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cc-by | In contrast, TD variations are not constrained by a potential TD value. A detailed list of all 132 equations, as well as the variables and the default parameter values is available at www1. clermont. inra. fr/urep/modeles/gemini. htm. The four studied traits refer specifically to the morphogenesis module. They all have... | 10.1371/journal.pone.0077372 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | For each species, an allometric relationship was derived, considering a constant leaf thickness and constant ratio between sheath and leaf lengths (Text S1). Variations in plant height H were achieved by changing the potential length of mature leaves L 0 (cm). For each species, plant height was calculated considering a... | 10.1371/journal.pone.0077372 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | For each species the model parameters reflecting the four traits were varied in ten equidistant steps (Table S1 ). The step values for each species were determined between minimum and maximum boundaries, which were selected to obtain for each trait a ±30% variation around the species' trait mean value observed in the ... | 10.1371/journal.pone.0077372 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Each simulation ran over ten years (repeating the 2003-2004 climate data five times), a necessary running time to check for the stability of the model response. In addition, simulations started from a quasiequilibrium state which was obtained by spin-up model runs. The two simulation campaigns (N+ and N-), correspondin... | 10.1371/journal.pone.0077372 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Data analyses In one simulation run, i. e. for each trait variation step, the annual biomass (below-and aboveground) was recorded for each simulated year and then averaged over the ten years simulation period for each species. For each species and for each N level, we generated an adaptive landscape in which the dynami... | 10.1371/journal.pone.0077372 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | For each species, we performed a regression analysis between the values of slope α i,j and slope α sum predicted by GEMINI and the corresponding observed species trait values under the high N treatment in the field. All statistical analyses were performed with the Statgraphics Plus (Manugistics, Rockville, MD, USA) sof... | 10.1371/journal.pone.0077372 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments We thank Romain Lardy for their precious help on data analysis; Hendrick Davi , Michel Lafarge , Sandra Lavorel , Isabelle Litrico , Robyn Butters , Alexandra Weigelt and five anonymous reviewers for their constructive and fruitful comments on a previous version of the paper. C. Wirth acknowled... | 10.1371/journal.pone.0077372 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | This study contributes to the French ANR DISCOVER project ( ANR-05-BDIV-010-01 ). V. Maire was funded by a Ph-D grant of French research ministry (MENRT). N. Gross was funded through a grant FEDER, 'l'Europe s'engage en région Auvergne'. The funders had no role in study design, data collection and analysis, deci... | 10.1371/journal.pone.0077372 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Downloaded from Ni-filtered CuKα radiation. All data were collected in the 2θ range of 3 • -70 • , with a step scan of 0. 02 • and a counting time of 8 s per step. For each analysis, 10 mg of powdered sample was mounted into the central hole of a nominally zero-background Si-sample holder (Li & Albe 1993). The identif... | 10.1093/gji/ggt265 | article | en | 2,013 | true | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Changes in physical and mechanical properties Standard rock characterization methods were employed as a tool to assess the impact of decarbonation under the various conditions implemented in this study. While the absolute values may not be representative of the in situ values (since our physical properties were measure... | 10.1093/gji/ggt265 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | oxfordjournals. org/ Downloaded from elastic moduli). The magnitude of the changes in rock physical properties at low levels of decarbonation (η dec = 0. 12) were greatly increased as temperature was increased. At 1200 • C the rock physical properties were drastically altered. Since the chemical changes at this stage a... | 10.1093/gji/ggt265 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 6, 1. 0, 1. 1, 1. 9, and 20 µg C-Ctx-1equiv. /kg fish, suggested that CFP by C-Ctx can be induced within a similar concentration range as P-Ctx-1 (CDC, 2009; Perez-Arellano et al. , 2005; Poli et al. , 1997). However, the above values where determined by various analytical and biochemical assays, thus making determina... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | In the current database, the amount consumed is either unknown or had to be estimated. the actual amount consumed however, can vary dramatically as in many moderate to severe intoxications patients react with immediate diarrhea or emesis and thus a major reduction of the meal consumed. As toxin concentrations, especial... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Intoxication timetable: In many cases a detailed description of when the meal was consumed, the timing of the onset of first symptoms and a detailed description of the clinical progression and intensity of symptoms and adverse effects is missing. A detailed description of the latter would help to understand differences... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Such a chain of custody was recently exemplified by a ciguatoxin intoxication of Germans exposed to contaminated fish from India (German Federal Institute for Risk Assessment, 2013). Simultaneously, medical primary care providers should be trained and provided with a national intoxication center where they can report i... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Consumption: there are some attempts to collect data on consumption habits involving surveys and questionnaires, but still the amount and quality of this type of information is insufficient. The uniformity and accuracy of questionnaires and surveys are important qualifiers in the establishment of robust datasets. Moreo... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | It is noteworthy that based on the available data from oral dose toxicity studies, humans appear to be several fold more sensitive to the DA excitotoxic effects than rodent model species (lefebvre and Robertson, 2010). It is primarily for this reason that an incidence of ASP outbreak in Canada in 1987 was employed for ... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | w. Because DA can be converted to epi-DA during storage, the ARfD applies to the sum of DA and epi-DA. eFSA recommends a safety threshold of 4. 5 µg DA/g shellfish in order not to exceed the acute reference dose (AR-fD), which is lower than the maximum tolerated residue level of 20 µg DA/g f. w. (20 mg DA/kg f. w. ) ef... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 4 μg AZA per 60 kg person that would result in symptoms (FSAI, 2006). As the latter risk estimate assumed equal potencies for all AZA analogues, the eFSA risk assessment on AZA (eFSA, 2008a) employed toxicity equivalent factors (TEF) that were based on very few mouse experiments using i. p. injection, suggesting teF a... | 10.14573/altex.2013.4.487 | review | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Thirteen balloon soundings were conducted from Sodankylä during 17 January-6 February, involving CFH and FLASH-B hygrometers flown together with the COBALD backscatter sonde. The measurements of water vapour, obtained using two independent techniques, are in excellent agreement, which allows for using FLASH-B and CFH p... | 10.5194/acp-13-11503-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. We thank the personnel of the FMI-ARC and RECONCILE coordination teams and the Myasischev Design Bureau. Through the same contract, the aircraft campaign in Kiruna and I. Engel and F. Wienhold , were partially funded by the EC as part of the FP7 project RECONCILE ( 226365-FP7-ENV-2008-1 ).... | 10.5194/acp-13-11503-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Bioinformatics workflow Sanger trace reads from SSH libraries clones were processed in batch for base-calling using Phred [44] (kindly provided by Phil Green, University of Washington) under default parameters and trimming all sequence regions with a Phred quality score lower than 20. For the 454-FLX sequencing of SS... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2. 6 (454 Life Sciences), with the cDNA mode option, a minimum overlap of 30 bases and 90% similarity, and with the rest of the computational parameters set to default values. The final dataset of isotigs (putative distinct transcripts; an equivalent term to the widely used ''contig'' given by Newbler software) and sin... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | GO mapping was done after the blastx search, and it included a final integration of the relational GO categories with the Annex option. The uniqueness of sequences per library was obtained from the final assembly using a program written in Perl that identifies isotigs resulting from sequences in both libraries. An enri... | 10.1371/journal.pone.0073176 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Gene expression analyses for meiotic transcripts Relative quantification of gene expression was performed on identified meiosis-related genes by qPCR on undifferentiated gonads, testis and ovary gonads, including both early and late maturation stages (Fig. 1 ). For each of these stages, six individual tissues were sele... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Relative quantities for each, target and reference genes, were estimated with the equation RQ = (1+E) (Cq mean -Cq). Relative expression values (RE) were calculated from the ratio of relative quantity (RQ) of each individual sample with the equation RE = RQ t / RQ nf (t = target gene and nf = normalization factor = geo... | 10.1371/journal.pone.0073176 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Microsatellite identification Microsatellites -single sequence repeats (SSR) -were screened in silico within the original unassembled reads using QDD2 software [49]. It is implemented in Perl language and uses ClustalW2 [50] and blast+ [51] to align the reads in flanking regions and thus reducing redundancy of pot... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Subtractive library sequencing, assembly and annotation Combining Sanger and 454-FLX sequences, we obtained a total of 34,276 valid reads of at least 50 bp with a quality score over Q20. The number of Sanger reads meeting these quality criteria were 352 and 177 from the maturing testis gonad and inactive gonad librarie... | 10.1371/journal.pone.0073176 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | With regard to each specific library, 1,153 transcripts from the late maturing testis and 833 from the inactive gonad library had a significant blast hit against the nr Genbank database (Table S2 ), and from those numbers, 768 (67%) and 697 (84%) respectively, had at least one Gene Ontology term significantly associat... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Functional annotation Subtraction efficiency was evidenced by finding that only 91 isotigs (from a total of 3,727) were built from both libraries. From those, 48 had at least one blastx hit and at least one significantly associated GO-term, and 3 had a blastx hit but no known annotation. Among the transcripts with anno... | 10.1371/journal.pone.0073176 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Identified microsatellites We identified 507 sequences with potential microsatellite loci, and successfully designed PCR primers for 310 of them. From these, a total of 272 pure and 38 compound microsatellites were found. A table of the microsatellite sequences, designed primers and the best-hit on Genbank is presented... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Finally, the last gene annotated as involved in sex differentiation was fkbp52 (peptidyl-prolyl cis-trans isomerase), which codes for a co-chaperone for HSP90, and is known to be critical for proper development and differentiation of male reproductive organs in mammals [97]. In the hermaphrodite nematode C. elegans, t... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | SSR in coding sequences Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. EST-SSRs have the advantage of being higher conservation across species than anonymous genomic SSRs, and hence are more transferable across taxonomic boundaries for genome mapping and co... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Some of the microsatellites for which an annotation of the nucleotide sequence was obtained were found to be located in the 3' UTR of mRNAs, as a tri-repeat of TAT with a flanking region similar to the troponin I of Patinopecten yessoensis cDNA (Genbank accession AB008006. 1). Expansions or contractions of SSRs located... | 10.1371/journal.pone.0073176 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgments We thank the technical assistance provided by JoseL. Ramı ´rez , Susana A ´vila , and Julio Hernandez Gonza ´lez; and Carmen Rodrı ´guez Jaramillo and Eulalia Meza Cha ´vez for their technical support in histological processing. We also thank Dr. Eduardo Romero-Vivas for his advice on bioinfor... | 10.1371/journal.pone.0073176 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | This work was funded by CIBNOR (grant AC0. 16 ) and CONACYT-CB-2011-1 (grant 166573 ). The first author is a Ph. D. student, financially supported by a CONACyT fellowship (number 204031 ). CAG wishes to thank CONACyT for a young investigator grant (number 133388 ). The funders had no role in study design, d... | 10.1371/journal.pone.0073176 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | For Classical T Tauri Stars (CTTSs), the resonance doublets of N v, Si iv, and C iv, as well as the He ii 1640 Å line, trace hot gas flows and act as diagnostics of the accretion process. In this paper we assemble a large high-resolution, high-sensitivity dataset of these lines in CTTSs and Weak T Tauri Stars (WTTSs). ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Most of the data for this paper comes from the Cycle 17 Hubble Space Telescope (HST) proposal "The Disks, Accretion, and Outflows (DAO) of T Tau stars" (PI G. Herczeg, Prop. ID HST- GO-11616). The DAO program is the largest and most sensitive high resolution spectroscopic survey of young stars in the UV ever undertake... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | OBSERVATIONS Tables 1, 2, and 3 list the 35 stars we will be analyzing in this paper and the references for all the ancillary data we consider. Table 4 indicates the origin of the data (DAO or some other project), the datasets and slit sizes used for the observations. Details about exposure times will appear in Herc... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Non-DAO COS data were downloaded from the Mikulski Archive for Space Telescopes (MAST) and reduced as described below. The sample of stars considered here includes objects with spectral types ranging from A7 (the Herbig Ae star DX Cha 18 ) to M2, although most objects have mid-K spectral types. We assume stellar ages ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 2007 ). The accretion rates listed in Table 3 are obtained from optical veiling and NUV excesses and represent total accretion for the overall system. At the end of this paper we will conclude that binarity may be affecting the line centroid determination only in AK Sco. For non-spectroscopic binaries, the effect of th... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 5" diameter circular aperture. The acquisition observations used the ACQ/SEARCH algorithm followed by ACQ/IMAGE (Dixon 2011). The absolute wavelength scale accuracy is ∼ 15 km s -1 (1σ), where the error is dominated by pointing errors. We obtained one dimensional, co-added spectra using the COS calibration pipeline (C... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | false | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | This reduction procedure provides a wavelength-scale accuracy of 1σ = 3 km s -1. Non-DAO STIS data were taken directly from StarCAT. For a given pointing, errors in the positioning of the target within the aperture result in an offset in the wavelength scale. As indicated above, these are supposed to be 15 km s -1 for ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Unlike the results reported by Linsky et al. 2012) , we do not observe a systematic increase in the line center as a function of wavelength, neither star by star nor in the average of all stars for a given line. This is likely the result of the different acquisition procedure followed here. For the STIS data, the aver... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | THE RELATIONSHIP BETWEEN ACCRETION RATE AND C IV LUMINOSITY As mentioned in the introduction, Johns-Krull et al. (2000) showed that the accretion rate is correlated with excess C iv luminosity. The excess C iv luminosity is obtained by subtracting the stellar atmosphere contribution to the observed line. They estimat... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | In the observations we present here, the C iv doublet lines are blueshifted by ∼-100 km s -1 , as can be seen from the position of the 1550 C iv line. This points to an origin in the approaching part of the outflow. The net result of these two outflows is that the blueshifted 1548 C iv line is buried under the redshift... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 6±0. 6 km s -1 ), derived by Nguyen et al. (2012) , which we use here, deviates significantly from the velocity of the surrounding molecular cloud (21 km s -1 ; Kenyon & Hartmann 1995). Using the cloud velocity would shift the C iv lines to the blue even more. France et al. 2012 finds that the H 2 lines have maxima ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | In our sample, we have 37% of targets with inclinations larger than 45 • , and the standard deviation of this count is 10%. Therefore, the observed difference in the number of stars with high and low inclinations is not significant. Over a hundred CTTSs with known inclinations are needed before we can distinguish 42% f... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | 2 that the errors in the COS dataset are ∼7 km s -1. Errors in the wavelength scale cause the data points to move parallel to the dotted line. We focus first on the upper right quadrant of Figure 9 , those objects with both v BC > 0 and v N C > 0. The hatched region of the plot corresponds to v BC ≥ 4 v N C. As we can... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | This is speculative and requires further study. We note here that Telleschi et al. (2007) find a mass-dependent inverse FIP-effect abundance pattern also in CTTSs. These statements are only intended to identify candidates for further study. What we can tell from our observations is that there is considerable scatter ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Indeed, we observe C iv and He ii redshifted, with the former redshifted more than the latter. This, however, is not a very constraining prediction. Linsky et al. (2012) have shown that C iv lines in dwarfs are redshifted by an amount correlated with their rotation period and Ayres et al. (1983) have shown that the ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | On the other hand, there is a large body of evidence (see the references in the introduction) suggesting that the accretion continuum and the (optical) line emission are well localized on the stellar surface. No unequivocal rotational modulation of the lines studied here has been reported in the literature, but this ma... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | C iv and He ii luminosities are also correlated with each other, and the C iv/He ii luminosity ratio is a factor of three to four times larger in CTTSs than in WTTS. This confirms that the ratio depends crucially on accretion phenomena and it is not an intrinsic property of the stellar atmosphere. • We do not find any ... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The other is the small range of accretion rates well-covered by objects. Future observational work should focus on resolving these limitations. Even with these limitations, it is clear that with this work we have only scratched the surface of this magnificent dataset. and the WTTS V396 Aur (blue line) for the four emis... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Note. -(a) In addition to the DAO data; we have made use of data from the following HST proposals: GO 8157: Molecular Hydrogen in the Circumstellar Environments of T Tauri Stars; PI Walter GO 8206: The Structure of the Accretion Flow on pre-main-sequence stars; PI: Calvet GTO 11533: Accretion Flows and Winds of Pre-Mai... | 10.1088/0067-0049/207/1/1 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Acknowledgements We thank all the members of the " French Young Neonatologist Club " for their fruitful discussions and critical reading of the review. | 10.1186/1471-2431-13-165 | review | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Lower boundary conditions As stated above, we placed the lower boundary of the hydrodynamic model at p 0 = 1 µbar and did not include H 2 or other molecules in the model. This decision was motivated by photochemical calculations for HD209458b (Lavvas et al. , in preparation) that we used to constrain the lower bounda... | 10.1016/j.icarus.2012.09.027 | article | en | 2,012 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Scene analysis, in urban environments, deals with street modeling and understanding. A street mainly consists of roadways, pavements (i. e. , walking areas), facades, still and moving obstacles. In this paper, we investigate the surface modeling of roadways and pavements using LIDAR data acquired by a mobile laser scan... | 10.5194/isprsannals-ii-3-w3-31-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Mobile laser scanning LIDAR data were obtained by a multi-sensor mobile laser scanning system called Stereopolis (see (Paparoditis et al. , 2012) ). The Stereopolis system is composed of a navigation device hybridating measurements from two GPSs, an inertial measurement unit, and a wheel odometer. The navigation devic... | 10.5194/isprsannals-ii-3-w3-31-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Fig. 17 presents result of street ground modeling in a Parisian street. It was obtained rapidly (thanks to simple interacting scheme) and is in a centimetric precision. Accurate street ground modeling is reachable for areas of any scale. Tests have only been performed on some parts of the Parisian network provided by ... | 10.5194/isprsannals-ii-3-w3-31-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | CONCLUSION In this paper, a road/walking areas surface modeling for MLS LI-DAR data is presented. It is composed of two parts, a model for road side and curb ramp detection is first described. Results of this first step are further used to model surfaces of both roads and walking areas. The process handle occlusions du... | 10.5194/isprsannals-ii-3-w3-31-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Assessment of risk factors of FRAXH and calculation of FRAXH tool All risk factors for fracture included in FRAXH were assessed baseline. Among the secondary osteoporosis categories in FRAXH, data on type 1 diabetes, osteogenesis imperfecta and chronic liver disease were not available. Prior non vertebral fractures wer... | 10.1371/journal.pone.0083436 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Using data of the SOF (Study of Osteoporotic Study) study, a cohort of older communitydwelling women (n = 6252, mean age of 71. 3 years), Ensrud et al showed that a simple model based on age and BMD predicted 10year risk of hip, major osteoporotic, and any clinical fracture as well as FRAXH models with BMD [30]. In t... | 10.1371/journal.pone.0083436 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Biochemical markers of bone turnover were not in FRAXH because of the biological variability, the lack of reference analytes and analytical standards [44]. An attempt to adjust the result of FRAXH based on dose of corticosteroid has been recently published [45]. Our study has several limitations. The first limitation... | 10.1371/journal.pone.0083436 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments We would like to acknowledge the contributions of the other members of the OPUS teams at the five participating centres: Rosie Reid (deceased), Lana Gibson and Alison Stewart in Aberdeen ; Antonia Gerwinn , Dr. Maren Glu ¨er , Roswitha John , Roswitha Marunde-Ott , Monika Mohr , Regina Schlen... | 10.1371/journal.pone.0083436 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Edges link gene functions that share genes. Edge thickness is proportional to number of shared genes and edge color is blue for shared worm genes and green for shared yeast genes. Clusters of functionally related nodes were manually circled and labeled. the BioGRID database (Breitkreutz et al, 2008) , 31 of which are ... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Rewiring scenarios The rewiring observed between worm and yeast may be due to a lack of conservation in: (i) the SH3 domain specificity (or the SH3 domain presence); (ii) the ligand; or (iii) both. For SH3mediated interactions whose ligand binding motif can be predicted using the phage-derived binding specificity, our ... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Protein localization assay in human cell lines Human skin melanoma SK-MEL-2 CLTA-TagRFP-T gene-edited cells (SK-MEL-2 CLTA EN-1 ) (Doyon et al, 2011) were maintained under 5% CO 2 at 371C in DMEM/F-12 (Invitrogen) supplemented with 10% FBS (fetal bovine serum, HyClone). SK-MEL-2 CLTA EN-1 cells were transiently trans... | 10.1038/msb.2013.9 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | At 16-24 h before imaging, cells were seeded onto uncoated glass coverslips in growth medium. During imaging, cells were maintained in DMEM without phenol red that was supplemented with 5% FBS, 10 mM HEPES and 1 Â GlutaMAX. A 488-nm solid-state laser (Melles Griot) and a 561-nm diode-pumped solid-state laser (Melles Gr... | 10.1038/msb.2013.9 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Peptides were identified by mass spectrometry as described (Rush et al, 2005; Guo et al, 2008). In total, 1139 human proteins were identified with this approach. We compared this data set with the predictions by orthology of human endocytosis proteins based on our worm SH3 interactome. The 55 predicted novel worm endo... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The score for any two GO terms is calculated based on their information content and ontology graph position. As recommended in previous work (Guo et al, 2006) , given a PPI involving two proteins, with A annotated by M terms and B annotated by N terms, we computed GO term similarity between all possible M Â N term pai... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | GO gene function term enrichment and construction of the enrichment map We used the DAVID v6. 7 service to compute GO term enrichment for our yeast and worm interactomes (http://david. abcc. ncifcrf. gov/; Dennis et al, 2003; Huang da et al, 2009). The worm SH3 interactome contains 520 unique proteins, mapped to WormBa... | 10.1038/msb.2013.9 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Protein interaction conservation To probe the degree of SH3-mediated protein interaction conservation from worm to yeast and human, proteins from the worm SH3 domain interactome, restricted to interactions with SH3 domains as baits, were mapped to their yeast and human orthologs. Protein interactions in yeast were retr... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Negative example proteins (105 in total) used to compute ROC curves were randomly selected from the Worm proteome, excluding ones with known endocytosis function in any organism. ROC curves were computed for each cross-validation run by varying k and used to compute an average AUC of 0. 69 (Po10 À 4 ). The k-core with ... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DG performed the bioinformatics analysis. XX cloned yeast two-hybrid (Y2H) baits. XX and LL performed Y2H screens. J-FR helped with ORFeome Y2H screening. RT cloned phage display baits. AP and AL performed phage display assays. RT and SSS supervised the phage display assays. JC, ATC, and DB performed co-localization as... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We thank Q Li , H Huang , J Gu , R Isserlin , H Fares , A Audhya , A Shi , S Pant , and D Carranza for experimental and computational support. This work was supported by the Canadian Institutes of Health Research (Grants MOP-84324 to GDB and MOP-93725 to SSS) and the US National Instit... | 10.1038/msb.2013.9 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data availability Phage display data and other data from this paper are available for download from http://www. baderlab. org/Data/SH3Worm. Phosphoproteomics data are available from the PhosphoSitePlus database for the following cell line samples under the following accession numbers: LAN-6 End1, End2, and Lys, which c... | 10.1038/msb.2013.9 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Alternatively, defective interfering particles could have served as a template 32, 33 , as the DNA forms had breakpoints and rearrangements similar to those identified in RNA1 defective interfering particles 11. Of note, we also identified DNA forms derived from FHV RNA2 that were similar in sequence to RNA2 defectiv... | 10.1038/ni.2542 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Methods and any associated references are available in the online version of the paper. Accession codes. NCBI Small Read Archive: sequences, SRA045427. After viral infection, viral genomes (viral RNA) or dsRNA intermediates (viral dsRNA) are propagated (red). Those viral forms are reverse-transcribed by cellular revers... | 10.1038/ni.2542 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Each unique sequence was given a unique identifier followed by the number of sequences that it represented in the library. First, unique sequences were filtered with Blastall software (National Center for Biotechnology Information) with the parameters '-W 9 -F F -e 1-g F', first against the Drosophila melanogaster refe... | 10.1038/ni.2542 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Second, the Blastall software was used with the parameters '-e 100 -W 9 -F F -q -100 -g F' for selection, among the remaining unique sequences, those with 9-12 bases with the most similarity to FHV RNA1 or RNA2 and their defective interfering particles without gaps or mismatches. Unique sequences without similarity or ... | 10.1038/ni.2542 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Results that allowed 0, 1 and 2 overlapping bases between the two hits were examined for all the unique sequences. Only unique sequences representing at least five reads on the original small-RNA library were retained. This second step was specifically designed to 'fish out' chimeric transcripts with high confidence. O... | 10.1038/ni.2542 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Mapping was done with Bowtie software, with applying a seed of 21 nts with a maximum of 2 mismatches. Each miRNA was quantified in the presence or absence of AZT with SAMtools. FHV small RNAs were mapped with Bowtie software for the alignment of short DNA sequences, and a maximum of two mismatches was allowed. The mapp... | 10.1038/ni.2542 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | ACKNOWLEDGMENTS We thank members of the Saleh lab , the Antoniewski lab and the Vignuzzi lab for discussions and technical support; M. Vignuzzi , J. Chandler and R. van Rij for critical reading of the manuscript; A. Schneemann ( The Scripps Research Institute, La Jolla, CA ) for antibody to FHV; P. Vargas ... | 10.1038/ni.2542 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Assay Miniaturization and Optimization HuH-7 cells were seeded in 384-well m clear-plate black (Greiner Bio-one, Germany) at 5610 3 cells per well containing 0. 5% DMSO vehicle, and treated with 50 mM CPZ or infected with CHIKV-118-GFP at a multiplicity of infection (M. O. I. ) of 0. 5 for 24, 48, 72 and 96 hrs at 37uC... | 10.1371/journal.pntd.0002471 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data Normalization, Compound Activity, and Assay Quality Control The measured RFU values obtained from the resazurin reduction assay was normalized as percent viability using the formula: % viability~RFU sample {mRFU CC100 À Á RFU MOCK {RFU CC100 ð Þ Â Ã |100% where m represents the mean value, and the RFU CC100 , RFU ... | 10.1371/journal.pntd.0002471 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Counter-screening against Dengue Virus Serotype 2 (DENV2) The inhibitory property of the CHIKV primary screening hits against DENV2 infection was investigated by retrieving the results from the a high-content, high-throughput screening of the BioFocus kinase inhibitor library against DENV2 infection in Huh-7. 5 cells (... | 10.1371/journal.pntd.0002471 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Structural Analysis of Hit Compounds Cluster analysis was done using a molecule-clustering module from Pipeline Pilot (Accelrys Software Inc. , San Diego, CA, USA). Structural relationship among the primary hit compounds was analyzed using the Tanimoto coefficient structural similarity [41]. The core scaffolds of hit ... | 10.1371/journal.pntd.0002471 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Image-Based High-Content Assay of CHIKV Infectivity CHIKV-118-GFP infection of HuH-7 in the presence of the hit compounds for 24 hours was analyzed by image-based highcontent assay. HuH-7 cells were seeded in 96-well m clear-plate black (Greiner Bio-one, Germany) at 5610 4 cells per well and kept under humidified condi... | 10.1371/journal.pntd.0002471 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Chemical Structures of Anti-CHIKV Compounds The chemical structures of the 6 confirmed hit compounds are shown in Figure 4. Based on the structural analysis using the molecule-clustering module from Pipeline Pilot, 4 of the compounds -CND0335, CND0364, CND0366, CND0415 share a benzofuran scaffold, with a common substi... | 10.1371/journal.pntd.0002471 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments The authors would like to acknowledge Katja Fink for the gift of HuH-7 cells and Claudia N. D. dos-Santos for the gift of C6/36 cells. | 10.1371/journal.pntd.0002471 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIP) (No. 2007-00559 ), Gyeonggi-do and KISTI. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | 10.1371/journal.pntd.0002471 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | In MS research, 118 studies that have reported QoL as an outcome were performed with MS patients in the Clinical Trials registry (ClinicalTrials. gov, December 31, 2012). Despite the acknowledged need to consider QoL issues, QoL assessment remains under-utilized in MS clinical practice [8]. QoL assessment may be consi... | 10.1155/2013/524894 | article | en | 2,013 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | Additionally, it becomes imperative to produce norms for the most popular MS-specific instruments. Aggregating datasets may contribute to produce valid and robust norms. Each patient would be compared to norms. | 10.1155/2013/524894 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The Ac H-NOX proteins lack a critical tyrosine residue in the non-polar distal heme pocket, making it likely that they are for nitric oxide (NO) rather than oxygen signaling [34]. Both Dd and Ac are responsive to light, although the photoreceptor that mediates phototaxis in Dictyostelium has yet to be identified [35]... | 10.1186/gb-2013-14-2-r11 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Ac encodes a NB-ARC-TPR homologue with a disease resistance domain (IPR000767) and an LRR-ROCO GTPase. | 10.1186/gb-2013-14-2-r11 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Sequencing and assembly Genome assembly was carried out using a two-step process. Firstly, the Illumina reads were assembled using the Velvet [96] short read assembler to generate a series of contigs. These assembled contigs were used to generate a set of pseudo-reads 400 bp in length. These pseudo reads were then as... | 10.1186/gb-2013-14-2-r11 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Gene structure prediction Gene finding was carried out on the largest 384 scaffolds of the Ac assembly using an iterative approach by firstly generating gene models directly from RNA. seq to train a gene-finding algorithm using a genome annotation pipeline followed by manual curation. Firstly, predicted transcripts wer... | 10.1186/gb-2013-14-2-r11 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | It identifies repeats, aligns ESTs (in this case the transcripts generated by the G. Mo. R-Se algorithm) and proteins from (nr) to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations. The 17,013 gene predictions generated by MAKER were then manually annotated usi... | 10.1186/gb-2013-14-2-r11 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Functional annotation assignments Functional annotation assignments were carried out using a combination of automated annotation as described previously [103] followed by manual annotation. Briefly, gene level searches were performed against protein, domain and profile databases, including JCVI in-house non-redundant... | 10.1186/gb-2013-14-2-r11 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
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