dataesr/scientific-paragraphs-categorization huggingface dataset:
The FlowCytomix multiplex assay was used to detect IL-1a, IL-1b, IL-2, IL-4, IL-6, IL-10, IL17A/F, IL-22, LAP, IFN-c, and TNF-a after 48 h of EC-PBMC coculture (data not shown). The only cytokine significantly produced was IL-6. The data in Figure  1(A)  show that activation of ECs with anti-HLA-DR L243 antibody before coculture with PBMCs significantly increased IL-6 secretion in comparison to that of ECs pretreated with an IgG2a control (423 AE 98. 04 vs. 236 AE 65. 7 pg/mL, p < 0. 01). In coculture experiments, prestimulation of ECs with the F(Ab 0 ) 2 HLA-DR antibody fragment also significantly increased IL-6 secretion compared with control cultures and to a similar level as that observed with the full-length antibody (359 AE 61. 3 pg/mL, p < 0. 05). Preactivation of ECs by HLA-DR antibody increases IL-6 production in EC cocultures with PBMCs from healthy donors independent of Fc receptor binding.
Because anti-HLA-DR antibody or the F(Ab 0 ) 2 fragment induced comparable levels of IL-6 production, the F(Ab 0 ) 2 fragment was used in subsequent experiments to avoid both complement activation and the implication of the Fc receptor expressing cells. In contrast, stimulation of ECs with the F(Ab 0 ) 2 antibody fragment alone (i. e. without PBMCs) did not increase IL-6 production by ECs (Figure  S2 ). The contribution of the EC to IL-6 production was determined by carrying out coculture experiments after anti-HLA-DR F(Ab 0 ) 2 stimulation of ECs, followed by paraformaldehyde fixation of ECs before coculture. The data shown in Figure  S3  indicate that the EC is the principal source of IL-6 secretion because EC fixation abrogated IL-6 production in the cocultures. To further confirm that the HLA-DR antibody-stimulated EC is the main source of IL-6 in cocultures, intracellular IL-6 was measured in either ECs or PBMCs after 3 days of coculture.
01 and p < 0. 05) and reveals that IL-6 secretion is Akt dependent in steady-state cultures (446 AE 21 vs. 276 AE 16 pg/mL), in cultures with control IgG2a (437 AE 10 vs. 270 AE 19 pg/mL) and in cultures in which ECs had been preactivated via HLA-DR (697 AE 24 vs. 376 AE 45 pg/mL) in the presence of the Akt inhibitor. This represents a significant reduction of almost 50% (p < 0. 05) in the presence of an Akt inhibitor. In contrast, Figure  2 (C) shows that treatment of ECs with U0126 did not alter IL-6 secretion by ECs prestimulated with the F (Ab 0 ) 2 fragment under any of the conditions (inhibition of ERK phosphorylation was verified by western blot) (data not shown). To further determine the role of Akt in the IL-6 secretion induced by activation with the F(Ab 0 ) 2 fragment of the or PBMCs cocultured with ECs that had been activated with interferon c for 3 days (activated EC).
Intracellular staining of IL-6 was then carried out on ECs (CD31 + Lin neg ) and PBMCs (Lin + ). The proportion of IL-6 + ECs was at least 10-fold higher than IL-6 + PBMCs. (B) also shows that EC activation by the HLA-DR antibody F(Ab 0 ) 2 fragment led to a significantly increased proportion of IL-6 + ECs, whereas the proportion of IL-6 + PBMCs remained unchanged. EC, endothelial cell; PBMC, peripheral blood mononuclear cell; SEM, standard error of the mean (*p < 0. 05, **p< 0. 01). anti-HLA-DR antibody (Figure  2B ), EC cultures were pretreated with increasing concentrations of two Akt inhibitors (Akt inhibitor IV [Figure  2D ] and Akt inhibitor X [Figure  2E ]) that have different molecular targets. These data revealed that IL-6 secretion is inversely related to the amount of Akt inhibitor and that significant inhibition was already detected after pretreatment with a concentration of 1 lM (p < 0.
5 lg/mL) for the indicated times. Western blotting was used to detect phosphorylated forms of MEK, ERK, or Akt (representative of four experiments). The time course of phosphorylation is shown in (A), as is the ratio of the phosphorylated forms of the kinases normalized to actin protein levels. Results were obtained by measuring the optical density of protein bands using Multigauge software (mean AE SEM). (B) shows that pretreatment of activated ECs with the Akt inhibitor IV (10 lM) significantly reduced the steady-state secretion of IL-6 and reduced IL-6 induced by EC preactivation with the variable fragment of the HLA-DR antibody to a level similar to that observed with ECs stimulated with control antibody (n = 4 donors). (C) shows that inhibition of MEK and ERK activation with the selective chemical inhibitor U0126 (10 lM) before HLA-DR antibody binding to activated ECs does not alter the secretion of IL-6 by ECs (n = 4 donors).
HMEC-1 cells were cultured in the presence of interferon c for 3 days and stimulated with the F(Ab 0 )2 fragment of the L243 antibody for 1 h, as described in Materials and Methods. HMEC-1 cells were then fixed with 2% paraformaldehyde or not and cultured for a further 3 days with PBMCs from nonrelated healthy donors before measuring the level of IL-6 in the culture supernatants. The data in Figure  S2  demonstrate that prestimulation of endothelial cells with the F(Ab 0 )2 significantly increases the secretion of IL-6 (as in Figure  1 ) and that disablement of secretion in paraformaldehyde-fixed endothelial cells abrogated IL-6 levels in the cocultures. The secretory capacity of the endothelial cell is thus required for IL-6 production in the PBMC-endothelial cell cocultures. (n = 4, *p < 0.
FigureS3: Fixation of endothelial cells abrogates IL-6 secretion in cocultures of endothelial cells and PBMCs. HMEC-1 cells were cultured in the presence of interferon c for 3 days and stimulated with the F(Ab 0 )2 fragment of the L243 antibody for 1 h, as described in Materials and Methods. HMEC-1 cells were then fixed with 2% paraformaldehyde or not and cultured for a further 3 days with PBMCs from nonrelated healthy donors before measuring the level of IL-6 in the culture supernatants. The data in FigureS2demonstrate that prestimulation of endothelial cells with the F(Ab 0 )2 significantly increases the secretion of IL-6 (as in Figure1) and that disablement of secretion in paraformaldehyde-fixed endothelial cells abrogated IL-6 levels in the cocultures. The secretory capacity of the endothelial cell is thus required for IL-6 production in the PBMC-endothelial cell cocultures.
Acknowledgments J. L. was supported by the  DIM Bioth erapies  and the  Roche Organ Transplantation Research Fund. This study was supported by the  Fondation pour la Recherche M edicale (FRM)  and l' Agence pour la Biom edicine. This work has been published under the framework of the  LABEX TRANSPLANTEX  [ ANR-11-LABX-0070_TRANSPLANTEX ] and benefits from funding from the  French government , managed by the  French National Research Agency (ANR)  as part of the  Investments for the future program. We are grateful for the technical help of Ghislaine Henry.
B. Data mining-based IDSs Since the initial studies by Denning  [4] , detection systems have continued to evolve. Data mining offers various solutions for the detection and analysis of computer attacks  [5]. Lee and Stolfo use data mining methods  [6] , which do not require an experts intervention. These methods tend to generate a lot of association rules and therefore exponentially increase the system's level of complexity. This work is based on network capture tool tcpdump and Unix audit data. To use this method, it is compulsory to install a sensor network with a large memory storage space and it is only for Unix systems. Using a hybrid (combine different data mining methods) approach is very interesting because it takes care about alert management  [7]   [8]. H. Nguyen et al. [9]  use an ensemble system of classifiers, called CBE based on K-mean algorithm but the classe number must be fixed a priori  [10].
This may take time depending on the number of servers to be monitored. A. R. Ajiboye et al. proposed to use the density-based DSB-CAN algorithm  [11]. In fact, even DBSCAN  [12]  or OPTICS algorithm  [13]  are capable of determining the cluster number. However, it is compulsory for us to define two hard-to-estimate input parameters chiefly the radius of the cluster and the minimum required points inside the cluster for DBSCAN and fix the minipoints argument for OPTICS. Moreover with such a large dataset, these algorithms require large memory and computing resource. Using PCA model with K nearest neighborhood for intrusion detection (on a KDD 99 dataset)  [14]  or Hierarchical Agglomerative Clustering (HAC)  [15]  have the advantage of providing good graphic visualization to assist with finding the relevant numbers of cluster.
A successful information request provides a list of available services (HTTP, HTTPS, FTP, mail, etc. ), the version of the services used (Microsoft Internet Information Services or Apache for a Linux server), and the base of the operating system. Scanning activities represent more than 80% of detected cyberattacks  [20]. Once this information is known, it is not difficult to find and/or create malicious tools/scripts to exploit known vulnerability in the target server. Hence, it is essential to be able to detect quickly whenever this kind of scanning and enumerating phase is taking place. The methods for information gathering have also evolved. It is now possible to use multiple IP addresses 2  , or use stretched intelligence to limit the arrival of access requests to different ports on a server.
It can also open the opportunity to trace and keep information to highlight these flows on events that have been either authorized and/or prohibited. Moreover, the firewall is the most security component used, the business equipment rate was 95% in 2010  [21]. Pre-treatments is made from logs connection filtering equipment (log option) and they are sent to the Syslog-ng server  3. Through its Perl compatible regular expression(PCRE) pattern matching and filtering options, all flows are saved on the databaseThereafter, computation is carried out via a Perl script. Finally, Graphviz Suite  4  and Afterglow  5  script components are used to create graphs. The terms of the variables listed below are exported to data containers. • source IP address, destination IP address • destination port, protocols (UDP and TCP) • date and time • firewall policy rule number matching • firewall action (accept or reject) Choosing these variables, we offer the possibilty to integrate several types of firewall of different brands.
B. Phase 2: Behavior analysis and alert Phase 2 is intended to allow for data analysis and the detection of abnormal behavior (if any, which in turn will trigger an alert (if needed). We feel it would be wise to use firewall event data mining methods for anomaly detection. Besides, Our work uses session data from firewall Logs as explained in section IV. Our main goal is to predict risks and threats according network transactions. After consideration of the data studied in Phase 1, we have to perform preprossing to reduce the available data range. This is required because, for example, the destination port variable includes 65535 possibilities. We opted for grouping variables in the three following categories: • well-known ports (under 1024) accept and deny; • port 1024 through 65535 accept and deny; • administration port (portadm), port activity for server or database administration accept and deny.
For instance, the computation time for 53 servers is approximately 0. 353 seconds. We have built a training data set and saved the class attribution result for reference. Which means that each server has a specific class number, and any derivation could be potentially considered as abnormal behavior. Further, we create a test data set for different kind of scans and we launched several brute force and path traversal attacks (Phase 2 obtain access)  6. Bydoing this, we saw that the number of class was directly detected in the target servers. For instance, the main server shifted from 6 to 2 classes. This source of behavior deviation is automatically identified as abnormal activity. We then extract data in order to trigger an alert. However, it is possible for an attacker to send massive amounts of data as decoy to try and hide a discreet attack.
So, we extract that to make new computations until a similar class number is obtained. Therefore, we can use a variation coefficient (CV) to generate a score  [25]. For the moment, we do not manage the score, but the variation coefficient provides a general overview which is good enough for the training dataset when compared to the test data set. We believe that Fig. 2 : Example of internal validation for one server with this kind of process, it will be possible to detect and identify destination servers that have undergone changes in behavior. Once we know this, we can then have a specific overview based on server class variation with CV, which allows to focus on the most critical activity. Our approach allows us to detect large scan, brute force attacks and path tranversal attacks, without any help from experts.
Result and Discussion The new aza-BDP 3 featuring nitrofluorene ethynyl substituents at positions 2/6 was easily obtained by Sonogashira cross-coupling between a dihalogenated aza-dipyrromethene (Scheme S1) and the nitrofluorene ethynyl synthon  [39] [40] [41]. Further chelation to boron trifluoride etherate in a basic medium afforded dye 3 to have a good yield. This dye and the intermediates were characterized by 1 H and  13  C NMR and HRMS (see supporting information). The absorption and fluorescence properties of chromophores 1-5 were recorded in a diluted dichloromethane solution (ca. 10 -5 M). The spectra are presented in Fig. 2 , and the photophysical data are compiled in Table  1. The photophysical properties of aza-BDPs were also dependent on the electronic and steric nature of substituents.
Acknowledgements This work was supported by the  National Research Foundation of Korea (NRF)  grant funded by the  Korea government (MSIP)  (No. 2007-0056091 ). This research was supported by a grant of the  Korea Health Technology R&D Project  through the  Korea Health Industry Development Institute (KHIDI) , funded by the  Ministry of Health & Welfare, Republic of Korea  (grant number :  HI15C0942 ).
10 -11 mol/L and the Fe concentration was < 2. 10 -8 mol/L. The Fe oxides were characterized by X-ray diffraction (XRD) with a D8 Advance diffractometer using Cu-Kα radiation and an energy-dispersive (Sol-X) detector (Bruker). Fits (Rietveld method) to the XRD data were provided by the TOPAS 4. 2 software (Bruker). The solids were further analyzed by scanning electron microscopy (SEM) with an ESEM Quanta 650 FEG (FEI) and the specific surface area was determined by the Brunauer-Emmett-Teller (BET) method  [4]  using N 2 adsorption with an AUTOSORB-1 (Quantachrome Corporation). Information on the valence states of Fe and adsorbed Am in the sorption samples was provided by X-ray photoelectron spectroscopy (XPS) analysis with a VersaProbe II (ULVAC-PHI). Am L 3 -edge EXAFS spectra were collected at the INE-Beamline  [5]  for actinide science at the ANKA Synchrotron Radiation Facility (Karlsruhe, Germany).
The energy calibration was done by assigning the first inflection point of a Zr foil at 17998 eV and this reference was measured in parallel with the samples. Data were collected in fluorescence mode using a 5-element low energy germanium solid state detector (Canberra-Eurisys). Data analysis was performed by using Athena and Artemis interfaces to the Ifeffit software  [6]  following standard procedures  [7] , with an amplitude reduction factor of S 0 2 = 0. 88.
Acknowledgements We thank  E. Soballa  ( KIT-INE ) for SEM analysis,  M. Lagos  and  F. Geyer  for ICP-MS measurements and  K. Dardenne  ( KIT-INE ) for assistance at the  INE-Beamline. ANKA (Karlsruhe, Germany)  is acknowledged for providing beamtime. This work has been supported by the  European FP7   TALISMAn (Transnational Access to Large Infrastructure for a Safe Management of ActiNides ) project under the grant agreement # 323300 , JRP no  TALI-C01-13.
Cleavage was performed at room temperature (RT) and 37 °C for the indicated incubation times. The inhibitor was used at 100 μ M and 250 μ M, shown as plus signs in regular and bold format, respectively. (C) Distinct populations of BR 187-385 were eluted using Superdex 200 HiLoad 16/600 at elution column volumes (CV) of 89, 78, 71 and 66 mL corresponding to apparent molecular weights of 22, 55 and 90, 150 kDa, as well as higher oligomers. In this study, we show that the irreversibly associated dimer of BR 187-385 is formed through a domain swap mechanism (PDB: 5JUI, Fig. S2 ) and that a low-affinity β -sheet dimer is created between two symmetry-related molecules in the previously determined crystal structure of the BR 187-385 monomer (PDB: 3ZGH, Fig. 3 ). (D) BR* 120-395 was eluted from the same column at CV of 79 and 69 mL corresponding to apparent MW of 50 and 115 kDa.
Indeed, we discovered intermolecular β -sheets between symmetry-related monomeric molecules in the P4 1 22 crystal form (PDB: 3ZGH) and in the P4 3 2 1 2 crystal form (PDB: 3ZGI) forming dimers with interface surface areas of 600 Å 2 and 440 Å 2 , respectively (Figs  3  and S4A ). Moreover, intermolecular β -sheets are also observed between symmetry-related domain-swapped dimers with similar interfaces and hydrogen bond patterns (Fig. S4B, C ). However, although the formation of such edge-to-edge β -sheets is regarded as a fundamental feature underlying molecular recognition in protein-protein interactions  34  , a predicted weak interaction of this interface could prevent its detection in the performed SEC, SAXS and AUC experiments (Figs 1C and 2A and S1B)  20. Single-cell and single-molecule atomic force microscopy have recently been applied to demonstrate that low-affinity (15 mM) homophilic interactions of the fibronectin binding protein A (FnBPA) of Staphylococcus aureus promote cellular aggregation  28.
5F, G ). A quantile is the fraction at which x% percent of the data fall below and (100x)% fall above that value. While two identical populations give a straight line (Fig. 5G , Scar-DUF in black), upward-shifted curves reveal increased particle sizes for Scar-BR 187-378 and Scar-BR 120-378 (Fig. 5G , Scar-BR 187-378 and Scar-BR 120-378 in red and blue, respectively). Similar results were -1 with the Boltzmann's constant k b , the charge of an electron e c at a temperature T of 298 K. The saddle-like structure snuggly fits an acidic helical non-specific DNA molecule, as predicted in a molecular model of the BR 187-385 -DNA complex. (E) Similar to the BR 187-385 dimer, the TATA-box binding protein (TBP, PDB: 1YTB) adopts a saddle-like structure. TBP was superimposed onto the BR 187-387 dimer via shape similarity and represented as white and blue ribbons.
Furin cleavage assay. Two units of Furin protease (New England Biolabs, P8077) were added to a total assay volume of 100 μ L with a concentration of 0. 7 mg/mL BR 120-395 and mutated BR* 120-395 in 20 mM HEPES, 500 mM NaCl, 10% glycerol, 1 mM CaCl 2 , pH 7. 5. Hexa-D-arginine amide (Sigma: SCP0148) was used as furin inhibitor at concentrations of 100 μ M and 250 μ M. The cleavage assays were carried out at room temperature and at 37 °C. Samples for SDS-PAGE were taken at after 0 h, 2 h, 4 h and overnight incubation. Small angle X-ray scattering. Sample preparation and data collection. Data were collected at beamline BM29 at the European Synchrotron Radiation Facility (ESRF, Grenoble)  42. Using a Pilatus 1 M detector at a sample to detector distance of 2. 9 m and a wavelength of λ = 0. 9919 Å, the range of momentum transfer 0.
006 < s < 0. 45 Å -1 was covered (s = 4π sin θ /λ , where 2θ is the scattering angle). Prior to data collection, proteins were buffer exchanged into phosphate buffered saline (PBS) with 5% glycerol, pH 7. 4. Samples were measured at concentrations between 0. 3 and 3 mg/ml using a continuous flow cell capillary. Data analysis. The forward scattering I(0), the radius of gyration R g along with the pair distribution function of the particle p(r) and the maximum dimension D max were derived using the automated SAXS data analysis pipeline  43. Using Ensemble Optimization Method (EOM)  44  analysis of BR 187-385 and BR 120-395 , a pool of 10,000 models comprising a rigid domain (residues K206-E375) and flexible N-and C-termini were generated. A subset of the pool was selected using a genetic algorithm such that the calculated averaged scattering of the selected models agreed with the experimental data.
Structural analysis. All figures were created using PyMOL version 1. 3. 0  45. Interfaces of macromolecular assemblies in the crystal structures were investigated using PBDePISA  46. The molecular model of the BR 187-385 -DNA complex was predicted using the non-specific DNA-rigid protein-docking algorithm ParaDock  47  , and the electrostatic surface was visualized using APBS  48, 49. The structure of TBP (PDB: 1YTB) was superimposed onto the BR 187-387 dimer using the shape similarity algorithm of subcomp in which three-dimensional models are represented as simplified ensembles of points  36, 50. Electrophoretic mobility shift assay (EMSA) and isolation of BR 187-378 -DNA 276bp complex using SEC. The 276 bp DNA molecule (DNA 276 sequence listed in supplemental information) was produced and isolated by PCR amplification and gel extraction (QIAEXII gel extraction kit, Qiagen).
1 mM CaCl 2 , 1% glucose, 1% casaminoacids, 1 mM Thiamine-HCl and 0. 05 mM nicotinamide, with or without the addition of herring sperm derived degraded DNA (D3159, Sigma Aldrich) at a concentration of 10 ug/mL that corresponds to approximately 1 μ M of 15 bp oligonucleotide fragments. The bacteria were adjusted in OD and imaged in the same way as described previously. Images were analyzed using the software cell profiler (www. cellprofiler. org), the particle parameter values were imported into the R software package for statistical analysis and visualization using density histogram and q-q plots  54, 55. Dotblot assays and fluorescence imaging. Polyclonal antibodies against the TEV-cleaved purified BR 187-385 monomer and a synthesized BR 143-156 (RKKPASDYVASVTN) peptide were raised in rabbits and the obtained sera yielded titers of about 75000 and 6000, respectively (Innovagen, Sweden).
(B) A protease cleavage assay confirmed that furin recognized the KRRKR motif, but did not cleave in the presence of the furin protease inhibitor or when the KRRKR sequence was substituted to KSRKS. Cleavage was performed at room temperature (RT) and 37 °C for the indicated incubation times. The inhibitor was used at 100 μ M and 250 μ M, shown as plus signs in regular and bold format, respectively. (C) Distinct populations of BR 187-385 were eluted using Superdex 200 HiLoad 16/600 at elution column volumes (CV) of 89, 78, 71 and 66 mL corresponding to apparent molecular weights of 22, 55 and 90, 150 kDa, as well as higher oligomers. In this study, we show that the irreversibly associated dimer of BR 187-385 is formed through a domain swap mechanism (PDB: 5JUI, Fig. S2) and that a low-affinity β -sheet dimer is created between two symmetry-related molecules in the previously determined crystal structure of the BR 187-385 monomer (PDB: 3ZGH, Fig.
Acknowledgements We gratefully acknowledge fruitful discussions with  Tatyana Sandalova  as well as access to synchrotron beamlines BM29 and ID23-1 at  ESRF (Grenoble, France). This work was facilitated by the  Protein Science Facility at Karolinska Institute/SciLifeLab  (http://psf. ki. se). We thank  John Löfblom  ( KTH, Stockholm ) and  Simon Elsässer  ( MBB, Karolinska Institute, Stockholm ) for providing the S. carnosus cells and access to the ZOE Fluorescent Cell Imager, respectively. This work was supported by grants from the  Swedish Research Council (AA, BHN) , the  Knut and Alice Wallenberg Foundation (AA, BHN) , the Swedish foundation for strategic research (AA and BHN), the  Wenner Gren Foundation and (TS) , the  European Community 's  Seventh Framework Programme  (FP7/2007-2013) under BioStruct-X (grant agreement No.