dataesr/scientific-paragraphs-categorization huggingface dataset:
The experimental data are compatible with these expectations. Among the three different nPDFs, the data tend to favour the result obtained with nCTEQ15. It is also interesting to note that the precision of the current data is already better than the nPDF uncertainties, especially in the forward region. This gives some hope that these measurements could ultimately be used to constrain the gluon density in heavy ions, provided that the impact of other nuclear effects could be disentangled. We also note that the shaded boxes on the right of the first two plots refer to the global systematical uncertainty. Such an information is not available for the ATLAS data. A good agreement with the LHCb and ALICE data is obtained; a slight discrepancy with the ATLAS data is observed. It is not clear whether it could be attributed to an offset in the data normalisation.
Doing so, the uncertainties in R FB would have been significantly larger. Finally, we recall that the global systematical uncertainties in the experimental data do cancel. On the experimental side, these results are usually much more reliable. Fig. 13  displays our results for the rapidity dependence of R FB for the three gluon nPDFs used before (EPS09LO, EPS09NLO, nCTEQ15). For the low P T data of LHCb and ALICE, the magnitude of the asymmetry is well compatible with that of nCTEQ15 and EPS09 LO, at the lower edge of the EPS09 NLO range. As for the ATLAS data with a P T cut, their current uncertainties and the reduced magnitude of the effects (since |y c. m. s. | is smaller) do not allow for any conclusions. results and the measurements by LHCb  [63] , ALICE  [66]  and ATLAS  [65]. [The uncertainty bands represent the nuclear PDF uncertainty only.
ALICE data are for inclusive J/ψ. ] , ALICE  [66]  and ATLAS  [65]  data. Fig. 14  shows our results for R FB versus P J/ψ T. A clear trend is seen in the LHCb and ALICE results with a ratio increasing with P T , starting at 0. 6. R FB at P T above 10 GeV are compatible with unity, but the larger uncertainties do not exclude values smaller than one. The magnitude of the ratio in the data is compatible with the 3 nPDFs. More advanced studies are needed to go further in the interpretation of the P T dependence using specific eigensets as opposed to bands. We also recall that a given nPDF set can be compatible with R FB and not with R pPb. This can happen due to specific cancellations in the magnitude of the forward and backward nuclear modifications or to a normalisation offset. In particular, we note that there is no tension at all with the ATLAS data for R FB (Fig.
13c  and Fig. 14c ) unlike the case of R pPb (Fig. 8c  and Fig. 9b ). We are inclined to attribute this to a normalisation offset from the pp baseline whose effect disappears in R FB. between our results and the measurements of LHCb  [67]  and ALICE  [68]. We have also computed R FB for Υ(1S ) (Fig. 15 ) and D 0 (Fig. 16 ). The same remarks as for the J/ψ case apply. No tension between the data and our computation are found. Just as for the ATLAS J/ψ data, the good agreement with the D 0 LHCb data may indicate that a slight offset in the normalisation affects R pPb as plotted on Fig. 11. Whereas the R pPb values point at a smaller suppression than those encoded in the nPDFs (in particular nCTEQ15), the magnitude of R FB is very well accounted by nCTEQ15 and corresponds to the strongest magnitude encoded in EPS09 NLO.
Conclusions We have devised a model-independent procedure to evaluate the impact of the nuclear modification of the gluon densities on hard probes produced in proton-nucleus collisions at colliders energies. It is particularly tailored for two-to-two partonic scatterings, relevant for quarkonium and heavy-meson production. The model independence of our procedure lies in the parametrisation of the partonic amplitude squared with parameters fit to pp collision data in similar kinematical conditions as the pPb data to be described. We have illustrated the capabilities of our approach by computing the cross sections as well as the nuclear modifications factor for J/ψ, Υ and D 0 production at the LHC. Even though our objective was not to argue that the nPDF effect is the dominant one in this energy range, we have not found out any significant tension between our computations using three common nPDFs (EPS09 LO & NLO and nCTEQ15) and the exisiting data.
Acknowledgements We are very grateful to  R. Arnaldi ,  E. G. Ferreiro ,  F. Fleuret ,  C. Hadjidakis ,  D. Kikola ,  Y. Kim ,  A. Kusina ,  S. Lee ,  A. Rakatozafindrabe ,  C. Salgado ,  I. Schienbein ,  R. Vogt ,  Z. Yang ,  Y. Zhang  for stimulating discussions. The work of J. P. L. is supported in part by the  French CNRS  via the LIA FCPPL (Quarkonium4AFTER) and the  Défi Inphyniti-Théorie LHC France. H. S. S. is supported by the  ERC  grant  291377  LHCtheory: Theoretical predictions and analyses of LHC physics: advancing the precision frontier.
ALICE has also measured low P T central J/ψ but with a limited statistical precision and a b feed-down contamination. The forward ALICE data are also prone to such a b feed-down contimanation. As such, we will focus on the LHCb data for our fits in the forward and low P T region. We also note that CMS has the capacity to cover P T down to 3 GeV (even below in specific cases) in its most forward/backward acceptance.
All these effects of FGF1 cooperate to protect PC12 cells from p53-dependent apoptosis. The FGF1 ΔNLS mutant, which only presents a cytosolic localization, has no effect on p53-dependent apoptosis in PC12 cells. Altogether, these data suggest that FGF1 regulates p53-dependent apoptosis and neuronal differentiation by new intracrine/nuclear pathways. 17 he aim of the present paper is to progress in the characterization of these nuclear pathways. For this purpose, the activity of new mutated forms of FGF1 in PC12 cells was examined. We studied the effect of three mutations located in the C terminus of FGF1 (i. e. , FGF1 K132E , FGF1 S130A and FGF1 S130D ) on its intracellular neurotrophic and anti-apoptotic activities. Previous studies using recombinant FGF1 K132E showed that it could bind FGF receptors, induced the mitogenassociated protein kinase pathway but it induced neither cell proliferation nor neuronal differentiation.
IC 50 values were averaged from 3 independent experiments with compound 15 and 27, and determined from at least one experiment for 29. IC 50 values obtained from elongation assays were averaged from >3 independent experiments for all three compounds. Hill slopes for IC 50 curves ranged from -0. 7 to -1. 6. All data points were measured in duplicates. Binding affinities (K d ) of compounds were determined by surface plasmon resonance using a Biacore T200 instrument as described in Materials and Methods and analyzed using Biacore T200 evalution with affinity-kinetics analysis. Effects of compounds on protein thermo-stability (melting temperature, T m ) was assessed using the thermo-denaturation assay as described in Materials and Methods, with in vitro expressed recombinant DENV4 FL NS5, RdRp domain (aa 268-900), or cell lysates from BHK-21 DENV2 (strain NGC) replicon cells following the cellular thermal shift assay described previously  [41].
Briefly, compounds were incubated for 20 min with enzyme alone, after which reactions were started with the ssRNA and nucleotide substrate components, and allowed to proceed for 2 hr  [39]. Hill slopes for IC 50 curves ranged from -0. 7 to -1. 6. All data points were measured in duplicates. doi:10. 1371/journal. ppat. 1005737. t005 completely abolished. Mutant replicons S710A, Y766A, and W803A were also non-replicative, despite showing 27-98% de novo initiation and elongation activities in vitro. Mutant replicons H800A and Q802A were poorly replicative, although their polymerase activities were only moderately decreased in the enzyme assays. In contrast, mutant replicons with T794A, S796A with similar reductions in polymerase activities, were more replicative, and continued to expand during the three-day incubation period.
1 M Tris/HCl, pH 8. 0 and 25% PEG 500 MME. DENV2 RdRp (Strain NGC, aa 266-900) protein expression was as described previously  (23). Protein crystallization was performed at 8 mg/ml in a sitting-drop vapor-diffusion setup with a well solution of 0. 1 M MES pH 7. 0, 0. 35 mM MgCl 2 and 16% PEG 4000 with a drop ratio of 2:1 (protein:well). Crystals appeared in one day and were transferred to the well solution supplemented with 10 mM compound 27 (prepared from a 100 mM DMSO stock to obtain a final concentration of 10% DMSO) for overnight incubation. For cryo-protection, crystals were transferred to the crystallization solution supplemented with 10% glycerol and 10% compound/DMSO and cooled in liquid nitrogen. Diffraction data were integrated using autoPROC (DENV2) or XDS (DENV3) and scaled using SCALA or AIMLESS, both part of the CCP4 suite  [49].
Surface plasmon resonance binding assay Biotinylated DENV3 and DENV4 RdRp were captured on flow cells 2 and 4 respectively in 50 mM Tris/HCl, pH 7. 5, 200 mM NaCl, 2 mM DTT, 0. 05% Tween 20, and 3% DMSO at 4°C. Flow cell 1 and 3 were left blank to serve as a reference  [37]. Compounds were tested in a 7-point 2-fold serial dilution, from 2. 5 μM and a zero-concentration sample was subtracted from each run. Compounds were injected at a flow rate of 30 μL/min, with 45 s contact time and 600 s dissociation, starting from the DMSO control and finishing with the highest concentration. The experiments were performed using a Biacore T200 instrument and the data were analyzed using Biacore T200 Evaluation software, version 2. 0. Compound testing with DENV dnI FAPA assays DENV1-4 FL NS5 dnI assays were performed as described previously  [39].
Generation of DENV4 NS5 mutant replicons Mutations in the DENV4 NS5 (GenBank accession number AF326825) sequence were engineered into the subclone, pACYC-DENV4-F shuttle, using the QuikChange II XL site-directed mutagenesis kit according to the manufacturer's protocol (Stratagene). This plasmid harbours nucleotides 7564-10653 (from NS3-3'UTR) from the DENV4, MY01-22713 strain, linked at the 3'end to the Hepatitis D virus ribozyme (HDVr) sequence. Following sequence verification, the plasmids were digested with NotI and KpnI and inserted with a PCR product comprising the sequence comprising nucleotides 1-7563 downstream of the T7 promoter in which the region from nucleotides 217-2291 in this cDNA has been replaced by renilla luciferase and foot-and-mouth disease virus 2A protease cDNAs  [50].
For determination of compound EC 50 values in mixed populations of 27-resistant or DMSO-cultured DENV2 replicon cells, cells were seeded into 96-well plates and treated with compounds, 27 and 29 (10-point, 2-fold serially diluted compounds from 0-100 μM), for 2 days. EC 50 values from replicon cells were determined by measuring cellular renilla luciferase levels. All data points were measured in duplicates. nd = not done. doi:10. 1371/journal. ppat. 1005737. t008.
Acknowledgments We thank  Thierry Diagana ,  David Beer ,  Paul Smith  and  Francesca Blasco  for support and useful discussions,  Nicole Tay ,  Ka Yan Chung ,  Katherine Chan ,  Lim Chin Chin ,  Hao Ying Xu ,  Agatha Susila  and  Alexander Theodore Chao , for technical support, and colleagues at  Novartis Biomedical Research Institute, Emeryville, CA, USA , for compound testing in human rhinovirus cell-based assays. We thank  Shamala Devi  for providing the clinical isolates of the four serotypes of dengue virus. JL and AES were supported by  National Medical Research Council  Grant  CBRG14May051  (to JL).
Compound inhibition of human rhinovirus replication in HeLa cells was measured by cytopathic inhibition over a period of 5 days. Determinations of compound inhibition (EC 50 ) in cell-based assays were performed once, except for DENV1-4 replication in A549 cells (high content imaging assay), where most compounds were tested 2 times. Compound cytotoxicity in HuH-7, BHK-21, A549, HeLa, and HepG2 were measured 1-2 times, after compound exposure for 2 (for HuH-7, BHK-21, A549) or 4-5 (HepG2 and HeLa) days. All data points were measured in duplicates. *Results of DENV1-4 HCI data for compounds 27 and 29 were previously reported in[38]. ╫denotesclinical DENV2 isolate MY97-10340. doi:10. 1371/journal. ppat. 1005737. t006withgraduallyincreasing concentrations of 27 (starting from 1. 5 μM; 0. 5X EC 50 ).
In the Netherlands, the biobank at the ILD Center of Excellence, St Antonius Hospital in Nieuwegein, is used for a nationwide registry of patients with LAM to enable countrywide insight, and enables participation in the global LAM registry of the LAM Foundation International Clinics programme to help identify patients and their availability for trials for research worldwide  [21]. There is also a French national LAM registry (RE-LAM-CE) co-ordinated in Lyon. The development of a European LAM registry to support research in larger clinical trials was a recommendation made at the workshop. There may be a role for the ERS to provide advice on tissue sharing. The increasing capture of LAM data internationally aims to increase awareness of the disease and its symptoms among both healthcare professionals and the wider public.
All stakeholders in LAM need to work together, to ensure that research can be adequately funded and coordinated. There are lessons to be learned from other respiratory diseases. Patient-powered research networks, such as the Patient-Centered Outcomes Research Institute (PCORI) in the USA  [27] , can be a way to ensure that patient data is collected and ready to be used for research across the globe. Examples in the respiratory field include chronic obstructive pulmonary disease. The aim of organisations such as the PCORI is to ensure that people make informed healthcare decisions, and improve healthcare delivery and outcomes, by producing and promoting high-integrity, evidence-based information that comes from research guided by patients, caregivers and the broader healthcare community.
The KM3NeT Collaboration is building a new generation of neutrino telescopes in the Mediterranean Sea. For these telescopes, a relational database is designed and implemented for several purposes, such as the centralised management of accounts, the storage of all documentation about components and the status of the detector and information about slow control and calibration data. It also contains information useful during the construction and the data acquisition phases. Highlights in the database schema, storage and management are discussed along with design choices that have impact on performances. In most cases, the database is not accessed directly by applications, but via a custom designed Web application server.
Overview The KM3NeT Collaboration [1] is installing water-Cherenkov neutrino telescopes  [2]  in several sites in the Mediterranean Sea. First data are expected by the end of 2015. The detectors of the telescopes comprise many detection units, i. e. vertical lines supporting 18 regularly spaced digital optical modules; each optical module hosts 31 photomultipliers, monitoring instruments and piezo elements for acoustic positioning of the modules. The detectors are subdivided into detector building blocks each comprising 115 detection units with 64,170 photomultipliers in total. The complexity of tasks of the detector and the inherently multi-site nature of the challenge call for suitable data management tools. A relational database system  [3]  has been set up and is already providing operational functionality while it is still partially in development.
Many tables and concepts in the design of the database are inherited from the database of ANTARES  [4] , but substantial evolution was needed scaling performances up to meet the KM3NeT needs. This work has already started a few years ago  [5]. The foundation of the system is Oracle Database Server  [6]. Reflecting the geographical distribution of the telescopes, a multi-master database network is in place: a cluster of 3 servers is hosted and managed by the CC-IN2P3 centre in Lyon; another database server is hosted at the University of Napoli (UNINA), under the management of the ReCaS consortium. Two web servers, also hosted at CC-IN2P3 and at UNINA/ReCaS, are used to provide access to the databases. Both servers have interchangeable links, i. e. each one can connect to either master database.
a e-mail: cbozza@unisa. it This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4. 0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Streams of calibration data from quasi-on-line post-processing and from acoustic sensors (mostly used to determine the position and orientation of the optical modules and the shape of the detection units) The database system is conceived as a living system that directly supports and takes part in several tasks, e. g. Collaboration management, detector construction and operation, data reconstruction and analysis and simulations. High performances both in writing and reading data are crucial for the whole system to be useful. System reliability and availability are very important as well for involving the database in real time data production and data collection; without these features the database would be just an offline container.
Security In order to ensure data security and reliable database operation, a layered security model has been adopted to provide user and batch process access. At the lowest layer, Oracle Database roles define consistent sets of privileges and permissions for access to tables, views, functions and procedures. Oracle Database accounts are provided to services with specific roles, such as the Web server and the shore station database interface. All duty accesses use HTTP(S) services, e. g. both the Web server and the shore station database interface behave as HTTP(S) servers. Physical users have KM3NeT accounts with irreversibly encrypted passwords that do not correspond to any Oracle account; and their privileges are defined in terms of KM3NeT responsibilities, e. g. membership of governing bodies, construction management or data-taking management.
Data flows All relevant information is described in terms of parameters. The scalar type for each parameter is defined, and, when applicable, also the international standard unit is declared. Datasheets and tests for qualification, characterisation and acceptance are all described in terms of the set of parameters they yield. In addition, the database contains the information needed to prepare commonly used plots and graphs from the data of each dataset. This enables the Web server to automatically prepare reports in a user-friendly fashion. The most relevant data flows in the KM3NeT database are related to detector construction, datataking and offline event-reconstruction/simulation. The construction data flow starts with the description of purchased components; next, each object that is the result of an integration of smaller components is Very Large Volume Neutrino Telescope (VLVnT-2015) described in terms of a template and the real components that were used to assemble the product; cabling information is also added when needed.
All results of tests (acceptance/qualification/characterisation) on objects are documented in the database. An object that is the result of an integration operation may on its turn be part of a more complex product, e. g. several optical modules are used to build a detection unit. This implies that the database is part of a loop in the information flow. A single photomultiplier test can involve up to about 10 5 measurements, corresponding to about 10 MB; this leads to the estimate of about 1 TB/building block for test results. The information collected about a complex product is later used to drive data acquisition tasks, which need the full description of the detector. In addition, for several operational parameters of the detector defaults are determined automatically from test information.
For instance, the supply voltage of a photomultiplier is extracted from the characterisation data provided by the vendor; then it is first optimized on a test bench; later it is re-optimized once the detection unit is fully assembled. This last value is then used during normal data acquisition tasks to set the working point of the photomultiplier. A runsetup is a full set of tuneable parameters for an acquisition task. It is possible to have several runsetups, according to different tasks and working conditions of the detector: for example, in times of high bioluminescence one might have a different tuning of supply voltage, threshold and trigger to reduce the trigger rate. The database hosts all available runsetups and the timeline of all runsetups used during the detector lifetime, so that data analysis and event reconstruction can be tuned accordingly.
The output parameters from detector monitoring and slow control are read continuously (10 -2 Hz) and fed into the database, with an estimated data rate of a few TB/y for a detector building block. The detector is calibrated and its shape is recomputed continuously. The expected data rate for calibration information and for acoustic data and shape parameters also tops a few TB/year. The KM3NeT detectors will be built incrementally: each detection unit can start taking data independently of the availability of the others, as soon as it is installed on the seabed and connected to the seabed infrastructure. Hence, the telescope as a whole has a history that requires bookkeeping. Finally, also for the purpose of simulating the expected output of the detector, detailed knowledge of detector configurations and working runsetups are needed.
Storage Tables in KM3NeT database belong to either of two categories: critical or non-critical, depending on the expected cardinality in 10 years: the criticality threshold is set at about 10 6 in 10 years. Non-critical objects get a database-wide unique ID from a single character sequence. Their storage and retrieval does not require special care. The category of critical object is worth some discussion. Critical tables all contain time series of parameters or event logs. Usual heap-organized tables with several fields per record would pose several problems: 1) With 10 12 records, adding or removing a single field is hardly feasible because the tables would be locked for more than one week. 2) Reading a single field requires reading the full row of the table, with extra disk activity and reduced access speed.
3) Accessing a time interval of values would require index scans of the primary key in addition to the table, implying sub-optimal performance. The solution is to use a columnar database storage scheme; more properly, it is quasi-columnar because each record also includes the timestamp. Data tables differ only by the data type: byte, 16-bit word, 32-bit double-word, 64-bit quad-word, single-precision floating point, double-precision floating point, string or event. The primary key includes the identifier of the parameter, its source (e. g. which photomultiplier or optical module it is related to) and the timestamp; a single value field contains the timestamped value of the parameter or the event code. Data are physically stored as if they were a stream, not repeating the unchanged key fields at every record, but storing only the timestamp and related value.