Comparative genomics of metabolic networks of free-living and parasitic eukaryotes

Background Obligate endoparasites often lack particular metabolic pathways as compared to free-living organisms. This phenomenon comprises anabolic as well as catabolic reactions. Presumably, the corresponding enzymes were lost in adaptation to parasitism. Here we compare the predicted core metabolic graphs of obligate endoparasites and non-parasites (free living organisms and facultative parasites) in order to analyze how the parasites' metabolic networks shrunk in the course of evolution. Results Core metabolic graphs comprising biochemical reactions present in the presumed ancestor of parasites and non-parasites were reconstructed from the Kyoto Encyclopedia of Genes and Genomes. While the parasites' networks had fewer nodes (metabolites) and edges (reactions), other parameters such as average connectivity, network diameter and number of isolated edges were similar in parasites and non-parasites. The parasites' networks contained a higher percentage of ATP-consuming reactions and a lower percentage of NAD-requiring reactions. Control networks, shrunk to the size of the parasites' by random deletion of edges, were scale-free but exhibited smaller diameters and more isolated edges. Conclusions The parasites' networks were smaller than those of the non-parasites regarding number of nodes or edges, but not regarding network diameters. Network integrity but not scale-freeness has acted as a selective principle during the evolutionary reduction of parasite metabolism. ATP-requiring reactions in particular have been retained in the parasites' core metabolism while NADH- or NADPH-requiring reactions were lost preferentially.

Effects of study precision and risk of bias in networks of interventions: a network meta-epidemiological study

BACKGROUND Empirical research has illustrated an association between study size and relative treatment effects, but conclusions have been inconsistent about the association of study size with the risk of bias items. Small studies give generally imprecisely estimated treatment effects, and study variance can serve as a surrogate for study size. METHODS We conducted a network meta-epidemiological study analyzing 32 networks including 613 randomized controlled trials, and used Bayesian network meta-analysis and meta-regression models to evaluate the impact of trial characteristics and study variance on the results of network meta-analysis. We examined changes in relative effects and between-studies variation in network meta-regression models as a function of the variance of the observed effect size and indicators for the adequacy of each risk of bias item. Adjustment was performed both within and across networks, allowing for between-networks variability. RESULTS Imprecise studies with large variances tended to exaggerate the effects of the active or new intervention in the majority of networks, with a ratio of odds ratios of 1.83 (95% CI: 1.09,3.32). Inappropriate or unclear conduct of random sequence generation and allocation concealment, as well as lack of blinding of patients and outcome assessors, did not materially impact on the summary results. Imprecise studies also appeared to be more prone to inadequate conduct. CONCLUSIONS Compared to more precise studies, studies with large variance may give substantially different answers that alter the results of network meta-analyses for dichotomous outcomes.

The scholarly networks of Albrecht von Haller and the Economic Society of Bern – a multi-level network analysis

Here, by the example of the transfer of cultivated plants in the context of the correspondence networks of Albrecht von Haller and the Economic Society, a multi-level network analysis is suggested. By a multi-level procedure, the chronological dynamics, the social structure, the spatial distribution and the functional networking are analyzed one after the other. These four levels of network analysis do not compete with each other but are mutually supporting. This aims at a deeper understanding of how these networks contributed to an international transfer of knowledge in the 18th century.

Networks of Information Exchange Under Uncertainty: The Case of Unconventional Gas Development in the United Kingdom

Modern policy-making is increasingly influenced by different types of uncertainty. Political actors are supposed to behave differently under the context of uncertainty then in “usual” decision-making processes. Actors exchange information in order to convince other actors and decision-makers, to coordinate their lobbying activities and form coalitions, and to get information and learn on the substantive issue. The literature suggests that preference similarity, social trust, perceived power and functional interdependence are particularly important drivers of information exchange. We assume that social trust as well as being connected to scientific actors is more important under uncertainty than in a setting with less uncertainty. To investigate information exchange under uncertainty analyze the case of unconventional shale gas development in the UK from 2008 till 2014. Our study will rely on statistical analyses of survey data on a diverse set of actors dealing with shale gas development and regulation in the UK.

Chow–Liu trees are sufficient predictive models for reproducing key features of functional networks of periictal EEG time-series

Seizure freedom in patients suffering from pharmacoresistant epilepsies is still not achieved in 20–30% of all cases. Hence, current therapies need to be improved, based on a more complete understanding of ictogenesis. In this respect, the analysis of functional networks derived from intracranial electroencephalographic (iEEG) data has recently become a standard tool. Functional networks however are purely descriptive models and thus are conceptually unable to predict fundamental features of iEEG time-series, e.g., in the context of therapeutical brain stimulation. In this paper we present some first steps towards overcoming the limitations of functional network analysis, by showing that its results are implied by a simple predictive model of time-sliced iEEG time-series. More specifically, we learn distinct graphical models (so called Chow–Liu (CL) trees) as models for the spatial dependencies between iEEG signals. Bayesian inference is then applied to the CL trees, allowing for an analytic derivation/prediction of functional networks, based on thresholding of the absolute value Pearson correlation coefficient (CC) matrix. Using various measures, the thus obtained networks are then compared to those which were derived in the classical way from the empirical CC-matrix. In the high threshold limit we find (a) an excellent agreement between the two networks and (b) key features of periictal networks as they have previously been reported in the literature. Apart from functional networks, both matrices are also compared element-wise, showing that the CL approach leads to a sparse representation, by setting small correlations to values close to zero while preserving the larger ones. Overall, this paper shows the validity of CL-trees as simple, spatially predictive models for periictal iEEG data. Moreover, we suggest straightforward generalizations of the CL-approach for modeling also the temporal features of iEEG signals.

Mechanisms of intrinsic beating variability in cardiac cell cultures and model pacemaker networks

Heart rate variability (HRV) exhibits fluctuations characterized by a power law behavior of its power spectrum. The interpretation of this nonlinear HRV behavior, resulting from interactions between extracardiac regulatory mechanisms, could be clinically useful. However, the involvement of intrinsic variations of pacemaker rate in HRV has scarcely been investigated. We examined beating variability in spontaneously active incubating cultures of neonatal rat ventricular myocytes using microelectrode arrays. In networks of mathematical model pacemaker cells, we evaluated the variability induced by the stochastic gating of transmembrane currents and of calcium release channels and by the dynamic turnover of ion channels. In the cultures, spontaneous activity originated from a mobile focus. Both the beat-to-beat movement of the focus and beat rate variability exhibited a power law behavior. In the model networks, stochastic fluctuations in transmembrane currents and stochastic gating of calcium release channels did not reproduce the spatiotemporal patterns observed in vitro. In contrast, long-term correlations produced by the turnover of ion channels induced variability patterns with a power law behavior similar to those observed experimentally. Therefore, phenomena leading to long-term correlated variations in pacemaker cellular function may, in conjunction with extracardiac regulatory mechanisms, contribute to the nonlinear characteristics of HRV.

Strange Relations. Cultural Translation of Noh Theatre in Ezra Pound’s Dance Poems and W. B. Yeats’s At the Hawk’s Well

Drawing on the reception of Noh drama by Ezra Pound and William Butler Yeats, the article analyses both the literary and cultural ‘translations’ of this form of Japanese theatre in their works, focusing on Yeats’s play At the Hawk’s Well (1917). I conceptualize ‘cultural translation’ as the staging of relations that mark a residual cultural difference. Referred to as ‘foreignizing’ in translation theory, this method enables what Erika Fischer-Lichte has termed a ‘liminal experience’ for the audience –– an effect Yeats intended for the performance of his play. It evokes situations in which opposites collapse and new ways of acting or new combinations of symbols can be tried out. Yeats’s play will be used to sketch how an analysis of relations could serve as a general model for the study of cultural transfer as cultural translation in general. Keywords: cultural translation, translation theory, performance, William Butler Yeats, Itō Michio, Ezra Pound, At the Hawk’s Well

Effects of forest management on bryophyte communities on deadwood

Epixylic bryophytes are important components of forest vegetation but are currently endangered by increment of wood harvest and intensive forest management. In this paper we present a study about the relationship between forest management, deadwood abundance, deadwood attributes and species richness of epixylic bryophytes on 30 plots comprising three forest types (managed coniferous, managed deciduous and unmanaged deciduous forests) in three regions in Germany. Additionally we analyzed the relations between deadwood attributes (wood species, decay, deadwood type, size) and bryophytes on deadwood items (n = 799) and calculated species interaction networks of wood species and bryophytes. Overall, species richness of epixylic bryophytes was positively related to deadwood abundance and diversity. The mean deadwood abundance was lowest in unmanaged forests (9.7 m³ ha^-1) compared with 15.0 m³ ha^-1 in managed deciduous and 25.1 m³ ha^-1 in managed coniferous forests. Accordingly, epixylic bryophyte species richness per plot increased from 7 species per 400 m 2 in unmanaged, 10 in managed deciduous and 16 in managed coniferous forests. The interaction network provided evidence of importance of tree-species diversity for bryophyte diversity and the relevance of particular wood species for rare bryophytes.

Generally, the results demonstrate a considerable lack of deadwood in all forest types, even in unmanaged forests. Species richness of epixylic bryophytes was strongly limited by available substrates within the observed deadwood abundance ranging up to only 60 m³ ha^-1. Altogether, this suggests a high demand to increase both abundance and diversity of deadwood in forests.