amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R.

Positive representations of finite groups in Riesz spaces

In this paper, which is part of a study of positive representations of locally compact groups in Banach lattices, we initiate the theory of positive representations of finite groups in Riesz spaces. If such a representation has only the zero subspace and possibly the space itself as invariant principal bands, then the space is Archimedean and finite dimensional. Various notions of irreducibility of a positive representation are introduced and, for a finite group acting positively in a space with sufficiently many projections, these are shown to be equal. We describe the finite dimensional positive Archimedean representations of a finite group and establish that, up to order equivalence, these are order direct sums, with unique multiplicities, of the order indecomposable positive representations naturally associated with transitive $G$-spaces. Character theory is shown to break down for positive representations. Induction and systems of imprimitivity are introduced in an ordered context, where the multiplicity formulation of Frobenius reciprocity turns out not to hold.Comment: 23 pages. To appear in International Journal of Mathematic

The development of a mapping tool for the evaluation of building systems for future climate scenarios on European scale

The paper presents a tool for the mapping of the performance of building systems on European scale for different (future) time periods. The tool is to use for users and be applicable for different building systems. Users should also be able to use a broad range of climate parameters to assess the influence of climate change on these climatic parameters. Also should the calculation time be reasonable short. The mapping tool is developed in MATLAB, which can be used by other users for their own studies.Comment: 21 pages, 24 figures, pre-conferenc

amsrpm: Robust Point Matching for Retention Time Aligment of LC/MS Data with R

Proteomics is the study of the abundance, function and dynamics of all proteins present in a living organism, and mass spectrometry (MS) has become its most important tool due to its unmatched sensitivity, resolution and potential for high-throughput experimentation. A frequently used variant of mass spectrometry is coupled with liquid chromatography (LC) and is denoted as "LC/MS". It produces two-dimensional raw data, where significant distortions along one of the dimensions can occur between different runs on the same instrument, and between instruments. A compensation of these distortions is required to allow for comparisons between and inference based on different experiments. This article introduces the amsrpm software package. It implements a variant of the Robust Point Matching (RPM) algorithm that is tailored for the alignment of LC and LC/MS experiments. Problem-specific enhancements include a specialized dissimilarity measure, and means to enforce smoothness and monotonicity of the estimated transformation function. The algorithm does not rely on pre-specified landmarks, it is insensitive towards outliers and capable of modeling nonlinear distortions. Its usefulness is demonstrated using both simulated and experimental data. The software is available as an open source package for the statistical programming language R

Computational protein profile similarity screening for quantitative mass spectrometry experiments

Motivation: The qualitative and quantitative characterization of protein abundance profiles over a series of time points or a set of environmental conditions is becoming increasingly important. Using isobaric mass tagging experiments, mass spectrometry-based quantitative proteomics deliver accurate peptide abundance profiles for relative quantitation. Associated data analysis workflows need to provide tailored statistical treatment that (i) takes the correlation structure of the normalized peptide abundance profiles into account and (ii) allows inference of protein-level similarity. We introduce a suitable distance measure for relative abundance profiles, derive a statistical test for equality and propose a protein-level representation of peptide-level measurements. This yields a workflow that delivers a similarity ranking of protein abundance profiles with respect to a defined reference. All procedures have in common that they operate based on the true correlation structure that underlies the measurements. This optimizes power and delivers more intuitive and efficient results than existing methods that do not take these circumstances into account. Results: We use protein profile similarity screening to identify candidate proteins whose abundances are post-transcriptionally controlled by the Anaphase Promoting Complex/Cyclosome (APC/C), a specific E3 ubiquitin ligase that is a master regulator of the cell cycle. Results are compared with an established protein correlation profiling method. The proposed procedure yields a 50.9-fold enrichment of co-regulated protein candidates and a 2.5-fold improvement over the previous method

Phenological and molecular studies on the introduced seaweed Dictyota cyanoloma (Dictyotales, Phaeophyceae) along the Mediterranean coast of the Iberian Peninsula

Dictyota cyanoloma, a distinctive brown algal species characterized by a blue-iridescent margin, was recently reported as an introduced species in the Mediterranean Sea but little is known about its distribution dynamics, morphological plasticity and genetic structure. In this integrative study, we evaluate its past and present occurrence along the Mediterranean Iberian coast, assess the species' phenology in Palamos (Girona, Spain) and analyze the haplotype diversity by sequencing 49 individuals from nine sampling sites for different chloroplast and mitochondrial DNA regions. Although D. cyanoloma currently occurs along all the Mediterranean Iberian coasts (in 19 of 36 localities sampled, mostly in marinas and harbour environments), we were not able to find any herbarium material of this species (at BCN-Phyc and MA) predating the year 1987. In Palamos, D. cyanoloma is present all through the year, with a maximum development in winter and a minimum in summer. Fertile specimens are absent during summer (July and August). Sporophytes are dominant from January to June and gametophytes were found only in February, March and June. Information about the antheridia, which has never been described before, is provided. Two chloroplast and three mitochondrial haplotypes were observed, indicating that multiple introductions of D. cyanoloma occurred in the study area. Additionally, the genetic structure suggests that spread did not occur through simple advancing wave fronts but by several longdistance dispersal events. Further studies employing microsatellite markers could potentially offer a better resolution to unravel expansion and colonisation dynamics of D. cyanoloma in the Mediterranean Sea

Viewpoint consistency in Z and LOTOS: A case study

Specification by viewpoints is advocated as a suitable method of specifying complex systems. Each viewpoint describes the envisaged system from a particular perspective, using concepts and specification languages best suited for that perspective. Inherent in any viewpoint approach is the need to check or manage the consistency of viewpoints and to show that the different viewpoints do not impose contradictory requirements. In previous work we have described a range of techniques for consistency checking, refinement, and translation between viewpoint specifications, in particular for the languages LOTOS and Z. These two languages are advocated in a particular viewpoint model, viz. that of the Open Distributed Processing (ODP) reference model. In this paper we present a case study which demonstrates how all these techniques can be combined in order to show consistency between a viewpoint specified in LOTOS and one specified in Z. Keywords: Viewpoints; Consistency; Z; LOTOS; ODP

Partial order and a T0T_0-topology in a set of finite quantum systems

A `whole-part' theory is developed for a set of finite quantum systems $\Sigma (n)$ with variables in ${\mathbb Z}(n)$. The partial order `subsystem' is defined, by embedding various attributes of the system $\Sigma (m)$ (quantum states, density matrices, etc) into their counterparts in the supersystem $\Sigma (n)$ (for $m|n$). The compatibility of these embeddings is studied. The concept of ubiquity is introduced for quantities which fit with this structure. It is shown that various entropic quantities are ubiquitous. The sets of various quantities become $T_0$-topological spaces with the divisor topology, which encapsulates fundamental physical properties. These sets can be converted into directed-complete partial orders (dcpo), by adding `top elements'. The continuity of various maps among these sets is studied