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cc-by | Covariables included sickle cell trait 33 gender, number of days present on site during the trimester, trimestrial incidence of P falciparum and age. Age was initially analysed as a continuous covariate. To assess the age-specific effect of allergy, age was categorised into two levels (<3. 5 years of age and ≥3. 5 ye... | 10.1136/bmjopen-2013-002835 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 22 The only other epidemiological study that has previously examined the link between malaria and atopy 38 also interpreted the result from the perspective of the impact of malaria on atopy. They examined the reinfection rate with P falciparum over a 5-year period in 91 children who were subsequently classified as atop... | 10.1136/bmjopen-2013-002835 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data sharing statement The allergy database will be made available on-line. The longitudinal malaria data set will be made available following discussion with the coordinators of the three Institutes that govern the dataset through contact with the corresponding author. | 10.1136/bmjopen-2013-002835 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data sharing statement The allergy database will be made available on-line. The longitudinal malaria data set will be made available following discussion with the coordinators of the three Institutes that govern the dataset through contact with the corresponding author. | 10.1136/bmjopen-2013-002835 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The central nervous system is especially vulnerable to perinatal injuries, including hypoxia, systemic inflammation and traumatic brain injury. Maternal exposure to neurotoxic compounds and drugs can have dramatic consequences for neurogenesis, leading to irreparable long-term neurodevelopmental disorders [28]. The pu... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Briefly, 10 μg of labelled cRNA was fragmented and denaturated in hybridization buffer, then hybridized on the chip for 6 h at 45°C with constant mixing by rotation at 60 rpm in an Genechip hybridization oven 640 (Affymetrix). After hybridization, arrays were washed and stained with streptavidin-phycoerythrin (GeneChip... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Refer to [34] for full methods and bioanalysis. Details of the analysis of the output from the high throughput RNA-Seq are published separately [34]. Briefly, reads were trimmed to remove ambiguous bases from the start and segments with low quality scores from the end. Trimmed reads were mapped with Bowtie version 0... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Quantitative real-time PCR RNA (1 μg) was spiked with 25 pg of bacterial AraB RNA from E. coli (GE Healthcare Bio-Sciences Freiburg, Germany), used as an external standard for normalization, as the expression of conventionally used house-keeping genes proved to be variable between developmental stages. RNA was reverse ... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Results and discussion Combined analysis of gene expression data by Affymetrix microarray, Illumina RNA-sequencing, and qRT-PCR The expression level of selected genes was assessed in E19, P2, and adult rat lateral ventricular choroid plexus using Affymetrix microarrays, and in E15 and adult lateral ventricular choroid ... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The profiles are grouped and interpreted for families of genes with similar functions. To optimize the reliability of the data generated by microarrays, mRNA samples were prepared from two separate pools of choroid plexuses, each being collected from several animals. The choroidal tissue was carefully controlled with a... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The duplicate choroidal mRNA populations analyzed for each stage were highly similar as the expression level of 99. 4% of all genes detected at level above a background of 100 fluorescence units as defined by Affymetrix software differed by less than a factor of two between samples (not shown). Finally, the expression ... | 10.1186/2045-8118-10-25 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Slc15, Slc28 and Slc29 transporters The Slc15 subfamily comprises proton-coupled oligopeptide transporters [66]. Among these, Slc15a2 transports peptidomimetic drugs such as the antiviral agent aciclovir or the β-lactam antibiotic cefadroxil. Slc15a2 protein was shown by immunocytochemistry to distribute at the apical... | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Endnotes a Gene official symbols (in italic), as defined on the NCBI website, other common gene or protein names, and accession numbers (NM; number mRNA) for all genes analyzed in this study are listed in Table 1. Symbols referring to human genes or proteins are written in capital letters. | 10.1186/2045-8118-10-25 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements The research leading to these results has received funding from the European Union Seventh Framework Program ( FP7/2007-2013) under grant agreement n°HEALTH -F2-2009-241778 and from the National Health and Medical Research Council, Australia. SAL is funded by the American-Australian Association... | 10.1186/2045-8118-10-25 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Refinement Approximate positions for all the H atoms were first obtained from the difference electron density map. However, the H atoms were situated into idealized positions and the H-atoms have been refined with the riding-model approximation. The applied constraints were as follow: C aryl -H aryl = 0. 95 Å; N aryl -... | 10.1107/s1600536813011951 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Crystal data (i) Àx þ 1; y þ 1 2 ; Àz þ 1; (ii) Àx; y À 1 2 ; Àz; (iii) x þ 1; y; z. Data collection: APEX2 (Bruker, 2012) ; cell refinement: SAINT (Bruker, 2012) ; data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008)... | 10.1107/s1600536813010398 | article | en | 2,013 | true | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | Computing details Data collection: APEX2 (Bruker, 2012) ; cell refinement: SAINT (Bruker, 2012) ; data reduction: SAINT (Bruker, 2012) ; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows (Farru... | 10.1107/s1600536813010398 | article | en | 2,013 | false | true | false | false | Chemistry | https://openalex.org/fields/16 |
cc-by | 3 mmol), and 4-dimethylaminopyridine (catalyst) in 5:1 tetrahydrofuran/triethylamine was stirred for 10 h at 60 °C. The solvents were removed to yield the desired triazole urea (85 mg; 0. 24 mmol; 78%) as a mixture of N2-and N1-carbamoylated regioisomers. The regioisomers were separated by silica gel chromatography (3:... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Then the plates were analyzed with a Spectramax Gemini XS microplate fluorometer (Molecular Devices, Sunnyvale, CA) using an excitation wavelength of 530 nm and an emission wavelength of 590 nm. Data were analyzed using the software Softmax Pro (Molecular Devices). A decrease of fluorescence (ϭinhibition) was expressed... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | We cannot exclude that other enzymes, below the detection limit of this experiment, might be affected upon treatment with the inhibitors. TgASH1 Is Encoded by a Close Homologue of hAPT1-As a means to determine the identity of the inhibitor targets, a mod-ified version of the FP probe containing biotin in place of rhoda... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Two candidates identified in the MS experiment (TGME49_ 028290 and TGME49_054690) and two further top candidates from the list in Table 3 (TGME49_023510 and TGME49_ 062490) were subjected to phylogenetic analysis along with their putative homologues in Apicomplexa, human APT1 and APT2 and their homologues in diverse eu... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | 2 ). The amino acid sequence alignment of ASH1 and hAPT1 (supplemental Fig. 2B ) highlights a highly charged region of low complexity that sits between the catalytic serine, aspartate, and histidine residues of ASH1. This insertion is also present in the ASH1 sequence of different T. gondii strains as well as in other ... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | To gain further information, the three genes most closely related to TgASH1 and present across Apicomplexa were characterized. TGME49_054690 (TgASH2; GenBank accession number KF114274) was identified in the MS of the inhibitor targets (supplemental Fig. 1 and Table 2 ), whereas TGME49_023510 (putative TgASH3; Gen-Ban... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Plaque assays were performed with knock-out strains, and no growth defect was detected over 10 days (data not shown). Furthermore, neither stimulated egress (Fig. 8D ) nor intracellular growth (Fig. 8E ) of these strains was negatively impacted, although the ash3-KO strain appeared to grow slightly faster than the cont... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments -We thank Dr. Karine Frenal and Leonardo Capponi for assistance during the early stage of this project. C. H. and M. R. thank Prof. Herbert Waldmann , Max Planck Institute for Molecular Physiology, Dortmund, Germany for unconditional support. | 10.1074/jbc.m113.460709 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | supplemental Figs. 1 and The nucleotide sequence(s) reported in this paper has been submitted to the Gen-Bank TM /EBI Data Bank with accession number(s) KC473455 , KF114274 , KF114275 , and KF1142761 Supported by FP7-funded Marie Curie Initial Training Network Project 215281-InterMal Training and Swiss National... | 10.1074/jbc.m113.460709 | article | en | 2,013 | true | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Confocal acquisition, 3D reconstruction and quantification Confocal acquisitions were performed using a spinning-disk Perkin-Elmer Ultraview RS Nipkow Disk, an inverted laser-scanning confocal microscope Zeiss Axiovert 200 M with an Apochromat 63Â/1. 4 oil objective and a Hamamatsu ORCA-II-ER camera (Imagopole, Institu... | 10.1093/nar/gkt015 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Real-time quantitative polymerase chain reaction Total RNA was isolated from HeLa cells using the RNAeasy Mini kit (Qiagen), treated with DNaseI (Qiagen), then reverse transcribed using Superscript Õ III Reverse transcriptase (Invitrogen). Real-time quantitative polymerase chain reaction (RT-qPCR) was performed using P... | 10.1093/nar/gkt015 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | mtDNA content analysis by quantitative polymerase chain reaction The quantification of mtDNA was performed by quantitative polymerase chain reaction (qPCR) amplification on 200 pg of total DNA using the StepOne TM Plus RealTime PCR system (Applied Biosystems) and Power Sybr Green PCR Master mix (ABI) following the manu... | 10.1093/nar/gkt015 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Protein extraction and western blot Cells were lysed by lysis solution [20 mM Tris, 18 mM NaCl, 0. 5 % Lauryl b Maltoside, 1 mM MgCl 2 , 200 mM Na 4 P 2 O 7 , 1 mM ethylene glycol tetraacetic acid (EGTA), 20 mM NaF, 2 mM NaVO 4 , 1 mM Pefabloc (Sigma), 1 mM Aprotinin (Sigma), 1 mM Leupeptin (Sigma)]. Protein content wa... | 10.1093/nar/gkt015 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Identification and quantification of mtDNA processing markers in single cells We recently developed an imaging approach, mitochondrial Transcription and Replication Imaging Protocol (mTRIP) that is a combination of DNA FISH and RNA FISH, and which can be also combined to immunofluorescence, as the treatment does not de... | 10.1093/nar/gkt015 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank F. Brandizzi , B. Dujon , S. Tajbakhsh and C. Zurzolo , for comments on the manuscript, and the Imagopole (PFID) of Institut Pasteur for advice. | 10.1093/nar/gkt015 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data analysis The slides were scanned on an Agilent G2505C DNA Microarray Scanner at a resolution of 5 mm, using default parameters. Acquisition of signals from the resulting scanned images and normalization were performed using the Feature Extraction v10. 5. 1. 1 software (Agilent Technologies), using default paramete... | 10.1016/j.breast.2012.07.010 | article | en | 2,012 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 10. 0 13 using the R statistical language. No clustering analysis was done due to the small sample size. The UCSC human genome build version hg18 of March 2006 was used for all the genomic coordinates [http://genome. ucsc. edu]. Raw data have been submitted to the Array Express database with the accession number E-TA... | 10.1016/j.breast.2012.07.010 | article | en | 2,012 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Multiannual satellite measurements of tropospheric NO 2 columns are used for evaluation of CO 2 emission changes in China in the period from 1996 to 2008. Indirect top-down annual estimates of CO 2 emissions are derived from the satellite NO 2 column measurements by means of a simple inverse modeling procedure involvin... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | son of our indirect top-down estimates of the CO 2 emission changes with the corresponding bottom-up estimates provided by the EDGAR (version 4. 2) and Global Carbon Project (GCP) glomal emission inventories reveals that while acceleration of the CO 2 emission growth in the considered period is a common feature of both... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | (2010) for studying NO x emission trends in megacities. Accordingly, our estimates of CO 2 emission changes are obtained by merging the top-down estimates of NO x emission changes and bottom-up estimates of the NO x -to-CO 2 emission conversion factors. Such CO 2 emission estimates can therefore be considered either a... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | , 2005; He et al. , 2007; Kim et al. , 2006 Kim et al. , , 2009;; Konovalov et al. , 2008 Konovalov et al. , , 2010)). The initial nominal horizontal resolution of the GOME measurements is 320 × 40 km 2 , and almost global coverage is achieved within three days. The SCIAMACHY measurements have a higher nominal horizont... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Data of emission inventories We used annual emission data from several emission databases, including the Emission Database for Global Atmospheric Research, version 4. 2 (EDGAR v4. 2), the Global Carbon Project (GCP) international inventories, the Regional Emission Inventory in Asia (REAS), and a new global data product... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Details can be found elsewhere (Wang et al. , 2013). The emission inventory data outlined above are considered below in comparison with corresponding estimates based on satellite measurements. Focus is given to the data of the global emission inventories (EDGAR and GCP) that have direct implications for climate change... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Taking into account that the effects of chemical nonlinearities in our case were found to be rather small (see the corresponding discussion in Sect. 5), we approximated monthly values of ζ for different years by linearly interpolating between unity and its values calculated (employing Eq. 3 to express α m ) with j = 20... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2 NO x emissions in the period from 1996 to 2001 in the both cases. The difference between the trends derived from satellite data for case II and calculated with the REAS v1. 11 data is almost insignificant. Similar to the estimates of the CO 2 emission changes, all of the considered estimates of the NO x emission chan... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The considerable difference in the behaviors of the hybrid vs. the bottom-up CO 2 emission estimates is further demonstrated in Fig. 7. Specifically, we have again fitted our estimates (for case I) and the EDGAR v4. 2 data with exponential curves, but this time without splitting the whole period 1996-2008 into two stag... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Therefore, we can conclude that the existence of the discussed sharp bend in emission time series is not corroborated by satellite measurements. The origin of the strong nonlinearity in the CO 2 and NO x emission trends found in the emission inventory data can be better understood after considering the dynamics of indi... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 9 , and also plotted in Fig. 10 versus the similar ratios calculated with the EDGAR v4. 2 and PKU-CO2 inventories. The scatterplots are presented separately for the two subsets of provinces depicted in Fig. 3. The first subset of provinces (see Fig. 3a ) has been considered above. The provinces in the second subset fe... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 9 ). Note that the distribution of the EDGAR v4. 2 emission data is performed with sector-specific spatial proxy datasets that are kept constant over time. As such, Fig. 9b visualizes only the impact of relative change in fraction of the different sectors, but not yet any urbanization process that might explain the sp... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | g. , due to a bias in estimation of a stratospheric part of the measured total NO 2 columns) and in simulations (e. g. , due to uncertainties in biogenic emissions). The fact that our estimates demonstrate much better agreement with the data of the PKU-CO2 inventory than with the EDGAR v4. 2 inventory may be considered... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2 inventory operates with the national fuel statistics, which are not all distributed to the point sources, but which uses proxy data for, e. g. , the residential sector. Interestingly, the correlation coefficient between our estimates of CO 2 emission ratios and the PKU-CO2 data increases from 0. 46 to 0. 52 when the ... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Specifically, correlations with our top-down estimates were found to be almost negligible both with the PKU-CO2 and EDGAR v4. 2 data. It seems unlikely that this result is due to a significantly different level of uncertainties in our top-down estimates. A more likely explanation is that both the PKU-CO2 and EDGAR v4. ... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | These results suggest that the atmospheric photochemistry in China is, on the whole, predominantly in the so-called high-NO x regime (Sillmann, 1999). Additional simulations were made to examine a possible effect of changes in emissions of volatile organic compounds (VOC) on our estimates. Specifically, along with the... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 4. 1. Any direct evidence of changes in biogenic NO x emissions in China during the considered period is not yet available. Nonetheless, the changes in biogenic NO x emissions are unlikely to exceed the changes in fertilizer consumption, which, according to the World Databank (http://databank. worldbank. org/ddp/home. ... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | An upper limit for the uncertainty associated with a possible trend in soil emissions is assessed above by means of a special case (case II) of our estimation procedure (see Figs. 4 and 5a ). To make sure that our estimates of NO x and CO 2 emission changes are indeed insensitive to the interannual meteorological vari... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 1 and 0. 3 % in the periods from 1996 to 2001 and from 2001 to 2008, respectively. It is important that using different estimates of conversion factors cannot "reconcile" our CO 2 and emission trend estimates with the corresponding EDGAR v4. 2 and GCP data for the first period. Moreover, possible uncertainties in the N... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Summary and conclusions This study explores the idea of verification of CO 2 emissions data by means of satellite measurements of tropospheric NO 2 column amounts. Indirect estimates of CO 2 emissions are obtained from the measurement-based estimates of NO x emissions by applying the emission factors from the EDGAR v4.... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | The performed analysis involving several variants of our estimation procedure indicates that these differences cannot be explained by systematic uncertainties in our baseline estimates. In contrast, some quantitative differences between the strong positive trends in the bottom-up and indirect topdown estimates for the ... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 2 and PKU-CO2 inventory data. The comparison has revealed that our estimates agree better with the PKU-CO2 inventory than with the EDGAR inventory. This result can be considered as evidence that the accuracy of our measurement-based estimates of emission changes is at least comparable with the accuracy of the correspon... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Acknowledgements. This study was supported by the Russian Government under the contract Nos. 11. G34. 31. 0014 and 11. G34. 31. 0048. The simulations were performed on the computer cluster of Siberian Federal University. I. B. Konovalov acknowledges support from the Russian Foundation for Basic Research (grant N... | 10.5194/acp-13-9415-2013 | article | en | 2,013 | false | false | true | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | We propose a novel fragment assembly method for low-resolution modeling of RNA and show how it may be used along with small-angle X-ray solution scattering (SAXS) data to model low-resolution structures of particles having as many as 12 independent secondary structure elements. We assessed this model-building procedure... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We propose a computational procedure that uses small-angle Xray solution scattering (SAXS) data to obtain low-resolution approximations of RNA structures. This process can be used as a diagnostic tool to help confirm predicted secondary structures with a higher degree of certainty than chemical footprinting approaches ... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Methods Here we describe a novel fragment assembly method RFR, which uses a sophisticated, variable-length fragment database, and insights into RNA secondary structure organization in order to significantly speed up the conformational search. | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | A fragment database may occasionally lack coverage; if it does, we resort to alternative strategies for subdividing secondary structure elements into strands and perform fine sampling of these subdivided flexible parts. Because these parts represent minor portions of the considered structures, we still substantially re... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | RNA Database We started our study with the RNAJunction database [33] , which contains only junction structures, and idealized helices produced by X3DNA [34]. This is not unlike the approach in [35] , where RDC data were used to determine the overall orientation of the helices to create a coarse-grained model of the ... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Our database contains tertiary structures of a total of 33,000 secondary structure elements and more than 62,000 strands, among which there are more than 11,000 loop strands. | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Sampling Algorithm Secondary structure definition provided as an input, is used to split predicted 3D structure into a tree of separate secondary structure elements. Thus, replacement of an element in any point of the tree with a 3D structure would only affect the placement of elements below it in the tree hierarchy (s... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Each replacement step consists of superimposing boundary atoms onto the boundary atoms of the previous element in the topology of the secondary structures, and then minimizing the 3 last dihedral angles of those boundary elements to assure a contiguous backbone. In the case of insufficient fragment coverage, version B ... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Experimental data are acquired by SAXS experiments and then fitted by scaling intensity so that the best x 2 measure is obtained using the CRYSOL program [39]. E exp ~x2 ~1 N p X Np i~1 ½ I e (s i ){c : I(s i ,r,dr) d(s i ) Where N p is the number of points of experimental data; I e (s) is the experimental data curve;... | 10.1371/journal.pone.0078007 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Scoring Function The scoring function is a sum of heuristic terms corresponding to the similarity of database fragment sequences to modeled sequences, geometric model quality terms, and fit to experimental data: E score ~wseqsim E seqsim zw geom E geom zw exp E exp E seqsim is a fragment match score that takes into acc... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SAXS Experiments Samples at concentrations of 2. 2-3. 8 mg/ml for stem loop 3 of 7SK RNA (HP3) and 0. 7 mg/ml to 1. 2 mg/ml for stem loop 4 of 7SK RNA (HP4), both in 50 mM cacodylate buffer at pH 6. 5, were measured on the X33 beamline [44] operated by European Molecular Biology Laboratory at DORIS III storage ring. ... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | SAXS Envelope Modeling Consistency checks between frames were performed automatically by X33 automated processing system [45] using ATSAS software [46]. The expected molecular masses of the solutes were estimated from intensity extrapolated to zero angle, and were found to be consistent with the expected masses for ... | 10.1371/journal.pone.0078007 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Model Visualization Atomic model structures were superimposed over SAXS envelopes using DAMSUP software [49]. Superpositions between atomic models were then improved using PyMol [31] , to minimize discrepancy between model best fitting to the envelope, and the other model. Secondary structure trees were created using... | 10.1371/journal.pone.0078007 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To facilitate the assessment of convergence speed, we have added the number of iterations (out of a maximum of 3000 for all runs) needed before the minimumenergy structure was found. Length in nucleotides and the number of different secondary structure elements are also indicated to facilitate assessment of the structu... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This comparison proves that while ROSETTA computed for a longer time, and produced more decoys, it didn't propose better models, even after filtering by fit to the SAXS data. The comparison of the accuracies and expected RMSD values from random modeling (table 2 ) clearly indicate the size and complexity of molecules ... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Comparison of the HP4 Model to the NMR-derived Structure SAXS data were measured for stem loop 4 (HP4) of 7SK RNA. The sequence used for the SAXS analysis (shown in Figure 7 ) is similar to that used for the NMR analysis (deposited in PDB as 2KX8 [51] ). Both are parts of the Homo sapiens 7SK sequence. We used a cons... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | HP3 Model Proposal We also used our method to propose two models for the stem loop 3 (HP3) of 7SK RNA (fig. 9 ), in accordance with two secondary structures of 7SK proposed by either [12] and [13]. The latter model [13] , was based upon evolutionary analysis of 7SK which suggested a more symmetric secondary structu... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Discussion We report a novel method for modeling RNA structures using pre-established secondary structure predictions, SHAPE-based determination for improved accuracy, and low-resolution tertiary structure reconstruction using SAXS data. Used together, these methods show great potential to overcome the difficulties cur... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments MJG and ACDB would like to thank Dmitry I. Svergun for discussions, and reading draft of the paper. MJG would like to thank Eckart Bindewald for providing the RNAJunction database in an SQL format [33], which was essential for the initial parts of the research and also gave us an excellent ''gold st... | 10.1371/journal.pone.0078007 | article | en | 2,013 | true | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The work of MJG was partially funded by the SAXIER ( RIDS-011934 ) grant from EU. ACDB and DMZ were funded by French Agency for Research (grant TrscrREGsnRNP ANR-06-BLAN-0072 ); CNRS, INSERM, University of Strasbourg and the SPINE-2 European project (Contract LSHG-CT-2006-031220 ). DMZ received a doctoral fell... | 10.1371/journal.pone.0078007 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We took advantage of our study to address this question by comparing our data with data freely available on public databases, in order to extend our analysis to a variety of stimulation conditions and to other mouse and human DC subsets. We identified, for the first time to the best of our knowledge, a core set of NF-κ... | 10.1002/eji.201243106 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | 1A ). In particular, pDCs did not undergo a cell-fate conversion into cDCs at MCMV infection leads to a profound and convergent genetic reprogramming of all splenic DC subsets in vivo. Genome-wide expression analysis was performed on quiescent (q) versus activated (a) immune cells isolated from the spleen of untreated ... | 10.1002/eji.201243106 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | The legend is the same as for Figure 1C. The GEO datasets used are listed in Table 1. For each condition, data are shown from pooled replicates of at least two independent experiments. specific membrane markers, Siglech and Ccr9. Similarly, a CD11b + cDCs and a CD8α + cDCs also kept the expression of their respective... | 10.1002/eji.201243106 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Microarray experiments and analyses Microarray and real-time PCR experiments were performed, processed, and analyzed as described [33]. Genes differentially expressed between quiescent and activated DC subsets (Fig. 2A and B ) in a statistically significant manner (false discovery rate ≤0. 05) were identified using V... | 10.1002/eji.201243106 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgements: We thank Pierre Grenot and Atika Zouine for technical support on cell sorting, Violaine Alunni and Christelle Thibault-Carpentier from the Plate-forme Biopuces ( Strasbourg, France ) for performing the microarray experiments (www. microarrays. ustrasbg. fr),and Dr. George S. Yap ( Center f... | 10.1002/eji.201243106 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Online Self-Assessment In the course of ALS, patients need alternative ways of communicating, especially because of dysarthria and progressing physical impairment. An increasing number of patients rely on novel methods, such as the Internet, for communication; therefore we chose the Internet self-assessment method for ... | 10.2196/ijmr.2463 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Data Analysis Relevant data was recorded via the Web-based database and analyzed with PASW Statistics version 19. 0 for Windows. Regarding the CNAQ independent two-sample t tests with between subject factor group (patients with "mild to severe" symptoms vs patients "not affected") and within subject factor symptoms (sw... | 10.2196/ijmr.2463 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | This result may be explained by early satiety after eating small amounts due to ALS-related weakness of the patients' diaphragm [26] , supported with evidence from patients with paralysis of the diaphragm who developed peri-or postprandial dyspnea and fatigue [26]. More speculatively, the known change of inflammatory... | 10.2196/ijmr.2463 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments The authors thank the study nurses Kerstin Krause , Dorit Strassenburg , and Birgit Koch , the institute for Biometry and Epidemiology under the leadership of Dr. Peter Martus , and the ALS patients for their participation and support. This study received funding from the German Federal Ministr... | 10.2196/ijmr.2463 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements. The authors acknowledge useful discussion with David J. Wilman , Massimo Dotti , and Emanuele Ripamonti. The authors thank the anonymous referee for a thorough report, which greatly improved this manuscript, and Astrid Peter for his helpful and detailed language revision. The authors would like t... | 10.1051/0004-6361/201220915 | article | en | 2,013 | false | false | true | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | R. G. and M. P. H. are supported by US NSF grants AST-0607007 and AST-1107390 and by a Brinson Foundation grant. This research has made extensive use of the GOLDmine database (Gavazzi et al. 2003) and of the NASA/IPAC Extragalactic Database (NED), which is operated by the Jet Propulsion Laboratory, California ... | 10.1051/0004-6361/201220915 | article | en | 2,013 | true | false | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | The few isolated pixels greater than the +3σ sky limit have been replaced with a 0 using a Python script. | 10.1051/0004-6361/201220915 | article | en | 2,013 | false | true | false | false | Physics and Astronomy | https://openalex.org/fields/31 |
cc-by | Sequencing and assembly We sequenced a 43-year-old root-grafted copy of the P. abies clone Z4006, which originated from a tree in Ragunda, central Sweden, collected in 1959. Many copies of this clone are available in clone archives and seed orchards, and it has been extensively used in Swedish breeding programs. We est... | 10.1038/nature12211 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | More than 86% of the elements remained as singletons, indicating that LTR-RTs are quite divergent and that there are several low-abundance families. We searched three LTR-RT families for signatures of unequal intra-element recombination events in scaffolds. 50 kb and 20 complete fosmids 33. For families ALISEI, 3K05 a... | 10.1038/nature12211 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Complete LTR-RTs were identified using a combination of de novo searches and manual inspection. WGS assemblies from shallow sequencing (3. 8-12. 53) of P. sylvestris, A. sibirica, J. communis, T. baccata and G. gnemon were produced using the CLC Bio de novo assembler. For website and accession number information, see S... | 10.1038/nature12211 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors would like to acknowledge support from the Knut and Alice Wallenberg Foundation. Additional funding was provided in particular by the Swedish Research Council (VR) , the Swedish Governmental Agency for Innovation Systems (Vinnova) , the Swedish Research Council for Environment, Agricult... | 10.1038/nature12211 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments Authors would like to thank RIIDFCM CYTED ( 209RT0380 ) network for supporting collaborative research on development of bioactive metal-based compounds and RIDIMEDCHAG CYTED , and also the financial support of Fundação para a Ciência e Tecnologia (FCT, Portugal ), PEst-OE/QUI/UI0100/2011 and CIÊN... | 10.1016/j.jinorgbio.2013.02.010 | article | en | 2,013 | false | false | true | false | Chemistry | https://openalex.org/fields/16 |
cc-by | In the present study, we used a new approach based on structural and in silico analyses to find new 4E-IPs. Using a refined eIF4E-binding motif to search databases for potential 4E-IPs, we found a CCR4 family member, Angel1, which displays an eIF4E-binding motif in its C-terminal domain. | 10.1093/nar/gkt569 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Cell lines Growth conditions and Angel1-shRNA accession numbers are detailed in Supplementary Methods. | 10.1093/nar/gkt569 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Angel1, a member of the CCR4 family, acquired an eIF4E-binding motif in vertebrates To find new eIF4E partners, our first approach was to look for sequences in protein databases that contained an eIF4E-binding consensus motif, YxxxxLÈ. However, scanning databases with the webserver Prosite (http:// www. expasy. org/too... | 10.1093/nar/gkt569 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The resulting set of sequences that were tolerated by the peptides and that could still interact with eIF4E constituted the refined eIF4E-binding motif matrix (Figure 1A ). Scanning the multi-species UniProtKb/Swiss-Prot database with Prosite revealed that the refined eIF4E-binding motif was present in 582 sequences (... | 10.1093/nar/gkt569 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS The authors thank Nahum Sonenberg , Xavier Fant and Simon Morley for antibodies, and Vincent Legagneux and Dominique Morello for helpful discussions. | 10.1093/nar/gkt569 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Representations and Formulation of the Problem The recovery of shallow meaning, and semantic role labels in particular, has a long history in linguistics (Fillmore 1968). Early attempts at systematically representing lexical semantics information in a precise way usable by computers, such as Levin's classification or ... | 10.1162/coli_a_00158 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
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