MultiD Analyses AB

Göteborg, Sweden

MultiD Analyses AB

Göteborg, Sweden
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Sjogreen B.,Multid Analyses AB | Yee H.C.,NASA
Journal of Physics: Conference Series | Year: 2017

Skew-symmetric splittings of the inviscid flux derivative for high order central schemes are studied and developed to improve their numerical stability without added high order numerical dissipation for long time wave propagations and long time integration of compressible turbulent flows. For flows containing discontinuities and multiscale turbulence fluctuations the Yee & Sjogreen [33] and Kotov et al. [15, 14] high order nonlinear filter approach is utilized in conjunction with the skew-symmetric form of high order central schemes. Due to the incomplete hyperbolic nature of the conservative ideal magnetohydrodynamics (MHD) governing equations, not all of the skew-symmetric splittings for gas dynamics can be extended to the ideal MHD. For the MHD the Ducros et al. [6] variants are constructed. In addition, four formulations of the MHD are considered: (a) the conservative MHD, (b) the Godunov/Powell non-conservative form, (c) the Janhunen MHD with magnetic field source terms [13], and (d) a MHD with source terms of [3]. The different formulation of the equations in conjunction with the variants of Ducros et al. type skew-symmetric splitting will be shown to have a strong effect on the stability of non-dissipative approximations. Representative test cases for both smooth flows and problems containing discontinuities for the ideal MHD are included. The results illustrate the improved stability by using the skew-symmetric splitting as part of the central base scheme instead of the pure high order central scheme. © Published under licence by IOP Publishing Ltd.


Bergkvist A.,MultiD Analyses AB | Rusnakova V.,Academy of Sciences of the Czech Republic | Sindelka R.,Whitehead Institute For Biomedical Research | Garda J.M.A.,University of Corunna | And 5 more authors.
Methods | Year: 2010

Advances in qPCR technology allow studies of increasingly large systems comprising many genes and samples. The increasing data sizes allow expression profiling both in the gene and the samples dimension while also putting higher demands on sound statistical analysis and expertise to handle and interpret its results. We distinguish between exploratory and confirmatory statistical studies. In this paper we demonstrate several techniques available for exploratory studies on a system of Xenopus laevis development from egg to tadpole. Techniques include hierarchical clustering, heatmap, principal component analysis and self-organizing maps. We stress that even though exploratory studies are excellent for generating hypotheses, results have not been proven statistically significant until an independent confirmatory study has been performed. An exploratory study may certainly be valuable in its own right, and there are often not enough resources to report both an exploratory and a confirmatory study at the same time. However, exploratory and confirmatory studies are intimately connected and we would like to raise that awareness among qPCR practitioners. We suggest that scientific reports should always have a hypothesis focus. Reports are either hypothesis generating, from an exploratory study, or hypothesis validating, from a confirmatory study, or both. In either case, we suggest the generated or validated hypotheses be specifically stated. © 2010 Elsevier Inc.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: ICT-2009.3.9 | Award Amount: 9.20M | Year: 2010

Cancer remains a prominent health concern afflicting modern societies. Continuous innovations and introduction of new technologies are essential to level or even reduce current healthcare spending. As the analysis of occult tumour cells (OTC) in blood or bone marrow is most promising in this respect, MIRACLE aims to develop a low-cost, fully automated, integrated lab-on-a-chip (LOC) system for the isolation, counting and characterization of OTCs starting from clinical samples.A major challenge for OTC detection is their extremely low concentration (below a single cell per mL) in clinical samples. Current detection methods are often based on enrichment techniques followed by cumbersome microscopic analysis of the cell phenotype. Some of these procedure steps have been semi-automated (Cellsearch, J&J), but the interpretation of the cell morphology requires expertise and remains partially subjective. In contrary to standard phenotyping tests, MIRACLE aims to determine the genotype by integrating all sample processing and detection steps in a miniaturized system. This envisaged, fully-automated MIRACLE test would yield decisive results within half a day for less than 50 EUR, as compared with contemporary diagnostics tests that may take days.With the essential individual modules recently demonstrated on automated chips in a joint project by some of the partners involved (MASCOT FP6 027652), the MIRACLEs consortium is uniquely positioned to lead the projects main objectives to a successful outcome, well ahead of the current state-of-the-art. Combining the teams multidisciplinary and unique expertise avoids unnecessary overlap. Integrating all components into a fully operational LOC platform will represent an immense advance for Europe to cope with interfacing and integration problems generic to microfluidic and smart miniaturized systems. More importantly, the realisation of the MIRACLE vision will revolutionise cancer diagnostics and individualized theranostics.


Grant
Agency: European Commission | Branch: FP7 | Program: CP | Phase: ICT-2007.5.1 | Award Amount: 12.70M | Year: 2008

The overall concept of the CD-MEDICS IP is to develop a technology platform for point-of-care diagnostics, capable of simultaneous genomic and proteomic detection, with embedded communication abilities for direct interfacing with hospital information systems. This will be achieved by exploiting breakthroughs at the confluences of bio-, micro- and nano- technologies to create a low-cost non-invasive intelligent diagnosis system. This platform will be developed in a modular format, which will allow each module to be developed and exploited individually. The modules will subsequently be integrated to facilitate the desired application. Advances in data communications, molecular biology and biosensor technology, with the integration of nanostructured functional components in macro and microsystems, will facilitate the realisation of a minimally invasive generic platform, which is capable of multi-parametric monitoring and will be interoperable with electronic medical records. The advantages of integrated biosensor systems include their ease of use, their sensitivity, their inherent selectivity (preventing problems due to interfering substances), their versatility (allowing in-field use) and their cost effectiveness. Addressing the future health care requirement of an individualised theranostic approach, the specific application that will be demonstrated in this IP will be for the management, monitoring and diagnosis of coeliac disease, with the proposed technology contributing to significant advances in sensitivity and specificity of diagnosis. The technology platform developed, however, could be applied to a variety of clinical screening applications, such as cancer. The radical innovation proposed in this IP will result in a concrete prime deliverable of a technology platform of wide application and unquestionable socio-economic benefit, increasing European competitiveness whilst contributing considerably to the quality of life well-being of the population.


Stahlberg A.,TATAA Biocenter | Stahlberg A.,Gothenburg University | Rusnakova V.,Academy of Sciences of the Czech Republic | Forootan A.,Gothenburg University | And 4 more authors.
Methods | Year: 2013

Individual cells represent the basic unit in tissues and organisms and are in many aspects unique in their properties. The introduction of new and sensitive techniques to study single-cells opens up new avenues to understand fundamental biological processes. Well established statistical tools and recommendations exist for gene expression data based on traditional cell population measurements. However, these workflows are not suitable, and some steps are even inappropriate, to apply on single-cell data. Here, we present a simple and practical workflow for preprocessing of single-cell data generated by reverse transcription quantitative real-time PCR. The approach is demonstrated on a data set based on profiling of 41 genes in 303 single-cells. For some pre-processing steps we present options and also recommendations. In particular, we demonstrate and discuss different strategies for handling missing data and scaling data for downstream multivariate analysis. The aim of this workflow is provide guide to the rapidly growing community studying single-cells by means of reverse transcription quantitative real-time PCR profiling. © 2012 Elsevier Inc.


PubMed | MultiD Analyses AB
Type: Journal Article | Journal: Methods (San Diego, Calif.) | Year: 2010

Advances in qPCR technology allow studies of increasingly large systems comprising many genes and samples. The increasing data sizes allow expression profiling both in the gene and the samples dimension while also putting higher demands on sound statistical analysis and expertise to handle and interpret its results. We distinguish between exploratory and confirmatory statistical studies. In this paper we demonstrate several techniques available for exploratory studies on a system of Xenopus laevis development from egg to tadpole. Techniques include hierarchical clustering, heatmap, principal component analysis and self-organizing maps. We stress that even though exploratory studies are excellent for generating hypotheses, results have not been proven statistically significant until an independent confirmatory study has been performed. An exploratory study may certainly be valuable in its own right, and there are often not enough resources to report both an exploratory and a confirmatory study at the same time. However, exploratory and confirmatory studies are intimately connected and we would like to raise that awareness among qPCR practitioners. We suggest that scientific reports should always have a hypothesis focus. Reports are either hypothesis generating, from an exploratory study, or hypothesis validating, from a confirmatory study, or both. In either case, we suggest the generated or validated hypotheses be specifically stated.

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