Classification Trees for Ordinal Responses in R: The rpartScore Package

This paper introduces rpartScore (Galimberti, Soffritti, and Di Maso 2012), a new R package for building classification trees for ordinal responses, that can be employed whenever a set of scores is assigned to the ordered categories of the response. This package has been created to overcome some problems that produced unexpected results from the package rpartOrdinal (Archer 2010). Explanations for the causes of these unexpected results are provided. The main functionalities of rpartScore are described, and its use is illustrated through some examples

Mixtures of multivariate generalized linear models with overlapping clusters

With the advent of ubiquitous monitoring and measurement protocols, studies have started to focus more and more on complex, multivariate and heterogeneous datasets. In such studies, multivariate response variables are drawn from a heterogeneous population often in the presence of additional covariate information. In order to deal with this intrinsic heterogeneity, regression analyses have to be clustered for different groups of units. Up until now, mixture model approaches assigned units to distinct and non-overlapping groups. However, not rarely these units exhibit more complex organization and clustering. It is our aim to define a mixture of generalized linear models with overlapping clusters of units. This involves crucially an overlap function, that maps the coefficients of the parent clusters into the the coefficient of the multiple allocation units. We present a computationally efficient MCMC scheme that samples the posterior distribution of the parameters in the model. An example on a two-mode network study shows details of the implementation in the case of a multivariate probit regression setting. A simulation study shows the overall performance of the method, whereas an illustration of the voting behaviour on the US supreme court shows how the 9 justices split in two overlapping sets of justices.Comment: 24 pages, 3 figure

Detecting relevant gene structure through independent component analysis Individuazione della struttura genica rilevante attraverso l'analisi in componenti indipendenti

Riassunto: Uno degli aspetti di maggior rilevanza nell'impiego di dati di espressione genica in problemi di classificazioneè rappresentato dalla necessità di procedere preliminarmente ad una selezione dei predittori. In questo lavoro sono approfonditi alcuni aspetti della procedura proposta i

Comparative targeted metabolomic profiles of porcine plasma and serum

Metabolomics has been used to characterise many biological matrices and obtain detailed pictures of biological systems based on many metabolites. Plasma and serum are two blood-derived biofluids commonly used to assess and monitor the organismal metabolism and obtain information on the physiological and health conditions of an animal. Plasma is the supernatant that is separated from the cellular components after centrifugation of the blood that is first added with an anticoagulant. Serum is obtained after centrifugation of the blood that has been coagulated. The choice of one or the other biofluid for metabolomic analyses is related to specific analytical needs and technical issues, to problems derived by the collection and preparation steps, in particular when specimens are sampled from animals involved in field studies. Thus far, most of the metabolomic studies that compared plasma and serum have been carried out in humans and very little is known on the pigs. In this study, we used a targeted metabolomic platform that can detect about 180 metabolites of five biochemical classes to compare plasma and serum profiles of samples collected from 24 pigs. To also obtain a cross-species comparative metabolomic analysis, information for human plasma and serum derived from the same platform was retrieved from previous studies. Statistical analyses included univariate and multivariate approaches aimed at identifying stable and/or differentially abundant metabolites between the two porcine biofluids. A total of 154 (∼83%) metabolites passed the initial quality control, indicating a good repeatability of the analytical platform in pigs. Discarded metabolites included aspartate and biogenic amines that were already reported to be unstable in human studies. More than 80% of the metabolites had similar profiles in both porcine biofluids (average correlation was 0.75). Concentrations were usually higher in serum than in plasma, in agreement with what was already reported in humans. The univariate analysis identified 44 metabolites that had statistically different concentrations between porcine plasma and serum, of which 28 metabolites were also confirmed by the multivariate analysis. The obtained picture described similarities and differences between these two biofluids in pigs and the related human-pig comparisons. The obtained information can be useful for the choice of one or the other matrix for the implementation of metabolomic studies in this livestock species. The results can also provide useful hints to valuing the pig as animal model, in particular when metabolite-derived physiological states are relevant

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes.

open9noBACKGROUND: Carcass fatness is an important trait in most pig breeding programs. Following market requests, breeding plans for fresh pork consumption are usually designed to reduce carcass fat content and increase lean meat deposition. However, the Italian pig industry is mainly devoted to the production of Protected Designation of Origin dry cured hams: pigs are slaughtered at around 160 kg of live weight and the breeding goal aims at maintaining fat coverage, measured as backfat thickness to avoid excessive desiccation of the hams. This objective has shaped the genetic pool of Italian heavy pig breeds for a few decades. In this study we applied a selective genotyping approach within a population of ~ 12,000 performance tested Italian Large White pigs. Within this population, we selectively genotyped 304 pigs with extreme and divergent backfat thickness estimated breeding value by the Illumina PorcineSNP60 BeadChip and performed a genome wide association study to identify loci associated to this trait. RESULTS: We identified 4 single nucleotide polymorphisms with P≤5.0E-07 and additional 119 ones with 5.0E-07<P≤5.0E-05. These markers were located throughout all chromosomes. The largest numbers were found on porcine chromosomes 6 and 9 (n=15), 4 (n=13), and 7 (n=12) while the most significant marker was located on chromosome 18. Twenty-two single nucleotide polymorphisms were in intronic regions of genes already recognized by the Pre-Ensembl Sscrofa10.2 assembly. Gene Ontology analysis indicated an enrichment of Gene Ontology terms associated with nervous system development and regulation in concordance with results of large genome wide association studies for human obesity. CONCLUSIONS: Further investigations are needed to evaluate the effects of the identified single nucleotide polymorphisms associated with backfat thickness on other traits as a pre-requisite for practical applications in breeding programs. Reported results could improve our understanding of the biology of fat metabolism and deposition that could also be relevant for other mammalian species including humans, confirming the role of neuronal genes on obesity.To June 10, 2013 the paper is labelled as "Highly accessed" on the BMC genomics website http://www.biomedcentral.com/1471-2164/13/583openFontanesi L;Schiavo G;Galimberti G;Calò DG;Scotti E;Martelli PL;Buttazzoni L;Casadio R;Russo VFontanesi L;Schiavo G;Galimberti G;Calò DG;Scotti E;Martelli PL;Buttazzoni L;Casadio R;Russo

The significance of sentinel lymph node micrometastasis in breast cancer: Comparing outcomes with and without axillary clearance.

Management of micrometastasis in the sentinel node is a controversial topic. Most of the guidelines don't recommend further axillary treatment if micrometastasis are the only finding in the sentinel node. However, some evidence suggests that micrometastasis have significant effect on long term outcomes and therefore indicate systemic treatment.Accepted manuscript (12 month embargo