Bayesian Analysis of Clustered Interval-censored Data

A novel approach to the analysis of Overall Survival (OS) as response with Progression-Free Interval (PFI) as condition based on the RNA-seq expression data in The Cancer Genome Atlas (TCGA)

BACKGROUND

Overall Survival (OS) and Progression-Free Interval (PFI) as survival times have been collected in The Cancer Genome Atlas (TCGA). It is of biomedical interest to consider their dependence in pathway detection and survival prediction. We intend to develop novel methods for integrating PFI as condition based on parametric survival models for identifying pathways associated with OS and predicting OS.

RESULTS

Based on the framework of conditional probability, we developed a family of frailty-based parametric-models for this purpose, with exponential or Weibull distribution as baseline. We also considered two classes of existing methods with PFI as a covariate. We evaluated the performance of three approaches by analyzing RNA-seq expression data from TCGA for lung squamous cell carcinoma and lung adenocarcinoma (LUNG), brain lower grade glioma and glioblastoma multiforme (GBMLGG), as well as skin cutaneous melanoma (SKCM). Our focus was on fourteen general cancer-related pathways. The 10-fold cross-validation was employed for the evaluation of predictive accuracy. For LUNG, p53 signaling and cell cycle pathways were detected by all approaches. Furthermore, three approaches with the consideration of PFI demonstrated significantly better predictive performance compared to the approaches without the consideration of PFI. For GBMLGG, ten pathways (e.g., Wnt signaling, JAK-STAT signaling, ECM-receptor interaction, etc.) were detected by all approaches. Furthermore, three approaches with the consideration of PFI demonstrated better predictive performance compared to the approaches without the consideration of PFI. For SKCM, p53 signaling pathway was detected only by our Weibull-baseline-based model. And three approaches with the consideration of PFI demonstrated significantly better predictive performance compared to the approaches without the consideration of PFI.

CONCLUSIONS

Based on our study, it is necessary to incorporate PFI into the survival analysis of OS. Furthermore, PFI is a survival-type time, and improved results can be achieved by our conditional-probability-based approach.

A Review of the Protocol of SDF Therapy for Arresting Caries

Objective

The aim of this work was to review the protocol of the use of silver diamine fluoride (SDF) for arresting caries, specifically the application time.

Method

Two researchers searched manufacturers’ instructions, YouTube videos, and 5 databases (Embase, Medline, PubMed, Scopus, and Web of Science). Manufacturers’ instructions, videos from national dental organisations, and peer-reviewed journal articles that published the SDF application protocol in English for arresting caries were selected.

Results

The review included 14 protocols from 15 publications from 4 manufacturers, 3 dental associations, and 7 author teams (one team had 2 articles). The American Dental Association and the British Society of Paediatric Dentistry provided their SDF application protocols on YouTube. The American Academy of Paediatric Dentistry and 7 author teams published their protocols in journal articles. Seven publications suggested an SDF application time of 60 seconds. Seven publications suggested a time range of 10 seconds to 240 seconds. Two publications suggested caries excavation, but 4 publications suggested no caries excavation before SDF application. The procedures from at least 5 publications involved protecting the gingiva with petroleum jelly, isolating the carious tooth with cotton rolls, drying the carious lesion with a 3-in-1 syringe, applying SDF solution with a micro brush for 60 seconds, removing excess SDF solution with gauze, and applying fluoride varnish to the SDF-treated lesion.

Conclusions

Although the SDF application protocol is simple and straightforward, the published protocols could be different. Most publications suggested an SDF application time of 60 seconds, which can be long, particularly for young children and older adults.

Thresholding of prominent biomarkers of breast cancer on overall survival using classification and regression tree

BACKGROUND

HER2, ER, PR, and ERBB2 play a vital role in treating breast cancer. These are significant predictive and prognosis biomarkers of breast cancer.

OBJECTIVE

We aim to obtain a unique biomarker-specific prediction on overall survival to know their survival and death risk.

METHODS

Survival analysis is performed on classified data using Classification and Regression Tree (CART) analysis. Hazard ratio and Confidence Interval are computed using MLE and the Bayesian approach with the CPH model for univariate and multivariable illustrations. Validation of CART is executed with the Brier score, and accuracy and sensitivity are obtained using the k-nn classifier.

RESULTS

Utilizing CART analysis, the cut-off value of continuous-valued biomarkers HER2, ER, PR, and ERBB2 are obtained as 14.707, 8.128, 13.153, and 6.884, respectively. Brier score of CART is 0.16 towards validation of methodology. Survival analysis gives a demonstration of the survival estimates with significant statistical strategies.

CONCLUSIONS

Patients with breast cancer are at low risk of death, whose HER2 value is below its cut-off value, and ER, PR, and ERBB2 values are greater than their cut-off values. This comparison is with the patient having the opposite side of these cut-off values for the same biomarkers.

Normal frailty probit model for clustered interval-censored failure time data

Clustered interval-censored data commonly arise in many studies of biomedical research where the failure time of interest is subject to interval-censoring and subjects are correlated for being in the same cluster. A new semiparametric frailty probit regression model is proposed to study covariate effects on the failure time by accounting for the intracluster dependence. Under the proposed normal frailty probit model, the marginal distribution of the failure time is a semiparametric probit model, the regression parameters can be interpreted as both the conditional covariate effects given frailty and the marginal covariate effects up to a multiplicative constant, and the intracluster association can be summarized by two nonparametric measures in simple and explicit form. A fully Bayesian estimation approach is developed based on the use of monotone splines for the unknown nondecreasing function and a data augmentation using normal latent variables. The proposed Gibbs sampler is straightforward to implement since all unknowns have standard form in their full conditional distributions. The proposed method performs very well in estimating the regression parameters as well as the intracluster association, and the method is robust to frailty distribution misspecifications as shown in our simulation studies. Two real-life data sets are analyzed for illustration.

Silver diamine fluoride versus sodium fluoride for arresting dentine caries in children: a systematic review and meta-analysis

Dental caries can compromise quality of life and is associated with demineralization of tooth structure by organic acids produced by microorganisms. This study systematically reviewed the dentine caries arrest capabilities of silver diamine fluoride (SDF) and sodium fluoride (NaF). A comprehensive search strategy was developed to identify the relevant publications in electronic databases and hand searched journals and reviews (to March 2018). By applying strict inclusion and exclusion criteria, only six papers (two randomized controlled trials, two follow-up articles and two secondary statistical analysis studies) were considered for full text qualitative and quantitative assessment. The included studies were critically appraised and statistically evaluated. Only four articles were considered for meta-analysis, as the other two were secondary analyses of included studies. When comparing the caries arrest lesions of SDF and NaF, SDF was found to be statistically more effective in dentine caries arrest of primary teeth during the 18 and 30 month clinical examinations. The weighted total effect size of the differences between SDF and NaF regarding arrested caries surfaces was calculated and showed nearly double the effectiveness of SDF to NaF at 30 months. Therefore, SDF is a more effective caries management reagent than NaF. Further clinical research is needed to consolidate the findings of this systematic review.

Non-surgical treatment of dentin caries in preschool children--systematic review

Background

Untreated dentin caries in primary teeth is commonly found in preschool children worldwide. Recently, the use of simple non-surgical approaches to manage the situation has been advocated.

The aim of the study was to systematically review and evaluate the literature on effectiveness of non-surgical methods in arresting or slowing down the progression of active dentin caries in primary teeth in preschool children.

Methods

A systematic search of the main electronic databases (Pubmed, Cochrane Collaboration, EMBASE) was conducted to identify peer reviewed papers published in English in the years 1947–2014. Keywords and MeSH terms used in the search were “dental caries”, “primary dentition” and various non-surgical treatments (fluoride, sealant, resin infiltration, xylitol, chlorhexidine, CPP-ACP, ozone, etc.). The inclusion criteria were clinical studies conducted in children under 6 years old, and reported findings on caries arrest or caries progression in primary teeth. Retrieved papers were read by two reviewers independently to assess suitability for inclusion, and the final decision was made by consensus. Quality of the included studies was assessed and data were extracted for analysis.

Results

The search identified 323 papers for screening. Among these, 290 papers did not satisfy the study inclusion criteria. Consequently, 33 full papers were retrieved and reviewed. Finally, 4 studies were included. Three studies reported that topical applications of silver diammine fluoride (SDF) solution could arrest dentin caries in preschool children. One study supported that having a daily toothbrushing exercise in kindergarten using toothpaste with 1000 ppm fluoride could stabilize the caries situation in young children.

Conclusions

There is limited evidence to support the effectiveness of SDF applications or daily toothbrushing with fluoride toothpaste in arresting or slowing down the progression of active dentin caries in primary teeth in preschool children. More well-designed randomized controlled trials are required to confirm these findings.

A marginal cure rate proportional hazards model for spatial survival data

Dental studies often produce spatially referenced multivariate time-to-event data, such as the time until tooth loss due to periodontal disease. These data are used to identify risk factors that are associated with tooth loss, and to predict outcomes for an individual patient.The rate of spatial referencing can vary with various tooth locations. In addition, these event time data are heavily censored, mostly because a certain proportion of teeth in the population are not expected to experience failure and can be considered 'cured'. We assume a proportional hazards model with a surviving fraction to model these clustered correlated data and account for dependence between nearby teeth by using spatial frailties which are modelled as linear combinations of positive stable random effects. This model permits predictions (conditioned on spatial frailties) that account for the survival status of nearby teeth and simultaneously preserves the proportional hazards relationship marginally over the random effects for the susceptible teeth, allowing for interpretable estimates of the effects of risk factors on tooth loss. We explore the potential of this model via simulation studies and application to a real data set obtained from a private periodontal practice, and we illustrate its advantages over other competing models to identify important risk factors for tooth loss and to predict the remaining lifespan of a patient's teeth.

Fluoride varnishes for preventing dental caries in children and adolescents

BACKGROUND

Topically-applied fluoride varnishes have been used extensively as an operator-applied caries-preventive intervention for over three decades. This review updates the first Cochrane review of fluoride varnishes for preventing dental caries in children and adolescents, which was first published in 2002.

OBJECTIVES

To determine the effectiveness and safety of fluoride varnishes in preventing dental caries in children and adolescents, and to examine factors potentially modifying their effect.

SEARCH METHODS

We searched the Cochrane Oral Health Group's Trials Register (to 13 May 2013), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2013, Issue 4), MEDLINE via OVID (1946 to 13 May 2013), EMBASE via OVID (1980 to 13 May 2013), CINAHL via EBSCO (1980 to 13 May 2013), LILACS and BBO via the BIREME Virtual Health Library (1980 to 13 May 2013), ProQuest Dissertations and Theses (1861 to 13 May 2013), and Web of Science Conference Proceedings (1945 to 13 May 2013). A search for ongoing trials was undertaken on ClinicalTrials.gov on 13 May 2013. There were no restrictions on language or date of publication in the search of the electronic databases.

SELECTION CRITERIA

Randomised or quasi-randomised controlled trials with blind outcome assessment used or indicated, comparing topically-applied fluoride varnish with placebo or no treatment in children up to 16 years during at least one year. The main outcome was caries increment measured by the change in decayed, missing and filled tooth surfaces in both permanent (D(M)FS) and primary (d(e/m)fs) teeth.

DATA COLLECTION AND ANALYSIS

At least two review authors assessed all search results, extracted data and undertook risk of bias independently. Study authors were contacted for additional information. The primary measure of effect was the prevented fraction, that is the difference in mean caries increments between the treatment and control groups expressed as a percentage of the mean increment in the control group. The caries increments nearest to three years were used from each included study. Random-effects meta-analyses were performed where data could be pooled. Potential sources of heterogeneity were examined in random-effects meta-regression analyses. Adverse effects information was collected from the included trials.

MAIN RESULTS

Twenty-two trials with 12,455 participants randomised (9595 used in analyses) were included. For the 13 that contributed data for the permanent tooth surfaces meta-analysis, the pooled D(M)FS prevented fraction estimate comparing fluoride varnish with placebo or no treatment was 43% (95% confidence interval (CI) 30% to 57%; P < 0.0001). There was substantial heterogeneity, confirmed statistically (P < 0.0001; I(2) = 75%), however this body of evidence was assessed as of moderate quality. The pooled d(e/m)fs prevented fraction estimate was 37% (95% CI 24% to 51%; P < 0.0001) for the 10 trials that contributed data for the primary tooth surfaces meta-analysis, also with some heterogeneity (P = 0.009; I(2) = 59%). Once again this body of evidence was assessed as of moderate quality. No significant association between estimates of D(M)FS or d(e/m)fs prevented fractions and the pre-specified factors of baseline caries severity, background exposure to fluorides, application features such as prior prophylaxis, concentration of fluoride, frequency of application were found. There was also no significant association between estimates of D(M)FS or d(e/m)fs prevented fractions and the post hoc factors: whether a placebo or no treatment control was used, length of follow-up, or whether individual or cluster randomisation was used, in the meta-regression models. A funnel plot of the trials in the main meta-analyses indicated no clear relationship between prevented fraction and study precision. In both methods, power is limited when few trials are included. There was little information concerning possible adverse effects or acceptability of treatment.

AUTHORS' CONCLUSIONS

The conclusions of this updated review remain the same as those when it was first published. The review suggests a substantial caries-inhibiting effect of fluoride varnish in both permanent and primary teeth, however the quality of the evidence was assessed as moderate, as it included mainly high risk of bias studies, with considerable heterogeneity.

Overweight and obesity: can we reconcile evidence about supermarkets and fast food retailers for public health policy?

The aim of this study is to determine whether access to fast food outlets and supermarkets is associated with overweight and obesity in New York City neighborhoods. We use a Bayesian ecologic approach for spatial prediction. Consistent with prior research, we find no association between fast food density and overweight or obesity. Consistent with prior research, we find that supermarket access has a salutary impact on overweight and obesity. Given the lack of empirical evidence linking fast food retailers with adverse health outcomes, policymakers should be encouraged to adopt policies that incentivize the establishment of supermarkets and the modification of existing food store markets and retailers to offer healthier choices. Reaching within neighborhoods and modifying the physical environment and public health prevention and intervention efforts based on the characteristics of those neighborhoods may play a key role in creating healthier communities.

Randomized clinical trial on effectiveness of silver diamine fluoride and glass ionomer in arresting dentine caries in preschool children

OBJECTIVE

To compare the effectiveness of annual topical application of silver diamine fluoride (SDF) solution, semi-annual topical application of SDF solution, and annual application of a flowable high fluoride-releasing glass ionomer in arresting active dentine caries in primary teeth.

METHODS

A total of 212 children, aged 3-4 years, were randomly allocated to one of three groups for treatment of carious dentine cavities in their primary teeth: Gp1-annual application of SDF, Gp2-semi-annual application of SDF, and Gp3-annual application of glass ionomer. Follow-up examinations were carried out every six months to assess whether the treated caries lesions had become arrested.

RESULTS

After 24 months, 181 (85%) children remained in the study. The caries arrest rates were 79%, 91% and 82% for Gp1, Gp2 and Gp3, respectively (p=0.007). In the logistic regression model using GEE to adjust for clustering effect, higher caries arrest rates were found in lesions treated in Gp2 (OR=2.98, p=0.007), those in anterior teeth (OR=5.55, p<0.001), and those in buccal/lingual smooth surfaces (OR=15.6, p=0.004).

CONCLUSION

Annual application of either SDF solution or high fluoride-releasing glass ionomer can arrest active dentine caries. Increasing the frequency of application to every 6 months can increase the caries arrest rate of SDF application.

CLINICAL SIGNIFICANCE

Arrest of active dentine caries in primary teeth by topical application of SDF solution can be enhanced by increasing the frequency of application from annually to every 6 months, whereas annual paint-on of a flowable glass ionomer can also arrest active dentine caries and may provide a more aesthetic outcome.

Randomized trial on fluorides and sealants for fissure caries prevention

To investigate the effectiveness of topical fluorides in preventing fissure caries, we conducted a randomized controlled trial with parallel groups. In total, 501 children (1,539 molars, 3,078 sites), mean age 9.1 years, who had at least one sound permanent first molar with deep fissures or fissures with signs of early caries were recruited. They were randomly allocated among four groups: (1) resin sealant, single placement; (2) 5% NaF varnish, semi-annual application; (3) 38% silver diamine fluoride (SDF) solution, annual application; and (4) placebo control. Follow-up examinations were conducted every 6 months by a masked examiner. After 24 months, 485 children (97%) were examined. Proportions of pit/fissure sites with dentin caries in the sealant, NaF, SDF, and control groups were 1.6%, 2.4%, 2.2%, and 4.6%, respectively. A multi-level logistic regression analysis accounting for the effects of data clustering and confounding factors showed that fissures in any of the three treatment groups had significantly lower risks of carious cavity development into dentin than did controls (p < 0.05). We concluded that placement of resin sealant, semi-annual application of NaF varnish, and annual application of SDF solution are all effective in preventing pit and fissure caries in permanent molars (ClinicalTrials.gov number CT01446107).

Quality of cluster randomized controlled trials in oral health: a systematic review of reports published between 2005 and 2009

OBJECTIVES

To assess the quality of methods and reporting of recently published cluster randomized trials (CRTs) in oral health.

METHODS

We searched PubMed for CRTs that included at least one oral health-related outcome and were published from 2005 to 2009 inclusive. We developed a list of criteria for assessing trial quality and reporting. This was influenced largely by the extended CONSORT statement for CRTs but also included criteria suggested by other authors. We examined the extent to which trials were consistent with these criteria.

RESULTS

Twenty-three trials were included in the review. In 15 (65%) trials, clustering had been accounted for in sample size calculations, and in 18 (78%) authors had accounted for clustering in analysis. Intraclass correlation coefficients (ICCs) were reported for eight (35%) trials; the outcome assessor was reported as having been blinded to allocation in 12 (52%) trials; 17 (74%) described eligibility criteria at individual level, but only nine (39%) described such criteria at cluster level. Sixteen of 20 trials (80%), in which individuals were recruited, reported that individual informed consent was obtained.

CONCLUSIONS

These results suggest that the quality of recent CRTs in oral health is relatively high and appears to compare favourably with other fields. However, there remains room for improvement. Authors of future trials should endeavour to ensure sample size calculations and analyses properly account for clustering (and are reported as such), consider the potential for recruitment/identification bias at the design stage, describe the steps taken to avoid this in the final report and report observed ICCs and cluster-level eligibility criteria.

Analysis of multilevel grouped survival data with time-varying regression coefficients

Correlated or multilevel grouped survival data are common in medical and dental research. Two common approaches to analyze such data are the marginal and the random-effects approaches. Models and methods in the literature generally assume that the treatment effect is constant over time. A researcher may be interested in studying whether the treatment effects in a clinical trial vary over time, say fade out gradually. This is of particular clinical value when studying the long-term effect of a treatment. This paper proposed to extend the random effects grouped proportional hazards models by incorporating the possibly time-varying covariate effects into the model in terms of a state-space formulation. The proposed model is very flexible and the estimation can be performed using the MCMC approach with non-informative priors in the Bayesian framework. The method is applied to a data set from a prospective clinical trial investigating the effectiveness of silver diamine fluoride (SDF) and sodium fluoride (NaF) varnish in arresting active dentin caries in the Chinese preschool children. It is shown that the treatment groups with caries removal prior to the topical fluoride applications are most effective in shortening the arrest times in the first 6-month interval, but their effects fade out rapidly since then. The effects of treatment groups without caries removal prior to topical fluoride application drop at a very slow rate and can be considered as more or less constant over time. The applications of SDF solution is found to be more effective than the applications of NaF vanish.

Application of Bayesian classifier for the diagnosis of dental pain

Toothache is the most common symptom encountered in dental practice. It is subjective and hence, there is a possibility of under or over diagnosis of oral pathologies where patients present with only toothache. Addressing the issue, the paper proposes a methodology to develop a Bayesian classifier for diagnosing some common dental diseases (D = 10) using a set of 14 pain parameters (P = 14). A questionnaire is developed using these variables and filled up by ten dentists (n = 10) with various levels of expertise. Each questionnaire is consisted of 40 real-world cases. Total 14*10*10 combinations of data are hence collected. The reliability of the data (P and D sets) has been tested by measuring (Cronbach's alpha). One-way ANOVA has been used to note the intra and intergroup mean differences. Multiple linear regressions are used for extracting the significant predictors among P and D sets as well as finding the goodness of the model fit. A naïve Bayesian classifier (NBC) is then designed initially that predicts either presence/absence of diseases given a set of pain parameters. The most informative and highest quality datasheet is used for training of NBC and the remaining sheets are used for testing the performance of the classifier. Hill climbing algorithm is used to design a Learned Bayes' classifier (LBC), which learns the conditional probability table (CPT) entries optimally. The developed LBC showed an average accuracy of 72%, which is clinically encouraging to the dentists.

Silver diamine fluoride: a caries "silver-fluoride bullet"

The antimicrobial use of silver compounds pivots on the 100-year-old application of silver nitrate, silver foil, and silver sutures for the prevention and treatment of ocular, surgical, and dental infections. Ag(+) kills pathogenic organisms at concentrations of <50 ppm, and current/potential anti-infective applications include: acute burn coverings, catheter linings, water purification systems, hospital gowns, and caries prevention. To distill the current best evidence relative to caries, this systematic review asked: Will silver diamine fluoride (SDF) more effectively prevent caries than fluoride varnish? A five-database search, reference review, and hand search identified 99 human clinical trials in three languages published between 1966 and 2006. Dual review for controlled clinical trials with the patient as the unit of observation, and excluding cross-sectional, animal, in vitro studies, and opinions, identified 2 studies meeting the inclusion criteria. The trials indicated that SDF's lowest prevented fractions for caries arrest and caries prevention were 96.1% and 70.3%, respectively. In contrast, fluoride varnish's highest prevented fractions for caries arrest and caries prevention were 21.3% and 55.7%, respectively. Similarly, SDF's highest numbers needed to treat for caries arrest and caries prevention were 0.8 (95% CI=0.5-1.0) and 0.9 (95% CI=0.4-1.1), respectively. For fluoride varnish, the lowest numbers needed to treat for caries arrest and prevention were 3.7 (95% CI=3.4-3.9) and 1.1 (95% CI=0.7-1.4), respectively. Adverse events were monitored, with no significant differences between control and experimental groups. These promising results suggest that SDF is more effective than fluoride varnish, and may be a valuable caries-preventive intervention. As well, the availability of a safe, effective, efficient, and equitable caries-preventive agent appears to meet the criteria of both the WHO Millennium Goals and the US Institute of Medicine's criteria for 21st century medical care.

Six-year follow up of atraumatic restorative treatment restorations placed in Chinese school children

OBJECTIVES

This study aimed to evaluate the clinical performance of atraumatic restorative treatment (ART) restorations placed in school children in China over a 6-year period.

METHODS

This study was implemented in 1996 and 294 ART restorations were placed in 197 children aged 12-13 years by five assistant dentists in four schools. Standard ART procedures and instruments were used combined with a high-strength glass-ionomer restorative material. One examiner evaluated the restorations annually using the ART criteria while at 5 years an independent external examiner used US Public Health Service (USPHS) criteria.

RESULTS

Fifty-eight per cent of the restorations were followed for 6 years. At the 6-year evaluation examination, 76% and 59% of the small and large restorations respectively were present and were without major wear or defect (P < 0.01). Similar results were obtained when using the USPHS criteria. Results of a multilevel survival analysis show that the correlation between restoration failure and operator was small but failure of restorations placed in the same child was substantial. Net wear of the small and large restorations after 6 years were 176 and 172 microm respectively (P > 0.05).

CONCLUSION

The 6-year survival rate of the class I ART restorations in this study, especially the smaller ones, was satisfactory. This suggests that the ART approach can be used in the school setting to improve the oral health of large populations of underserved children.