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In this article we propose a penalized clustering method for large-scale data with multiple covariates through a functional data approach. In our proposed method, responses and covariates are linked together through nonparametric multivariate functions (fixed effects), which have great flexibility in modeling various function features, such as jump points, branching, and periodicity. Functional ANOVA is used to further decompose multivariate functions in a reproducing kernel Hilbert space and provide associated notions of main effect and interaction. Parsimonious random effects are used to capture various correlation structures. The mixed-effects models are nested under a general mixture model in which the heterogeneity of functional data is characterized. We propose a penalized Henderson's likelihood approach for model fitting and design a rejection-controlled EM algorithm for the estimation. Our method selects smoothing parameters through generalized cross-validation. Furthermore, Bayesian confidence intervals are used to measure the clustering uncertainty. Simulation studies and real-data examples are presented to investigate the empirical performance of the proposed method. Open-source code is available in the R package MFDA. [ABSTRACT FROM AUTHOR]

We propose a Bayesian procedure to cluster temporal gene expression microarray profiles, based on a mixed-effect smoothing-spline model, and design a Gibbs sampler to sample from the desired posterior distribution. Our method can determine the cluster number automatically based on the Bayesian information criterion, and handle missing data easily. When applied to a microarray dataset on the budding yeast, our clustering algorithm provides biologically meaningful gene clusters according to a functional enrichment analysis. [ABSTRACT FROM AUTHOR]

Testing the hypothesis of parallelism is a fundamental statistical problem arising from many applied sciences. In this paper, we develop a nonparametric parallelism test for inferring whether the trends are parallel in treatment and control groups. In particular, the proposed nonparametric parallelism test is a Wald type test based on a smoothing spline ANOVA (SSANOVA) model which can characterize the complex patterns of the data. We derive that the asymptotic null distribution of the test statistic is a Chi-square distribution, unveiling a new version of Wilks phenomenon. Notably, we establish the minimax sharp lower bound of the distinguishable rate for the nonparametric parallelism test by using the information theory, and further prove that the proposed test is minimax optimal. Simulation studies are conducted to investigate the empirical performance of the proposed test. DNA methylation and neuroimaging studies are presented to illustrate potential applications of the test. [ABSTRACT FROM AUTHOR]

Background: Accurate identification of differentially expressed (DE) genes in time course RNA-Seq data is crucial for understanding the dynamics of transcriptional regulatory network. However, most of the available methods treat gene expressions at different time points as replicates and test the significance of the mean expression difference between treatments or conditions irrespective of time. They thus fail to identify many DE genes with different profiles across time. In this article, we propose a negative binomial mixed-effect model (NBMM) to identify DE genes in time course RNA-Seq data. In the NBMM, mean gene expression is characterized by a fixed effect, and time dependency is described by random effects. The NBMM is very flexible and can be fitted to both unreplicated and replicated time course RNA-Seq data via a penalized likelihood method. By comparing gene expression profiles over time, we further classify the DE genes into two subtypes to enhance the understanding of expression dynamics. A significance test for detecting DE genes is derived using a Kullback-Leibler distance ratio. Additionally, a significance test for gene sets is developed using a gene set score. Results: Simulation analysis shows that the NBMM outperforms currently available methods for detecting DE genes and gene sets. Moreover, our real data analysis of fruit fly developmental time course RNA-Seq data demonstrates the NBMM identifies biologically relevant genes which are well justified by gene ontology analysis. Conclusions: The proposed method is powerful and efficient to detect biologically relevant DE genes and gene sets in time course RNA-Seq data. [ABSTRACT FROM AUTHOR]

Phenylthiourea (PTU) is commonly used for inhibiting melanization of zebrafish embryos. In this study, the standard treatment with 0.2 mM PTU was demonstrated to specifically reduce eye size in larval fish starting at three days postfertilization. This effect is likely the result of a reduction in retinal and lens size of PTU-treated eyes and is not related to melanization inhibition. This is because the eye size of tyr, a genetic mutant of tyrosinase whose activity is inhibited in PTU treatment, was not reduced. As PTU contains a thiocarbamide group which is presented in many goitrogens, suppressing thyroid hormone production is a possible mechanism by which PTU treatment may reduce eye size. Despite the fact that thyroxine level was found to be reduced in PTU-treated larvae, thyroid hormone supplements did not rescue the eye size reduction. Instead, treating embryos with six goitrogens, including inhibitors of thyroid peroxidase (TPO) and sodium-iodide symporter (NIS), suggested an alternative possibility. Specifically, three TPO inhibitors, including those that do not possess thiocarbamide, specifically reduced eye size; whereas none of the NIS inhibitors could elicit this effect. These observations indicate that TPO inhibition rather than a general suppression of thyroid hormone synthesis is likely the underlying cause of PTU-induced eye size reduction. Furthermore, the tissue-specific effect of PTU treatment might be mediated by an eye-specific TPO expression. Compared with treatment with other tyrosinase inhibitors or bleaching to remove melanization, PTU treatment remains the most effective approach. Thus, one should use caution when interpreting results that are obtained from PTU-treated embryos. [ABSTRACT FROM AUTHOR]

Irx7, a member in the zebrafish iroquois transcription factor (TF) family, has been shown to control brain patterning. During retinal development, irx7's expression was found to appear exclusively in the inner nuclear layer (INL) as soon as the prospective INL cells withdraw from the cell cycle and during retinal lamination. In Irx7-deficient retinas, the formation of a proper retinal lamination was disrupted and the differentiation of INL cell types, including amacrine, horizontal, bipolar and Muller cells, was compromised. Despite irx7's exclusive expression in the INL, photoreceptors differentiation was also compromised in Irx7-deficient retinas. Compared with other retinal cell types, ganglion cells differentiated relatively well in these retinas, except for their dendritic projections into the inner plexiform layer (IPL). In fact, the neuronal projections of amacrine and bipolar cells into the IPL were also diminished. These indicate that the retinal lamination issue in the Irx7- deficient retinas is likely caused by the attenuation of the neurite outgrowth. Since the expression of known TFs that can specify specific retinal cell type was also altered in Irx7-deficient retinas, thus the irx7 gene network is possibly a novel regulatory circuit for retinal development and lamination. [ABSTRACT FROM AUTHOR]

A low-cost yet highly sensitive colorimetric sensor array for the deteclion and identification of toxic industrial chemicals (TICs) has been developed. The sensor consists of a disposable array of cross-responsive nanoporous pigments whose colors are changed by diverse chemical interactions with analytes. Clear differentiation among 20 differentTlCs has been easily achieved at both their IDUI (immediately dangerous to life or health) concentration within 2 mm of exposure and PEL (permissible exposure limit) concentration within 5 mm of exposure with no errors or misclassifications. Detection limits are generally well below the PEL (in most cases below 5% of PEL) and are typically in the low ppb range. The colorimetric sensor array is not responsive to changes in humidity or ternperature over a substantial range. The printed arrays show excellent batch to batch reproducibility and long shelf life (greater than 3 months). [ABSTRACT FROM AUTHOR]

Molecular recognition of sugars and a practical method to detect and discriminate among a large number of such similar analytes remain substantial scientific challenges. We report here a low-cost, simple colorimetric sensor array capable of identification and quantification of sugars and related compounds. Fifteen different monosaccharides, disaccharides, and artificial sweeteners were differentiated without error in 80 trials. Limits of detection at pH 7.4 for glucose were <1 mM, which is below physiologically important levels. [ABSTRACT FROM AUTHOR]

Objective--To test the hypotheses that the densities of macrophages in the synovial membranes and capsules of stifle joints in dogs with ruptured cranial cruciate ligaments are greater than those of normal joints and that those densities in affected joints are positively correlated with the chronicity and severity of the disease. Animals--17 dogs with naturally occurring rupture of the cranial cruciate ligament and 5 healthy control dogs. Procedure--All dogs underwent orthopedic and radiographic evaluations. In affected dogs, duration of clinical signs was used as an indicator of disease chronicity and the severity of osteoarthritis in the stifle joint was determined radiographically. Joint capsule specimens were evaluated histologically; macrophages, interleukin-6, and tumor necrosis factor-α were identified by use of immunocytochemical techniques. Results--Compared with unaffected joints, macrophage density was increased in all affected joints. Duration of disease was significantly associated with radiographic severity of osteoarthritis and synovial macrophage density. Synovial macrophage density was significantly associated with severity of osteoarthritis and with the presence of interleukin-6 and tumor necrosis factor-α. Conclusions and Clinical Relevance--Results suggest that synovial macrophages may be involved in the development of pathologic changes (including osteophyte formation) in the stifle joints of dogs with osteoarthritis secondary to rupture of the cranial cruciate ligament. Determination of the importance of synovial macrophages in the development of changes in osteoarthritic joints may result in new treatment strategies that involve elimination of the deleterious effects of those cells. [ABSTRACT FROM AUTHOR]