Metabolic network discovery through reverse engineering of metabolome data

Reverse engineering of high-throughput omics data to infer underlying biological networks is one of the challenges in systems biology. However, applications in the field of metabolomics are rather limited. We have focused on a systematic analysis of metabolic network inference from in silico metabolome data based on statistical similarity measures. Three different data types based on biological/environmental variability around steady state were analyzed to compare the relative information content of the data types for inferring the network. Comparing the inference power of different similarity scores indicated the clear superiority of conditioning or pruning based scores as they have the ability to eliminate indirect interactions. We also show that a mathematical measure based on the Fisher information matrix gives clues on the information quality of different data types to better represent the underlying metabolic network topology. Results on several datasets of increasing complexity consistently show that metabolic variations observed at steady state, the simplest experimental analysis, are already informative to reveal the connectivity of the underlying metabolic network with a low false-positive rate when proper similarity-score approaches are employed. For experimental situations this implies that a single organism under slightly varying conditions may already generate more than enough information to rightly infer networks. Detailed examination of the strengths of interactions of the underlying metabolic networks demonstrates that the edges that cannot be captured by similarity scores mainly belong to metabolites connected with weak interaction strength

Multivariate paired data analysis: multilevel PLSDA versus OPLSDA

Metabolomics data obtained from (human) nutritional intervention studies can have a rather complex structure that depends on the underlying experimental design. In this paper we discuss the complex structure in data caused by a cross-over designed experiment. In such a design, each subject in the study population acts as his or her own control and makes the data paired. For a single univariate response a paired t-test or repeated measures ANOVA can be used to test the differences between the paired observations. The same principle holds for multivariate data. In the current paper we compare a method that exploits the paired data structure in cross-over multivariate data (multilevel PLSDA) with a method that is often used by default but that ignores the paired structure (OPLSDA). The results from both methods have been evaluated in a small simulated example as well as in a genuine data set from a cross-over designed nutritional metabolomics study. It is shown that exploiting the paired data structure underlying the cross-over design considerably improves the power and the interpretability of the multivariate solution. Furthermore, the multilevel approach provides complementary information about (I) the diversity and abundance of the treatment effects within the different (subsets of) subjects across the study population, and (II) the intrinsic differences between these study subjects

Strategic responses to global challenges: The case of European banking, 1973–2000

In applying a strategy, structure, ownership and performance (SSOP) framework to three major clearing banks (ABN AMRO, UBS, Barclays), this article debates whether the conclusions generated by Whittington and Mayer about European manufacturing industry can be applied to the financial services sector. While European integration plays a key role in determining strategy, it is clear that global factors were far more important in determining management actions, leading to significant differences in structural adaptation. The article also debates whether this has led to improved performance, given the problems experienced with both geographical dispersion and diversification, bringing into question the quality of decision-making over the long term

Double-check: validation of diagnostic statistics for PLS-DA models in metabolomics studies

Partial Least Squares-Discriminant Analysis (PLS-DA) is a PLS regression method with a special binary ‘dummy’ y-variable and it is commonly used for classification purposes and biomarker selection in metabolomics studies. Several statistical approaches are currently in use to validate outcomes of PLS-DA analyses e.g. double cross validation procedures or permutation testing. However, there is a great inconsistency in the optimization and the assessment of performance of PLS-DA models due to many different diagnostic statistics currently employed in metabolomics data analyses. In this paper, properties of four diagnostic statistics of PLS-DA, namely the number of misclassifications (NMC), the Area Under the Receiver Operating Characteristic (AUROC), Q2 and Discriminant Q2 (DQ2) are discussed. All four diagnostic statistics are used in the optimization and the performance assessment of PLS-DA models of three different-size metabolomics data sets obtained with two different types of analytical platforms and with different levels of known differences between two groups: control and case groups. Statistical significance of obtained PLS-DA models was evaluated with permutation testing. PLS-DA models obtained with NMC and AUROC are more powerful in detecting very small differences between groups than models obtained with Q2 and Discriminant Q2 (DQ2). Reproducibility of obtained PLS-DA models outcomes, models complexity and permutation test distributions are also investigated to explain this phenomenon. DQ2 and Q2 (in contrary to NMC and AUROC) prefer PLS-DA models with lower complexity and require higher number of permutation tests and submodels to accurately estimate statistical significance of the model performance. NMC and AUROC seem more efficient and more reliable diagnostic statistics and should be recommended in two group discrimination metabolomic studies

Advances on antiviral activity of Morus spp. plant extracts: Human coronavirus and virus-related respiratory tract infections in the spotlight

(1) Background: Viral respiratory infections cause life-threatening diseases in millions of people worldwide every year. Human coronavirus and several picornaviruses are responsible for worldwide epidemic outbreaks, thus representing a heavy burden to their hosts. In the absence of specific treatments for human viral infections, natural products offer an alternative in terms of innovative drug therapies. (2) Methods: We analyzed the antiviral properties of the leaves and stem bark of the mulberry tree (Morus spp.). We compared the antiviral activity of Morus spp. on enveloped and nonenveloped viral pathogens, such as human coronavirus (HCoV 229E) and different members of the Picornaviridae family—human poliovirus 1, human parechovirus 1 and 3, and human echovirus 11. The antiviral activity of 12 water and water–alcohol plant extracts of the leaves and stem bark of three different species of mulberry—Morus alba var. alba, Morus alba var. rosa, and Morus rubra—were evaluated. We also evaluated the antiviral activities of kuwanon G against HCoV-229E. (3) Results: Our results showed that several extracts reduced the viral titer and cytopathogenic effects (CPE). Leaves’ water-alcohol extracts exhibited maximum antiviral activity on human coronavirus, while stem bark and leaves’ water and water-alcohol extracts were the most effective on picornaviruses. (4) Conclusions: The analysis of the antiviral activities of Morus spp. offer promising applications in antiviral strategies

Detecting Regulatory Mechanisms in Endocrine Time Series Measurements

The regulatory mechanisms underlying pulsatile secretion are complex, especially as it is partly controlled by other hormones and the combined action of multiple agents. Regulatory relations between hormones are not directly observable but may be deduced from time series measurements of plasma hormone concentrations. Variation in plasma hormone levels are the resultant of secretion and clearance from the circulation. A strategy is proposed to extract inhibition, activation, thresholds and circadian synchronicity from concentration data, using particular association methods. Time delayed associations between hormone concentrations and/or extracted secretion pulse profiles reveal the information on regulatory mechanisms. The above mentioned regulatory mechanisms are illustrated with simulated data. Additionally, data from a lean cohort of healthy control subjects is used to illustrate activation (ACTH and cortisol) and circadian synchronicity (ACTH and TSH) in real data. The simulation and the real data both consist of 145 equidistant samples per individual, matching a 24-hr time span with 10 minute intervals. The results of the simulation and the real data are in concordance

Have Anglo-Saxon concepts really influenced the development of European qualifications policy?

This paper considers how far Anglo-Saxon conceptions of have influenced European Union vocational education and training policy, especially given the disparate approaches to VET across Europe. Two dominant approaches can be identified: the dual system (exemplified by Germany); and output based models (exemplified by the NVQ ‘English style’). Within the EU itself, the design philosophy of the English output-based model proved in the first instance influential in attempts to develop tools to establish equivalence between vocational qualifications across Europe, resulting in the learning outcomes approach of the European Qualifications Framework, the credit-based model of European VET Credit System and the task-based construction of occupation profiles exemplified by European Skills, Competences and Occupations. The governance model for the English system is, however, predicated on employer demand for ‘skills’ and this does not fit well with the social partnership model encompassing knowledge, skills and competences that is dominant in northern Europe. These contrasting approaches have led to continual modifications to the tools, as these sought to harmonise and reconcile national VET requirements with the original design. A tension is evident in particular between national and regional approaches to vocational education and training, on the one hand, and the policy tools adopted to align European vocational education and training better with the demands of the labour market, including at sectoral level, on the other. This paper explores these tensions and considers the prospects for the successful operation of these tools, paying particular attention to the European Qualifications Framework, European VET Credit System and European Skills, Competences and Occupations tool and the relationships between them and drawing on studies of the construction and furniture industries

Statistical validation of megavariate effects in ASCA

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Simplivariate Models: Ideas and First Examples

One of the new expanding areas in functional genomics is metabolomics: measuring the metabolome of an organism. Data being generated in metabolomics studies are very diverse in nature depending on the design underlying the experiment. Traditionally, variation in measurements is conceptually broken down in systematic variation and noise where the latter contains, e.g. technical variation. There is increasing evidence that this distinction does not hold (or is too simple) for metabolomics data. A more useful distinction is in terms of informative and non-informative variation where informative relates to the problem being studied. In most common methods for analyzing metabolomics (or any other high-dimensional x-omics) data this distinction is ignored thereby severely hampering the results of the analysis. This leads to poorly interpretable models and may even obscure the relevant biological information. We developed a framework from first data analysis principles by explicitly formulating the problem of analyzing metabolomics data in terms of informative and non-informative parts. This framework allows for flexible interactions with the biologists involved in formulating prior knowledge of underlying structures. The basic idea is that the informative parts of the complex metabolomics data are approximated by simple components with a biological meaning, e.g. in terms of metabolic pathways or their regulation. Hence, we termed the framework ‘simplivariate models’ which constitutes a new way of looking at metabolomics data. The framework is given in its full generality and exemplified with two methods, IDR analysis and plaid modeling, that fit into the framework. Using this strategy of ‘divide and conquer’, we show that meaningful simplivariate models can be obtained using a real-life microbial metabolomics data set. For instance, one of the simple components contained all the measured intermediates of the Krebs cycle of E. coli. Moreover, these simplivariate models were able to uncover regulatory mechanisms present in the phenylalanine biosynthesis route of E. coli

European skills framework? - but what are skills? Anglo-Saxon versus German concepts

With the proposed introduction of a common framework for comparing qualifications within the European Union (EU), as a result of the Lisbon agreement of 2000, the question of commonly agreed transnational concepts of skills and qualifications is has become a pressing political and practical issue. The paper argues that there are grounds for doubting that there is a ready translation of the English terms 'skill'and 'qualification' in a way that avoids problems of comparing and calibrating German and English vocational qualifications. Reasons for this difficulty are explored, the most important of which relate to: a) the conceptual structure of skill and its cognates in the two languages; b) the differing socio-political role of qualifications; c) different industrial structures and labour processes; d) differences in institutions regulating vocational education and training (VET). These problems are discussed in relation to examples of similar industries and occupations and apparently similar levels of qualification in England and Germany