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cc-by | Analysis of sequence and structure databases addresses a fundamental safety question: does the introduced protein share any sequence or structural similarity with proteins known to pose possible toxicological hazards? These databases range from repositories of protein sequences derived from translations of nucleic acid... | 10.3109/10408444.2013.842956 | review | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Recently, population threshold doses for elicitation of allergic reactions to peanut allergens were proposed based on the review of clinical records for 286 peanut-allergic patients in France (Taylor et al. , 2010). The threshold dose was low for the most sensitive population (approximately 2-4 mg/person) and consider... | 10.3109/10408444.2013.842956 | review | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | CP4. TTC levels were estimated for acute and chronic exposures based on available toxicology data for a variety of different proteins, many of which are enzymes used in food processing. TTC levels were determined following adjustments to correct for purity of enzymes in fermentation batches tested in animals and applyi... | 10.3109/10408444.2013.842956 | review | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | approximately 100 times what humans might consume (based on the European and North American maize consumption Dietary Exposure Evaluation Model [DEEM] UK and DEEM US databases, Exponent, Inc;WHO GEMS, 2006), and no treatment-related adverse effects were reported. These studies have been reviewed by the EFSA and results... | 10.3109/10408444.2013.842956 | review | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements The authors and Task Force members thank the following individuals for participating in the review process and for providing many constructive comments and suggestions: Bruce Chassy , University of Illinois, Urbana-Champaign; Andrew Cockburn, University of Newcastle and Toxico-Logical Consulting Ltd.... | 10.3109/10408444.2013.842956 | review | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements. The experimental part of this work was partially supported by Chapman Chair funds, kindly supplied by the late Norbert Untersteiner during F. Domine's stay at the Geophysical Institute, University of Alaska Fairbanks. F. Domine is very indebted to W. R. Simpson for organizing his stay at UAF , and... | 10.5194/tc-7-1915-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Back Close Full specifically on understanding the atmospheric natural variability at the annual and interannual time scale (de Angelis et al. , 2003; Correia et al. , 2003; Vimeux et al. , 2008). However, logistical constraints and harsh weather conditions prevailing over the high altitude cold glaciers of the Andean ... | 10.5194/cpd-9-3399-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | We assessed the percentage errors and the mean angular errors. These direction estimates are expected to be accurate when participants have memorized a well-developed, map-like representation of the environment [10]. This task measures survey knowledge. Real wayfinding task: This task consisted of reproducing the lear... | 10.1007/978-3-642-40483-2_1 | book-chapter | en | 2,013 | true | false | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | For the Allocentric Sketch mapping task, the ANOVA did not reveal any significant effects for the Input Devices or Rotation factors (p>0. 800; p>0. 300; two-way interaction, p>0. 100). The performances did not reveal any differences among the four VR learning conditions. Concerning the Allocentric starting point estima... | 10.1007/978-3-642-40483-2_1 | book-chapter | en | 2,013 | true | false | false | false | Engineering | https://openalex.org/fields/22 |
cc-by | Methods GLobal epidemic and mobility model. We use the GLobal Epidemic and Mobility (GLEaM) model 24, [33] [34] [35] [36] [37] [38] , which is based on a high definition geographically structured metapopulation approach 39, 40. The model is composed of three layers. The first one, the population layer, integrates di... | 10.1038/srep00810 | article | en | 2,013 | true | false | false | false | Mathematics | https://openalex.org/fields/26 |
cc-by | Acknowledgements We are grateful to the IATA and OAG for making the airline commercial flight database available to develop GLEaM. This work was partially funded by the DTRA -1-0910039 award to A. V. The views and conclusions contained in this document are those of the authors and should not be interpreted as rep... | 10.1038/srep00810 | article | en | 2,013 | true | false | true | false | Mathematics | https://openalex.org/fields/26 |
cc-by | , 2011). The recognition and lysis of target cells by NK cells pass through sensing "missing self " due to the lack of MHC class I molecules and through interaction of activating receptors with specific ligands. How does the interaction between monocytes or macrophages and NK cells trigger immune response? Both cell to... | 10.3389/fimmu.2012.00403 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | NKp46-DNAM-1 INTERACTIONS In human, the susceptibility of macrophages to be lysed by autologous NK cells can also be mediated by the activating receptors NKp46 and DNAM-1. Thus, blocking of NKp46 and DNAM-1 decreases NK cell cytotoxicity against cytomegalovirusinfected macrophages and LPS-stimulated macrophages derived... | 10.3389/fimmu.2012.00403 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | 2012 ). In the present study, CD-1 fetuses and neonates were exposed to low doses of BPA [0. 025, 0. 25, or 25 μg BPA/kg body weight (bw)/day] administered to their mothers from the end of gestation day (GD) 8 through day 16 of lactation. Female offspring were examined for reproductive outcomes and found to have decrea... | 10.1289/ehp.1205588 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 1 H NMR analyses. All 1 H NMR spectra were obtained on a Bruker DRX-600-Avance NMR spectrometer (Bruker, Wissembourg, France) operating at 600. 13 MHz for 1 H resonance frequency using an inverse detection 5 mm 1 H-13 C-15 N cryoprobe attached to a cryoplatform (the preamplifier cooling unit). The 1 H NMR spectra were ... | 10.1289/ehp.1205588 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | 3 Hz to the free induction decay. To confirm the chemical structure of metabolites of interest, we performed two dimensional (2D) 1 H-1 H COSY (correlation spectroscopy) and 2D 1 H-13 C-HSQC (heteronuclear single quantum coherence spectroscopy) NMR experiments on selected samples. Data reduction and multivariate statis... | 10.1289/ehp.1205588 | article | en | 2,013 | true | false | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | SIMCA-P software (V12; Umetrics AB, Umea, Sweden) was used to perform the multivariate analyses. | 10.1289/ehp.1205588 | article | en | 2,013 | false | true | false | false | Environmental Science | https://openalex.org/fields/23 |
cc-by | Background: While a large body of work exists on comparing and benchmarking descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 amino acid descriptor sets have been benchmarked with respect to their ability of establishing bioactivity... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Background: While a large body of work exists on comparing and benchmarking descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 amino acid descriptor sets have been benchmarked with respect to their ability of establishing bioactivity... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Summary of the benchmarking performed In the current work all descriptor sets are used on four different data sets by constructing structure-bioactivity models and comparing their performance (see Table 2 for details). The datasets are firstly a previously published set of 58 dipeptides that have an inhibitory effect... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 70-30 validation on ACE inhibitors The first benchmark performed on the dataset of dipeptides inhibiting ACE was a 70-30 validation experiment where a random 70% of the data set was used for training and 30% for testing. The results of this validation on the test set are shown in Figure 1. The figure shows that all de... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 627 log units and R 0 2 0. 566). Given that the ProtFP (Feature) descriptor set merely encodes for presence or absence of features (amino acids) and that dipeptides are modeled (hence only two features per datapoint) a slightly lowered performance was expected. The BLOSUM, ProtFP (PCA5) and ProtFP (PCA8) (RMSE 0. 496 -... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The well-performing descriptor sets ProtFP (PCA3), Z-scales (3) and MS-WHIM also display a clustering similar to Z-scales (Binned). The PCA shows the highly active peptides to cluster together and the lesser actives are separated from these actives. Hence, overall investigating the 'Neighbourhood Behavior' in the descr... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Furthermore, the descriptor sets on the protein side now describe a smaller part of the entire data set as we also have the presence of chemical descriptors, which are held constant in the different models. The best performance has been obtained in this case by the Z-scales (3) and Z-Scales (3) combined with Z-Scales (... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | LOSO validation GPCRs In order to benchmark the extrapolation capabilities of the descriptor set a Leave-One-Sequence-Out experiment was performed on the GPCR dataset, the results of which are shown in Figure 4. The overall performance is worse compared to the 70-30 benchmark (MCC values between 0. 367 and 0. 400 and ... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Analysis of GPCR target space From the PCA analysis of target space we can rationalize the poor performance on the histamine receptors (Figure 5 , and Additional file 1: Figures S6, S7, S8). In the PCA of all GPCR targets used in this dataset, and employing the different descriptor sets, the histamine receptors are no... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 70-30 validation on NNRTIs While the above GPCR ligand dataset was based on rather diverse ligands, the NNRTI dataset employed in this study covers a more neatly defined area of both chemical (ligand) space as well as biological (target) space and hence we also included the set. Moreover, this set has been very difficu... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | It is striking that ProtFP (Feature) performs significantly better on this data set than the other two sets. On the NNRTI set, ProtFP (Feature) ranks 1st in the 70-30 validation and 4th in the LOSO validation, in the ACE inhibitor set it ranks 16th and also in the GPCR set the descriptor ranks 16th. A PCA analysis was ... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Conclusions for NNRTIs and mutants The NNRTI set represented a different data set compared to the GPCR ligand dataset evaluated above, as it consists of a number of highly similar sequences and compounds and, hence, resembles a typical data set one might encounter in lead optimization. It is concluded that in these cas... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | LOSO validation on PIs The LOSO experiment was performed slightly different on this dataset. Given the very large size and the computational infeasibility to repeat this for 16 descriptor sets, not a single target was left out but 10% at a time. From earlier work it was known that this can indeed be done and that the r... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Final descriptor set ranking The final ranking of the individual descriptor sets is given in Table 3 and Figure 12. The table included the individual ranks of all descriptor set in each experiment (on a scale of 1 to 16) and a final overall ranking (which is calculated as the median of the individual rankings). Also... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 0 (±2. 5)), Z-Scales (3) (median rank 4. 5 (±1. 5)), MSWHIM (median rank 5. 5 (±2. 5)), Z-Scales ( 5 ) (median rank 6. 5 (±3. 5)), and ProtFP (PCA3) (median rank 7 (±2. 0)). Following from the results it is apparent that combining Z-Scales (a physicochemical descriptor) with complementary information leads to synergy,... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In this respect it would be interesting to investigate the use of non-alignment dependent descriptors such as PROFEAT [42] , CTD [43] , or descriptors from the PROPY package [44]. A final option could be the usage of chemogenomics based descriptors. These can consist of phylogenetic trees which are generated based o... | 10.1186/1758-2946-5-42 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Training times One final property of the descriptor sets has not been highlighted yet. On a workstation with a core i7 860 CPU and 16 GB memory, considerable differences in training times were found for the individual descriptor sets. On the datasets used in this work, as a rule of thumb ProtFP (Feature) showed the fas... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Conclusions Overall performance differences between amino acid descriptor sets used in this study were rather small, with differences in the order of RMSE differences between 0. 01 -0. 1 log units. Hence, as a first approximationand with some differences between datasets -all descriptor sets considered in this study ca... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | On the other hand there are 3 descriptor sets that consistently score less well on the datasets used here, namely ProtFP (PCA8), ProtFP (Feature), and ST-Scales. Based on the information available, these would be less ideal for use in PCM models. | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Benchmark datasets for the descriptor sets Analyzing similar and different behavior of AA descriptor sets is relevant to judge how similarly two descriptor sets behave as shown previously [21]. However, this analysis does not yet give any information how relevant the information captured by a particular descriptor wou... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | GPCR data set The second bioactivity data set employed for benchmarking different amino acid descriptor sets comprised a subset of 32 human monoamine receptors (class A GPCRs listed in Additional file 1: Table S2 ; see also Additional file 1: Figure S17 regarding the subset of receptors used) obtained from ChEMBL ve... | 10.1186/1758-2946-5-42 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Finally compounds were clustered (using the ECFP_6 fingerprint, also used to train the models) to obtain a total of 100 chemically diverse 'actives' and 75 chemically diverse 'inactives' per receptor, in addition a random 25 compound from ChEMBL were included as presumed inactives (based on the work of Heikamp and Bajo... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 70-30 validation The first benchmark employed in this study was a '70-30' validation experiment. Each descriptor set was used in turn in combination with each of the datasets, and a model was trained on a random 70% of the data available and used to predict the bioactivities of the remaining 30% of the data. This proce... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For the bioactivity datasets employed for PCM modeling (which takes both ligand-side and protein-side descriptors into account) this benchmark provides an answer to two different questions. Firstly, the model was asked to make bioactivity predictions for those compounds that are not present in the training set and henc... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Leave-one-sequence-out validation This validation experiment was performed for each target in order to assess extrapolation abilities of the PCM models in the biological / target domain. Hence this validation was only applied to the datasets containing targets (GPCR set, NNRTI set, and PI set). In this part of the work... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | PCM modeling method Both regression and classification models were generated in Pipeline Pilot Version 8. 5 using the R-statistics modeling package version 2. 12. 1 [50, 59]. Modeling was performed using the 'randomForest' package in R Statistics [60]. The size of the forest was experimentally determined to be optima... | 10.1186/1758-2946-5-42 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Comparison to QSAR models For the PCM datasets (GPCR, NNRTI, and PI) also dedicated QSAR models were trained per target using a 70% -30% approach. Of these models the average RMSE / MCC and R 0 2 / sensitivity were calculated along with the standard deviation. The results of these models are shown in Additional file 1:... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Descriptor set ranking Finally, to obtain a broadly derived performance measure all 16 amino acid descriptor sets were ranked based on their performance per dataset per experiment per validation parameter. This rank-based assessment prevents a single dataset that is modeled very well or very badly (as expressed in RMSE... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Figure12Median rank of the descriptor sets in the bioactivity benchmarks. The median is calculated over all 14 ranks (1 rank per dataset, per experiment, per validation type), also shown the median average deviation (MAD). The best three descriptor sets have a median rank < 5 among which the combinations of Z-scales (3... | 10.1186/1758-2946-5-42 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The financial support of Tibotec BVBA is gratefully acknowledged. ICC was supported by a stipend from the Pasteur -Paris University (PPU) International PhD programme. | 10.1186/1758-2946-5-42 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DNA Microarray Analysis We analyzed TTK DNA copy number in the different tumor subtypes (46 TNBC; 33 Her2; 39 LB and 35 LA) and in 17 healthy tissue samples. We purified DNA from frozen tumor samples with the use of a standard phenol/chloroform procedure, as described in [30] and hybridized 500 ng of genomic DNA onto... | 10.1371/journal.pone.0063712 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We then fitted a linear mixed model by using the nlme package using Restricted Maximum Likelihood (REML) [34]. The model included the tumors, and in normal breast tissues (N). (C) Correlation between TTK protein and RNA levels. Omic data obtained in panels A and B reveal the consistency of TTK measurements between RNA... | 10.1371/journal.pone.0063712 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We dried the processed slides by centrifugation and scanned them using a GenePix 4000B microarray scanner (Molecular Devices). We determined spot intensity with MicroVigene software (VigeneTech Inc). The data obtained for TTK was part of a larger set of 27 RPPA arrays that we used to analyze the same tumor samples and ... | 10.1371/journal.pone.0063712 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Immunoblot (IB) For each extract, we separated 10 mg of protein on 4-12% TGX gels (BioRad) and transferred onto nitrocellulose membranes (BioRad). We saturated membranes with TBST-BSA and incubated them overnight at 4uC with the appropriate primary antibodies diluted in TBST-BSA. After washes, we incubated membranes wi... | 10.1371/journal.pone.0063712 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Cell Cycle Analysis by Flow Cytometry We collected siRNA-treated floating and detached (after trypsinization) cells. Then, we washed them once with PBS and then with PBS containing 0. 5% BSA. We fixed the cells in cold 70% ethanol with gentle vortexing. After fixation, we incubated the cells in PBS containing 10 mg/ml ... | 10.1371/journal.pone.0063712 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The error bars represent the standard deviation of the mean and asterisks, the p values from Student's t test (*p,0. 05; **p,0. 01; ***p,0. 001). doi:10. 1371/journal. pone. 0063712. g004 Annexin V assay: Additionally, we determined the proportion of apoptotic cells by using the annexin-V-FLUOS staining kit (Roche) acc... | 10.1371/journal.pone.0063712 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Soft-agar Tumorigenicity Assay A day after siRNA transfection, we trypsinized MDA-MB-231, MDA-MB-468 and HCC70 cells. We resuspended 5610 3 cells in 0. 35% soft-agar medium, consisting of equal volumes of 0. 70% agarose (A4018, Sigma) and 2X culture medium, and plated onto 1 ml of solidified 0. 5% soft-agar in 6-well p... | 10.1371/journal.pone.0063712 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | High Expression of TTK is Associated with Triple-negative Breast Cancers We have constituted our tumor collection to get a similar number of biopsies for each of the 4 main breast cancer subgroups. Biopsies (46 TNBC, 33 Her2, 35 LA and 40 LB), obtained from patients treated at the hospital of Institut Curie (Biological... | 10.1371/journal.pone.0063712 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For in vitro analysis, we selected three TNBC cell lines, MDA-MB-468, MDA-MB-231 and HCC70 with high, intermediate and low TTK protein levels, respectively (Figure 3 ). These three cell lines are mutated for TP53 gene (www. sanger. ac. uk/genetics/CGP/ cosmic). In addition, we included in our study the non-malignant c... | 10.1371/journal.pone.0063712 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | TTK Depletion in Triple-negative Breast Cancer Cell Lines Induces Apoptosis We performed additional experiments to assay whether TTKdepleted cells undergo cell death by apoptosis. For the same reasons as previously mentioned, we measured the induction of apoptosis at different times, 72 h post-transfection for MCF10A c... | 10.1371/journal.pone.0063712 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments We are grateful to Dr Bernard Asselain ( Institut Curie, Research center, Inserm U900 ) and Martine Yann for their help during the selection of the human tumors of our cohort. We are indebted to Dr Xavier Sastre-Garau ( Institut Curie, Department of Tumor Biology ), his colleagues from the Biolog... | 10.1371/journal.pone.0063712 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Introduction Making health-related decisions can be difficult due to the amount and complexity of information available. Audio-visual information may improve memory for health information but whether audio-visual information can enhance health-related decisions has not been explored using quantitative methods. The obje... | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Eligibility criteria Peer-reviewed articles will be included, as well as ongoing research where datasets are available (eg, via clinicaltrials. gov, opengrey. eu or the Open Science Framework). The Participant/Intervention/Comparator/Outcome framework will be used to identify papers. Only articles published in English ... | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | true | Computer Science | https://openalex.org/fields/17 |
cc-by | Participants Research which includes adults aged 18 years and above will be included. If other age groups are included within studies, but data can be separated, those studies will be eligible for inclusion. | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Outcomes Health-related decision-making must be measured by one or all of the following: decisional conflict, confidence in decision or quality of decision. Subgroup analyses: if data allow, we will conduct separate meta-analyses for younger versus older adults or include age group as a subgroup analysis. | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Information sources Databases to be searched: Cochrane Database of Systematic Reviews; Database of Abstracts of Reviews of Effects; Cochrane Central Register of Controlled Trials; Cochrane database of methodology reviews; Cochrane methodology register: EBSCO, Ovid EMBASE, Ovid MEDLINE, PubMed, PsychINFO, Scopus and Web... | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | We have included the Cochrane Database of Systematic Reviews so that the reference lists of review articles can be checked to ensure relevant articles are captured. Data extraction process JES will be responsible for the creation of the data extraction form. The data extraction process will be subject to piloting by bo... | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Data items The data extracted will include the aim, comparator, study design (eg, RCT), the decision-making task (eg, choosing a treatment option), setting, conflicts of interest, demographic information about the population, randomisation process, effect sizes reported for the primary outcomes: decision-making measure... | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Synthesis methods For eligible studies, if effect sizes are not reported, they will be calculated from means and SDs, or from analysis of Open access variance or t-tests. Where sufficient data can be extracted, we will conduct random-effects meta-analyses of the SMDs, as we anticipate significant heterogeneity across i... | 10.1109/icc.2013.6654788 | article | en | 2,013 | true | false | false | false | Computer Science | https://openalex.org/fields/17 |
cc-by | This review is funded by the Economic HH, KLR, HAA and SPB provided feedback on the manuscript and all authors approved the final draft of the protocol. JES is the guarantor of the review. Funding This work was funded by the Economic and Social Research Council (ESRC) (grant number ES/V000071/1 ) and Open Access... | 10.1109/icc.2013.6654788 | article | en | 2,013 | false | false | true | false | Computer Science | https://openalex.org/fields/17 |
cc-by | Pseudosections P-T and T-X pseudosections have been calculated (1) to precise metamorphic P-T conditions and more particularly conditions of partial melting, and (2) to determine the type of prograde melting reactions. Phase relations have been modeled in the Ti(Mn)NKFMASH system using Perple_X'07 software (Connolly, ... | 10.1016/j.lithos.2012.10.005 | article | en | 2,012 | true | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 7 mW. The spectral resolution was 1 cm -1 using 600 g/mm grating. The spectral region from 1200 to 1800 was investigated in order to characterize the vibration mode of carbonaceous matter following the method proposed by Beyssac et al. (2002). Treatments of the RSCM data were undertaken using Peakfit software. | 10.1016/j.lithos.2012.10.005 | article | en | 2,012 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | 207 Pb. 208 Pb. 232 Th and 238 U masses are acquired. The occurrence of common Pb in the sample can be monitored by the evolution of the 204 (Pb + Hg) signal intensity, but no common Pb correction was applied owing to the large isobaric interference from Hg. The 235 Usignaliscalculated from 238 U on the basis of the ra... | 10.1016/j.lithos.2012.10.005 | article | en | 2,012 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | , 2010). At the beginning and at the end of every run, repeated analyses of the Manangoutry monazite (Paquette and Tiepolo, 2007) standard were treated as unknowns to independently control the reproducibility and accuracy of the corrections. Data reduction was carried out with the software package GLITTER® developed ... | 10.1016/j.lithos.2012.10.005 | article | en | 2,012 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | (1992) and Smith et al. (1998). The spot size used during all the sessions was around 20 μm. In this study, six data collection cycles (scans) were performed per analysis and count times (per scan) were 10 s for the 204 Pb. 206 Pb and 208 Pb mass peaks and background and 30 s for the 207 Pb mass peak. Unknown analyse... | 10.1016/j.lithos.2012.10.005 | article | en | 2,012 | false | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements This research was funded by the SEDIT programme (INSU , 2008(INSU, -2009 )). We thank the IRD-Quito for logistical support during the 2008 and 2010 field campaigns. We thank Francis Coeur , François Senebier , Jean-Luc Devidal and Gilles Montagnac , for their help in sample preparation, microp... | 10.1016/j.lithos.2012.10.005 | article | en | 2,012 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | , 1958; Hopson and McCroskey, 1972; Prigge et al. , 1981). Considering the potential interest of PEG as a faecal marker and its rapid determination by NIRS, Hassoun et al. (2007a) set up a 1000-sample database with wide ranges of PEG content in faeces. In an in vivo experiment with sheep (Hassoun et al. , 2007b) , v... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | PEG preparation, administration and NIRS measurement The PEG used was PEG 6000 (molecular weight 6000 da, Panreac Qimica SA, Barcelona, Spain). It was administered in solution form with plastic syringes. The PEG solution, with a concentration of 333. 33 g/l, was prepared a few days before in the laboratory with double ... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The PEG 1 faeces mixtures were dried (508C until constant dry weight) and ground through a 1-mm sieve, similarly to the procedure applied for faeces preparation during trials. The samples were scanned on a monochromator NIR spectrophotometer (NIRS 6500, Foss NIRSystems, Silver Spring, MD, USA). Measurement was done in ... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | , Port Matilda, PA, USA). Only wavelengths in the 1100 to 2500 nm range were used, because of the unstability of models built with visible wavelengths. Mathematical pre-processing was applied to spectra with detrending and normalization (SNV) of data, and use of the second derivative calculated on five consecutive poin... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The RPD (5s. d. /SECV) was calculated as an indicator of the quality of the models (Williams and Sobering, 1993). The Mahalanobis distance was used to compare spectra with the database and identify spectral outliers following Shenk and Westerhaus (1991). | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | NIRS calibration for PEG content The calibration itself had an R 2 5 0. 99 and a residual standard error (SEC) of 3. 05 g/kg. No major bias was observed in the calibration process, and there were only 13 outlier samples, that is, 2. 5% of the calibration database. The validation of the calibration model by cross-valida... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Discussion The precision of NIRS calibration was high, with a low measurement error (3. 47 g/kg) and high R 2 and RPD values. The analytical precision is of extreme importance in studies with markers because a small error in the quantification of markers in faeces has a strong effect on the calculation of feed intake... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | This is also confirmed by the fact that the spectra of experimental samples were well fitted to the calibration database, that is, no major change was observed between PEG added in vitro and PEG having transited in vivo. The estimation of PEG concentration in faeces by NIRS proved to be very efficient. As no alternativ... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Conclusions These results confirm that faecal PEG content can be estimated by NIRS with good accuracy, provided that faeces obtained from sheep fed the diet on which measurements are to be made are included in the general NIRS database for calibration. Because PEG is rapidly excreted, it is recommended that faeces be c... | 10.1017/s1751731113000323 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements The authors would like to thank J. M. Capron , S. Douls , V. Thiers and the technical staff of La Fage for their expertise in animal management and sample preparation. They are also grateful to L. Bonnal for his assistance in NIRS analysis. | 10.1017/s1751731113000323 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Background: Mobile phone text messaging (SMS) has the potential to promote adherence to tuberculosis treatment. This systematic review aims to synthesize current evidence on the effectiveness of SMS interventions in improving patients' adherence to tuberculosis treatment. Methods: We searched electronic databases (PubM... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Background: Mobile phone text messaging (SMS) has the potential to promote adherence to tuberculosis treatment. This systematic review aims to synthesize current evidence on the effectiveness of SMS interventions in improving patients' adherence to tuberculosis treatment. Methods: We searched electronic databases (PubM... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Databases We searched the following electronic databases: PubMed; EMBASE; Cochrane Central Register of Controlled Trials (CENTRAL); ISI Web of Science (Science Citation Index); Africa-Wide Information; Cumulative Index of Nursing and Allied Health (CINAHL); and World Health Organization (WHO) library databases (WHOLIS)... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Searching other sources We also searched the WHO International Clinical trials Registry Platform, Clinicaltrials. gov, and the Pan African Clinical Trials Registry (PACTR) for ongoing studies. In addition, we searched the website of the mHealth Alliance and the mHealth in Low Resource Settings' resources database [21]... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | true | Health Professions | https://openalex.org/fields/36 |
cc-by | Data extraction and management References were managed using Thomson ISI Research-Soft Endnote 9. 0 [23]. Two authors independently extracted descriptive and outcome data for each included article using a standardized data collection form, resolving any discrepancies by discussion and consensus. MN entered the final d... | 10.1186/1471-2334-13-566 | review | en | 2,013 | false | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Measures of treatment effect Data analysis was conducted using the Cochrane Collaboration Review Manager Version 5. 2 statistical software [24]. The outcomes of interest were all dichotomous. We calculated risk ratios (RR) and their corresponding 95% confidence intervals (CI) and p-values, when count data were availab... | 10.1186/1471-2334-13-566 | review | en | 2,013 | false | true | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Data synthesis and investigation of heterogeneity We assessed clinical heterogeneity by examining types of participants, interventions and outcomes in each study. We also assessed methodological heterogeneity by examining differences between studies in methodological factors such as the comparability of groups. All inc... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Frequency matching was utilized to match participants from the pilot study with controls in a 1: 4 ratio. We analyzed participants according to whether or not they received SMS reminders. Rates of sputum smear conversion and TB cure were provided for two scenarios. Scenario one included all 24 participants who took par... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Methods The evaluation used both qualitative and quantitative data collection methods. Structured interviews using a questionnaire were conducted among patients and staff. Additional information was collected from patient records, background documents and reports and clinic visits. | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Regarding completeness of outcome data, one study was judged to have an unclear risk of bias because it was unclear whether the proportion of missing data was balanced across intervention groups. Two studies were judged to have a low risk of bias because there were no missing data. One study was judged to have a high r... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Effects of intervention A meta-analysis of data from included studies was not done because of significant clinical and methodological heterogeneity among the studies. Findings for each study are described individually. Bridges. org 2005 [37] found that the SMS intervention and the clinic-based DOTS groups were simila... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Potential biases in the review process Although this systematic review adheres to the standardized guidelines of conduct and reporting of systematic reviews [22] , there are certain limitations. Although we did not set out to exclude non-English studies in this review, non-English studies may have been missed because ... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Acknowledgements We did not receive any dedicated funding for this manuscript. MN received salary support as an operational research fellow from the International Union against Tuberculosis and Lung Disease, Paris, France. | 10.1186/1471-2334-13-566 | review | en | 2,013 | false | false | true | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Frequency matching was utilized to match participants from the pilot study with controls in a 1: 4 ratio. We analyzed participants according to whether or not they received SMS reminders. Rates of sputum smear conversion and TB cure were provided for two scenarios. Scenario one included all 24 participants who took par... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | Potential biases in the review process Although this systematic review adheres to the standardized guidelines of conduct and reporting of systematic reviews [22] , there are certain limitations. Although we did not set out to exclude non-English studies in this review, non-English studies may have been missed because ... | 10.1186/1471-2334-13-566 | review | en | 2,013 | true | false | false | false | Health Professions | https://openalex.org/fields/36 |
cc-by | For each sample, three different LB films were taken to ensure reproducibility. For data processing, AFM data were processed using the Nanoscope (version 7. 30, Veeco) and the Gwiddion softwares. Each time, six images were recorded at the same time: trace and retrace height images (topography), trace and retrace amplit... | 10.1504/ijnt.2013.053511 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We thank the Région Aquitaine-Limousin and CNRS for supporting this work through the PhD grant of N. R. Faye and the equipment of the NSI platform ( CPER COLA2 ). | 10.1504/ijnt.2013.053511 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
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