Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs
© Chen et al; licensee BioMed Central Ltd. 2008
Received: 06 September 2007
Accepted: 18 February 2008
Published: 18 February 2008
As one of the most common protein post-translational modifications, glycosylation is involved in a variety of important biological processes. Computational identification of glycosylation sites in protein sequences becomes increasingly important in the post-genomic era. A new encoding scheme was employed to improve the prediction of mucin-type O-glycosylation sites in mammalian proteins.
A new protein bioinformatics tool, CKSAAP_OGlySite, was developed to predict mucin-type O-glycosylation serine/threonine (S/T) sites in mammalian proteins. Using the composition of k-spaced amino acid pairs (CKSAAP) based encoding scheme, the proposed method was trained and tested in a new and stringent O-glycosylation dataset with the assistance of Support Vector Machine (SVM). When the ratio of O-glycosylation to non-glycosylation sites in training datasets was set as 1:1, 10-fold cross-validation tests showed that the proposed method yielded a high accuracy of 83.1% and 81.4% in predicting O-glycosylated S and T sites, respectively. Based on the same datasets, CKSAAP_OGlySite resulted in a higher accuracy than the conventional binary encoding based method (about +5.0%). When trained and tested in 1:5 datasets, the CKSAAP encoding showed a more significant improvement than the binary encoding. We also merged the training datasets of S and T sites and integrated the prediction of S and T sites into one single predictor (i.e. S+T predictor). Either in 1:1 or 1:5 datasets, the performance of this S+T predictor was always slightly better than those predictors where S and T sites were independently predicted, suggesting that the molecular recognition of O-glycosylated S/T sites seems to be similar and the increase of the S+T predictor's accuracy may be a result of expanded training datasets. Moreover, CKSAAP_OGlySite was also shown to have better performance when benchmarked against two existing predictors.
Because of CKSAAP encoding's ability of reflecting characteristics of the sequences surrounding mucin-type O-glycosylation sites, CKSAAP_ OGlySite has been proved more powerful than the conventional binary encoding based method. This suggests that it can be used as a competitive mucin-type O-glycosylation site predictor to the biological community. CKSAAP_OGlySite is now available at http://bioinformatics.cau.edu.cn/zzd_lab/CKSAAP_OGlySite/.
Representing one of the most common but complicated protein post-translational modifications (PTMs), protein glycosylation is abundant in many cell surface and secreted eukaryotic proteins [1–3]. Glycosylation is involved in a variety of important biological processes including protein stability, solubility, secretion of signal, regulation of interactions, extracellular recognition, etc . Glycosylation is also strongly associated with marketed therapeutic proteins, since more than one-third of approved biopharmaceuticals are glycoproteins .
The detection of glycosylation sites in a query protein is very helpful to understand its biological function. Compared with the huge number of known protein sequences obtained from genomic and proteomic studies, the experimentally identified glycosylation sites are still limited. Proteomics analysis of glycoproteins by mass spectrometry (MS) is very promising to speed up the experimental identification of glycosylation sites . Meanwhile, computational detection of glycosylation sites is also playing an increasingly important role [4, 5].
N-linked and O-linked are two major types of glycosylation. N-linked glycosylation (N-glycosylation) is characterized by the β-glycosylamine linkage of N-acetylglucosamine (GlcNac) to asparagine (Asn) . It has been well established that the consensus sequence motif Asn-X-Ser/Thr is essential in N-glycosylation . The most abundant form of O-linked glycosylation (O-glycosylation), called "mucin-type", is characterized by α-N-acetylgalactosamine (GalNac) attached to the hydroxyl group of serine/threonine (Ser/Thr) side chains [7, 8]. Therefore, S and T (i.e. the one-letter abbreviations of serine and threonine) are regarded as mucin-type O-glycosylation sites. Mucin-type O-glycosylation is commonly found in many secreted and membrane-bound mucins in mammal, although it also exists in other higher eukaryotes [8, 9]. As the main component of mucus, a gel playing crucial role in defending epithelial surface against pathogens and environmental injury, mucins are in charge of organizing the framework and conferring the rheological property of mucus. Beyond the above properties exhibited by mucins, mucin-type O-glycosylation is also known to modulate various protein functions in vivo . For instance, mucin-like glycans can serve as receptor-binding ligands during an inflammatory response . Unlike N-glycosylation, the consensus motif has not been identified in the sequence context of O-glycosylation sites. Thus, computational prediction of mucin-type O-glycosylation sites in mammalian proteins is challenging and has received considerable attention. Prediction of O-glycosylation sites could offer valuable information for characterizing a new protein's functional and structural properties, like explaining mass spectrometry results as well as improving protein structure prediction . Considering the roles of mucin-type O-linked glycoproteins involved in different diseases, computational identification of O-glycosylation sites can also be helpful in drug design . In the current study, we focus on developing a new algorithm to detect mucin-type O-glycosylation sites in mammalian proteins.
A series of important prediction methods for mucin-type O-glycosylation sites have been elegantly developed. In 1993, Elhammer et al. used a matrix statistics method to initiate the prediction of O-glycosylation sites . Subsequently, a vector projection method was developed [12, 13]. Furthermore, a few state-of-the-art machine learning methods such as Neural Network (NN) and Support Vector Machine (SVM) were also heavily employed to perform the prediction [8, 14–18]. Some well-maintained O-glycosylation site prediction web-servers, such as NetOGlyc 3.1 , are also publicly available. Even so, the prediction accuracy of these methods is generally not high enough. Some methods revealed less convincing performance when benchmarked with independent experimental studies [19–21]. Therefore, development of more accurate O-glycosylation site predictor is required.
The input feature vector (i.e. encoding scheme) is very important in obtaining a machine learning algorithm based predictor. Generally the input for an O-glycosylation site predictor is presented by a 2n+1 residue long sequence with S or T in the center (i.e. the window size is equal to 2n+ 1). The common position-specific features such as the standard binary encoding have been widely used as input features [8, 15, 18]. Some predicted structural properties like the solvent accessibility and secondary structure of a glycosylation site's sequence context were also used as input features [8, 16]. Another possible useful encoding is the evolutionary information in the form of multiple sequence alignment profiles generated by PSI-BLAST program , which has also been integrated into the NetOGlyc 3.1 . Parallel to the method development of O-glycosylation site prediction, the sequence and structural characters of O-glycosylation sites were also investigated [14, 23, 24]. These analyses are very helpful in guiding the selection of new encoding scheme to predict O-glycosylation sites.
In the present study, the prediction of O-glycosylation sites was improved by seeking new encoding schemes. After evaluating different encoding schemes, it was found that the composition of k-spaced amino acid pairs (CKSAAP) is suitable for representing an O-glycosylation site's sequence context. The CKSAAP reflects the short-range interactions of amino acids within a sequence or sequence fragment, which has been successfully employed for the prediction of protein flexible/rigid regions  and protein crystallization . When k = 0, the CKSAAP reduces to the dipeptide composition, which has been applied in diverse prediction topics in the field of protein bioinformatics [27–29]. With the assistance of SVM, a predictor named CKSAAP_OGlySite has been set up to detect mucin-type O-glycosylation sites in mammalian proteins. The proposed encoding scheme resulted in a higher accuracy than the conventional binary encoding. The details about this proposed predictor are reported and the overall performance is benchmarked against two existing predictors.
Results and Discussion
Prediction accuracy of O-glycosylation sites based on different encoding schemesa
74.2 ± 1.7
81.9 ± 3.0
78.0 ± 1.9
0.567 ± 0.039
76.5 ± 3.5
74.6 ± 3.6
75.6 ± 3.1
0.523 ± 0.060
77.9 ± 1.7
86.5 ± 3.0
82.2 ± 1.8
0.655 ± 0.037
79.0 ± 5.2
83.0 ± 2.4
81.0 ± 2.6
0.628 ± 0.050
80.7 ± 3.3
85.6 ± 3.9
83.1 ± 2.8
0.671 ± 0.055
82.1 ± 2.3
83.9 ± 3.8
83.0 ± 2.4
0.665 ± 0.048
74.8 ± 4.1
78.3 ± 1.7
76.6 ± 2.3
0.536 ± 0.045
77.8 ± 3.4
76.6 ± 3.2
77.2 ± 2.4
0.548 ± 0.048
80.4 ± 2.2
82.3 ± 2.9
81.3 ± 2.3
0.631 ± 0.045
80.3 ± 1.9
85.7 ± 1.9
83.0 ± 1.8
0.666 ± 0.038
80.3 ± 1.8
82.5 ± 2.3
81.4 ± 1.3
0.632 ± 0.026
80.8 ± 1.5
81.9 ± 3.1
81.3 ± 2.2
0.631 ± 0.045
Comparison of CKSAAP_OGlySite with NetOGlyc 3.1
49.7 ± 4.8
88.0 ± 0.8
81.7 ± 1.4
0.364 ± 0.054
56.7 ± 3.2
95.6 ± 0.4
89.1 ± 0.8
0.575 ± 0.040
54.9 ± 0.3
91.6 ± 0.7
85.6 ± 0.5
0.473 ± 0.011
60.8 ± 0.8
85.4 ± 1.3
81.3 ± 1.2
0.416 ± 0.026
68.8 ± 1.7
92.9 ± 0.3
88.9 ± 0.2
0.608 ± 0.009
76.9 ± 0.0
86.1 ± 0.6
84.6 ± 0.5
0.549 ± 0.009
The negative dataset may contain numerous un-annotated positive sites, which is one of the major limitations of the machine learning based O-glycosylation site predictors. To remove these "potential" O-glycosylation sites within the data sets of negative sites, those with >40% identity with any positive site were discarded. The definition of the identity between two sites is detailed in the section of Datasets. Based on this strategy, some "true" negative sites with relatively high sequence identity with any positive site were filtered. Thus, it seems that only the "easy" negative sites remain in the training datasets, then one may argue that such a filtration may "artificially" result in a higher performance. To clarify this point, we performed another computational experiment by selecting negative sites without the filtration of 40% identity, and then the proposed prediction method was re-trained and assessed. As shown in Table 1, the predictor based on the new negative datasets only cause a minor difference of accuracy (-1.2% in predicting S sites and +1.7% in predicting T sites). Therefore, the filtration of 40% identity did not result in an overestimated accuracy.
Top ranked amino acid pairs
The top 20 features selected by correlation coefficient (CC-) and information entropy (IE-) based methods
Top 20 features
Performance of S+T predictora
82.9 ± 1.3
83.4 ± 1.8
83.2 ± 1.6
0.667 ± 0.033
63.7 ± 1.7
95.1 ± 0.3
89.8 ± 0.4
0.617 ± 0.017
Further analysis on the top k-spaced amino acid pairs may strengthen our understanding on the characteristics of the sequence surrounding O-glycosylation sites. As shown in Table 3, P, S and T frequently occur in these important amino acid pairs, which are in line with the observation that P, S and T residues frequently appear in the vicinity of O-glycosylation sites . As reported by Christlet and Veluraja , P at +3 and/or -1 positions strongly favors O-glycosylation sites, which is also correlated with our analysis that SXXP, TXXP, PS and PT are top ranked amino acid pairs (cf. Table 3). Moreover, the listed amino acid pairs also support the observation that the residues with small side chains are preferred to be located in O-glycosylation sites .
Comparison of different encoding schemes
Prediction performance based on the datasets filtered by amino acid compositiona,b
73.9 ± 3.8
83.1 ± 5.9
78.5 ± 3.2
0.590 ± 0.068
79.3 ± 2.0
86.8 ± 2.0
83.1 ± 1.8
0.677 ± 0.032
77.7 ± 2.7
83.1 ± 3.0
80.4 ± 2.5
0.612 ± 0.052
81.1 ± 1.8
88.0 ± 1.1
84.5 ± 1.1
0.699 ± 0.023
Why the CKSAAP encoding is better than the binary encoding in predicting O-glycosylation sites? The question may be answered from the following aspects. The binary encoding clearly characterizes amino acids in different positions surrounding a potential glycosylation site, but it is weak in reflecting the coupling effect of amino acid pairs at different positions. On the other hand, the CKSAAP pays attention on the correlation of amino acid pairs at different positions, but position specific amino acid information can not be inferred from the CKSAAP alone. It has been well known that there was no consensus motif identified for the neighbouring residues around O-glycosylation sites, but some frequently occurred amino acids were observed. Therefore, the CKSAAP encoding is particularly suitable for the prediction of O-glycosylation. Additionally, a similar conformation may be generally required by O-glycosylation sites. For example, it has been well established that O-glycosylation sites are preferred in coil or turn regions either situated near the termini of proteins, or in linker regions between domains . The CKSAAP encoding can elegantly reflect short-range interactions of amino acids and it is very informative in predicting the local conformation of a sequence fragment . That is probably another reason why the CKSAAP encoding can surpass the binary encoding in predicting O-glycosylation sites.
Comparison of CKSAAP_OGlySite with other predictors
The proposed CKSAAP_OGlySite method was benchmarked against NetOGlyc 3.1 , one of the best O-glycosylation site predictors. The benchmark was based on 1:5 datasets, almost the same ratio as used in NetOGlyc 3.1. To perform a comparison, all the testing examples in 1:5 datasets were submitted to the NetOGlyc 3.1 server  and the average prediction accuracy was also calculated.
The performance of our method is significantly better than that of NetOGlyc 3.1 by showing about 0.102 and 0.059 higher MCC value in predicting O-glycosylation S and T sites, respectively (cf. Table 2). It should be pointed out that some testing examples were possibly already selected in training NetOGlyc 3.1. Since the developers of NetOGlyc 3.1 did not distribute their training data set publicly, we were not able to exclude these examples from the analysis. In case the comparison is based on a completely independent dataset, the increased accuracy resulted from our method may be more significant. As reported in the paper of NetOGlyc 3.1 , different encoding schemes were jointly employed, including the binary encoding, predicted structural information and evolutionary information inferred from PSI-BLAST search. Noted that the structural properties used in NetOGlyc 3.1 were predicted from the sequence information with the assistance of other programs, the major input of NetOGlyc 3.1 is the sequence context of O-glycosylation sites and the corresponding evolutionary information. The sequence conservation is not highly required for O-glycosylation sites, the power of evolutionary information is limited . Using the current training and testing datasets, we also benchmarked the evolutionary information based encoding, and the result is only slightly better than that of binary encoding (data not shown). Therefore, it is reasonable that our CKSAAP_OGlySite is able to provide better performance than NetOGlyc 3.1.
The proposed CKSAAP_OGlySite method was also benchmarked against OGlyC method, a SVM-based O-glycosylation site predictor . When trained and tested in balanced datasets, OGlyC based on the binary encoding scheme reached an accuracy of 85.0% . Using the similar strategy for selecting the positive and negative sites, the same ratio of positive and negative sites (1:1), the same encoding scheme, window size (i.e. 2n+1 = 41) and machine learning method (i.e. SVM), the prediction accuracy of our method based on the binary encoding is much less impressive (about 78.0% accuracy in predicting S sites and 76.6% accuracy in predicting T sites) (cf. Table 1). The selection of training dataset in our method is based on a newer version of the Swiss-Prot database. The accuracy difference may be resulted from the different selection of datasets, especially the selection of negative sites. Using the same datasets and the same cross-validation, it has been clearly proved that the CKSAAP encoding based SVM model has a much higher accuracy than that of the binary encoding. Given the same datasets, the performance of our CKSAAP_OGlySite should be better than that of OGlyC.
With more and more O-glycosylation sites experimentally verified, we hope some standard training and testing datasets will be available in the near future. Thus, different prediction methods can be reliably benchmarked. Meanwhile, some well-established strategies in assessing different protein structure prediction methods (e.g. Live-Bench  and EVA ) should also be considered in evaluating different O-glycosylation site predictors.
A competitive mucin-type O-glycosylation site predictor named as CKSAAP_OGlySite has been developed in the present study. The proposed CKSAAP_OGlySite demonstrated higher prediction accuracy than some other existing predictors, although the overall accuracy is still not satisfactory and there is possibility to develop more accurate predictors in the foreseeable future. With the ability of reflecting the characteristics of the sequence surrounding the O-glycosylation sites, the CKSAAP encoding has been proved to be particularly suitable for the prediction of O-glycosylation sites. By using other state-of-the-art machine learning methods as well as combining other encoding schemes, it is expected the CKSAAP encoding can play an important role in developing new O-glycosylation site predicting systems.
To facilitate the biological community, a web-server of CKSAAP_OGlySite was constructed, which can be used for proteome-wide O-glycosylation site prediction. Since the training dataset used in the current method is merely based on a limited number of experimentally verified O-glycosylated proteins, it should be pointed out that the performance for proteome-wide prediction may be less impressive in comparison to the accuracy reported in this paper. On the other hand, if we have the prior knowledge that query proteins are known to be O-glycosylated, the prediction of such proteins may result in an expected accuracy close to the value reported in this paper.
The experimentally validated mucin-type O-glycosylation sites from mammalian proteins were extracted from the Swiss-Prot database (Release 52.4), which contains 103 proteins covering 125 S and 242 T sites, and were compiled into two positive datasets (Pos_S and Pos_T). Each site within the datasets is represented by a sequence fragment of 41 amino acids, where S or T is in the central position. For the sites located in N- or C-terminus, the number of upstream or downstream residues may be less than 20. To ensure a sequence fragment with a unified length, we assigned a non-existing amino acid O to fill in the corresponding positions. Thus, 21 different amino acids are considered in the present study to reflect the sequence context of a glycosylation site, which are ordered as ACDEFGHIKLMNPQRSTVWYO. To remove redundant fragments within the datasets, the initial datasets (Pos_S and Pos_T) were further filtered by a 40% sequence identity cut-off. Since each site is represented by a sequence fragment with fixed length, the sequence identity is simply based on the match between two fragments (i.e. no-gap alignment). Considering the middle residue in each fragment is always the same (S/T), the central position is excluded when calculating the sequence identity, meaning that only sixteen residues are maximally allowed to be identically matched in the alignment. The similar filtration method was previously used for the preparation of training datasets in the prediction of phosphorylation sites [34, 35]. Thus, our final positive datasets included 116 S and 212 T respectively [see Additional file 1 and Additional file 2]. It should be emphasized that the annotation of Swiss-Prot was regarded as a golden standard for selecting positive O-glycosylation sites, and the original publications for these O-glycosylation sites were not checked. Due to the potential annotation errors, the quality of the compiled O-glycosylation dataset was inevitably limited by the knowledge of Swiss-Prot database.
All S and T residues in these 103 protein sequences with no annotation related to O-glycosylation site were selected as negative sites. In the present study, 1506 non-glycosylated S residues and 2529 non-glycosylated T residues were initially selected, and were further compiled into two negative datasets (Neg_S and Neg_T). Likewise, we also filtered the negative data sets using a 40% sequence identity to avoid the redundancy. Furthermore, the negative site sharing over 40% identity with any of the positive sites was also discarded. Finally, we got 1153 non-glycosylated S and 1702 non-glycosylated T residues [see Additional file 3 and Additional file 4].
A new feature construction, the composition of k-spaced amino acid pairs (CKSAAP) based encoding, was employed. The detailed procedures are described as follows. Generally, a sequence fragment of 2n+1 amino acids (i.e. the window size is equal to 2n+1, and the maximal window size is 41 as defined in the section of Datasets) is used to define a glycosylation site. For k-spaced amino acid pairs (i.e. pairs that are separated by k other amino acids) within this sequence fragment, there are 441 possible types (AA, AC, AD, ..., OO). Then, a feature vector of that size is used to represent the composition of these pairs, which can be described as(c AA c AC c AD ... c OO )441
The value of each feature denotes the composition of the corresponding amino acid pair in the fragment. For instance, if an AD pair occurs m times in this fragment, the corresponding value in the vector (i.e.c AD ) is equal to m. The amino acid pairs for k = 0, 1, ..., k max are jointly considered in this study, so the total dimension of the proposed feature vector is 441 × (k max +1).
To benchmark the proposed CKSAAP encoding, the prediction based on the binary encoding was also carried out. In this encoding scheme, each amino acid is represented by a 21-dimensional binary vector, e.g. A (100000000000000000000), C (010000000000000000000), ..., O (000000000000000000001), etc. For a query O-glycosylation site represented by a fragment of 2n+1 residues, the central residue is always S/T, which is not necessary to be taken into account. Therefore, the total dimension of the proposed binary feature vector is 21 × 2n.
Due to the high dimensionality as well as the sparse nature of the CKSAAP encoding, the dimensionality reduction seems to be required. CC- and IE-based dimensionality reduction methods, previously reported by Chen et al. , were employed in this work.
CC-based feature selection
For each variable from the CKSAAP based feature vector (X) and the known predicted variable (Y), the correlation coefficient cor(X,Y) is computed. The value of cor(X,Y) is in the range from -1 to 1. Higher value of | cor(X,Y)| means the corresponding variable X is more significantly correlated with Y. To reduce the dimensionality, therefore only those variables with higher | cor(X,Y)| were kept.
IE-based feature selection
Where P(x i |y j ) is the posterior probability of x i given the value y j of Y. Then, information gain IG(X|Y) is given byIG(X|Y) = I(X) - I(X|Y)
The information gain IG(X|Y) indicates the additionally increased information about X provided by Y. For any two features (X1 and X2) from the CKSAAP encoding, if IG(X 1|Y) > IG(X 2|Y), the feature Y is regarded as more correlated with X1 than X2. To reduce the dimensionality, therefore the features with higher IG are selected.
Support Vector Machine (SVM)
The SVM is a machine-learning algorithm for two classes of classification with the goal to find a rule that best maps each member of training set to the correct classification , which has been widely used in the field of protein bioinformatics [37–41]. In linearly separable cases, SVM constructs a hyperplane that separates two different groups of feature vectors in the training set with a maximum margin. The orientation of a test sample relative to the hyperplane gives the predicted score, and hence the predicted class can be derived. The implementation of SVM algorithm used in this work was SVM-Light . The applied kernel functions were the linear function, polynomial function, and radial basis function (RBF). The selection of the kernel function parameters is important for SVM training and testing, because it implicitly determines the structure of the high dimensional feature space when constructing the optimal hyperplane . In the current study, several parameters need to be determined in advance to optimize SVM training, such as the regularization parameter C, which controls the trade-off between training error and margin, the width parameter γ in the RBF kernel , and the degree d in the polynomial kernel . Other than changing the kernel functions and the necessary regulation of the kernel function parameters, the algorithm was run with the default settings in a Linux Platform.
In this study, two subsets (Neg_S_Sub and Neg_T_Sub) were randomly constructed from Neg_S and Neg_T to have the same size as Pos_S and Pos_T, respectively. Each set of Pos_S and Pos_T with the corresponding negative sets of Neg_S_Sub and Neg_T_Sub was used to construct predictors for S and T sites. Then, a 10-fold cross-validation was performed. To check the difference of predictive accuracy caused by the different choices of negative data sets, the above 10-fold cross-validation was repeated 5 times by randomly changing the negative datasets (i.e. Neg_S_Sub and Neg_T_Sub). Finally, the overall performance was averaged over these 5 times of 10-fold cross-validation tests. Thus, the current cross-validation generally reflected the overall performance of the proposed method over the selected data sets. The same training and testing procedures were used in assessing the binary encoding based predictor.
Similar to the above procedures, datasets with 1:5 ratio of positive to negative sites were also used to train the proposed predictors. Then, 10-fold cross-validation tests were carried out. The negative dataset was also randomly changed for five times and the average prediction accuracy was obtained.
TP, FP, FN and TN denote true positives, false positives, false negatives and true negatives.
The prediction accuracy was also measured by using the ROC analysis [44, 45]. For a prediction method, the curve of ROC plots true positive rate (i.e. Sn) as a function of false positive rate (i.e. 1-Sp) for all possible thresholds. The AUC was also calculated to provide a comprehensive understanding for the proposed prediction method. Generally, the closer the AUC value is to 1, the better the prediction method is.
Availability and requirements
Project Name: CKSAAP_OGlySite predictor
Project home page: http://bioinformatics.cau.edu.cn/zzd_lab/CKSAAP_OGlySite/
Operating system: Online service is web based; local version of the software [see Additional file 5] should be run in Linux platform.
Programming language: Perl.
Other requirements: None.
Any restrictions to use by non-academics: None.
The authors thank Dr. Carlos A Canchaya at Parma University, Italy and Dr. Ziad Ramadan at Nestlé Purina Petcare PTC, USA for their critical reading on this manuscript. The authors are also indebted to Dr. Zhen Su (China Agricultural University) and his lab members for the excellent assistance in setting up the web server. The authors are thankful to the developers of NetOGlyc 3.1 for making their software free available to the community. YZC is also grateful to Dr. Ke CHEN (University of Alberta, Canada) for helpful discussion on the dimensionality reduction methods. This research was supported by the Program for New Century Excellent Talents in University (NCET-06-0116).
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