dataesr/scientific-paragraphs-categorization huggingface dataset:
Moreover, an enrichment analysis within 'Segment 3+4' of a large number of publicly available datasets for the occupancy of various TFs and cofactors was performed using ReMap  (53). These analyses confirmed the significant enrichment of AP1-bound regions on 'Segment 3+4' (Figure  5D ) and further identified a significant overlap with additional TFs including Signal Transducer and Activator of Transcription 3 (STAT3) and CCAAT/Enhancer-Binding Protein-␤ (C/EBPb). Notably, based on RNA-seq data, all the identified TFs are expressed in hFOBs and only RUNX2 and Fos-related antigen 2 (FOSL2) expression were dependent on BRD4 (Supplementary Figure  S5D ), suggesting that these factors may serve as central mediators to facilitate BRD4 recruitment to osteoblast-specific enhancer regions. ChIP-qPCR analyses on the overlapping regions identified by ReMap showed a significant enrichment for C/EBPb, TEAD1, STAT3, JUND and FOSL2 (Supplementary Figure  S5E-H ).
Thus, the predictive value of utilizing a combination of chromatin segmentation of differentially bound osteoblast-specific BRD4-enriched regions, motif analyses and integration of publically available TF genome occupancy datasets, could be confirmed by genome-wide occupancy studies for four out of five predicted TFs (C/EBPb, TEAD1, JUND and FOSL2). Moreover, the association of these putative enhancers with osteoblast-related genes and the dependence of these genes on functional activity of BRD4 support a role for BRD4 in regulating gene expression and controlling lineage determination.
ACKNOWLEDGEMENTS The authors thank  M. Thomas-Chollier  and  D. Thieffry  for guiding the work of R. T. M. ;  C. Hernandez  and  S. Collombet  for useful discussions and invaluable assistance on the data analysis;  G. Salinas-Riester ,  B. Downey ,  F. Ludewig  and  T. Lingner  for excellent support with next generation sequencing; and  C. -M. Chiang  for kindly providing the BRD4 antibody.
FUNDING German Academic Exchange Service (DAAD)  (to S. N. ); EpiGeneSys consortium travel grant (to R. T. M. ); Erasmus Mundus External Cooperation Window EURINDIA and the  G öttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences  (to U. B. );  German Research Foundation (DFG)  [ JO 815/3-1 ];  Deutsche Krebshilfe  [ 111600  to S. A. J. ];  German Ministry for Science and Education (BMBF)  and  Agence Nationale de la Recherche -funded iBONE consortium [ 01KU1401A  to S. A. J. ,  01KU1401B  to  E. H. ,  ANR-14-CE11-0006  to M. Thomas-Chollier];  German Research Foundation  [ HE 5208/2-1  to E. H. ];  NIH  [ DE14036  to J. R. H. , M. S. ]. Funding for open access charge: Internal house funding/university funding.
The amplification conditions were as follows: preheating at 50°C for 2 min, then at 95°C for 15 s followed by 40 cycles at 94°C for 15 s, 60°C for 30 s and 72°C for 30 s. Serially diluted 16S rRNA gene amplicons from Paracoccus denitrificans (Bacteria), Nitrosotalea devanaterra (Archaea) or ITS gene amplicons from Suillus variegatus (Fungi) were used as standards. Melting curves were performed to confirm the purity of the amplified product. Amplification efficiency (E) of the primers was within the prescribed values (0. 9<E<1. 1) with linearity (r 2 >0. 99). Gene abundance is expressed g -1 soil dry weight. The sum of gene abundances of Archaea, Bacteria and Fungi was used to estimate total microbial biomass. Fungal:bacterial ratios (F:B) were also calculated based on the qPCR data. M-TRFLP analysis employed universal 16S rRNA gene primers or internal transcribed spacer (ITS) region primers (Applied Biosystems, UK) to target bacterial and fungal communities, respectively, with sample preparation and data analysis as described in Singh et al.
Similar tests were applied to determine statistically significant differences in the percentage of total OTUs. The significance of differences could not be determined between the compensatory response soil, for which n = 1 as previously demonstrated by Karhu et al. [21] , and the no-response or enhancing response soils. Linear regression analysis was used to relate the magnitude of the respiration responses (RR MT ) in different soils to changes in these microbial parameters, soil properties and other parameters describing microbial community composition across all data. Analyses were conducted using SPSS Statistics 22 (IBM, USA). Statistical analysis of the M-TRFLP samples was based on the complete sample profiles as expressed by the pattern of M-TRFLP peaks and the relative abundance (percentage) of individual peaks in each profile  [38].
To determine whether information on the initial microbial community composition could help to predict the respiratory response, Canonical Variates Analysis (CVA) was performed on M-TRFLP data (precooling treatment samples) using Gen-Stat 14 th edition (VSN International Ltd, UK) and coordinates were obtained (S1 Fig). Each CVA axis shows the best separation between groups defined by their respiratory response and using microbial community structure data obtained at the end of the incubation. Pyrosequencing data analysis was performed using the 'Quantitative Insights Into Microbial Ecology' (QIIME v1. 6. 0) software package  [46]. Strict quality filtering steps were performed before affiliation to phylogenetic clusters and operational taxonomic units (OTU; SI Materials and Methods).
Acknowledgments We thank  J-A. Subke  from  University of Stirling ,  G. Bergkvist  from  Swedish University of Agricultural Sciences ,  F. Gouriveau  from  Forest Sciences Centre of Catalonia ,  P. Meir  from  University of Edinburgh  and the  Australian National University ,  A. Nottingham  from  University of Edinburgh ,  N. Salinas  from  Pontificia Universidad Catolica del Peru , and  M-T Sebastià  from  Forest Sciences Centre of Catalonia and University of Lleida  for help with site selection, soil sampling and for the use of the Stirling incubator facility as well as the review of this manuscript. We would like to thank  Lorna English  for help with the enzyme assays and  Lucinda Robinson  and  Jenna Ross  for technical assistance.
Binary nucleation of sulfuric acid and water as well as ternary nucleation involving ammonia are thought to be the dominant processes responsible for new particle formation (NPF) in the cold temperatures of the middle and upper troposphere. Ions are also thought to be important for particle nucleation in these regions. However, global models presently lack experimentally measured NPF rates under controlled laboratory conditions and so at present must rely on theoretical or empirical parameterizations. Here with data obtained in the European Organization for Nuclear Research CLOUD (Cosmics Leaving OUtdoor Droplets) chamber, we present the first experimental survey of NPF rates spanning free tropospheric conditions. The conditions during nucleation cover a temperature range from 208 to 298 K, sulfuric acid concentrations between 5 × 10 5 and 1 × 10 9 cm À3 , and ammonia mixing ratios from zero added ammonia, i.
[2016]  are extended to the ternary ammonia system. We present experimentally determined nucleation rates that were obtained during three different campaigns conducted at the European Organization for Nuclear Research (CERN) CLOUD (Cosmics Leaving OUtdoor Droplets) chamber. The measurements were made during CLOUD3 (October/November 2010), CLOUD5 (October/November 2011), and CLOUD7 (October-December 2012). For the data analysis, ammonia calibration measurements from CLOUD6 (June 2012) were used. The investigated parameter space covers a wide range of tropospheric conditions and is summarized in Table  1. The relative humidity (RH) was sometimes varied (at 223 K, see Text S3 in the supporting information and at 298 K, see section 3. 1. 6) but no systematic investigation of the RH effect was performed; for most experiments the RH was set to 38%.
When data from instruments with detection thresholds between 1. 3 and 2. 7 nm are available, these are used to constrain the formation rates in this size range, but we can always calculate J 1. 7 based solely on adjusting J 3. 2 obtained from the CPC 3776. In general, the various methods agree to within a factor of 2, as shown in Figure  S3  in the supporting information. For consistency, we use the J 1. 7 values obtained from the CPC 3776 in this work. During CLOUD3 when the chamber was operated at temperatures below 292 K, the particle counters were cooled to about 280 K to minimize the residence time of particles inside the warm instrument inlets and tubes. During CLOUD5, when the chamber temperature was as low as 208 K, the particle counters were contained in thermal huts, which were cooled to 243 K when the chamber was held at 208 or 223 K  [Wimmer et al.
However, this attempt was not made since the comparison to the CLOUD data should provide a qualitative picture of the functional dependencies certain parameters have on the NPF. When simulating cluster formation under GCR or pion beam conditions, ions are introduced via a constant charger ion source term of 3 or 75 ion pairs cm À3 s À1 , respectively. These generic charger ions, O 2 À and H 3 O + , can then collide with either sulfuric acid or ammonia molecules, or with clusters, thereby transferring their charge. Hydration of the charger ions is neglected although it could potentially affect the number concentration of generated HSO 4 À and NH 4 + ions by influencing the charging rate of the primary ions. This effect is, however, within the overall uncertainty related to the ion-neutral collision rate parameterization.
Therefore, the increase in RH could lead to a displacement of ammonia from the chamber walls and lead to an elevated NH 3 background level and consequently to higher nucleation rates. It is interesting to note that the slope of J versus [H 2 SO 4 ] is very flat at the lowest RH of 20%. This could indicate that nucleation is limited with respect to the availability of H 2 O or contaminant NH 3. However, the number of data points is quite low, so this cannot be unambiguously shown. Clearly, in future CLOUD studies, the effect of varying RH should be studied in more detail while ensuring that the level of contaminants is insignificant. 3. 1. 7. Comparison Between CLOUD Data and Previous Studies at 292 and 298 K Recently,  Glasoe et al. [2015]  investigated the effect of seven bases on the particle formation rate for the system of sulfuric acid and water (plus the added base).
3 pptv (estimated contaminant level of ammonia at 292 K; Figure  4 , dash-dotted blue line) and 1000 pptv (Figure  4 , dash-dotted red line). Both lines show relatively good agreement with the CLOUD data, especially for the nominally binary conditions with an estimated ammonia level of 4. 3 pptv. Regarding this estimation the comparison between data from this study and from  Glasoe et al. [2015]  indicates that our reported ammonia background should be quite accurate. For higher NH 3 mixing ratio the agreement is also quite good, which is discussed further below (section 3. 3. 3). The data at 298 K (Figure  4 , bottom) are also compared to equation (  1 ) for an estimated ammonia background level of 6 pptv (Figure  4 , dash-dotted cyan line). Equation (  1 ) is derived for conditions of 28% RH; the agreement with the CLOUD data for an RH of 38% (cyan data points) is relatively good.
Summary and Conclusions More than 300 individual particle formation rates at a mobility diameter of 1. 7 nm were presented from measurements at the CLOUD chamber. Different temperatures between 208 and 298 K were adjusted probing a range of sulfuric acid concentrations and ammonia mixing ratios. Furthermore, the effect of ion-induced nucleation was extensively studied by either eliminating the effect of ions through the use of a high-voltage clearing field (neutral conditions) or by allowing ions from galactic cosmic rays (GCR conditions) or a pion beam (pion beam conditions) from the CERN proton synchrotron to participate in the formation of new particles. The data set is used to derive a parameterization, which is presented elsewhere  [Dunne et al. , 2016]. The parameterized particle formation rates are implemented into the GLObal Model of Aerosol Processes  [Dunne et al.
At even higher temperatures (278 and 292 K), both the binary and the ternary system show elevated nucleation rates under the presence of ions because the neutral cluster evaporation rates are high and therefore the addition of charge efficiently stabilizes the clusters. Regarding the importance of ion-induced nucleation, we want to emphasize that the CLOUD data suggest where this effect should be most important. At 248 K and the lowest ammonia levels (i. e. , under nominally binary conditions) the enhancement in the nucleation rates due to the presence of charges is high, while nucleation is efficient at the same time due to the rather low temperature. Consequently, in clean upper tropospheric regions where ionization rates are high and the levels of ternary substances are low, the ioninduced nucleation pathway could be dominant  [Lee et al.
, 2003; Lovejoy et al. , 2004]. Neutral and ion-induced nucleation rates were also calculated with the Atmospheric Cluster Dynamics Code (ACDC) and evaporation rates calculated by quantum chemistry. The nucleation rates were calculated for different levels of sulfuric acid and ammonia. The effect of water vapor was not taken into account; therefore, it is unreasonable to expect the simulations to reliably predict the formation rates for conditions when the ammonia levels are low and binary nucleation is the preferred pathway. Given this limitation, the formation rates at the two lowest temperatures (208 and 223 K) agree with the simulations within the uncertainties. Other model approaches, using, e. g. , thermochemical data from experiments for binary nucleation could be used for such conditions  [Panta et al.
Acknowledgments We would like to thank  CERN  for supporting CLOUD with important technical and financial resources and for providing a particle beam from the  CERN Proton Synchrotron. We also thank  P. Carrie ,  L. -P. De Menezes ,  J. Dumollard ,  K. Ivanova ,  F. Josa ,  I. Krasin ,  R. Kristic ,  A. Laassiri ,  O. S. Maksumov ,  B. Marichy ,  H. Martinati ,  S. V. Mizin ,  R. Sitals ,  A. Wasem , and  M. Wilhelmsson  for their important contributions to the experiment. We thank  T. Olenius  for helpful discussion. This research has received funding from the  EC Seventh Framework Programme  ( Marie Curie Initial Training Networks  " CLOUD-ITN" 215072  and " CLOUD-TRAIN" 316662, ERC-Starting "MOCAPAF " grant no. 57360  and  ERC-Advanced  " ATMNUCLE" grant   227463 ), the  German Federal Ministry of Education and Research  (projects  01LK0902A  and  01LK1222A ), the  Swiss National Science Foundation  (Projects  200020_135307 ,  206620_130527 , and  206620_141278 ), the  Väisälä Foundation , the  U.
(2) Since C V t C V t C V t p ac p ac p ac 2 2 1 2 1 1 ( ) = ( ) ≈ - ( ) (3) the total charges qtotal, feeding the amplifier is q t q q V t C V t V C t V t C total a c p ac dc ac p ( ) = + = ( ) + ( )+ ( ) ( )+ ( ) 1 2 1 1 1 1 1 2 2 , q q t V t V C t total a c d c ( ) = ( )+ ( ) ( ) 1 1 1. ( 4 ) This quantity of charges was then amplified using a charge amplifier and fed into a network analyzer. The resulting data were subtracted with the background signal at Vdc1 = 0 V and filtered using the moving average method to remove the noise. In addition to the integrated capacitive detection measurements, optical detection of the resonant frequency of the active devices was achieved using a Fabry-Perot setup for comparison means  (Bhaswara et al. , 2014). The center of each nanoplate was chosen as the optical measurement spot, since it corresponds to the maximum amplitude of the first vibration mode of a circular plate.
75  [12]. For this purpose, considering a proportion of VO 2 responders of 21 %  [8] , 51 fluid-responder's patients are required for a power of 90 % and an alpha risk of 0. 05. Assuming a proportion of responders close to 50 %, about 102 patients would be necessary. Statistical analysis was performed using STATA 14. 0 (StataCorp LP, College Station, Texas, USA) and SPSS for Windows release 17. 0 (Chicago, Illinois, USA). p < 0. 05 was considered statistically significant. All reported P values are two-sided.
Analysis A t-test analysis was used to compare the quantitative data of satisfaction ratings for 1 st and 2 nd years using SPSS Version 21. A 5 % level of significance was used for all statistical tests. Qualitative feedback was analysed using thematic analysis  [60]. Thematic analysis is the most common form of analysis in qualitative research. It pinpoints, examines, and records patterns (or "themes") within data and the themes become the categories for analysis. Thematic analysis is performed through a process of coding to create established, meaningful patterns.
We present a complete census of all Herschel -detected sources within the six massive lensing clusters of the HST Frontier Fields (HFF). We provide a robust legacy catalogue of 263 sources with Herschel fluxes, primarily based on imaging from the Herschel Lensing Survey (HLS) and PEP/HerMES Key Programmes. We optimally combine Herschel, Spitzer and WISE infrared (IR) photometry with data from HST, VLA and ground-based observatories, identifying counterparts to gain source redshifts. For each Herschel -detected source we also present magnification factor (µ), intrinsic IR luminosity and characteristic dust temperature, providing a comprehensive view of dust-obscured star formation within the HFF. We demonstrate the utility of our catalogues through an exploratory overview of the magnified population, including more than 20 background sub-LIRGs unreachable by Herschel without the assistance gravitational lensing.
3, ΩΛ = 0. 7. Herschel imaging, catalogues and source IR SEDs associated with this paper can be downloaded from the public flavour of the Rainbow Database. 2  The PACS instrument allowed an observer to choose between 70 or 100 µm bands in a blue channel, collected simultaneously with the red channel at 160 µm. For all six central Frontier Fields footprints, imaging is available within the PACS 100 and 160 µm bands. In addition, M1149 and AS1063 were also covered at 70 µm. Five clusters were observed by PACS as part of the Herschel Lensing Survey (HLS;  Egami et al. 2010 Egami et al. , 2015 in prep. ) in prep. ) , which combines an Open-Time Key Programme (KPOT) and an Open-Time Cycle 2 (OT2) Programme (both PI: E. Egami). These (100, 160 µm) observations consist of two orthogonal scan maps, each comprising 18 repetitions of thirteen parallel 4-arcmin scan legs (total observing time per cluster, t obs = 4.
2012 (Piazzo et al. , 2015)). Unimap employs a Generalised Least Squares (GLS) method to produce the final maps (combining all OBSIDS), and includes a second timeline deglitcher, detection and correction for detector signal jumps, and an advanced drift removal via an Alternate Least Square method. This algorithm has several advantages compared to the naive map-maker photProject (the erstwhile standard for archive products), as it removes the need to filter 1/f noise drift in the PACS bolometers: 1) variations in background flux are conserved rather than smoothed; 2) source fluxes are not truncated, removing the need to mask known sources and allowing blind PSF-fit photometry without using correction functions; 3) all turnaround data can be used, including those observed at zero scan speed, which increases the depth at the edge of the map.
MERGED IR FLUX CATALOGUE In this section we describe the band-merged photometry methodology, culminating in the presentation of our Herschel flux catalogue for HFF. Band-merged catalogues in the wavelength range covered by WISE, Spitzer and Herschel were produced within the Rainbow Cosmological Surveys Database framework  (Pérez-González et al. 2008). Photometric extraction follows the method described in  Pérez-González et al. (2010). The same procedure was followed for each cluster.
view of the full Herschel Lensing Survey (HLS;  Egami et al. 2010) , covering 10× the cluster sample, and many thousands of Herschel -detected sources  (Egami et al. 2015 in prep. ). Herschel imaging, catalogues and source IR SEDs can be downloaded from the public flavour of the Rainbow Database. 10. from STFC (ST/L00075X/1), the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. Based on observations made with the NASA/ESA Hubble Space Telescope, which is operated by the Association of Universities for Research in Astronomy, Inc. , under NASA contract NAS 5-26555. These observations are associated with  programmes #11689, 13389, 13495, 13496, 13498, 13504. This publication also uses data products from the Wide-field Infrared Survey Explorer (WISE ), which is a joint project of UCLA and JPL, Caltech, funded by NASA.
This research made use of the NASA/IPAC Infrared Science Archive, which is operated by JPL, Caltech, under contract with NASA. We made use of a private version of the Rainbow Cosmological Surveys Database, operated by the Universidad Complutense de Madrid (UCM), and PGP-G acknowledges support from Spanish Government MINECO grant AYA2012-31277. A2744 C -28. 3 ± 2. 3 41. 6 ± 3. 5 23. 9 ± 4. 1 11. 9 ± 2. 9 5. 1 ± 1. 5 HLSJ001421. 0-302336 (P) A2744 C -9. 9 ± 1. 0 19. 6 ± 1. 9 17. 5 ± 2. 6 --HLSJ001422. 1-302254 (P) A2744 C -4. 6 ± 0. 7 7. 0 ± 1. 2 15. 6 ± 2. 5 9. 0 ± 2. 5 -HLSJ001422. 4-302304 (P) A2744 C -41. 5 ± 3. 3 46. 5 ± 3. 8 15. 0 ± 2. 5 3. 9 ± 3. 7 -HLSJ001422. 7-302350 (P) A2744 C -3. 6 ± 0. 7 6. 1 ± 1. 2 ---HLSJ001421. 7-302401 (P) A2744 C -33. 2 ± 2. 6 41. 3 ± 3. 6 24. 9 ± 2. 7 6. 9 ± 4.
ACKNOWLEDGMENTS TDR was supported by a  European Space Agency (ESA)  Research Fellowship at the  European Space Astronomy Centre (ESAC) , in Madrid, Spain. RJI acknowledges support from the  ERC  in the form of the Advanced Investigator Program, 321302, COSMICISM. IRS acknowledges support Complete census of Herschel sources within HFF 21 This work also utilises gravitational lensing models produced by  PIs Ebeling  (CATS) and  Merten & Zitrin , funded as part of the  HST Frontier Fields program  conducted by  STScI. STScI is operated by the  Association of Universities for Research in Astronomy, Inc. under  NASA  contract  NAS 5-26555. The lens models were obtained from the  Mikulski Archive for Space Telescopes (MAST).
Study Design This is a pooled analysis of data from nine national registries of RA patients: ARTIS (Sweden), ATTRA (Czech Republic), DANBIO (Denmark), GISEA (Italy), NOR-DMARD (Norway), ORA (France), REUMA. PT (Portugal), RHUMADATA (Canada), and SCQM (Switzerland), collected from 2006 to 2015. Each of the registries was approved by the local Ethics Committee and national guidelines for collection of informed consent form before enrolment in the study in accordance with the Declaration of Helsinki were followed. A more detailed description of the registries is available elsewhere  (Curtis et al. , 2010; Finckh et al. , 2015). Inclusion criteria for this analysis were a diagnosis of RA, initiation of ABA treatment and at least two assessments of DAS28. The primary outcome to model response trajectories was the disease activity score based on 28 joints (DAS28)  (Prevoo et al.