Statistical Analyses and Reproducible Research

For various reasons, it is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, etc. with the documents that describe and rely on them. This integration allows readers to both verify and adapt the statements in the documents. Authors can easily reproduce them in the future, and they can present the document's contents in a different medium, e.g. with interactive controls. This paper describes a software framework for authoring and distributing these integrated, dynamic documents that contain text, code, data, and any auxiliary content needed to recreate the computations. The documents are dynamic in that the contents, including figures, tables, etc., can be recalculated each time a view of the document is generated. Our model treats a dynamic document as a master or ``source'' document from which one can generate different views in the form of traditional, derived documents for different audiences. We introduce the concept of a compendium as both a container for the different elements that make up the document and its computations (i.e. text, code, data, ...), and as a means for distributing, managing and updating the collection. The step from disseminating analyses via a compendium to reproducible research is a small one. By reproducible research, we mean research papers with accompanying software tools that allow the reader to directly reproduce the results and employ the methods that are presented in the research paper. Some of the issues involved in paradigms for the production, distribution and use of such reproducible research are discussed.

Identification and in silico analyses of novel TGFBR1 and TGFBR2 mutations in Marfan syndrome-related disorders

Very recently, heterozygous mutations in the genes encoding transforming growth factor beta receptors I (TGFBR1) and II (TGFBR2) have been reported in Loeys-Dietz aortic aneurysm syndrome (LDS). In addition, dominant TGFBR2 mutations have been identified in Marfan syndrome type 2 (MFS2) and familial thoracic aortic aneurysms and dissections (TAAD). In the past, mutations of these genes were associated with atherosclerosis and several human cancers. Here, we report a total of nine novel and one known heterozygous sequence variants in the TGFBR1 and TGFBR2 genes in nine of 70 unrelated individuals with MFS-like phenotypes who previously tested negative for mutations in the gene encoding the extracellular matrix protein fibrillin-1 (FBN1). To assess the pathogenic impact of these sequence variants, in silico analyses were performed by the PolyPhen, SIFT, and Fold-X algorithms and by means of a 3D homology model of the TGFBR2 kinase domain. Our results showed that in all but one of the patients the pathogenic effect of at least one sequence variant is highly probable (c.722C > T, c.799A > C, and c.1460G > A in TGFBR1 and c.773T > G, c.1106G > T, c.1159G > A, c.1181G > A, and c.1561T > C in TGFBR2). These deleterious alleles occurred de novo or segregated with the disease in the families, indicating a causative association between the sequence variants and clinical phenotypes. Since TGFBR2 mutations found in patients with MFS-related disorders cannot be distinguished from heterozygous TGFBR2 mutations reported in tumor samples, we emphasize the importance of segregation analysis in affected families. In order to be able to find the mutation that is indeed responsible for a MFS-related phenotype, we also propose that genetic testing for sequence alterations in TGFBR1 and TGFBR2 should be complemented by mutation screening of the FBN1 gene.

Robust Inferences For Covariate Effects On Survival Time With Censored Linear Regression Models

Various inference procedures for linear regression models with censored failure times have been studied extensively. Recent developments on efficient algorithms to implement these procedures enhance the practical usage of such models in survival analysis. In this article, we present robust inferences for certain covariate effects on the failure time in the presence of "nuisance" confounders under a semiparametric, partial linear regression setting. Specifically, the estimation procedures for the regression coefficients of interest are derived from a working linear model and are valid even when the function of the confounders in the model is not correctly specified. The new proposals are illustrated with two examples and their validity for cases with practical sample sizes is demonstrated via a simulation study.

On the Accelerated Failure Time Model for Current Status and Interval Censored Data

This paper introduces a novel approach to making inference about the regression parameters in the accelerated failure time (AFT) model for current status and interval censored data. The estimator is constructed by inverting a Wald type test for testing a null proportional hazards model. A numerically efficient Markov chain Monte Carlo (MCMC) based resampling method is proposed to simultaneously obtain the point estimator and a consistent estimator of its variance-covariance matrix. We illustrate our approach with interval censored data sets from two clinical studies. Extensive numerical studies are conducted to evaluate the finite sample performance of the new estimators.

Checking Assumptions in Latent Class Regression Models via a Markov Chain Monte Carlo Estimation Approach: An Application to Depression and Socio-Economic Status

Latent class regression models are useful tools for assessing associations between covariates and latent variables. However, evaluation of key model assumptions cannot be performed using methods from standard regression models due to the unobserved nature of latent outcome variables. This paper presents graphical diagnostic tools to evaluate whether or not latent class regression models adhere to standard assumptions of the model: conditional independence and non-differential measurement. An integral part of these methods is the use of a Markov Chain Monte Carlo estimation procedure. Unlike standard maximum likelihood implementations for latent class regression model estimation, the MCMC approach allows us to calculate posterior distributions and point estimates of any functions of parameters. It is this convenience that allows us to provide the diagnostic methods that we introduce. As a motivating example we present an analysis focusing on the association between depression and socioeconomic status, using data from the Epidemiologic Catchment Area study. We consider a latent class regression analysis investigating the association between depression and socioeconomic status measures, where the latent variable depression is regressed on education and income indicators, in addition to age, gender, and marital status variables. While the fitted latent class regression model yields interesting results, the model parameters are found to be invalid due to the violation of model assumptions. The violation of these assumptions is clearly identified by the presented diagnostic plots. These methods can be applied to standard latent class and latent class regression models, and the general principle can be extended to evaluate model assumptions in other types of models.

Studying Effects of Primary Care Physicians and Patients on the Trade-Off Between Charges for Primary Care and Specialty Care Using a Hierarchical Multivariate Two-Part Model

Objective. To examine effects of primary care physicians (PCPs) and patients on the association between charges for primary care and specialty care in a point-of-service (POS) health plan. Data Source. Claims from 1996 for 3,308 adult male POS plan members, each of whom was assigned to one of the 50 family practitioner-PCPs with the largest POS plan member-loads. Study Design. A hierarchical multivariate two-part model was fitted using a Gibbs sampler to estimate PCPs' effects on patients' annual charges for two types of services, primary care and specialty care, the associations among PCPs' effects, and within-patient associations between charges for the two services. Adjusted Clinical Groups (ACGs) were used to adjust for case-mix. Principal Findings. PCPs with higher case-mix adjusted rates of specialist use were less likely to see their patients at least once during the year (estimated correlation: –.40; 95% CI: –.71, –.008) and provided fewer services to patients that they saw (estimated correlation: –.53; 95% CI: –.77, –.21). Ten of 11 PCPs whose case-mix adjusted effects on primary care charges were significantly less than or greater than zero (p < .05) had estimated, case-mix adjusted effects on specialty care charges that were of opposite sign (but not significantly different than zero). After adjustment for ACG and PCP effects, the within-patient, estimated odds ratio for any use of primary care given any use of specialty care was .57 (95% CI: .45, .73). Conclusions. PCPs and patients contributed independently to a trade-off between utilization of primary care and specialty care. The trade-off appeared to partially offset significant differences in the amount of care provided by PCPs. These findings were possible because we employed a hierarchical multivariate model rather than separate univariate models.

Caching and Visualizing Statistical Analyses

We present the cacher and CodeDepends packages for R, which provide tools for (1) caching and analyzing the code for statistical analyses and (2) distributing these analyses to others in an efficient manner over the web. The cacher package takes objects created by evaluating R expressions and stores them in key-value databases. These databases of cached objects can subsequently be assembled into “cache packages” for distribution over the web. The cacher package also provides tools to help readers examine the data and code in a statistical analysis and reproduce, modify, or improve upon the results. In addition, readers can easily conduct alternate analyses of the data. The CodeDepends package provides complementary tools for analyzing and visualizing the code for a statistical analysis and this functionality has been integrated into the cacher package. In this chapter we describe the cacher and CodeDepends packages and provide examples of how they can be used for reproducible research.

INTERACTING WITH LOCAL AND REMOTE DATA RESPOSITORIES USING THE stashR PACKAGE

The stashR package (a Set of Tools for Administering SHared Repositories) for R implements a simple key-value style database where character string keys are associated with data values. The key-value databases can be either stored locally on the user's computer or accessed remotely via the Internet. Methods specific to the stashR package allow users to share data repositories or access previously created remote data repositories. In particular, methods are available for the S4 classes localDB and remoteDB to insert, retrieve, or delete data from the database as well as to synchronize local copies of the data to the remote version of the database. Users efficiently access information from a remote database by retrieving only the data files indexed by user-specified keys and caching this data in a local copy of the remote database. The local and remote counterparts of the stashR package offer the potential to enhance reproducible research by allowing users of Sweave to cache their R computations for a research paper in a localDB database. This database can then be stored on the Internet as a remoteDB database. When readers of the research paper wish to reproduce the computations involved in creating a specific figure or calculating a specific numeric value, they can access the remoteDB database and obtain the R objects involved in the computation.

Development, feasibility and performance of a health risk appraisal questionnaire for older persons

BACKGROUND: Health risk appraisal is a promising method for health promotion and prevention in older persons. The Health Risk Appraisal for the Elderly (HRA-E) developed in the U.S. has unique features but has not been tested outside the United States. METHODS: Based on the original HRA-E, we developed a scientifically updated and regionally adapted multilingual Health Risk Appraisal for Older Persons (HRA-O) instrument consisting of a self-administered questionnaire and software-generated feed-back reports. We evaluated the practicability and performance of the questionnaire in non-disabled community-dwelling older persons in London (U.K.) (N = 1090), Hamburg (Germany) (N = 804), and Solothurn (Switzerland) (N = 748) in a sub-sample of an international randomised controlled study. RESULTS: Over eighty percent of invited older persons returned the self-administered HRA-O questionnaire. Fair or poor self-perceived health status and older age were correlated with higher rates of non-return of the questionnaire. Older participants and those with lower educational levels reported more difficulty in completing the HRA-O questionnaire as compared to younger and higher educated persons. However, even among older participants and those with low educational level, more than 80% rated the questionnaire as easy to complete. Prevalence rates of risks for functional decline or problems were between 2% and 91% for the 19 HRA-O domains. Participants' intention to change health behaviour suggested that for some risk factors participants were in a pre-contemplation phase, having no short- or medium-term plans for change. Many participants perceived their health behaviour or preventative care uptake as optimal, despite indications of deficits according to the HRA-O based evaluation. CONCLUSION: The HRA-O questionnaire was highly accepted by a broad range of community-dwelling non-disabled persons. It identified a high number of risks and problems, and provided information on participants' intention to change health behaviour.

The development and evaluation of a computer-based program to test and to teach the recognition of facial affect

Autism is a chronic pervasive neurodevelopmental disorder characterized by the early onset of social and communicative impairments as well as restricted, ritualized, stereotypic behavior. The endophenotype of autism includes neuropsychological deficits, for instance a lack of "Theory of Mind" and problems recognizing facial affect. In this study, we report the development and evaluation of a computer-based program to teach and test the ability to identify basic facially expressed emotions. 10 adolescent or adult subjects with high-functioning autism or Asperger-syndrome were included in the investigation. A priori the facial affect recognition test had shown good psychometric properties in a normative sample (internal consistency: rtt=.91-.95; retest reliability: rtt=.89-.92). In a prepost design, one half of the sample was randomly assigned to receive computer treatment while the other half of the sample served as control group. The training was conducted for five weeks, consisting of two hours training a week. The trained individuals improved significantly on the affect recognition task, but not on any other measure. Results support the usefulness of the program to teach the detection of facial affect. However, the improvement found is limited to a circumscribed area of social-communicative function and generalization is not ensured.

Collapsed cone convolution and analytical anisotropic algorithm dose calculations compared to VMC++ Monte Carlo simulations in clinical cases

The purpose of this work was to study and quantify the differences in dose distributions computed with some of the newest dose calculation algorithms available in commercial planning systems. The study was done for clinical cases originally calculated with pencil beam convolution (PBC) where large density inhomogeneities were present. Three other dose algorithms were used: a pencil beam like algorithm, the anisotropic analytic algorithm (AAA), a convolution superposition algorithm, collapsed cone convolution (CCC), and a Monte Carlo program, voxel Monte Carlo (VMC++). The dose calculation algorithms were compared under static field irradiations at 6 MV and 15 MV using multileaf collimators and hard wedges where necessary. Five clinical cases were studied: three lung and two breast cases. We found that, in terms of accuracy, the CCC algorithm performed better overall than AAA compared to VMC++, but AAA remains an attractive option for routine use in the clinic due to its short computation times. Dose differences between the different algorithms and VMC++ for the median value of the planning target volume (PTV) were typically 0.4% (range: 0.0 to 1.4%) in the lung and -1.3% (range: -2.1 to -0.6%) in the breast for the few cases we analysed. As expected, PTV coverage and dose homogeneity turned out to be more critical in the lung than in the breast cases with respect to the accuracy of the dose calculation. This was observed in the dose volume histograms obtained from the Monte Carlo simulations.

Cerebellar disorders in childhood: cognitive problems

Over the last decade, increasing evidence of cognitive functions of the cerebellum during development and learning processes could be ascertained. Posterior fossa malformations such as cerebellar hypoplasia or Joubert syndrome are known to be related to developmental problems in a marked to moderate extent. More detailed analyses reveal special deficits in attention, processing speed, visuospatial functions, and language. A study about Dandy Walker syndrome states a relationship of abnormalities in vermis lobulation with developmental problems. Further lobulation or volume abnormalities of the cerebellum and/or vermis can be detected in disorders as fragile X syndrome, Downs's syndrome, William's syndrome, and autism. Neuropsychological studies reveal a relation of dyslexia and attention deficit disorder with cerebellar functions. These functional studies are supported by structural abnormalities in neuroimaging in these disorders. Acquired cerebellar or vermis atrophy was found in groups of children with developmental problems such as prenatal alcohol exposure or extreme prematurity. Also, focal lesions during childhood or adolescence such as cerebellar tumor or stroke are related with neuropsychological abnormalities, which are most pronounced in visuospatial, language, and memory functions. In addition, cerebellar atrophy was shown to be a bad prognostic factor considering cognitive outcome in children after brain trauma and leukemia. In ataxia teleangiectasia, a neurodegenerative disorder affecting primarily the cerebellar cortex, a reduced verbal intelligence quotient and problems of judgment of duration are a hint of the importance of the cerebellum in cognition. In conclusion, the cerebellum seems to play an important role in many higher cognitive functions, especially in learning. There is a suggestion that the earlier the incorrect influence, the more pronounced the problems.

Complication rates and associated factors in alveolar distraction osteogenesis: a comprehensive review

Despite its growing popularity, alveolar distraction osteogenesis (DO) is a technically challenging operation. The purpose of this review is to estimate the types and frequencies of complications in alveolar DO and to identify factors associated with them. 26 reports of alveolar DO found in the PubMed database that met the criteria for inclusion were studied. 256 patients underwent 270 DO procedures; 109 complications arose in 77 patients (30%) with 77 distractions (29%). In 27/77 patients, more than 1 complication occurred. 20 complications (7%) were a consequence of surgery, 32 (12%) occurred during distraction, 22 (8%) during the consolidation period and 35 (13%) post-distraction. The most common complications were insufficient bone formation following the consolidation period (22 cases, 8%), regression of distraction distance (18 cases, 7%) and problems related to the distractor device (16 cases, 6%). The most severe complications occurred in 4 cases (2%). The type of device used and an augmentation rate of more than 0.5 mm/24 h were significantly related to insufficient bone formation and evidence of complications. This review indicates that complications in alveolar DO are frequent, but rarely cause severe problems or clinical decline. Appropriate treatment selection, surgical technique and adjusted protocol should decrease the number of complications.

A STUDY ON REGIONAL CIRCULAR ECONOMY SYSTEM AND ITS CONSTRUCTION, OPERATION AND SUGGESTION FOR SHANGHAI

The characteristics of the traditional linear economic model are high consumption, high emission and low efficiency. Economic development is still largely at the expense of the environment and requires a natural resource investment. This can realize rapid economic development but resource depletion and environmental pollution become increasingly serious. In the 1990's a new economic model, circular economics, began to enter our vision. The circular economy maximizes production and minimizes the impact of economic activities on the ecological environment through organizing the activities through the closed-loop feedback cycle of "resources - production - renewable resource". Circular economy is a better way to solve the contradictions between the economic development and resource shortages. Developing circular economy has become the major strategic initiatives to achieving sustainable development in countries all over the world. The evaluation of the development of circular economics is a necessary step for regional circular economy development. Having a quantitative evaluation of circular economy can better monitor and reveal the contradictions and problems in the process of the development of recycling economy. This thesis will: 1) Create an evaluation model framework and new types of industries and 2) Make an evaluation of the Shanghai circular economy currently to analyze the situation of Shanghai in the development of circular economy. I will then propose suggestions about the structure and development of Shanghai circular economy.