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cc-by | Planck Number Counts Compared with Other Datasets The number counts are in fairly good agreement at lower frequencies (100 to 217 GHz) with the counts published in the Planck early results, based on a 30 GHz selected sample (Planck Collaboration XIII (2011); represented as diamonds in Fig. 9 and 10). The effect of inc... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The ACT and SPT data, when added to the Planck data at 143 GHz, cover more than four orders of magnitude in flux density. Finally, we checked that our counts are in agreement with the Planck Sky Model (Delabrouille et al. , 2012). Figure 10. Same as Fig. 9 , but on a wider flux density scale and with the addition of ... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | (2009 ), Franceschini et al. (2010) , Lacey et al. (2010) , Marsden et al. (2011) , Wilman et al. (2010), and Rahmati & van Der Werf (2011). A comparison is given with these models in Fig. 12 based on an analysis of all the main source populations at GHz frequencies. It currently provides a good fit to all data on... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Dusty sources The Serjeant & Harrison (2005) model performs reasonably well at 857 GHz, but is lower than our observations at 545 and 353 GHz. The Bethermin et al. (2011) model has the same trend -it is compatible with the data at 857 GHz, but is lower than the observations by a factor of about 3 at 353 and 545 GHz... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | , 2009) and in all bands (Massardi et al. , 2009; de Zotti et al. , 2010) , and finally IRAS 25, 60 and 100 µm results (Lonsdale & Hacking, 1989; Hacking & Soifer, 1991; Bertin & Dennefeld, 1997). The Spitzer level at 24, 70 and 160 µm comes from counts above 8, 70 and 300 mJy, respectively (Bethermin et al. , 2010... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | We might instead want to use the luminosity density estimated at 850 µm from previous studies, and correct it to account for the excess observed by Planck. We can thus use: Luminosity density ρ ν (in units of h L ⊙ Mpc -3 ) of dusty galaxies, derived from the Euclidean level p and scaled to the luminosity density of: ... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | (2011) agrees marginally at 857 GHz but is too low at 545 GHz and at lower frequencies, while the model of Serjeant & Harrison (2005) is marginally lower at 857 GHz, fits the data well at 545 GHz, but is too low at 353 GHz. The likely origin of the discrepancies is an inaccurate description of the SEDs for galaxies ... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | We derive a range of values for the local luminosity density for dusty galaxies, based on simple considerations and using the SCUBA 850 µm and IRAS 60 µmluminosity density as a reference. The Planck multi-frequency all-sky survey is very rich dataset, in particular for extragalactic studies (e. g. Negrello et al. 2012)... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Figure14. Luminosity density ρ ν (in units of h L ⊙ Mpc -3 ) of dusty galaxies, derived from the Euclidean level p and scaled to the luminosity density of: SCUBA 850 µm data (Dunne et al. , 2000; Serjeant & Harrison, 2005 ) (see Eq. 12); or IRAS 60 µm data (Soifer & Neugebauer, 1991; Bertin & Dennefeld, 1997; Takeuchi ... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgements. Based on observations obtained with Planck (http://www. esa. int/Planck), an ESA science mission with instruments and contributions directly funded by ESA Member States , NASA , and Canada. The development of Planck has been supported by: ESA ; CNES and CNRS/INSU-IN2P3-INP (France) ; ASI , ... | 10.1051/0004-6361/201220053 | article | en | 2,012 | true | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The first technique we use for the final reconstruction of the map is PhotProject. We first remove the 1/f noise (correspond- ing to data with low spatial frequencies or large scale structures in the map) using a high-pass filter. We then use PhotProject to reproject the data on the sky. The high-pass filtering step is... | 10.1051/0004-6361/201321602 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Nevertheless, MADmap is more efficient than PhotProject in reconstructing the extended structures within a map. Scanamorphos is another technique specially developed to process scan observations (Roussel 2012). The particularity of Scanamorphos, compared to MADmap, is that no particular noise model is assumed to deal ... | 10.1051/0004-6361/201321602 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Determination of unc sum : For each pixel there is a contribution from the background noise to the total measured flux density. This error, σ sky , is the same for a pixel in the source aperture as well as in the background aperture, repeated N ap times here. The error, σ sky , is the standard deviation of all pixels i... | 10.1051/0004-6361/201321602 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | This will affect the determination of the flux density for each pixel summed in the aperture : unc bg = N ap unc bg level (6) The uncertainty due to background noise in the source aperture, unc source , is determined the same way as the PACS unc ap since it is the uncertainty arising from summing the pixels in a given ... | 10.1051/0004-6361/201321602 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | MIPS photometry The table of the available MIPS data for the DGS is given in Madden et al. (2013) and Bendo et al. (2012) who give a detailed description of the photometry for total galaxy flux densities. Of the DGS sample, 34 galaxies have been observed by MIPS in the considered bands. Bendo et al. (2012) MIPS fl... | 10.1051/0004-6361/201321602 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The very faint and discrepant galaxies at 70 µm are HS1222+3741 (ratio of 0. 40) and Tol1214-277 (ratio of 0. 24). For HS1222+3741, the MIPS image contains some bright pixels near the edge of the photometry aperture used for MIPS, and this may have driven the 70 µm MIPS flux density up. For Tol1214-277, a nearby source... | 10.1051/0004-6361/201321602 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgements. The authors would like to thank the referee, Simone Bianchi , for his valuable comments that helped improve the quality of this paper. ARR is supported by a CFR grant from the AIM laboratory (Saclay, France). This research was, in part, made possible through the financial support of the Agence Na... | 10.1051/0004-6361/201321602 | article | en | 2,013 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Relationship between Wt and reduced heat flow In general we assume that the mantle and crust heat flux is proportional to the average surface heat flux. Pollack and Chapman (1977) argued that mantle heat flux represents 40% of the regional average surface heat flux. Despite the fact that their measures were based on a... | 10.1186/2193-1801-2-513 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Study of the equilibria The basic reproductive number of a disease, R 0 , is the expected number of secondary cases caused by one infected individual introduced into a susceptible population [40]. A disease is expected to spread only if R 0 is greater than unity. We calculated R 0 in our model using the Next Generatio... | 10.1371/journal.pcbi.1003039 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Stochastic analyses To assess the effect of population structure on the persistence of the disease, we use a stochastic version of our model without resistant rats (system (S1. 1) in the Supporting Text S1), based on the Gillespie algorithm [47] that is implemented in the GillespieSSA R package [48]. It simulates a ... | 10.1371/journal.pcbi.1003039 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We are grateful to the staff of the Plague Laboratory of the Institut Pasteur de Madagascar and to the Malagasy Health Ministry who largely contributed to the acquisition of the biological data that were used in the model, and to Alexandre Dehne-Garcia for his help with the computing cluster of the ... | 10.1371/journal.pcbi.1003039 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As for data collection methods, legal and literature research, document analysis, informal interviews with experts and informed participants (such as judges, ICT and administrative personnel and lawyers etc. ) as well as on-site observations have been carried out by the authors. In particular, the direct involvement of... | 10.18352/ulr.211 | article | en | 2,013 | true | false | false | false | Social Sciences | https://openalex.org/fields/33 |
cc-by | Technically, it is a webbased service retrieving data in the courts' local Oracle databases, using Microsoft Visual Studio. NET technology. Users have voiced their strong satisfaction with Sagace: the service was used in 95% of cases during the first year, each case file being visited on 2 or 3 occasions. By the end of... | 10.18352/ulr.211 | article | en | 2,013 | true | false | false | false | Social Sciences | https://openalex.org/fields/33 |
cc-by | 12 ± 0. 06 Pg C yr -1. There is insufficient data available to provide a quantitative assessment of interannual variability or long-term trends in CO 2 flux in the Arctic, although the dynamic nature of the region suggests that the former would be relatively large. Speculation over the future trend of the carbon flux i... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Further, it is critical to distinguish whether the significant decadal climate variability in this region is responsible for observed changes, as opposed to long-term trends. McKinley et al. (2011) addressed these issues by using an updated pCO 2 database (Takahashi et al. , 2009) to estimate pCO 2 trends in three N... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Methods Consistent with the RECCAP methodology, we use global "Tier 1" methodologies for our primary analysis (Canadell et al. , 2011). These are sea-air CO 2 fluxes from (1) a sea surface pCO 2 climatology, (2) ocean inversions, (3) atmospheric inversions, and (4) ocean biogeochemical models. Additionally, we use flu... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The gas transfer velocity k was calculated using the wind formulation by Wanninkhof (1992) with bomb 14 C corrections by Sweeney et al. (2007). Wind speed data, taken from the 6-hourly CCMP Wind Vector Analysis dataset (Atlas et al. , 2011) , were provided for the RECCAP project (Wanninkhof et al. , 2012 ). The so... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | f CO 2 was then computed as sea surface pCO 2 minus atmospheric pCO 2. It is worth noting here that the non-ideal behavior of CO 2 gas is corrected for in f CO 2 ; the f CO 2 is generally indistinguishable from the pCO 2 , provided atmospheric f CO 2 is used in the former. Uncertainty is estimated as 50 % of the region... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 4a ), yet is not found in the other Tier 1 methodologies. The spatial mean seasonal cycles of the CO 2 flux densities [mol m -2 yr -1 ] for each region are shown in Fig. 5 for Tier 1 methodologies: pCO 2 climatology, median of atmospheric inversions, and median of ocean biogeochemical models; additionally, we include ... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | This pattern is consistent with detailed studies in the subpolar gyre (Chierici et al. , 2009; Olsen et al. , 2008; Rödenbeck et al. , 2012; Watson et al. , 2009). However, the mean SOCAT MPR sink is much lower than that of the other methodologies (Fig. 3b ). It should be noted, however, that the SOCAT MPR only extend... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The spread of 2007 ) have been added to the ocean model estimates as required (described in text). Uncertainty is the median absolute deviation for the atmospheric inversions and ocean models, 50 % of the mean for the pCO 2 climatology and SOCAT MPR, the mean annual uncertainty for the pCO 2 database trend, and the... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2009) , SOCAT MPR and pCO 2 database estimates are derived. climatology (light blue), atmospheric inversions (black), and ocean biogeochemical models (magenta), SOCAT MPR (green), pCO 2 database (cyan), and at the BATS and ESTOC sites in the North Subtropics (dark blue and red, respectively). Shading indicates the sp... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Interannual variability (IAV) Figure 6 shows the low-frequency IAV and trends for Tier 1 methodologies for the atmospheric inversions, ocean biogeochemical models, and the pCO 2 database. High-frequency IAV can be found in the Supplement. Note that fluxes at BATS and ESTOC in [Pg C yr -1 ] assume the same flux intens... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The integrated Arctic/Atlantic regional sink varies by ±0. 055 Pg C yr -1 for the atmospheric inversions, ±0. 029 Pg C yr -1 in the ocean biogeochemical models, ±0. 015 Pg C yr -1 in the SOCAT MPR, and ±0. 046 Pg C yr -1 in the pCO 2 database. Correlation of the low-frequency interannual variability is presented in Tab... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Linear trends of the sea-air CO 2 flux Table 8 presents the linear trends of the sea-air CO 2 flux for 1995-2009 in each region from the atmospheric inversions, ocean biogeochemical models, and observation-based trends from the pCO 2 database. The SOCAT MPR is not included as its time-period is shorter than this. For... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The strong increasing trend for the pCO 2 database is dominated by the trend in the South Subtropics where data are extremely limited. Even in other regions, the pCO 2 database method suggests the largest trends, and these should be considered upper-bound estimates for the trends because this approach estimates the flu... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2008; Takahashi et al. , 2009; Watson et al. , 2009). Estimates of the seasonal cycle of the CO 2 flux in the North Subpolar region agree between the pCO 2 database and the ocean biogeochemical models, but include a significant CO 2 efflux in the summer that is a subtropical, temperature-driven signal. The RECCAP Nor... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | We recommend that future assessments use regional boundaries that are defined by biogeochemical provinces (McKinley et al. , 2011; Sarmiento et al. , 2004) as opposed to lines of latitude. Interannual variability in the North Subpolar region is small, ranging from 0. 004 to 0. 016 Pg C yr -1 (Table 6 ). There is lim... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2002; Santana-Casiano et al. , 2007). Statistically significant negative linear trends are found for the sea-air CO 2 flux from 1995 to 2009 (Table 8 ) as determined by the atmospheric inversions, ocean biogeochemical models, and the pCO 2 database, indicating a longterm increase in the CO 2 sink. This is in contras... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Conclusions We have summarized and compared sea-air CO 2 fluxes estimated for the Atlantic and Arctic across many realizations of the dominant methodologies presently in use to quantify regional and global carbon budgets: pCO 2 climatology, ocean inversion, atmospheric inversions and ocean biogeochemical models. Origin... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Correlations of seasonal cycle for each region and each methodology. Significant correlations (p < 0. 05) are in bold. (a) Arctic pCO 2 climatology Atmospheric inversions Ocean models SOCAT MPR pCO 2 database. | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Linear trends of the spatially integrated sea-air CO 2 flux for each region and whole Arctic + Atlantic, 1995 to 2009 [Tg C yr -1 decade -1 ], for the atmospheric inversions, the ocean biogeochemical models and the pCO 2 database. Trends are a linear fit to the low-frequency median flux IAV (i. e Fig. 6), with 2σ confi... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements. U. Schuster and G. A. McKinley contributed equally to this manuscript and should be considered as joint first authors. We thank P. Canadell , P. Ciais , C. Le Quéré , and C. Sabine for coordinating the global effort of RECCAP. We thank captains, officers, and crew of all ships on which measure... | 10.5194/bg-10-607-2013 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 14 0. 30 -0. 06 SOCAT MPR 1 0. 08 0. 02 0. 35 0. 20 pCO 2 database 1 0. 20 0. 49 0. 11 NAO 1 0. 17 -0. 35 BATS 1 0. 26 (d) Equatorial Atm. inversions 1 0. 40 0. 39 -0. 39 -0. 51 Ocean models 1 0. 72 0. 13 -0. 43 SOCAT MPR 1 0. 06 0. 11 pCO 2 database 1 0. 35 (e) South Subtropics Atm. inversions 1 0. 56 -0. 50 -0. 31 0.... | 10.5194/bg-10-607-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Bioassays Guidelines for test procedures and interpretation of results are available from the WHOPES 3 (see http://www. who. int/whopes/resistance/en/). It is important that the mosquitoes used for the bioassays are standardized for age, sex and physiological status as all of these can affect the outcome of the tests. ... | 10.5772/56117 | review | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The WHO/AFRO African Network for Vector Resistance was established in 2000 and amongst its objectives was the important goal of improving the dissemination of resistance data. Accordingly a database was established to store the results of resistance monitoring activities by the African Network for Vector Resistance (AN... | 10.5772/56117 | review | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | org/ir/; MARA http://www. mara. org. za; Arthropod Pesticide Resistance Database, http:// www. pesticideresistance. org. ; and IR mapper, http://www. irmapper. com. | 10.5772/56117 | review | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 0 LLINs was initiated in one of the most affected island provinces, Karuzi [225]. Initially, one round per year of pyrethroid-IRS was carried out in all human dwellings and cattle sheds before the seasonal increase in transmission. LLIN distribution preceded the first IRS round in the same year. The S-form of An. gamb... | 10.5772/56117 | review | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Considered time step Figure 1 : Scheme explaining the nature of the series we study and the procedure used to obtain them. For each time window, we observe the last trade (trades are dashed vertical lines, randomly spaced) and consider the bid and ask prices immediately before the transaction (blue and red large point... | 10.1080/14697688.2012.723821 | article | en | 2,012 | true | false | false | false | Economics, Econometrics and Finance | https://openalex.org/fields/20 |
cc-by | The paper is organized as follow. In section 2 we present the dataset we use for the study, together with the sampling rules. In section 3 the main statistical objects (autocorrelation and Hurst exponent) are presented and discussed. Section 4 is devoted to the explanation of the tools and procedures we follow looking ... | 10.1080/14697688.2012.723821 | article | en | 2,012 | true | false | false | false | Economics, Econometrics and Finance | https://openalex.org/fields/20 |
cc-by | Data set The original data set consists of all trades registered in the primary markets of the analyzed stocks. The data are stored in the Thomson Reuters TRTH data base made available to the Chair of Quantitative Finance by Thomson Reuters and BNP Paribas. For the purpose of our study, we extract from the TRTH databas... | 10.1080/14697688.2012.723821 | article | en | 2,012 | true | false | false | false | Economics, Econometrics and Finance | https://openalex.org/fields/20 |
cc-by | Acknowledgement F. A. would like to acknowledge that the idea of optimizing a basket of stocks with respect to statistical properties arose from a collaboration with Laurent Jaillet while they were colleagues at CAI Cheuvreux. | 10.1080/14697688.2012.723821 | article | en | 2,012 | false | false | true | false | Economics, Econometrics and Finance | https://openalex.org/fields/20 |
cc-by | Quantitative PCR. For detection of viral RNA, we used the one-step real-time RT-PCR upE assay (30) ; for the detection of mRNA, we used an ORF1-and ORF5-specific SYBR green assay. See SI Materials and Methods for detailed information. Microarray Data and Functional Analysis. RNA extracted from lung tissue samples and ... | 10.1073/pnas.1310744110 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | ACKNOWLEDGMENTS. We thank Drs. Bart Haagmans and Ron Fouchier at the Erasmus Medical Center for providing Middle East respiratory coronavirus isolate HCoV-EMC/2012; Ralph Baric at the University of North Carolina at Chapel Hill for subgenomic RNA primer sequences; Laura Baseler , Tina Thomas , Dan Long , a... | 10.1073/pnas.1310744110 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Motivation: Cancer cells are often characterized by epigenetic changes, which include aberrant histone modifications. In particular, local or regional epigenetic silencing is a common mechanism in cancer for silencing expression of tumor suppressor genes. Though several tools have been created to enable detection of hi... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Results: We present HMCan (Histone modifications in cancer), a tool specially designed to analyze histone modification ChIP-seq data produced from cancer genomes. HMCan corrects for the GC-content and copy number bias and then applies Hidden Markov Models to detect the signal from the corrected data. On simulated data,... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , 2010). Many tools have been developed to facilitate the analysis of histone modification data obtained with the ChIP-Seq technique. Some tools are designed to detect narrow peaks of type of H3K4me3 (Kharchenko et al. , 2008; Rozowsky et al. , 2009; Zhang et al. , 2008). Other methods are able to identify epigenetic ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | GC-content is known to influence read depth in both Illuminaand SOLiD-generated datasets (Boeva et al. , 2011; Dohm et al. , 2008). A possible difference in GC-content dependencies between ChIP and control datasets can result in false predictions of enrichment in histone modification marks (Chen et al. , 2012). Here ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Only HMCan and CCAT did not show copy number bias. Separately, on an experimental ChIP-seq dataset of H3K27me3 in a bladder cancer cell line, HMCan provided better results than CCAT. | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | HMCan algorithm The HMCan workflow consists of (i) estimation of the copy number profile using a window approach on the control dataset (usually, input DNA), (ii) calculation of the density profile, (iii) normalization of the density profile by copy number, GC-content and background signal and (iv) application of HMMs ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data profile construction Reads of ChIP and control datasets are transformed into density profiles. To construct the profiles, the reads are extended from read starts to the length of DNA fragments. Similarly to FindPeaks, we use the triangular distribution for read extension (Fejes et al. , 2008). This method allows ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data size correction Assuming that the ChIP dataset contains N reads and the control dataset contains M reads, the ChIP density profile is multiplied by the ratio between these numbers (M/N). | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Initial peak calling To calculate the correct GC-content profile on the ChIP data and correctly estimate the initial parameters of HMM, preliminary peak (enrichment signal) calling should be applied to serve as a guide for both operations. A one-sided exact Poisson test is used to label whether a bin belongs to a peak ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We denote the expected density for each gc value as gc , defined as: gc ¼ D gc =N gc : ð1Þ We will denote the average expected density along the genome by , defined as: ¼ P gc D gc P gc N gc : ð2Þ Fig. 1. HMCan framework. HMCan initially estimates copy numbers from control data and it builds density profiles for both l... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Applying the described method to the control data is straightforward, as the control data are not supposed to contain any signal. In the case of ChIP data, the process is trickier because the signal contained in the ChIP data may interfere with the GC bias, e. g. some histone modifications can occur more frequently in ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The transition probabilities of HMM are estimated by counting four possible combinations of the states. The emission probabilities are derived from the distributions of the normalized densities over the peak and nonpeak data independently. | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Evaluation on simulated data To investigate the performance of HMCan on cancer samples, we constructed a simulated ChIP-seq dataset for a fictional histone mark. The signal covered multiple regions across chromosome 1 (human genome, hg19), with each region being of length from 1 to 20 Kb. These regions comprised 5% of ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As sequencing depth depends on GC-content, we used the experimentally observed GC-content dependency function from the ENCODE dataset for the MCF-7 cell line (input and H3K9me3). The code for read generation together with parameters used and necessary files can be found at the HMCan webpage (package 'GenerateReadsChIP-... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , 2010) , MACS (Zhang et al. , 2008) and SICER (Zang et al. , 2009) (Fig. 2 ). CCAT applies an iterative method to estimate the noise-to-signal ratio in ChIP-seq and control data based on a linear model. MACS shifts the reads toward the fragment centers and uses a dynamic Poisson model that is able capture the mean... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Evaluation on H3K27me3 data To assess the performance of HMCan on real data, we generated ChIP-seq dataset for trimethylation of lysine 27 on histone H3 (H3K27me3) for the CL1207 human bladder transitional cell carcinoma cell line (see Materials and Methods). We compared HMCan and CCAT on this dataset. As the MACS and ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | g. MACS, CCAT or SICER) and may require up to 1 h on a standard PC (Supplementary Table S4 ). Running iterative HMMs is the most time-consuming step. However, we believe that the greater accuracy of HMCan demonstrated in this study compensates for a longer run time. In some cases, it might be interesting to detect dif... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | CONCLUSION HMCan was specifically developed to analyze histone modification data obtained for cancer genomes. Cancer genomes are characterized by frequent copy number alterations: gains and losses of large regions of chromosomal material. The designed algorithm explicitly corrects for copy number alterations, and thus ... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | HMCan accepts the most common alignment formats: SAM/BAM and BED, and outputs predicted regions in BED and WIG formats. We successfully applied HMCan on both simulated and experimental data. On simulated data, we demonstrated HMCan's higher accuracy in signal prediction compared with the tools designed for normal genom... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank A. Zinovyev for helpful suggestions and critical comments and K. Bleakley for english proofreading. Funding: Project ABS4NGS , funded by the ' Bioinformatique 2011' call, action 'Sante´Biotechnologie' of Investissement d'avenir and Agence Nationale de la Recherche , under contr... | 10.1093/bioinformatics/btt524 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | (2010b) and Boselli et al. (2012) , while the dust properties of the early-type systems in Smith et al. (2012a). Some of these works are already taking advantage of the spectroscopic data presented here. The spectroscopic data presented in this work, as well as those collected at other frequencies, will be made avai... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | cluster, to loose groups and fairly isolated systems. As defined, the present sample is ideal for any statistical study of the mean galaxy population of the nearby universe. This paper is focused on the late-type galaxies of the sample. We present new spectroscopic observations of 134 galaxies 2 , and we combine this ... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | For those few objects with angular size larger than the size of the slit, the drift was done in the direction perpendicular to the major axis. Drifting was obtained by slewing manually several times the telescope between two extreme positions checked on one offset star or on the galaxy itself. Not unexpectedly spectra ... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Data reduction In order to form a homogeneous dataset with the existing observations of Gavazzi et al. (2004) , we apply the same data reduction method to the new observations presented in this work. The reduction of the observations from the raw, two-dimensional images into calibrated, one-dimensional spectra is perf... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 1%, and this increases to 3. 6% at the blue end (λ < 5500Å). The largest discrepancy occurs at λ < 4000 Å, where the difference in one object reaches ∼ 20 %. In the red (λ > 6800 Å) the differences are 15%. Although we are limited by the low number of objects for comparison, it appears that the largest discrepancies oc... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The relative scatter of the red portion (λ > 5500Å) of the spectrum is around 5. 7%, and it increases to 8. 9% at the blue end (λ < 5500Å). The Moustakas et al. (2010) spectra are typically redder than our spectra. The differences between our and the Moustakas et al. (2010) spectra reach ∼ 60 % at λ ∼ 4000 Å and 35... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | We further test our spectrophotometric accuracy by comparing magnitudes synthesized from our spectra to the recently published broadband photometry from Cortese et al. (2012a). Synthesized spectroscopic gr colours were obtained by deconvolving the continua with the profiles of the g and r SDSS filters. Figure 4 show... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 38 Å). Variations with the metallicity are at most of 0. 3 Å, thus 10 % of the E. W. Hα abs. Sandage model star formation histories give values of E. W. Hα abs in the range 2. 3-3 Å, slightly lower than those predicted by the Boissier & Prantzos models (2. 6 E. W. Hα abs 3. 5 Å) in the range of τ and M star expected fo... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Comparison with integrated spectra A few HRS galaxies have been observed using the same drift scan technique adopted in this work by Kennicutt (1992a; 4 objects) , Jansen et al. (2000; 5) , Moustakas & Kennicutt (2006; 16) and Moustakas et al. (2010; 8). Their integrated spectroscopic data are given in Tables 10 ... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | g. Elbaz et al. 2011; Smith et al. 2012b ). We thus use either of the two parameters in the following analysis. Gas metallicities, 12+log(O/H), are derived using the set of data described in this paper as indicated in Paper II (Hughes et al. 2012). We follow the conversions of Kewley & Ellison (2008) for five differ... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Interferometric data, mainly taken in order of preference from VIVA (Chung et al. 2009a) , Cayatte et al. (1994) and Warmels (1986) , are used to measure HI gas column densities (in M⊙ pc -2 ). For the VIVA galaxies, column densities are determined using the isophotal HI radius 14. For the sake of homogeneity, we n... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Line diagnostic Spectral line emission is often used to characterise, using different diagnostic diagrams, the nature of the emitting source. The set of data in our hands allow us to construct two of the three mostly used diagnostic diagrams, the [Oiii]λ5007/Hβ vs. [Nii]λ6584/Hα and the [Oiii]λ5007/Hβ vs. [Sii]λ6717-67... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The contribution of the nuclear emission to the integrated spectrum is thus more important in HI-deficient objects than in gas rich systems. Despite the contribution of the AGN to the integrated spectra is minor, objects hosting an active nucleus should be removed in any study of the physical properties of the ISM sinc... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Blue symbols are for galaxies with a normal HI gas content (HIde f ≤ 0. 4), red symbols for HI-deficient objects (HIde f > 0. 4). Filled symbols are for galaxies hosting an AGN. The black cross shows the typical uncertainty on the data. The blue and red lines indicate the best fit to the data for HI-normal and HI-defic... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Spearman correlation coefficients ρ of the relations between the Balmer decrement and the underlying Hβ absorption and the physical parameters for all galaxies (Fig. 14 ). Blue symbols are for galaxies with a normal HI gas content (HIde f ≤ 0. 4), red symbols for HI-deficient objects (HIde f > 0. 4). Filled symbols... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 2000 , Witt & Gordon 2000) , and the slope of the UV spectrum β (Meurer et al. 1999 , Calzetti et al. 2000 , Calzetti 2001 ). The far-IR to UV flux ratio has been generally measured using FUV GALEX and either IRAS or Spitzer IR Fig. 16. The relationship between the Balmer decrement C(Hβ) and the UV slope β GALEX deter... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Blue symbols are for galaxies with a normal HI gas content (HIde f ≤ 0. 4), red symbols for HI-deficient objects (HIde f > 0. 4). Filled symbols indicate galaxies hosting an AGN. The black cross shows the typical uncertainty on the data for a galaxy of equivalent width of 5 Å. of the observed galaxies. The correlation ... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | We want to thank the OHP telescope operators J. Taupenas et J. P. Troncin for their invaluable support during the observations and the PNCG for their generous allocation of time at the OHP telescope. A. B thanks the ESO visiting program committee for inviting him at the Garching headquarters for a two months staying. W... | 10.1051/0004-6361/201219200 | article | en | 2,012 | true | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | For crystallization, we reconstituted and purified telomeric DNA complexes with all three binding constructs, but only one (G233-A345) yielded crystals when reconstituted with a duplex telomeric DNA (5 0 -cTGTTAGGGTTA GGGTTAG-3 0 and 3 0 -ACAATCCCAATCCCAATCt-5 0 ) similar to the one present in the crystal structures of... | 10.1038/emboj.2013.105 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Again, depletion of both HOT1 and TCAB1 led to shorter telomere length with a shortening of on average 700 and 600 bp, respectively. Given the short nature of telomeres in this cell line (on average, 5 kb measured by STELA) and the substantial contribution of variant repeats and subtelomeric DNA to this value (Aubert ... | 10.1038/emboj.2013.105 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | MS data acquisition In-gel digestion and MS analysis was performed essentially as previously described by Butter et al, 2010. Peptides were desalted on StageTips and analysed by nanoflow liquid chromatography on an EASY-nLC system from Proxeon Biosystems coupled to a LTQ-Orbitrap XL or a Orbitrap-Velos (Thermo Electron... | 10.1038/emboj.2013.105 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | MS spectrum and data analysis The raw files were processed with MaxQuant (Cox and Mann, 2008) and searched with the Mascot search engine (Matrix Science) against IPI human v3. 37 protein database concatenated with a decoy of the reversed sequences. Carbamidomethylation was set as fixed modification, while methionine ... | 10.1038/emboj.2013.105 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 5) and 100 mM KSO 4. For data collection, crystals were cryoprotected by soaking in a mother liquor supplemented with 20% glycerol and was flash-frozen in liquid nitrogen. Diffraction data were collected at the PXII beam line of the Swiss Light Source (SLS; Villigen, Switzerland) and processed using XDS (Kabsch, 1993)... | 10.1038/emboj.2013.105 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Telomeric quantitative FISH For metaphase preparation, cells were incubated for 4 h with 200 nM nocodazole in order to induce mitotic arrest. A hypotonic shock was achieved in 0. 03 M sodium citrate at 371C for 40 min. Cells were fixed in an ethanol/acetic acid solution (3:1) and washed three times in this fixing reage... | 10.1038/emboj.2013.105 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements We thank members from the Buchholz, Mann and London ˜o laboratories for helpful comments on the manuscript, Charlott-Amelie Teutsch , an internship student selected by the Fo ¨rderverein der Biologieolympiade e. V. , for performing DNA pull-down experiments, Sebastian Rose for technical assistanc... | 10.1038/emboj.2013.105 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Since the 1980s several spaceborne sensors have been used to retrieve the aerosol optical depth (AOD) over the Mediterranean region. In parallel, AOD climatologies coming from different numerical model simulations are now also available, permitting to distinguish the contribution of several aerosol types to the total A... | 10.5194/amt-6-1287-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
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