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cc-by | This curve corresponds well to the computational results presented in the paper of Fedosov et al. [4] , who report a maximal axial diameter of 16 mm and a minimal transversal diameter between 4 and 5 mm at a force of 200 pN, as well as experimental data by Suresh et al. [12]. RBC relaxation. In order to validate the di... | 10.1371/journal.pcbi.1003267 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | BS acknowledges the Agency for Innovation by Science and Technology in Flanders (IWT) for financial support (www. iwt. be). The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme ( FP7/2007-2013)/ERC Grant Agreement Nu 3... | 10.1371/journal.pcbi.1003267 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements The authors would like to thank BRE Global, UK, and FM Global, USA , for their financial support to this research. | 10.1016/j.firesaf.2013.08.015 | article | en | 2,013 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | Atmospheric CO 2 observations Atmospheric surface CO 2 observations are obtained from a global network of more than 100 sites where CO 2 is measured either continuously (∼ 50 sites), or via discrete flask air samples (weekly; ∼ 100 sites). The current network is part of an international effort that started 55 yr ago wi... | 10.5194/bg-10-6699-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | CO 2 observing networks Previous work (Law et al. , 2003; Patra et al. , 2006; Gurney et al. , 2008) has shown that the fluxes estimated in the inverse approach can be very sensitive to the composition of the CO 2 observing network used (Fig. 1 ). This is particularly true for parts of the world where there are few o... | 10.5194/bg-10-6699-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Note that the two Carbon-Tracker estimates (CT2011_oi, CTE2013) assimilate all data that were positively quality controlled by the inverse modelling team (i. e. removing outliers). The list of the observation sites and data selection criteria used in each of the participating inversion systems can be found in the Suppl... | 10.5194/bg-10-6699-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | However, even with the "fossil fuel" correction, the global annual totals show significant differences, up to 1 Pg C yr -1 , among the different inversions in particular years. The differences are not systematic and reflect differences between atmospheric transport mixing properties, especially the mixing of surface fl... | 10.5194/bg-10-6699-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | These differences are also seen in the prior fluxes (Supplement, Fig. S6 ) used by most inversions, which are mainly based on the CASA model (Randerson et al. , 1997). It is worth noting that the inversions that do not use this prior (MACC-II, LSCEa, JENA) nevertheless largely agree with the other inversion estimates.... | 10.5194/bg-10-6699-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements. We first thank all PIs of the atmospheric stations whose data are the principal component of the atmospheric inversions and those who maintain instruments and collect samples (including those whose data is included in ObsPack). We also thank those who put significant work into providing atmospheric da... | 10.5194/bg-10-6699-2013 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | (i) x þ 1; y; z; (ii) x À y; x À 1; Àz þ 1; (iii) Ày þ 1; x À y À 1; z; (iv) Àx þ y þ 1; Àx; z; (v) Àx þ y þ 1; Àx þ 1; z; (vi) Ày þ 1; x À y; z; (vii) x; y; Àz þ 3 2 ; (viii) Àx þ 1; Ày; Àz þ 1; (ix) y þ 1; Àx þ y þ 1; Àz þ 1; (x) Ày; x À y; Àz þ 3 2 ; (xi) x À 1; y; z. Intensity data were collected on the Nonius Kapp... | 10.1107/s1600536813025907 | article | en | 2,013 | true | false | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | 1997 , Theurillat & Guisan 2001 , Schumacher & Bugmann 2006 , Gehrig-Fasel et al. 2007 , Wastl et al. 2012) we regard the investigation of the human-caused fire ignition as substantial for a better understanding of fire danger for Austrian forests and the goods and services they provide. The objective of this study is... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Study area and fire database Austria is a central European country covering 83 855 km 2 and a population size of 8. 47 million people. Austria is a largely alpine country (68%) with a temperate to alpine climate. Average temperatures range from -10 °C in winter to 20 °C in summer. Austria has a total number of 2357 mun... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Wildfire records have been obtained from municipalities, fire brigades, the OEBB (Austrian Railway Company) as well as the Federal Ministry of Agriculture and Forestry, Environment and Water Management (BMLFUW). The database includes information for each fire record on geographical coordinates and other characteristics... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Lightning caused fires have been analyzed in a separate study and are not part of this dataset (Müller et al. 2013). Fires in agricultural areas have not been considered. | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 1995). Model events with binary or dichotomous variables -such as the presence or absence of fire ignition -are best described by means of logistic regression. Forward stepwise logistic regression has been chosen for this study, since the interest was on identifying the significance of a group of predicting variables a... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Ignition and non-ignition points were coded in a binary format (0: no fire; 1: fire) representing the dependent variable fire ignition. In order to be able to test the final model, 100 fire ignition points and 100 no-fire ignition points were selected randomly from each of the five datasets for validation, resulting in... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | g. , agricultural area, intensity of agricultural operations); • Factors related to forest management (e. g. , density of forest area, forest roads, forestry operations, storm blow-down salvage harvesting); • Factors related to infrastructure and their density (e. g. , roads, railroads). Tab. 1 shows all independent so... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Model construction In order to eliminate multicollinearity between the variables selected for this study, the Pearson correlation analysis has been conducted for all five datasets independently. All variables with a correlation higher than 0. 5 were not further considered for the model building procedure. Five differen... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Even though other levels and approaches for assessing probability could be used (see Castedo-Dorado et al. 2011 ) the cut-off point 0. 5 -the midpoint of the logistic function -was chosen for this study, since it is the one most extensively used in other comparable studies (Jamnick & Beckett 1988 , Vasconcelos et al.... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Results The best logistic model to analyze the influence of socio-economic factors on forest fire ignition has been selected out of the five models computed (Tab. 2 and Tab. 3) in order to identify the best combination of explaining variables. Railroad density (RAIL/ TOTAREA), density of forest roads (FOR- ) computed f... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 8 % for the model building dataset and 63. 0 % for the validation dataset). Fig. 1 shows the probabilities distribution of the logistic model for the "fire" and "no fire" events from the model data set (Fig. 1a ) and the validation data set (Fig. 1b ). In the model data set, a left-sided distribution was obtained, whe... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Two maps have been generated with the selected model with the aim of illustrating model predictions for all municipalities which data were included in this analysis. Fig. 5 displays the spatial distribution of the forest fire danger at the level of municipalities, and Fig. 6 reports the model prediction for the fores... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Discussion The logistic regression carried out in this study provides a model based on a set of socio-economic factors potentially affecting forest fire ignition, in addition to the driving factors of climate and fuel. The logistic model obtained correctly classified 63. 1 % of the calibration and 59. 5 % of the valida... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Although a high average density of forest fire ignitions per forest area occurs in the highest fire danger class, the probability of fire occurrence was found to be higher in districts further away from areas densely populated or with a high density of infrastructure. According to Brosofske et al. (2007) the explanat... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2002). First attempts using Geographic Weighted Regression have provided interesting results in the European Mediterranean (Koutsias et al. 2005 (Koutsias et al. , 2010)). The logistic probabilities would allow human factors to be integrated with meteorological factors (Arpaci et al. 2013 ) and fuel conditions. Stati... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2011 , Eastaugh & Vacik 2012 ). For the above reasons and the overall small dataset available, in this study we did not consider the causes underlying forest fire ignition in Austria. Therefore, the analysis carried out can be seen as the first step of this research. | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Tab. 5 -Classification table for model building dataset and validation dataset. Percentage of correctly classified: p=0. 5. | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments This research has been partly conducted within the frame of the Austrian Forest Research Initiative (AFFRI) , which is funded by the Austrian Science Funds (FWF) -reference number L539-N14 , and within the European Project ALP FFIRS (Alpine Forest Fire Warning System ), which is funded by the Euro... | 10.3832/ifor0936-006 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Tab. 5 -Classification table for model building dataset and validation dataset. Percentage of correctly classified: p=0. 5. Dataset Class Predicted No fire Fire % Correct (a) Model building data Observed No fire 622 233 72. 7 Fire 392 463 54. 2 Total percentage 63. 4 (b) Validation dataset Observed No fire 63 37 63 Fir... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Evaluation of the fire danger map classification with the validation dataset. Change in -2LL (iv) Regression Coefficient B (v) Global Score (Sum) RAIL/TOTAREA 1 1 1 5 1 8 HIKETRAIL/TOTAREA 3 2 1 2 2 9 FORROAD/TOTAREA 2 3 1 3 3 11 AGRPAST 4 4 1 4 4 16 Tab. 7 -Fire danger classes Forest area (%) Ignitions observed (%) Av... | 10.3832/ifor0936-006 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | ACKNOWLEDGEMENTS The authors thank Be´ne´dicte Michel and Ivan Matic for insightful discussions. They thank France-Audrey Peltier for the V. cholerae over-expression library and the Institut Pasteur Microbiology 2012 Master students for the genetic screening and identification of the mfd mutant in neomycin and ... | 10.1093/nar/gkt1259 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The paper is organized as follows. Section 2 provides a description of the COSMIC RO data set and the methodology used. The results are described in Sect. 3, followed by a discussion in Sect. 4 and a summary of conclusions in Sect. 5. | 10.5194/acp-13-6391-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | , 2011). The data include latitude and longitude of the tangent point, pressure, temperature, water vapor pressure, refractivity and altitude of the perigee above sea level. The data in NetCDF format are available from the CDACC (COSMIC Data Analysis and Archive Center) website hosted by the University Corporation for ... | 10.5194/acp-13-6391-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. The COSMIC RO data used in this study are those available from the Data Analysis and Archive Center (CDAAC) of the University Corporation for Atmospheric Research (http://cdaac-www. cosmic. ucar. edu/cdaac/). The work was supported by the French Agence Nationale de la Recherche (ANR) Tro- Pico p... | 10.5194/acp-13-6391-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Grazing-incidence X-ray Diffraction: The grazing-incidence X-ray diffraction (GIXD) measurements were done at beam line 11-3 at the Stanford Synchrotron Radiation Laboratory. The measurements were done with a beam energy of 12. 735 keV and an incidence angle of 0. 12°. The samples were enclosed in a He environment to l... | 10.1002/adma.201300027 | article | en | 2,013 | true | false | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | Acknowledgements The authors would like to acknowledge Scott E. Watkins ( CSIRO Materials Science and Engineering, VIC 3169, Victoria, Australia ) for PESA measurements. This work was in part carried out under the EPSRC Project EP/F056710/1 , EP/G037515/1 , EC FP7 ONE-P 245 Project 212311 and DPI Grant 678 , w... | 10.1002/adma.201300027 | article | en | 2,013 | false | false | true | false | Engineering | https://openalex.org/fields/22 |
cc-by | A final extension step was carried out for 5 min at 72°C. The amplified products were detected by electrophoresis as above. Negative control was included in each nested PCR analysis to monitor contamination and false-positive amplification. To rule out amplicon carry-over, nucleotide-free water negative control was use... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Sequence alignment and phylogenetic inferences All sequences obtained were aligned using ClustalW (v. 1. 8. 1 in BioEdit v. 7. 0. 5. 3. ) [50]. Maximum Likelihood (PhyML) tree reconstruction was conducted from the 16S rRNA aligned sequences (457 nucleotides) of ticks. For each Borrelia of soft tick, the FlaB gene (FLA,... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | pasteur. fr/cgi-bin/portal) using NNI (Nearest Neighbor Interchange) branch swapping and 100 bootstrap replicates [53]. Molecular distances with standard error estimate were conducted using the Kimura 2-parameter model among Ornithodoros 16S sequences and among Borrelia concatened IGS-FLA sequences as used in other ph... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | turicata (GenBank acc. no. L34327), and O. parkeri (GenBank acc. no. EU009925) were treated as outgroups. Borrelia crocidurae (GenBank acc. no. GU350723 and NC017808), B. duttonii (GenBank acc. no. DQ000279 and DQ346833), B. hispanica (GenBank acc. no. GU350718 and GU357614), B. merionesi (GenBank acc. no. JX257047 and... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | The holotypes and paratypes of the new species are deposited at the Institut Royal des Sciences Naturelles de Belgique, Brussels, Belgium (IRSNB). Sequences obtained from a segment of leg of one or several specimens of the type series are deposited in GenBank. | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Diagnostic SNPs of Ornithodoros ticks To allow a rapid molecular identification of Ornithodoros species, we highlighted 25 single nucleotide polymorphisms among the 9 species in 16S rRNA sequence dataset (Table 6 ). We detected at least one diagnostic SNP for each species, i. e. at a given position of the 16S sequence... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgments We thank Jean-Louis Camicas ( IRD, Montpellier ) for assistance in tick determination and Stephen C. Barker ( University of Queensland, Brisbane ) for useful comments on a first draft of the manuscript. We thank all those in Dakar, Bamako, Ouagadougou, Niamey, NDjamena, Yaoundé, Cotonou, Lomé, Lamt... | 10.1371/journal.pone.0078473 | review | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | • O. occidentalis Trape, Diatta, Durand & Renaud, sp. nov. Diatta, Bouattour, Durand, Renaud & Trape, sp. nov. Holotype: IRSNB IG. 32. 280/004/1; ZooBank: urn:lsid:zoobank. org:act:DC0E7B5B-FBC3-4A7B- A223-77E0F2CFF2F5; GenBank: KC311536, KC311537. Holotype: IRSNB IG. 32. 280/002/1; ZooBank: urn:lsid:zoobank. org:act:D... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | 32. 280/003/1; C807-4194-97C7-1FE7CFA3398D; GenBank: KC311545. ZooBank: The four other species identified were: O. erraticus, GenBank: KC311539, KC311540, KC311541, neotype: IRSNB 32. 280/006; O. marocanus, GenBank: KC11533, KC311537, KC311535; neotype: IRSNB 32. 280/007; O. sonrai, GenBank: KC311525, KC311526, KC31152... | 10.1371/journal.pone.0078473 | review | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | In this paper, we critique the methods commonly used in evaluation studies and propose a number of new ideas. The plan of the paper is as follows. Section 2 describes some data from the CMIP5 archive that are used throughout the paper for illustration. Section 3 discusses the choice of performance measure. Section 4 fo... | 10.1002/met.1409 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | In such cases, the adjusted ensemble CRPS will still be unfair. In the case of independent and identically distributed ensemble members that we considered above, however, the convergence holds and the adjusted ensemble CRPS is fair. If there is only one ensemble member (m = 1) then the measures listed above typically c... | 10.1002/met.1409 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements This work was part of the EQUIP project (http://www. equip. leeds. ac. uk) funded by NERC Directed Grant NE/H003509/1. The authors thank Leon Hermanson , Doug Smith and Holger Pohlmann for useful discussion, Helen Hanlon for assistance with obtaining data, and two anonymous reviewers for co... | 10.1002/met.1409 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | However, empirical examples of the relationships between host biodiversity and parasite transmission are still relatively rare, in part because suitable datasets that may allow comparisons are deficient [4]. Further complexities are encountered when the distribution range of a pathogen covers a large number of host co... | 10.1371/journal.pntd.0002045 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Environmental and climate data. Monthly and yearly average rainfall and temperature for China were extracted from the 0. 5 degree [23] gridded dataset of the FAO Global maps (http://www. fao. org/geonetwork). Altitude maps were derived from the Global Land One-km Base Elevation (GLOBE) Project [24]. Using the same g... | 10.1371/journal.pntd.0002045 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data handling and models. Land cover was estimated as the proportion of pixels belonging to a Global Land Cover 2000 category in question within a circular buffer centered at a given pixel. Elevation, yearly rainfall and yearly average temperature, were extracted from a 0. 1 degree gridded dataset of the FAO Global map... | 10.1371/journal.pntd.0002045 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Selected GAMMs were further subjected to Bayesian analysis using the software BayesX [30, 31] which enabled the inclusion of a spatial random effect to account for otherwise unexplained between-pixel spatial autocorrelation. The spatial random effect was modeled as a Markov random field [32, 33] on the 20 km resolu... | 10.1371/journal.pntd.0002045 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments The authors thank Dr. Chen Xingwang , Professors Qiu Dongchuan , Wang Qian , Yang Wen and Xiao Ning ( Institute of Parasitic Diseases, Sichuan Centers for Disease Control and Prevention ) and Professor Mark Danson ( University of Salford ) for their participation and dedication throughout our p... | 10.1371/journal.pntd.0002045 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | This asymmetry in the cause-effect relationships can be used to predict change. Additionally, the statistical estimation of time lags can shed light on cause-and-effect relationships in temporal data. Second, time is uni-dimensional, whereas space has three dimensions. In this respect, strictly temporal patterns are si... | 10.1098/rspb.2012.1931 | review | en | 2,012 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | These patterns would not be expected to occur on unbounded temporal series. For bounded time series, directionality means that the effect of a starting boundary is different from that of an ending boundary. The starting point is an important part of the successional pattern that follows [17]. Moreover, when studying t... | 10.1098/rspb.2012.1931 | review | en | 2,012 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In practice, the study of autocorrelation in space and time typically differs in three ways. First, temporal data are typically collected at constant time intervals, allowing easy calculation of lags between points, whereas spatial variables are often recorded at irregular locations distributed continuously in space, r... | 10.1098/rspb.2012.1931 | review | en | 2,012 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Most statistical methods that are used to forecast future trajectories of biodiversity implicitly assume that the mechanisms driving historical and recent trends continue into the future, albeit with new levels for some covariates. However, drastic changes often involve pressures upon ecosystems, generating novel syste... | 10.1098/rspb.2012.1931 | review | en | 2,012 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Conclusions Availability of long-term, large-scale, high-resolution data is the single most important factor limiting progress in understanding temporal patterns in biodiversity. Given the difficulty of obtaining data from the past, we reiterate the appeal to preserve data and associated metadata in publicly accessible... | 10.1098/rspb.2012.1931 | review | en | 2,012 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Figure2. Tools for assessing temporal autocorrelation. These data examine changes in species richness of a small rodent community over 26 years at the long-term research site in Portal, Arizona run by James Brown, Morgan Ernest and others [50, 51] at control un-manipulated sites. All analysis done in R v. 2. 12. 2 [52... | 10.1098/rspb.2012.1931 | review | en | 2,012 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Experimental Crystal data Data collection: APEX2 (Bruker, 2004 ); cell refinement: SAINT (Bruker, 2004) ; data reduction: SAINT; program(s) used to solve structure: SIR2002 (Burla et al. , 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 for Windows (Farrugia, 2012... | 10.1107/s1600536813011914 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Supplementary data and figures for this paper are available from the IUCr electronic archives (Reference: YK2093). | 10.1107/s1600536813011914 | article | en | 2,013 | true | false | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Computing details Data collection: APEX2 (Bruker, 2004 ); cell refinement: SAINT (Bruker, 2004) ; data reduction: SAINT (Bruker, 2004 ); (Farrugia, 2012) and DIAMOND (Brandenburg & Berndt, 2001) ; software used to prepare material for publication: WinGX (Farrugia, 2012) and CRYSCAL (local program). | 10.1107/s1600536813011914 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Thus, if Bik ubiquitylation process is turned off in the model, only the formation term remains in equation 1 which is now the same for parental and transformed cells, with different initial conditions. This equation can be solved analytically: ½Bik(t)~Bik 0 zk fBik t ð3Þ where Bik 0 stands for Bik initial concentratio... | 10.1371/journal.pcbi.1003011 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Estimating parameters of the mitochondrial apoptosis model Parameters of this model of mitochondrial apoptosis were estimated by fitting experimental data in parental and Src-transformed cells from [5] and integrating biological results from literature. First, we assessed quantitative molar values of considered Bcl-2... | 10.1371/journal.pcbi.1003011 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Confocal microscopy For the analysis of Bik relocalization to mitochondria upon staurosporine exposure, cells were pre-incubated with Mitotracker-red (1:10,000) for 20 min before a 20 min washing in fresh medium. Then, cells were fixed by addition of paraformaldehyde (4%). Mitotracker-red background was removed by a 10... | 10.1371/journal.pcbi.1003011 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mathematical modeling and parameter estimation Matlab ode15s solver was used to solve the systems of ordinary differential equations. Parameter estimation for Bik kinetics model consisted of a least-square approach in which minimization tasks were performed by the CMAES algorithm ( [63] , Text S1). Parameter estimatio... | 10.1371/journal.pcbi.1003011 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We acknowledge the permission from Nature Publishing Group to reprint Figures 2A and3 , which contain images from [5]. | 10.1371/journal.pcbi.1003011 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The work was supported by the Agence Nationale de la Recherche through grant number ANR-09-BLAN-0218 TOPPAZ, by the European Union through the Network of Excellence BioSim ( LSHB-CT-2004-005137 ), the Specific Targeted Research Project TEMPO ( LSHC-CT-2006-037543 ) and ErasysBio+ Circadian and Cell Cycle C... | 10.1371/journal.pcbi.1003011 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome sequencing, assembly and automated annotation In order to identify the genetic bases of our two metal-tolerant mesorhizobia and to use them as references to map sequence reads from the transcriptome data sets, the draft genomes of the two studied strains were first sequenced using half a 454 run (Titanium kit) w... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genome sequences are also available from European Nucleotide Archive under accession numbers CAUM01000001-CAUM01000191 for strain STM 2683 and CAAF010000001-CAAF010000089 for strain STM 4661. The general genome characteristics for the two analyzed strains are listed in Table 1. As expected, CDS located on the plasmids... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | metallidurans CH34 where most metal-responsive genes are plasmidborne [14]. In order to estimate genomic divergence between the two strains, we explored the proportions of homologous CDS as a function of the identity percentage. Homologous genes present in the two strains were retrieved with the comparative genomics p... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | RNAseq analysis, mapping and statistical analyses using DESeq The universal bacterial rRNA subtraction kit (Microbe Express, Ambion) allowed for the removal of most rRNAs. Qualitative analyses of RNA samples prior and after depletion indicated that total RNA was of high quality (RIN values ranging from 7 to 10) and tha... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Interestingly, sequence reads were successfully assigned to all predicted genomic objects, suggesting that all CDS were transcribed and that sequencing was deep enough to cover the full transcriptomes. All read mapping data for STM 2683 and STM 4661 are accessible from the Microscope interface [15]. Using the MicroSco... | 10.1186/1471-2164-14-292 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Because we observed a wide magnitude in the read count numbers per CDS, a logarithmic transformation of these data was performed. A logarithmic base-2 transformation of fold changes was used to represent expression differences. The Additional file 2 reports the descriptive statistics obtained from our quantitative RNAs... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Quantitative PCR on selected genes The reliability of our RNAseq data can be assessed by comparing the differential expression of a set of regulated genes using an alternative approach such as quantitative real time PCR (qPCR). The relative expression of five genes present in both studied microbial genomes was estimate... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 9 was found for both isolates when plotting the log2 (Metal / control) values obtained for the five selected genes using the genomewide RNAseq approach against the qPCR data (Additional file 7C and F). Differences in the amplitude of the deregulation between the two techniques could be attributed to the PCR step used t... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Identification of genes regulated by metals in Mesorhizobium strains STM 2683 and STM 4661 Transcriptional profiles obtained using the genome-wide RNAseq approach was performed on pooled samples. The high reproducibility between treatments, as exemplified by the high correlation factors of read counts and relative expr... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | These products were then purified on a gel to select a size range at 200 pb and enriched by PCR to create the final cDNA library. The efficacy of the library construction was checked in a quality control step that involved measuring the adapter-cDNA size and concentration on an Agilent DNA 1000 chip. Sequencing librari... | 10.1186/1471-2164-14-292 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | PCR efficiency (E) for each amplicon was calculated using the linear regression method on the log (fluorescence)per-cycle-number data using Stratagen MXpro software. All qPCRs were performed in three technical replicates using either total pooled RNA used for RNAseq (two replicates for each mesorhizobial strain) or tot... | 10.1186/1471-2164-14-292 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The average relative quantity for each gene under study was calculated and log2-transformed. Means and standard deviations of these final log2 ratios were calculated using data from three technical replicates. Mean comparison was performed with a multiple comparison of Conover-Iman, using XLSTAT software, to determine ... | 10.1186/1471-2164-14-292 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The plates were incubated at 28°C with shaking at 450 rpm. OD 600nm and fluorescence (excitation filter at 485 nm and emission filter at 535 nm) were recorded 48 hours post inoculation using a spectrofluorometer plate reader (TECAN Infinite M200). Three transcriptional assays were performed for each bacterial strain ca... | 10.1186/1471-2164-14-292 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments This work was supported by the Agence Nationale de la Recherche Programme « Contaminants, Ecosystèmes et Santé » (CES 2008-12, APTITUDE). G. M. , received a PhD grant from the Ministère de la Recherche et de l'Education Nationale. We thank Dr. Klonowska A. and Dr. Cartieaux F. for help in qPCR assa... | 10.1186/1471-2164-14-292 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genotyping Genomic DNA was obtained from all subjects enrolled in the study. We then obtained the genotypes for 31 SNPs that span approximately 320 kb of genomic DNA in the promoter region, exon 1 and intron 1 of PARK2. Based on the tag SNP information available from the International HapMap project database (www. hapm... | 10.1371/journal.pntd.0002015 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Human cytokine ELISA Macrophages were seeded into 24-well plates at a density of 5610 5 cells per well and Schwann cells at a density of 5610 4 cells per well. Cells were treated with stimuli for 6-24 hours; the supernatants were collected, cleared by centrifugation and assayed using Milliplex MAP 42-plex human cytokin... | 10.1371/journal.pntd.0002015 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Statistical analysis The expression levels of IL6 and CCL2 in M. leprae sonicate stimulated and non-stimulated whole blood assays for all 62 subjects were used as quantitative traits in an eQTL analysis. Association between expression levels of CCL2 and IL6 and SNP alleles in PARK2/PACRG was tested by means of the Like... | 10.1371/journal.pntd.0002015 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments We thank all subjects who participated in this study. AC is a Banting postdoctoral fellow of the Canadian Institutes of Health Research. | 10.1371/journal.pntd.0002015 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Image Acquisition and Data Analysis Images were acquired with a Nikon Eclipse Ti using a plan Apochromatic 3100 oil-immersion objective with a 1. 4 numerical aperture. A Nikon Intensilight C-HGFI lamp was used to illuminate the coverslips. Dichroic filters for Cy3 (Semrock Cy3-4040B) and DAPI (Semrock DAPI-1160A) were ... | 10.1016/j.celrep.2013.10.013 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACCESSION NUMBERS The microarray data presented in this article have been deposited in the Gene Expression Omnibus under accession number GSE32980. | 10.1016/j.celrep.2013.10.013 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS We thank Daniel Larson and Robert H. Singer for sharing algorithms, J. Boulay for technical assistance, A. Aguilera and C. Cullin for the gift of yeast strains, and T. H. Jensen and F. Stutz for critical reading of the manuscript. This work was supported by the CNRS (to D. L. ), the Dan... | 10.1016/j.celrep.2013.10.013 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For some experiments, protein shape was visualized in samples measured at 12% contrast (12% D 2 O). For these studies, the scattering intensity of the protein was enhanced by preparing nHDL with deuterated apoA1. Both SANS at multiple levels of contrast and mass spectrometry studies independently confi rmed that 70% of... | 10.1194/jlr.m032763 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 25 UltraMicro Tip Columns (Nest Group, Southborough, MA). The samples were prepared for SCX chromatography by adding acetonitrile (5% v/v fi nal) to the cross-linked peptide solution and adjusting to pH 3. 0 with H 3 PO 4 prior to being loaded onto the columns. The column was washed with PBS, pH 3. 0 and eluted with 5%... | 10.1194/jlr.m032763 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The samples were measured at 6-8°C in 12% ( q range 0. 005-0. 304 Å Ϫ 1 ) and 42% D 2 O solution ( q range 0. 007-0. 453 Å Ϫ 1 ). The radius of gyration (R g ) was obtained based on the Guinier approximation ( 36 ) from the corresponding scattering curves. The SANS data collected were processed as follows. The program ... | 10.1194/jlr.m032763 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Atom clashes in the all-atom model, which resulted from manual adjustment of chain residues and individual lipid molecules, were removed by performing a short geometry optimization in vacuum. The CHARMM22 force fi eld was used for protein ( 43 ) , and CHMARMM27 for lipids ( 44 ). The vacuum model of nHDL DMPC was fur... | 10.1194/jlr.m032763 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Electron microscopy studies Negative stained nHDL samples (dilution 1:300) were obtained by applying them to the clear side of the carbon-mica interface and staining with 2% (w/v) uranyl acetate. Images were recorded under low-dose conditions with a CM12 (Philips) electron microscope equipped with an LaB6 fi lament and... | 10.1194/jlr.m032763 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Biochemical characterization of nHDL preparations formed using native human apoA1 and perdeuterated human apoA1 Reconstituted nHDL particles generated for SANS analyses in the present study were prepared with either isolated human apoA1 or recombinant human perdeuterated apoA1, as described under Materials and Methods.... | 10.1194/jlr.m032763 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Computational modeling of nHDL DMPC In earlier SANS with contrast variation studies ( 15, 27 ) we matched computational models of HDL at multiple contrast levels (0, 12, 42, and 90% D 2 O) and established that two contrast levels (12 and 42% D 2 O) are suffi cient to produce a consistent model for the entire particle... | 10.1194/jlr.m032763 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Following energy minimization, the crude proposed three-dimensional model obtained for the apoA1 chains within nHDL DMPC is shown in Fig. 4B (stereo views in supplementary Fig. IV ), and its superposition onto the lowresolution structure of apoA1 is given in Fig. 4C. It should be noted that this hypothetical exercise ... | 10.1194/jlr.m032763 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SAR acquisitions may then be used, together with an electromagnetic backscattering model (EBM) able to simulate the reflectivity of a snowpack from a set of physical descriptors, in order to constrain a physical snowpack model. In this study, we introduce a variational data assimilation scheme coupling TerraSAR-X radio... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | After evaluating the sensitivity of the EBM to snowpack parameters, a 1D-Var data assimilation scheme is implemented in order to minimize the discrepancies between EBM simulations and observations obtained from TerraSAR-X acquisitions by modifying the physical parameters of the Crocus-simulated snowpack. The algorithm ... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The new generation of synthetic-aperture radar (SAR) satellite data provides images with metric resolution and short revisit time. The TerraSAR-X satellite, with 1. 477 m ⇥ 2. 44 m resolution and revisit time of 11 days, gives dense information both spatially and temporally on snowpack evolution. In this study, we prop... | 10.5194/tcd-7-4881-2013 | preprint | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
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