White spot syndrome virus impact on the expression of immune genes and gut microbiome of black tiger shrimp Penaeus monodon.

The gut microbiome plays an essential role in the immune system of invertebrates and vertebrates. Pre and pro-biotics could enhance the shrimp immune system by increasing the phenoloxidase (PO), prophenoloxidase (ProPO), and superoxide dismutase activities. During viral infection, the host immune system alteration could influence the gut microbiome composition and probably lead to other pathogenic infections.

Depthgram: Visualizing outliers in high-dimensional functional data with application to fMRI data exploration.

Functional magnetic resonance imaging (fMRI) is a non-invasive technique that facilitates the study of brain activity by measuring changes in blood flow. Brain activity signals can be recorded during the alternate performance of given tasks, that is, task fMRI (tfMRI), or during resting-state, that is, resting-state fMRI (rsfMRI), as a measure of baseline brain activity. This contributes to the understanding of how the human brain is organized in functionally distinct subdivisions.

Censored functional data for incomplete follow-up studies.

Functional data analysis plays an increasingly important role in medical research because patients are followed over time. Thus, the measurements of a particular biomarker for each patient are often registered as curves. Hence, it is of interest to estimate the mean function under certain conditions as an average of the observed functional data over a given period.

Variable selection with P-splines in functional linear regression: Application in graft-versus-host disease.

This paper focuses on the problems of estimation and variable selection in the functional linear regression model (FLM) with functional response and scalar covariates. To this end, two different types of regularization (L and L ) are considered in this paper. On the one hand, a sample approach for functional LASSO in terms of basis representation of the sample values of the response variable is proposed.

A novel predictive approach for GVHD after allogeneic SCT based on clinical variables and cytokine gene polymorphisms.

Despite considerable advances in our understanding of the pathophysiology of graft-versus-host disease (GVHD), its prediction remains unresolved and depends mainly on clinical data. The aim of this study is to build a predictive model based on clinical variables and cytokine gene polymorphism for predicting acute GVHD (aGVHD) and chronic GVHD (cGVHD) from the analysis of a large cohort of HLA-identical sibling donor allogeneic stem cell transplant (allo-SCT) patients. A total of 25 SNPs in 12 cytokine genes were evaluated in 509 patients.

Diastereoselective and Catalytic α-Alkylation of Chiral N-Acyl Thiazolidinethiones with Stable Carbocationic Salts.

Direct nickel-catalyzed alkylation of chiral N-acyl-4-isopropyl-1,3-thiazolidine-2-thiones using a commercially available nickel(II) complex, (MeP)NiCl, has been developed for tropylium and trityl tetrafluoroborate salts. The reaction provides a single diastereomer of the corresponding adducts in good to high yields, which, in turn, can be easily converted into a wide array of enantiomerically pure compounds that are difficult to obtain by other asymmetric procedures.

Stereoselective Synthesis of the C9-C19 Fragment of Peloruside A.

A concise synthesis of the C9-C19 fragment of peloruside A that is both highly stereoselective and efficient is described. Achieving an overall yield of 23% over 14 steps, this synthesis not only is high yielding but also involves four chromatography steps. This approach is based on the addition of metal enolates of chiral auxiliary scaffolds generated by either catalytic or stoichiometric amounts of nickel(II) or titanium(IV) Lewis acids.

Stereoselective Alkylation of (S)-N-Acyl-4-isopropyl-1,3-thiazolidine-2-thiones Catalyzed by (Me3P)2NiCl2.

The structurally simple (Me3P)2NiCl2 complex catalyzes SN1-type alkylations of chiral N-acyl thiazolidinethiones with diarylmethyl methyl ethers and other stable carbenium cations. The former can contain a variety of functional groups and heteroatoms at the α-position. The resultant adducts are isolated as single diastereomers in high yields and can be converted into enantiomerically pure derivatives in a straightforward manner.

Stereoselective aminoxylation of biradical titanium enolates with TEMPO.

A highly efficient and straightforward aminoxylation of titanium(IV) enolates from (S)-N-acyl-4-benzyl-5,5-dimethyl-1,3-oxazolidin-2-ones with TEMPO has been developed. A wide array of functional groups on the acyl moiety, including alkyl and aryl substituents, olefins, esters, or α-cyclopropyl, as well as α-trifluoromethyl groups, are well tolerated. This transformation can therefore produce the α-aminoxylated adducts in excellent yields with high diastereomeric ratios (d.

Shape outlier detection and visualization for functional data: the outliergram.

We propose a new method to visualize and detect shape outliers in samples of curves. In functional data analysis, we observe curves defined over a given real interval and shape outliers may be defined as those curves that exhibit a different shape from the rest of the sample. Whereas magnitude outliers, that is, curves that lie outside the range of the majority of the data, are in general easy to identify, shape outliers are often masked among the rest of the curves and thus difficult to detect.

DepthTools: an R package for a robust analysis of gene expression data.

Background: The use of DNA microarrays and oligonucleotide chips of high density in modern biomedical research provides complex, high dimensional data which have been proven to convey crucial information about gene expression levels and to play an important role in disease diagnosis. Therefore, there is a need for developing new, robust statistical techniques to analyze these data.

Results: depthTools is an R package for a robust statistical analysis of gene expression data, based on an efficient implementation of a feasible notion of depth, the Modified Band Depth.

Comparing quantile residual life functions by confidence bands.

In this article we present a nonparametric method for constructing confidence bands for the difference of two quantile residual life (qrl) functions. These bands provide evidence for two random variables ordering with respect to the qrl order. The comparison of qrl functions is of importance, specially in the treatment of cancer when there exists a possibility of benefiting from a new secondary therapy.

Robust depth-based estimation in the time warping model.

In functional data analysis, the time warping model aims at representing a set of curves exhibiting phase and amplitude variation with respect to a common continuous process. Many biological processes, when observed across the time among different individuals, fit into this concept. The observed curves are modeled as the composition of an "amplitude process," which governs the common behavior, and a "warping process" that induces time distortion among the individuals.

Robust depth-based tools for the analysis of gene expression data.

Microarray experiments provide data on the expression levels of thousands of genes and, therefore, statistical methods applicable to the analysis of such high-dimensional data are needed. In this paper, we propose robust nonparametric tools for the description and analysis of microarray data based on the concept of functional depth, which measures the centrality of an observation within a sample. We show that this concept can be easily adapted to high-dimensional observations and, in particular, to gene expression data.