: left (intact) side, R: right side, B: Baseline; LD: L-DOPA treatment, K d : binding affinity, B max : Receptor density.
For this purpose, we compared the in vivo DA release properties and D2R occupancy under 4 conditions: (1) intact striatum where the DA terminal network is intense and far above the endogenous 5HT terminal density; (2) lesioned striatum with near complete loss of DA innervation while the 5HT fiber terminals are at least partially retained; (3) denervated striatum grafted with 5HT neurons in which the total 5HT fiber density is enhanced beyond the sparse network present endogenously; and (4) denervated striatum transplanted with DA-neuron rich grafts that partially reconstitutes the normal DA terminal network, and in fact also contained some 5HT neurons as well. Although the data we obtained confirmed that 5HT terminals were recruited to ectopically synthesize and store DA upon L-DOPA administration, the level of extracellular DA measured by OMD did not exceed those seen in intact animals -either in parkinsonian rats or in animals where grafts rich in 5HT neurons generated a supra-normal serotonergic terminal density in the dopamine denervated striatum.
Acknowledgments The authors wish to thank  Anneli Josefsson ,  Ulla Samuelsson ,  Ulrika Sparrhult-Bjo  ¨rk and  Ulrika Schagerlo  ¨f for their excellent technical assistance,  Tomas Bjo  ¨rklund for advice in D2 receptor assay,  Fredrik Nilsson  for designing the generalized non-linear model for analysis of the D1 and D2 receptor assays and  Erik Ahlm Cederfja  ¨ll for the art design of Figure 9. Authors are also grateful to  Martine Guillermier ,  Marion Chaigneau  and  Diane Houitte  for expert technical assistance with animal handling during PET experiments.
3 must be less than 0. 4 GeV + 0. 04p γ T. These isolation variables are corrected for the presence of additional reconstructed vertices associated with extra interactions in the same bunch crossing (pileup) by subtracting the average energy calculated from the typical energy density in the event, as computed using the FASTJET package  [19]. The signal efficiency is found to be ∼70% for the photon identification and isolation selection criteria. Anomalous calorimeter signals  [20] , caused by isolated large noise in the detector could be reconstructed as photon candidates. A selection is therefore applied on the shower shape variables to largely remove such photon candidates from the event. In addition, to reduce the anomalous calorimeter noise signals  [21] , the ECAL crystals with energy greater than 1 GeV are required to be within a 5 ns window relative to the supercluster time.
Resonance shape and background fit The invariant mass distributions of the γ + jet events in the collected data and for simulated events, after applying all the selections, are shown in Fig. 1. The γ + jet and dijet MC predictions are generated using PYTHIA 6. 426  [23] , based on a LO calculation, while the electroweak backgrounds are taken from the MADGRAPH  [24]  event generator. The underlying event tune Z2  [25, 26]  and the CTEQ6L1  [27, 28]  parton distribution functions (PDFs) are used. The generated events are processed with a full detector simulation based on GEANT4  [29]  and the same event reconstruction package as used for data. The MC prediction is normalized to the integrated luminosity of the data sample. A K-factor of 1. 3  [30, 31]  is used to scale the PYTHIA γ + jet and dijet predictions to account for the next-to-leading-order contributions.
Acknowledgements We thank  Debajyoti Choudhury  for inspiring this work and continuing to provide theoretical insight throughout its course. We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centres and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWFW  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MES (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES  and  CSF (Croatia) ;  RPF (Cyprus) ;  MoER ,  ERC IUT  and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NIH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  NRF  and  WCU (Republic of Korea) ;  LAS (Lithuania) ;  MOE  and  UM (Malaysia) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MBIE (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Dubna) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MESTD (Serbia) ;  SEIDI  and  CPAN (Spain) ;  Swiss Funding Agencies (Switzerland) ;  MST (Taipei) ;  ThEPCenter, IPST, STAR  and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU  and  SFFR (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
Data Source The CIBMTR is a working group of more than 450 transplantation centers worldwide that contribute detailed data on hematopoietic cell transplantations to a Statistical Center at the Medical College of Wisconsin in Milwaukee and the National Marrow Donor Program (NMDP) in Minneapolis. Participating centers are required to report all transplants consecutively and patients are followed longitudinally. Computerized checks for discrepancies, physicians' review of submitted data and on-site audits of participating centers ensure data quality. Data are collected before transplant, 100 days and six months after transplant, and annually thereafter, or until death. The followup research forms specifically inquire whether a recipient has developed AVN post-transplantation. Observational studies conducted by the CIBMTR are performed under guidance of the Institutional Review Board of the NMDP and are in compliance with all applicable federal regulations pertaining to the protection of human research participants.
If feasible, categories with a small number of patients were combined with related categories. Patients receiving transplant from HLA-mismatched related donors (N=23), patients with unknown conditioning regimen intensity (N=2) and patients with unknown date of GVHD onset (N=14) were excluded from the risk factor analysis All P-values are two-sided. All analyses were carried out using SAS statistical software (SAS Institute Inc. , Cary, NC, USA).
Acknowledgments CIBMTR sources of support: The  Center for International Blood and Marrow Transplant Research (CIBMTR)  is supported by  Public Health Service Grant/Cooperative Agreement   U24-CA76518  from the  National Cancer Institute (NCI) , the  National Heart, Lung and Blood Institute (NHLBI)  and the  National Institute of Allergy and Infectious Diseases (NIAID) ; a Grant/Cooperative Agreement  5U01HL069294  from  NHLBI  and  NCI ; a contract  HHSH234200637015C  with  Health Resources and Services Administration (HRSA/DHHS ); two Grants  N00014-06-1-0704  and  N00014-08-1-0058  from the  Office of Naval Research ; and grants from  Allos, Inc. ;  Amgen, Inc. ; Angioblast; Anonymous donation to the  Medical College of Wisconsin ; Ariad; Be the  Match Foundation ;  Blue Cross and Blue Shield Association ;  Buchanan Family Foundation ; CaridianBCT;  Celgene Corporation ;  CellGenix, GmbH; Children's Leukemia Research Association; Fresenius-Biotech North America, Inc.
[11]. An effort has been made to reduce bias effects due to dead time, background, γ-ray attenuation in the sample, shape of the neutron flux, normalization and corrections for self-shielding and multiple interaction events. An internal normalization procedure based on the well-isolated and saturated 4. 9 eV resonance of 197 Au  [6, 12]  was applied and verified by complementary measurements on a thin Au sample. For an accurate determination of the background level, all measurements were performed with fixed background filters. The use of fixed background filters improves the accuracy but results in an upper limit of the data to 84 keV. The accuracy of the correction for self-shielding and multiple interaction events was verified by experiment. To study the impact of resonance fluctuations additional capture measurements on 197 Au at a 30 m measurement station were carried out.
5 ns resolution, developed at the IRMM  [19]. The TOF and the pulse height of the detected events were recorded in list mode using a data acquisition system developed at the IRMM  [20] , allowing for a continuous stability check of the detection systems and an off-line application of the weighting function. The stability of the two detection systems and the accelerator operating conditions (i. e. frequency, current and neutron output) were verified in cycles of 1 hour. Only cycles with a 800 Hz operating frequency and for which the total neutron intensity and response of the detection systems deviated from the average by less than 2. 5% were selected. The stability of the C 6 D 6 detectors was monitored on a weekly basis by measurements of the 2. 6 MeV γ-ray from the 232 Th decay chain. Each detection system produced a veto signal that created a fixed dead-time as soon as an event was detected.
The fixed dead time of the capture and neutron detection chains were monitored continuously by registering the time-interval between successive events. For the flux measurements the dead time was 3500 ns, with a maximum dead time correction less than 1%. The dead time for the capture measurement systems was 2800 ns, with dead time corrections that were less than 20%. In refs. [11, 21]  it was shown that uncertainties for such dead time corrections are very small and can be neglected. Capture cross section data for 197 Au were deduced from results of measurements with a 0. 52 mm and 1. 01 mm thick metallic gold disc. Additional measurements with a 0. 01 mm thick Au metallic disc were performed to verify the normalization. A 0. 5 mm thick metallic 208 Pb disc was used to determine the sample dependent background contribution in the C 6 D 6 response.