dataesr/scientific-paragraphs-categorization huggingface dataset:
Its properties make it an ideal tool for exploring computational principles of spiking systems consisting of both spiking sensors and cortical-like processing units. This type of tools are an essential resource for understanding how to leverage the physical properties of the electronic substrate as well as the most robust theories of neural computation in light of the design of a new generation of cortex-like processors for real-world applications. The multi-chip system is supported by the use of a newly developed software front-end, PyNCS, which allows rapid integration of heterogeneous spiking neuromorphic devices in unique hardware infrastructure and continuous online monitoring and interaction with the system during execution  (Stefanini et al. , 2014). In order to integrate the DVS and ROLLS in the existing software and hardware infrastructure, it was necessary to list the address specifications for the spiking events and for the configuration events in Neuromorphic Hardware Mark-up Language (NHML) files, the neuromorphic mark-up language used by PyNCS to control the neuromorphic system.
Acknowledgments Some of the circuits described in this work were developed jointly with  Chiara Bartolozzi ,  Elisabetta Chicca , and  Srinjoy Mitra. We thank  Stefano Fusi ,  Mattia Rigotti ,  Paolo Del Giudice , and  Massimiliano Giulioni  for fruitful discussions on the learning mechanisms and silicon neuron attractor networks; we thank  Adrian Whatley  and  Sadique Sheik  for their helpful comments on the overall chip architecture,  Hongzhi You  for his work on minimizing mismatch in the silicon neuron circuit,  Giovanni Rovere  for designing the rail-to-rail voltage buffer used to read out the analog signals, and  Tobi Delbruck  for technical support on designing the on-chip Bias Generator. We also acknowledge all our other colleagues at the  Institute of Neuroinformatics  for fruitful discussions and collaborations.
Study design This was a randomised, multi-centre, placebo-controlled, observer-blind, phase III study performed at eight centres in Australia between 5 October 2010 and 12 June 2012 (NCT01134263). The study was conducted in accordance with the Declaration of Helsinki and the International Conference on the Harmonization-Good Clinical Practice. The study protocol and amendments were approved by the respective Institutional Review Boards or Independent Ethics Committees at each study site. Written informed consent was obtained from all participants. The site selection criteria included locations outside of dengue endemic regions.
In order to have over 90% power to determine GMT equivalence between the three phase III lots for all four serotypes and to provide 97. 5% power for each serotype, assuming a 2-fold maximum acceptable difference between GMTs, an alpha level of 5% (two-sided hypotheses), a standard deviation of 0. 54 (log 10 titres) for each serotype, and that approximately 80% of participants would be included in the per-protocol analysis set, the sample size required for each dengue vaccine group was set at 165. With a placebo control group of 55, the total sample size required was set at 715. Statistical analyses were performed with SAS ® software. PRNT 50 titres and their 95% CIs were calculated for each of the four serotypes assuming normal distribution of the log 10 transformed PRNT 50 titres. The primary immunogenicity analyses were performed on the per-protocol analysis set, and confirmed on the full analysis set.
Older participants aged 46-60 years had a similar safety profile compared with younger participants aged 18-45 years (data not shown). Among the adverse events of special interest sought, there were no cases of serious or severe allergic reactions, no serious neurotropic or viscerotropic events, and no hospitalized dengue disease reported. While allergic reactions within seven days after study injection (1 pruritus, 7 rash, 1 facial swelling) were reported by: 8/488 (2%) participants receiving any phase III vaccine and 1/167 (1%) receiving the phase II vaccine, and none in the placebo group. Four pregnancies were reported; all in CYD-TDV groups. One pregnancy was 'exposed to vaccine', i. e. the vaccine was administered 18 days before the last menstrual period. The woman chose to have an elective abortion for unrelated personal reasons.
Acknowledgements Editorial assistance with the preparation of the manuscript was provided by  Richard Glover , in  Science Communications ,  Springer Healthcare. Funding for this assistance was provided by  Sanofi Pasteur. We thank  Maureen McKeirnan  ( Brisbane South Clinical Research Centre, Australia ) for her participation in this study. We also thank  Sutee Yoksan  from  CVD Mahidol, Thailand , for his dengue assay contributions,  Linghua Zhou  for her comments on the manuscript,  Edith Langevin  for assistance with the statistical analyses, and  Charlene Stevens  for coordinating study activities. We acknowledge the valuable contributions of each participant who volunteered to participate in the study and the staff who contributed to the conduct of the study at each site.
Genotyping Five polymorphisms that were observed in previous studies to be associated with DTC were selected for genotyping: the nonsynonymous SNP rs1801516 (D1853N) in ATM, the GWAS SNP rs944289 near PTCSC3 and NKX2-1 at 14q13. 3, the GWAS SNP rs965513 near FOXE1 at 9q22. 33, rs1867277 in the 5′UTR of FOXE1, and the poly-alanine stretch polymorphism rs71369530 in FOXE1 that is the result of a variable number of alanine repeats. For SNPs rs944289, rs965513, rs1867277, and rs1801516, 25 ng of gDNA were analysed using High-Resolution Melting curve (HRM) with a specific probe. Some representative samples were re-sequenced by dye-terminator to confirm the genotype  [28]. Fluorescence readings and data analyses were done with the Idaho Technology LightScanner Inc. Hi-Res Melting System (Idaho Technology, Salt Lake City, UT).
For rs71369530, 30 ng of gDNA was amplified by PCR with fluorescently end-labelled forward primers (5′-6-FAM or 5′-HEX) using KAPA 2G Fast HotStart ReadyMix (KAPA Biosystems, Woburn, MA, US) in a 10 μl final reaction volume (0. 5 mM MgCl2, 5% DMSO, 0. 25 mM primers). The fluorescently-labelled PCR product was loaded on an ABI 3730 capillary sequencer and analysed as a variable length fragment polymorphism using GenScan size standards (ROX-500) as internal size standards. Data were collected and visualized with Genotyper Software v3. 7. To determine the number of repeats corresponding to each allele identified in the genotyping assay, the PCR products from 6 homozygous individuals were Sanger sequenced. The sequences of all PCR primers, HRM probes, and all PCR conditions are available from the authors on request.
Thus, any generated odorant elicits an equal average response, given equal odorant concentrations. Odorant concentration varies between 0 and a max-concentration value of 1, the saturation point for OSN activation. For ease of visualization, raster plots are centered around glomerulus 50. All simulations were implemented using the MATLAB programming language using the Euler integration method for differential equations with a time step of 0. 5 ms. This model can be accessed from the modelDB website  (Hines et al. , 2004)  at the link senselab. med. yale. edu/ModelDb/ accession number 146813. The significance of the result in Figures  5 6 7 were corrected for multiple comparisons using the Bonferroni method.
Data collection The participants were involved in a structured transfer of knowledge of Sherbrooke model theory and practice. After this 3-hour training session, data were collected by semi-structured individual interview (N=22) and focus groups (N=7) led by an investigator. Focus groups were homogeneous in terms of background and occupation with no primary intention to explore divergences or reach consensus among the participants. The questions were based on the conceptual framework  (14)  and concerned perceived needs for a Sherbrooke-type intervention, perceived difficulties of understanding and use, perceived pros and cons, perceived usefulness, and compatibility with the participants' values and practices. In two rehabilitation centers, triangulation of data collection modes was used to improve accuracy.
Strong and weak points of the study The multiple case study design (15) allowed a complex notion to be dealt with in a real life setting. Several measures were taken to ensure the validity of the results  (16). Drawing up an eclectic conceptual framework allowed barriers and facilitators to be identified in the various agents and at the various levels. Triangulation of data collection and investigators at the time of analysis was performed. The investigators' interpretation of the results was fed back to the participants. Use of a single database and software package ensured process traceability. Analytical categories were saturated at the end of the analysis. A log-book kept during data collection enabled results to be contextualized and investigator subjectivity to be included. For all these reasons, the results can be presumed to have good construct validity and reliability.
Molecular modeling studies of P19 and F4 peptides both display a type I β-turn at the N-terminus Visualization of the different trajectories showed that both P19 and F4 peptides, independently of the starting conformation (displayed in Figure  6A ), adopted a small amount of hydrogen secondary structure (β-bridge, β-sheet or helix), low number of β-bridge, β-sheet or helix local structure. Globally, the peptides adopted mostly random structures. These observations were confirmed by the analysis of the local secondary structures performed using the DSSP (Define Secondary Structure of Proteins) algorithm as implemented in the GROMACS package  [30]. In all simulations, along the 200 ns, the coil local structure proportion was above 40%. The fractions of bends and turns were more important when starting from conformations generated with the Itasser or the Pepfold servers.
Fluorescence was analyzed by the Data Analysis software (Stratagene). Crossing points (Cp or Ct) were established using the second derivative method. The qPCR efficiency was calculated from the slope of the standard curve. Target gene expression levels were normalized to reference gene. The results were calculated using the delta-delta method. tPA detection by immunocytofluorescence 24 h after siRNA transfection, SKMEL28 cells were plated on glass slides and incubated in 10% serumcontaining medium for 48 h. They were fixed for 5 min with 4% paraformaldehyde. The slides were washed with PBS and saturated in PBS-T with 5% BSA. Cells were then incubated for 1 h at room temperature with an anti-tPA antibody diluted 1/400 in PBS-T with 1% BSA. Slides were washed in PBS and cells were incubated for 30 min with the Alexa-488-conjugated secondary antibody diluted 1/1000 in PBS-T with 1% BSA.
Molecular dynamics simulations Molecular dynamic simulations on the different peptides were conducted using the GROMACS simulation package  [48]. OPLSAA force field was chosen as the set of parameters for describing the atoms and their interactions  [49]. Isolated peptides were placed in boxes with side length varying from 50 Å to 90 Å depending on their size. These values were chosen so that a given peptide would not interact with its image when the periodic boundary conditions are applied. Water (TIP3P model) and counter ions were added prior to the simulations. In order to relax the structures, 500 steps of energy minimization were performed using the steepest descent algorithm. The systems were equilibrated for 500 ps at the temperature of 310 K in the isothermalisobaric ensemble. The equilibration steps were followed by Molecular Dynamics (MD) simulations carried out for 200 ns, maintaining a pressure of 1 bar (Berendsen algorithm) and a temperature of 310 K (V-rescale algorithm).
ACKNOWLEDGMENTS This work was supported by grants from the  « Université de Reims-Champagne-Ardenne » , the  « Centre National de la Recherche Scientifique » , the  « Ligue Nationale contre le Cancer » , the  « Region Champagne-Ardenne »  and the  « Fonds Européen de Développement Régional (FEDER)  ». The authors thank the  HPC-Regional Center ROMEO  (https://romeo. univ-reims. fr)and the  Multiscale Molecular Modeling Platform  (https://p3m. univ-reims. fr) of the  University of Reims Champagne-Ardenne (France)  for providing CPU time and support. The authors thank  Pr Hans-Peter Bächinger  and  Dr Serguey Budko  for providing some of the peptides necessary for the studies.
e. at least one cfu). Molecular identification and typing of Aspergillus isolates. This study was performed on Aspergillus isolates belonging to the same species or section based on mycological examination, and that were found in both clinical and environmental samples taken at the same period. DNA was extracted for isolates to be genotyped and A. fumigatus strains were typed with a set of 4 microsatellites as previously described  [10]. Signals were read with an automatic sequencer (ABI Prism 310, Applied Biosystems) and data were stored and analyzed with Genescan software (version 2. 1, Applied Biosystems). Multilocus sequence typing was used for Aspergillus isolates for which microsatellite typing was not available. Internal transcribed spacer (ITS) 1 and 2 loci, the β-tubulin gene and the actin gene were amplified and sequenced via the fluorescent dideoxynucleoside triphosphate method  [11] [12] [13].
Acknowledgments We thank  A. Stoclin  ( LTU ) and all medical staff members of the  SICU  for their help in collecting patient data. We thank  S. Bretagne  for critical review of the manuscript and the  Centre National de Référence des Mycoses  invasives et antifongiques for microsatellite typing of Aspergillus fumigatus isolates. This article is dedicated to  Pr Francis Derouin  whose work was devoted to fungal infectious diseases and particularly to the prevention of hospital-acquired fungal infections and who passed away before the submission of the final version of this manuscript. Dr Christine Bonnal  accepts responsibility for the integrity and validity of the data collected and analyzed.
Deletion constructs and COS cell immunofluorescence assays Deletion constructs based on TM284var1 (Genbank accession number JQ684046) DBL4 were amplified and cloned into the pRE4 vector as described previously  [9, 17]. The amino acid boundaries and primers used are shown in Table  S1. Immunofluorescence assays (IFAs) were carried out as described previously  [9]. Briefly, COS-7 cells were seeded in wells containing 12 mm coverslips and transfected with constructs using FuGene (Roche) according to the manufacturer's protocol. IFAs were carried out forty-eight hours after transfection on cells that were washed with Phosphate Buffered Saline (PBS) and fixed for 10 min in PBS/2% formaldehyde. Cells were blocked for 1 h with PBS/5% Bovine Serum Albumin (BSA) and incubated with PBS containing 10 % pooled human serum as a source of IgM for 1 h.
Binding of recombinant TM284var1DBL4 mutants to human IgM Surface Plasmon Resonance (SPR) was used to assess the binding of single (E1663R and R1764E), double (E1663R, R1764E) and quadruple (E1663R, E1665R, R1764E, E1779K) mutants to immobilized IgM. All mutants bound IgM similarly to the wild type (Fig. 4 ), with binding affinities (K D ) in the nanomolar range for all proteins (Table  3 ). There were minor differences in K D between some of the proteins, but further investigation with completely pure protein preparations would be required to determine the significance of these minor changes. All mutants containing R1764E showed biphasic association and dissociation curves (Fig. 4 ). Fitting the data to a model with two independent binding sites gave a K D similar to the value obtained for the single-site model, together with a much tighter complex with no detectable dissociation over the time course of the experiment (koff < 10 -6 s -1 , the lower limit of the SPR machine).
K-next neighbours For the K-next neighbours parametrisation we made use of the Statistics Toolbox provided by MATLAB (The Math-Works, Inc. 3 ) to characterise the ionisation patterns of the tracks by calculating the distances between K-next neighbours. Figure  1  gives the average euclidean distances from one energy transfer point to the next ten neighbouring transfer points for proton energies as indicated in the figure legend. In Figure  2  the same is shown for carbon ions. We calculated the distances to the next ten neighbouring ionisations for each ionisation point in all available tracks for the respective energy. Data was then divided into ten subgroups and we took the arithmetic mean value of the arithmetic mean values from each subgroup. The corresponding error is then given by the standard deviation of the mean values from the subgroups.
RESULTS AND DISCUSSION Detection and classification of episomes. We screened 660 Vibrionaceae isolates for the presence of episomes using multiple gel electrophoretic assays to resolve DNA of different sizes (see Materials and Methods). This identified 140 DNA bands distributed across 101 of the isolates and varying in size between 1 and 200 kbp. To further investigate these putative episomes, we excised all bands from gels and determined their sequence by the Illumina and 454 technologies. Although in many cases assembly produced single and frequently circular episomes (see Table  S1  in the supplemental material), there were instances where several contigs resulted from a single band on electrophoresis gels. Because this may indicate incomplete assembly of a single episome or comigration of multiple, similarly sized episomes, we used additional in-formation contained in the data to differentiate these possibilities.
Genetic diversity. The episomes detected in this study carry a diversity of genes, albeit with 43% (2,043 ORFs), the largest portion are hypotheticals when annotated using both RAST  (28)  and the ACLAME database  (29)  (see Materials and Methods). This is consistent with the notion that mobile elements are enriched in genes with poorly understood function  (30, 31). The most important category of known functions is membrane transport, with 296, 70, and 10 genes annotated as members of T4SS, type 6 secretion systems (T6SS), and ABC transporters, respectively. As mentioned above, T4SS is most likely involved in conjugative transfer, and of the 27 T4SS detected, 19 were type F, 6 type T, and 2 type G. Conjugation systems of the F-type have thin, flexible pili that allow high frequency of conjugation in liquid media  (32) , while type T pili are rigid and are thought to perform better on surfaces  (33) , providing some indirect support for the biased occurrence (and potential transfer) of episomes among free-living hosts (Fig.
Multicontig episomes and their matching references were subsequently used to define families by applying variable sequence cutoffs. Episomes without matches in the similarity network were considered singletons. Classification of episomes. Based on previous identification of broad categories of episomes, we searched our data for evidence of conjugative, mobilizable, and nontransmissible plasmids and of phage. To identify conjugative plasmids, we searched for cooccurrence of genes encoding the type IV secretion system (T4SS) and the relaxosome. Plasmids encoding both components were classified as conjugative, while plasmids encoding a relaxase only were classified as mobilizable. The episomes that did not encode either of these elements and could not be identified as phage (see below) were classified as putatively nontransmissible plasmids following the logic of Smillie et al.
This led to a database of protein profiles associated with conjugation that correspond in general to the known essential proteins in each system (albeit a few evolve too fast and give poor sequence similarity hits). The profiles were then searched using HMMER in the proteomes of all episomes. We filtered the results by using an E value of Յ0. 01 and coverage (ratio between the target and query lengths) of more than 0. 5. Clusters are based on the findings in the entire replicon. For phage identification, we blasted the episome contigs against the ACLAME Database of Mobile Elements v. 0. 4 (29) using BLASTp with an E value of Յ1eϪ10. We unified the phage and prophage categories into a single "phage" category so that we broadly classified proteins into phageand plasmid-like. Phage episomes were identified based on the density of proteins matching phage proteins in the ACLAME database.
0 (62), followed by the clustering of ORFs using OrthoMCL  (63, 64) , in which a minimum 97% coverage of the longer sequence was required as well as an E value of Յ1eϪ5. Whole genomes of episomes were then clustered based on these shared proteins, using the FT ClustNSee clustering algorithm in cytoscape  (65, 66). Nucleotide sequence accession numbers. Sequence data can be retrieved from GenBank under accession numbers KP795445 to KP795714.
Study design This prospective study was performed in a real-life cohort approved by the Transplantation Prospective Group of the Association Française pour l'Etude du Foie (AFEF, French Association for the Study of the Liver) in October 2011. This was an observational study. The physicians chose to treat patients for HCV recurrence in accordance with current guidelines. Patients were enrolled in 17 transplant centers in France, Belgium and Switzerland. They were included when at least one dose of anti-HCV therapy was administered. Data were collected prospectively between March 2011 and January 2014.
The exclusion criteria were HIV co-infection and contraindications to the use of one of the antiviral drugs, including uncontrolled biopsy-proven acute rejection (BPAR). Cirrhotic patients were enrolled when compensated. Data were collected on the testing of recipient DNA for interleukin (IL) 28B polymorphism rs12979860C/T using the ABI TaqMan allelic discrimination kit and the ABI7900HT Sequence Detection System (Applied Biosystems, Carlsbad, CA). Before the initiation of PI, a minimal calcineurin inhibitor (CNI) trough concentration (C0) was targeted and all patients were at a steady state regarding the IS. Whole blood concentrations were assayed using a chemiluminescent microparticulate immunoassay on an Architect autoanalyzer for CNI, and liquid chromatography coupled to tandem mass spectrometry for everolimus.
Safety assessments Adverse events were assessed at each consultation visit: at baseline, at weeks 4, 8, 12, 24 and 48 during therapy and at weeks 4, 12 and 24 after therapy. However, investigators were able to schedule supplementary visits when the condition of their patients required close follow-up; for example, if any adverse events occurred. For the purposes of this paper, serious adverse events (SAE) were defined as all unexpected events occurring during treatment whatever their cause, and required treatment discontinuation. Severe cytopenia was defined as cytopenia requiring treatment discontinuation. Data on the type of SAE and on clinical and biological parameters were collected during the period of antiviral therapy and for 6 months after administration of the last dose. The estimated glomerular filtration rate (eGFR) was assessed using the Cockcroft-Gault formula  [18].
Statistical Analysis Analyses were performed in the modified intention-to-treat population, which included all patients who had received at least one dose of anti-HCV therapy. SAS software, Version 9. 3 (SAS Institute Inc. , Cary, NC, USA) was used for these analyses. All statistical tests and 95% confidence intervals were two-sided, with a significance level of 0. 05. When data were supplied as mean values, ranges were provided [minimum-maximum] and when data were supplied as median values, interquartile ranges were provided [IQR1-IQR3]. Differences in baseline characteristics between the two treated groups were evaluated using the chi-square test for categorical data and one-way analysis of variance for continuous data. Comparisons of efficacy, adverse events and laboratory abnormalities were performed using Fisher's exact test.