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1.  Nasopharyngeal carcinoma with paranasal sinus invasion: the prognostic significance and the evidence-based study basis of its T-staging category according to the AJCC staging system 
BMC Cancer  2014;14(1):832.
To evaluate the prognostic significance of paranasal sinus invasion for patients with NPC and to provide empirical proofs for the T-staging category of paranasal sinus invasion according to the AJCC staging system for nasopharyngeal carcinoma.
The clinical records and imaging studies of 770 consecutive patients with newly diagnosed, untreated, and nondisseminated NPC were reviewed retrospectively. The overall survival, distant metastasis-free survival, and local relapse-free survival of these patients were analyzed using the Kaplan-Meier method, and the differences were compared using the log-rank test.
The incidence of paranasal sinus invasion was 23.6%, with the rate of incidence of sphenoid sinus invasion being the highest. By multivariate analysis, paranasal sinus invasion was shown to be an independent prognostic factor for overall survival, distant metastasis-free survival, and local relapse-free survival (p < 0.05 for all). No significant differences in overall survival, distant metastasis-free survival, and local relapse-free survival were observed between patients with sphenoid sinus invasion alone and those with maxillary sinus and ethmoid sinus invasion (p = 0.87, p = 0.80, and p = 0.37, respectively). The overall survival, distant metastasis-free survival, and local relapse-free survival for patients with stage T3 disease with paranasal sinus invasion were similar to the survival rates for patients with stage T3 disease without paranasal sinus invasion (p = 0.22, p = 0.15, and p = 0.93, respectively). However, the rates of overall survival and local relapse-free survival were better for patients with stage T3 disease with paranasal sinus invasion than for patients with stage T4 disease (p < 0.01, and p = 0.03, respectively).
Paranasal sinus invasion is an independent negative prognostic factor for NPC, regardless of which sinus is involved. Our results confirm that it is scientific and reasonable for the AJCC staging system for nasopharyngeal carcinoma to define paranasal sinus invasion as stage T3 disease.
PMCID: PMC4247012  PMID: 25403714
Nasopharyngeal carcinoma; Paranasal sinus; Invasion; Prognosis; Staging
2.  A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets 
BMC Systems Biology  2014;8(Suppl 3):S1.
As an abstract mapping of the gene regulations in the cell, gene regulatory network is important to both biological research study and practical applications. The reverse engineering of gene regulatory networks from microarray gene expression data is a challenging research problem in systems biology. With the development of biological technologies, multiple time-course gene expression datasets might be collected for a specific gene network under different circumstances. The inference of a gene regulatory network can be improved by integrating these multiple datasets. It is also known that gene expression data may be contaminated with large errors or outliers, which may affect the inference results.
A novel method, Huber group LASSO, is proposed to infer the same underlying network topology from multiple time-course gene expression datasets as well as to take the robustness to large error or outliers into account. To solve the optimization problem involved in the proposed method, an efficient algorithm which combines the ideas of auxiliary function minimization and block descent is developed. A stability selection method is adapted to our method to find a network topology consisting of edges with scores. The proposed method is applied to both simulation datasets and real experimental datasets. It shows that Huber group LASSO outperforms the group LASSO in terms of both areas under receiver operating characteristic curves and areas under the precision-recall curves.
The convergence analysis of the algorithm theoretically shows that the sequence generated from the algorithm converges to the optimal solution of the problem. The simulation and real data examples demonstrate the effectiveness of the Huber group LASSO in integrating multiple time-course gene expression datasets and improving the resistance to large errors or outliers.
PMCID: PMC4243122  PMID: 25350697
Gene Regulatory Network; Reverse Engineering; Group LASSO; Optimization; Gene Expression Data
3.  Prognostic Value and Staging Classification of Retropharyngeal Lymph Node Metastasis in Nasopharyngeal Carcinoma Patients Treated with Intensity-modulated Radiotherapy 
PLoS ONE  2014;9(10):e108375.
The development of intensity-modulated radiotherapy (IMRT) has revolutionized the management of nasopharyngeal carcinoma (NPC). The purpose of this study was to evaluate the prognostic value and classification of TNM stage system for retropharyngeal lymph node (RLN) metastasis in NPC in the IMRT era.
Material and Methods
We retrospectively reviewed data from 749 patients with biopsy-proven, non-metastatic NPC. All patients received IMRT as the primary treatment. Chemotherapy was administered to 86.2% (424/492) of the patients with stage III or IV disease.
The incidence of RLN metastasis was 64.2% (481/749). Significant differences were observed in the 5-year disease-free survival (DFS; 70.6% vs. 85.4%, P<0.001) and distant metastasis-free survival (DMFS; 79.2% vs. 90.1%, P<0.001) rates of patients with and without RLN metastasis. In multivariate analysis, RLN metastasis was an independent prognostic factor for disease failure and distant failure (P = 0.005 and P = 0.026, respectively), but not for locoregional recurrence. Necrotic RLN metastases have a negative effect on disease failure, distant failure and locoregional recurrence in NPC with RLN metastasis (P = 0.003, P = 0.018 and P = 0.005, respectively). Survival curves demonstrated a significant difference in DFS between patients with N0 disease and N1 disease with only RLN metastasis (P = 0.020), and marginally statistically significant differences in DMFS and DFS between N1 disease with only RLN metastasis and other N1 disease (P = 0.058 and P = 0.091, respectively). In N1 disease, no significant differences in DFS were observed between unilateral and bilateral RLN metastasis (P = 0.994).
In the IMRT era, RLN metastasis remains an independent prognostic factor for DFS and DMFS in NPC. It is still reasonable for RLN metastasis to be classified in the N1 disease, regardless of laterality. However, there is a need to investigate the feasibility of classifying RLN metastasis as N1a disease in future by a larger cohort study.
PMCID: PMC4193733  PMID: 25302611
4.  Elevated levels of plasma D-dimer predict a worse outcome in patients with nasopharyngeal carcinoma 
BMC Cancer  2014;14(1):583.
Hemostatic alterations occur during the development of cancer. Plasma D-dimer is a hypercoagulability and fibrinolytic system marker that is increased in patients with various solid tumours. The aim of this study was to evaluate the hemostatic status of nasopharyngeal carcinoma (NPC) patients by assessing plasma D-dimer levels to investigate its value as a prognostic marker.
We retrospectively analysed 717 patients with nasopharyngeal carcinoma, and we applied Cox regression and log-rank tests to assess the association of D-dimer levels with disease-free survival (DFS), distant metastasis-free survival (DMFS), and overall survival (OS). D-dimer levels were measured using a quantitative D-dimer latex agglutination assay.
Using the 3rd quartile values (0.8 μg/L) as the optimal cut-offs, we found that patients with high D-dimer levels have a shorter 3-year DFS, (79%, 95%CI (73.1–84.9)) vs. (69%, 95%CI (59.2–78.8)), DMFS (87%, 95%CI (83.1–90.9)) vs. (77%, 95%CI (69.2–84.8)), and overall survival (82%, 95%CI (76.1–87.9)) vs. (76%, 95%CI (66.2–85.8)). Multivariate analysis revealed that pre-treatment D-dimer levels and EBV DNA were significant independent factors for DFS, DMFS, and OS in NPC patients. Subgroup analyses indicated that the plasma D-dimer levels could effectively stratify patient prognosis for early cancer, advanced stage cancer, and patients with EBV DNA ≥4000 copies/ml.
High D-dimer levels were associated with poor disease-free survival, distant metastasis-free survival, overall survival, and increased risk of mortality in NPC patients. Prospective trials are required to assess the prognostic value of D-dimer levels.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2407-14-583) contains supplementary material, which is available to authorized users.
PMCID: PMC4242497  PMID: 25109220
Nasopharyngeal carcinoma; D-dimer; Survival
5.  Translation and validation of the Chinese version of the quality of life radiation therapy instrument and the head & neck module (QOL-RTI/H&N) 
To translate and validate the Chinese version of the Quality Of Life Radiation Therapy Instrument and the Head & Neck Module (QOL-RTI/H&N), a disease-specific scale to measure quality of life (QOL) for patients with head and neck cancer (HNC) who received radiotherapy.
The QOL-RTI/H&N was translated and validated according to the standard process: a translation and back-translation procedure, pilot testing and a validation study. HNC patients were enrolled from the Cancer Center of Sun Yat-sen University and assessed using the QOL-RTI/H&N, QLQ-C30 and QLQ-H&N35. Reliability (internal consistency reliability, split-half reliability and test-retest reliability), validity (content validity, construct validity, criterion validity and discriminant validity), and responsiveness analysis were performed to evaluate the psychometric characteristics of the QOL-RTI/H&N.
A total of 238 patients (99.2%) completed the questionnaire. Item RTI23 had 16.0% missing data. Other items had low percentages of missing data (0.4% or 0.8%) or no missing data. The average time to finish the scale was 9.8 minutes. Cronbach's alpha of the domains ranged from 0.41 to 0.77. The split-half reliability coefficients ranged from 0.43 to 0.77. All of the intra-class correlation coefficients were equal to or greater than 0.8. All of the item-own domain correlation coefficients were greater than those of the item-other domain. Confirmatory factor analysis showed that Comparative Fit Index, Normed Fit Index and Non-Normed Fit Index were equal to 1.00. Root Mean Square Error of Approximation was 0.01, with 90% CI (0.00, 0.10). The domain scores of the QOL-RTI/H&N were significantly correlated with those of the QLQ-C30 or QLQ-H&N3. All domain scores of patients in different radiotherapy stages were statistically significant (P < 0.05), apart from the speech domain.
The Chinese version of the QOL-RTI/H&N is a valid, reliable and responsive scale to measure QOL in HNC patients and can be used to assess the effects of radiotherapy treatment on these patients.
PMCID: PMC4022371  PMID: 24731442
Head and neck cancer; Quality of Life; QOL-RTI/H&N; Translation; Validation
6.  Nonlinear-Model-Based Analysis Methods for Time-Course Gene Expression Data 
The Scientific World Journal  2014;2014:313747.
Microarray technology has produced a huge body of time-course gene expression data and will continue to produce more. Such gene expression data has been proved useful in genomic disease diagnosis and drug design. The challenge is how to uncover useful information from such data by proper analysis methods such as significance analysis and clustering analysis. Many statistic-based significance analysis methods and distance/correlation-based clustering analysis methods have been applied to time-course expression data. However, these techniques are unable to account for the dynamics of such data. It is the dynamics that characterizes such data and that should be considered in analysis of such data. In this paper, we employ a nonlinear model to analyse time-course gene expression data. We firstly develop an efficient method for estimating the parameters in the nonlinear model. Then we utilize this model to perform the significance analysis of individually differentially expressed genes and clustering analysis of a set of gene expression profiles. The verification with two synthetic datasets shows that our developed significance analysis method and cluster analysis method outperform some existing methods. The application to one real-life biological dataset illustrates that the analysis results of our developed methods are in agreement with the existing results.
PMCID: PMC3910117  PMID: 24516364
7.  Long-term outcome and late toxicities of simultaneous integrated boost-intensity modulated radiotherapy in pediatric and adolescent nasopharyngeal carcinoma 
Chinese Journal of Cancer  2013;32(10):525-532.
The application of simultaneous integrated boost-intensity modulated radiotherapy (SIB-IMRT) in pediatric and adolescent nasopharyngeal carcinoma (NPC) is underevaluated. This study aimed to evaluate long-term outcome and late toxicities in pediatric and adolescent NPC after SIB-IMRT combined with chemotherapy. Thirty-four patients (aged 8–20 years) with histologically proven, non-disseminated NPC treated with SIB-IMRT were enrolled in this retrospective study. The disease stage distribution was as follows: stage I, 1 (2.9%); stage III, 14 (41.2%); and stage IV, 19 (55.9%). All patients underwent SIB-IMRT and 30 patients also underwent cisplatin-based chemotherapy. The prescribed dose of IMRT was 64–68 Gy in 29–31 fractions to the nasopharyngeal gross target volume. Within the median follow-up of 52 months (range, 9–111 months), 1 patient (2.9%) experienced local recurrence and 4 (11.8%) developed distant metastasis (to the lung in 3 cases and to multiple organs in 1 case). Four patients (11.8%) died due to recurrence or metastasis. The 5-year locoregional relapse–free survival, distant metastasis–free survival, disease-free survival, and overall survival rates were 97.1%, 88.2%, 85.3%, and 88.2%, respectively. The most common acute toxicities were grades 3–4 hematologic toxicities and stomatitis. Of the 24 patients who survived for more than 2 years, 16 (66.7%) and 15 (62.5%) developed grades 1–2 xerostomia and ototoxicity, respectively. Two patients (8.3%) developed grade 3 ototoxicity; no grade 4 toxicities were observed. SIB-IMRT combined with chemotherapy achieves excellent long-term locoregional control in pediatric and adolescent NPC, with mild incidence of late toxicities. Distant metastasis is the predominant mode of failure.
PMCID: PMC3845542  PMID: 24016394
Pediatric and adolescent; nasopharyngeal carcinoma; SIB-IMRT; outcome; late toxicity
8.  Prognostic scoring system for locoregional control among the patients with nasopharyngeal carcinoma treated by intensity-modulated radiotherapy 
Chinese Journal of Cancer  2013;32(9):494-501.
The prognostic value of T category for locoregional control in patients with nasopharyngeal carcinoma (NPC) has decreased with the extensive use of intensity-modulated radiotherapy (IMRT). We aimed to develop a prognostic scoring system (PSS) that incorporated tumor extension and clinical characteristics for locoregional control in NPC patients treated with IMRT. The magnetic resonance imaging scans and medical records of 717 patients with nonmetastatic NPC treated with IMRT at Sun Yat-sen University Cancer Center between January 2003 and January 2008 were reviewed. Age, pathologic classification, primary tumor extension, primary gross tumor volume (GTV-p), T and N categories, and baseline lactate dehydrogenase (LDH) level were analyzed. Hierarchical cluster analysis as well as univariate and multivariate analyses were used to develop the PSS. Independent prognostic factors for locoregional relapse included N2–3 stage, GTV-p ≥26.8 mL, and involvement of one or more structures within cluster 3. We calculated a risk score derived from the regression coefficient of each factor and classified patients into four groups: low risk (score 0), intermediate risk (score >0 and ≤1), high risk (score >1 and ≤2), and extremely high risk (score >2). The 5-year locoregional control rates for these groups were 97.4%, 93.6%, 85.2%, and 78.6%, respectively (P < 0.001). We have developed a PSS that can help identify NPC patients who are at high risk for locoregional relapse and can guide individualized treatments for NPC patients.
PMCID: PMC3845563  PMID: 23981849
Nasopharyngeal carcinoma; prognostic scoring system; locoregional control; intensity-modulated radiotherapy
9.  Radiation-induced temporal lobe injury after intensity modulated radiotherapy in nasopharyngeal carcinoma patients: a dose-volume-outcome analysis 
BMC Cancer  2013;13:397.
To identify the radiation volume effect and significant dosimetric parameters for temporal lobe injury (TLI) and determine the radiation dose tolerance of the temporal lobe (TL) in nasopharyngeal carcinoma (NPC) patients treated with intensity modulated radiation therapy (IMRT).
Twenty NPC patients with magnetic resonance imaging (MRI)-diagnosed unilateral TLI were reviewed. Dose-volume data was retrospectively analyzed.
Paired samples t-tests showed all dosimetric parameters significantly correlated with TLI, except the TL volume (TLV) and V75 (the TLV that received ≥75 Gy, P = 0.73 and 0.22, respectively). Receiver operating characteristic (ROC) curves showed V10 and V20 (P = 0.552 and 0.11, respectively) were the only non-significant predictors from V10 to V70 for TLI. D0.5cc (dose to 0.5 ml of the TLV) was an independent predictor for TLI (P < 0.001) in multivariate analysis; the area under the ROC curve for D0.5cc was 0.843 (P < 0.001), and the cutoff point 69 Gy was deemed as the radiation dose limit. The distribution of high dose ‘hot spot’ regions and the location of TLI were consistent.
A D0.5cc of 69 Gy may be the dose tolerance of the TL. The risk of TLI was highly dependent on high dose ‘hot spots’ in the TL; physicians should be cautious of such ‘hot spots’ in the TL during IMRT treatment plan optimization, review and approval.
PMCID: PMC3851326  PMID: 23978128
Nasopharyngeal carcinoma; Temporal lobe injury; Intensity modulated radiotherapy; Radiation volume effect; Dose tolerance
10.  Radiation-Induced Temporal Lobe Injury for Nasopharyngeal Carcinoma: A Comparison of Intensity-Modulated Radiotherapy and Conventional Two-Dimensional Radiotherapy 
PLoS ONE  2013;8(7):e67488.
To compare the radiation-induced temporal lobe injury (TLI) in patients with nasopharyngeal carcinoma (NPC) treated with intensity-modulated radiotherapy (IMRT) or two-dimensional conventional radiotherapy (2D-CRT).
Patients and Methods
1276 cases of NPC treated with IMRT or 2D-CRT were retrospectively reviewed. A diagnosis of TLI was made on follow-up magnetic resonance imaging (MRI).
The crude incidence of TLI was 7.5% and 10.8% (P = 0.048), and the actuarial 5-year incidence was 16% and 34.9% (P<0.001) for the IMRT and 2D-CRT groups, respectively. Multivariate analysis revealed both T stage (P<0.001) and radiation technique (P<0.001) as independent predictors. Patients with T1, T2 and T3 disease had a significantly higher risk when treated with 2D-CRT (P = 0.005, 0.016, <0.001, respectively). This trend was not evident for T4 patients (P = 0.680). The 2D-CRT group had a longer latency for the development of TLI (P<0.001). Those with T4 disease had a shorter median time to TLI (P = 0.006, 0.042, <0.001 when compared with T1, T2 and T3, respectively).
IMRT is superior to 2DRT for the management of T1-T3 NPC in terms of sparing the temporal lobe. The high incidence of TLI in T4 disease needs to be addressed.
PMCID: PMC3707870  PMID: 23874422
11.  Locoregional extension patterns of nasopharyngeal carcinoma and suggestions for clinical target volume delineation 
Chinese Journal of Cancer  2012;31(12):579-587.
Clinical target volume (CTV) delineation is crucial for tumor control and normal tissue protection. This study aimed to define the locoregional extension patterns of nasopharyngeal carcinoma (NPC) and to improve CTV delineation. Magnetic resonance imaging scans of 2366 newly diagnosed NPC patients were reviewed. According to incidence rates of tumor invasion, the anatomic sites surrounding the nasopharynx were classified into high-risk (>30%), medium-risk (5%–30%), and low-risk (<5%) groups. The lymph node (LN) level was determined according to the Radiation Therapy Oncology Group guidelines, which were further categorized into the upper neck (retropharyngeal region and level II), middle neck (levels III and Va), and lower neck (levels IV and Vb and the supraclavicular fossa). The high-risk anatomic sites were adjacent to the nasopharynx, whereas those at medium- or low-risk were separated from the nasopharynx. If the high-risk anatomic sites were involved, the rates of tumor invasion into the adjacent medium-risk sites increased; if not, the rates were significantly lower (P < 0.01). Among the 1920 (81.1%) patients with positive LN, the incidence rates of LN metastasis in the upper, middle, and lower neck were 99.6%, 30.2%, and 7.2%, respectively, and skip metastasis happened in only 1.2% of patients. In the 929 patients who had unilateral upper neck involvement, the rates of contralateral middle neck and lower neck involvement were 1.8% and 0.4%, respectively. Thus, local disease spreads stepwise from proximal sites to distal sites, and LN metastasis spreads from the upper neck to the lower neck. Individualized CTV delineation for NPC may be feasible.
PMCID: PMC3777458  PMID: 22854064
Nasopharyngeal carcinoma; magnetic resonance imaging; local extension; lymph node spread; clinical target volume
12.  Characterizing the Clustered Microcalcifications on Mammograms to Predict the Pathological Classification and Grading: A Mathematical Modeling Approach 
Journal of Digital Imaging  2011;24(5):764-771.
In this study, we explore a mathematical model to characterize the clustered microcalcifications on mammograms for predicting the pathological classification and grading. Our database consists of both retrospective cases (78 cases) and prospective cases (31 cases) with pathologically diagnosed clusters of microcalcifications on mammograms. The microcalcifications were divided into four grades: grade 0, benign breast disease including mastopathies (n = 12) and fibroadenomas (n = 20); grade 1, well-differentiated infiltrating ductal carcinoma (n = 12); grade 2, moderately differentiated infiltrating ductal carcinoma (n = 38); grade 3, poorly differentiated infiltrating ductal carcinoma (n = 27). A feature parameter, defined as the pattern form factor of microcalcification cluster θ by us, combines five computer-extracted image parameters of microcalcification clusters of those mammograms. In every case, only one imaging was selected for modeling analysis. A total of 109 imagings were adopted in current study. We find the existence of a positive relationship between the feature parameter θ and pathological grading G of microcalcifications in retrospective cases, which was expressed as G =  6.438 + 1.186 ×  Ln <θ>. The model above has been verified further by the prospective study with a comparative evaluation accuracy of approximately 77.42%. The binary predication simply for both benignancy and malignancy was also included using same but reshuffled data, and the receiver operating characteristic (ROC) analysis was performed with ROC value 0.74351∼0.79891. As one candidate for feature parameter in computer-aided diagnosis, the pattern form factor θ of clustered microcalcifications may be useful to predict the pathological grading and classification of microcalcification clusters on mammography in breast cancer.
PMCID: PMC3180539  PMID: 21512853
Algorithms; computer-aided diagnosis (CAD); mammography CAD; breast diseases; clustered microcalcification detection
13.  Nuclear overexpression of metastasis-associated protein 1 correlates significantly with poor survival in nasopharyngeal carcinoma 
Metastasis-associated protein 1 (MTA1) has been associated with poor prognosis in several malignant carcinomas. The purpose of this study was to investigate the expression and prognostic value of MTA1 in nasopharyngeal carcinoma (NPC).
MTA1 expression was assessed using immunohistochemistry in paraffin-embedded tumor specimens from 208 untreated NPC patients. Cox regression analysis was used to calculate the hazard ratio (HR), 95% confidence interval (CI) and identify independent prognostic factors, and recursive partitioning analysis was used to create a decision tree.
Nuclear overexpression of MTA1 was observed in 48.6% (101/208) of the NPC tissues. Nuclear overexpression of MTA1 correlated positively with N classification (P = 0.02), clinical stage (P = 0.04), distant metastasis (P < 0.01) and death (P = 0.01). Additionally, nuclear overexpression of MTA1 correlated significantly with poorer distant metastasis-free survival (DMFS; P <0.01) and poorer overall survival (OS; P < 0.01). MTA1 had prognostic significance in NPC patients with stage II disease, but not stage III or IV disease. Multivariate analysis demonstrated that nuclear overexpression of MTA1 was independently associated with poorer DMFS (HR, 2.05; 95% CI, 1.13–3.72; P = 0.02) and poorer OS (HR, 1.98; 95% CI, 1.09–3.59; P = 0.03). Using recursive partitioning analysis, the NPC patients could be classified with a low, intermediate or high risk of distant metastasis and death, on the basis of clinical stage, age and MTA1 expression.
The results of this study suggest that nuclear overexpression of MTA1 correlates significantly with poorer DMFS and poorer OS in NPC. MTA1 has potential as a novel prognostic biomarker in NPC.
PMCID: PMC3478212  PMID: 22537306
Nasopharyngeal carcinoma; Biomarker; MTA1; Prognosis
14.  Promising treatment outcomes of intensity-modulated radiation therapy for nasopharyngeal carcinoma patients with N0 disease according to the seventh edition of the AJCC staging system 
BMC Cancer  2012;12:68.
Intensity-modulated radiation therapy (IMRT) provides excellent locoregional control for nasopharyngeal carcinoma (NPC), and has gradually replaced two-dimensional conventional radiotherapy as the first-line radiotherapy technique. Furthermore, in the new seventh edition of the American Joint Committee on Cancer (AJCC) staging system, retropharyngeal lymph nodes were upgraded from N0 to N1 disease as a result of their negative impact on the distant metastasis-free survival (DMFS) rates of NPC. This retrospective study was conducted in order to review the treatment outcomes and patterns of failure in NPC patients with N0 disease after IMRT in order to effectively guide treatment in the future.
We retrospectively reviewed data from 506 biopsy-proven nonmetastatic NPC patients. There were 191 patients with negative cervical lymph node involvement. According to the seventh edition of the American Joint Committee on Cancer (AJCC) staging system, 110 patients (21.7%) were staged with N0 disease, and 81 patients (16.0%) were reclassified with N1 disease due to the presence of RLN metastasis. All patients received IMRT as the primary treatment.
In patients with negative cervical lymph node involvement, distant metastasis-free survival (DMFS) was significantly higher in patients without retropharyngeal lymph node (RLN) metastasis than those with RLN metastasis (95.9% vs. 88.1% respectively, P = 0.04). For N0 disease, the 5-year overall survival (OS), local relapse-free survival (LRFS), nodal relapse-free survival (NRFS) and DMFS rates were 93.8%, 97.1%, 99.1% and 95.9%, respectively. For T1N0, T2N0, T3N0 and T4N0, OS was 97.8%, 100%, 93.8% and 76.9%, LRFS was 100%, 92.9%, 100% and 88.9% and DMFS was 96.6%, 90.9%, 100% and 93.3%, respectively. OS and LRFS were higher in T1-3 N0 patients than T4N0 patients (P < 0.01 and P = 0.01, respectively).
The seventh edition of the AJCC N-staging system improves prognostic accuracy by upgrading RLN metastasis to N1 disease. IMRT produces excellent survival rates in T1-3 N0 disease; however, T4N0 disease remains a challenge and additional improvements are required to achieve a favorable prognosis for these NPC patients.
PMCID: PMC3332280  PMID: 22336097
15.  Nonlinear Model-Based Method for Clustering Periodically Expressed Genes 
TheScientificWorldJournal  2011;11:2051-2061.
Clustering periodically expressed genes from their time-course expression data could help understand the molecular mechanism of those biological processes. In this paper, we propose a nonlinear model-based clustering method for periodically expressed gene profiles. As periodically expressed genes are associated with periodic biological processes, the proposed method naturally assumes that a periodically expressed gene dataset is generated by a number of periodical processes. Each periodical process is modelled by a linear combination of trigonometric sine and cosine functions in time plus a Gaussian noise term. A two stage method is proposed to estimate the model parameter, and a relocation-iteration algorithm is employed to assign each gene to an appropriate cluster. A bootstrapping method and an average adjusted Rand index (AARI) are employed to measure the quality of clustering. One synthetic dataset and two biological datasets were employed to evaluate the performance of the proposed method. The results show that our method allows the better quality clustering than other clustering methods (e.g., k-means) for periodically expressed gene data, and thus it is an effective cluster analysis method for periodically expressed gene data.
PMCID: PMC3217600  PMID: 22125455
Gene expression data; nonlinear model; periodicall expressed genes; clustering; average adjusted Rand index

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