Modeling biochemical transformation processes and information processing with Narrator

BACKGROUND: Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. RESULTS: Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. CONCLUSION: Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from

Taking Differences in Institutional Quality into Account in Global Forest Modelling

Forest cover and land-use change models are commonly used for climate scenarios and provide policy advice. The IIASA Global Forest Model (G4M) compares the net present value of agriculture and forestry, and makes a land-use change decision, based on this comparison. Moving beyond this purely economic rationale, we aimed at understanding in how far integrating differences in environmental institutional quality, could allow improving the representation of forest cover change processes of the model. Through an econometric regression analysis, we identified the most significant out of a larger set of variables on environmental institutional quality and created a composite index. We then implemented the composite index into the model. Its components are: the internalization of environmental norms, the strength of institutions, the ability of the institutions to guarantee macroeconomic stability, the quality of the administration and the efficiency of the bureaucracy. Through the inclusion of the composite index, the model’s residual could be significantly reduced. The results suggest that future research should consider taking differences in environmental institutional quality into account to improve modeling of deforestation processes. Moreover, the implementation of the index into the model allows for the first time to create scenarios for institutional quality and its impact on forest cover

Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations

Progress in our understanding of ultrafast light-induced processes in molecules is best achieved through a close combination of experimental and theoretical approaches. Direct comparison is obtained if theory is able to directly reproduce experimental observables. Here, we present a joint approach comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay of the photoelectron signal and an induction time prior to excited state depopulation in dynamics simulations. As a benchmark molecule, we have chosen hexamethylcyclopentadiene, which shows an unprecedentedly large spectral delay of (310 \ub1 20) fs in TRPES experiments. For the dynamics simulations, methyl groups were replaced by "hydrogen atoms" having mass 15 and TRPES spectra were calculated. These showed an induction time of (108 \ub1 10) fs which could directly be assigned to progress along a torsional mode leading to the intersection seam with the molecular ground state. In a stepladder-type approach, the close connection between the two phenomena could be elucidated, allowing for a comparison with other polyenes and supporting the general validity of this finding for their excited state dynamics. Thus, the combination of TRPES and AIMS proves to be a powerful tool for a thorough understanding of ultrafast excited state dynamics in polyenes.Peer reviewed: YesNRC publication: Ye

Research priorities for negative emissions

Carbon dioxide removal from the atmosphere (CDR)—also known as ‘negative emissions’—features prominently in most 2 °Cscenarios and has been under increased scrutiny by scientists, citizens, and policymakers. Critics argue that ‘negative emission technologies’ (NETs) are insufficiently mature to rely on them for climate stabilization. Some even argue that 2 °Cis no longer feasible or might have unacceptable social and environmental costs. Nonetheless, the Paris Agreement endorsed an aspirational goal of limiting global warming to even lower levels, arguing that climate impacts— especially for vulnerable nations such as small island states—will be unacceptably severe in a 2 °C world. While there are few pathways to 2 °Cthat do not rely on negative emissions, 1.5 °Cscenarios are barely conceivable without them. Building on previous assessments of NETs, we identify some urgent research needs to provide a more complete picture for reaching ambitious climate targets, and the role that NETs can play in reaching them

Working conditions and Work-Family Conflict in German hospital physicians: psychosocial and organisational predictors and consequences

<p>Abstract</p> <p>Background</p> <p>Germany currently experiences a situation of major physician attrition. The incompatibility between work and family has been discussed as one of the major reasons for the increasing departure of German physicians for non-clinical occupations or abroad. This study investigates predictors for one particular direction of Work-Family Conflict – namely work interfering with family conflict (WIF) – which are located within the psychosocial work environment or work organisation of hospital physicians. Furthermore, effects of WIF on the individual physicians' physical and mental health were examined. Analyses were performed with an emphasis on gender differences. Comparisons with the general German population were made.</p> <p>Methods</p> <p>Data were collected by questionnaires as part of a study on <it>Psychosocial work hazards and strains of German hospital physicians </it>during April–July 2005. Two hundred and ninety-six hospital physicians (response rate 38.9%) participated in the survey. The Copenhagen Psychosocial Questionnaire (COPSOQ), work interfering with family conflict scale (WIF), and hospital-specific single items on work organisation were used to assess WIF, its predictors, and consequences.</p> <p>Results</p> <p>German hospital physicians reported elevated levels of WIF (mean = 74) compared to the general German population (mean = 45, <it>p </it>< .01). No significant gender difference was found. Predictors for the WIF were lower age, high quantitative demands at work, elevated number of days at work despite own illness, and consequences of short-notice changes in the duty roster. Good sense of community at work was a protective factor. Compared to the general German population, we observed a significant higher level of quantitative work demands among hospital physicians (mean = 73 vs. mean = 57, <it>p </it>< .01). High values of WIF were significantly correlated to higher rates of personal burnout, behavioural and cognitive stress symptoms, and the intention to leave the job. In contrast, low levels of WIF predicted higher job satisfaction, better self-judged general health status, better work ability, and higher satisfaction with life in general. Compared to the German general population, physicians showed significantly higher levels of individual stress and quality of life as well as lower levels for well-being. This has to be judged as an alerting finding regarding the state of physicians' health.</p> <p>Conclusion</p> <p>In our study, work interfering with family conflict (WIF) as part of Work-Family Conflict (WFC) was highly prevalent among German hospital physicians. Factors of work organisation as well as factors of interpersonal relations at work were identified as significant predictors for WIF. Some of these predictors are accessible to alteration by improving work organisation in hospitals.</p

The interplay between total mercury, methylmercury and dissolved organic matter in fluvial systems: A latitudinal study across Europe.

Large-scale studies are needed to identify the drivers of total mercury (THg) and monomethyl-mercury (MeHg) concentrations in aquatic ecosystems. Studies attempting to link dissolved organic matter (DOM) to levels of THg or MeHg are few and geographically constrained. Additionally, stream and river systems have been understudied as compared to lakes. Hence, the aim of this study was to examine the influence of DOM concentration and composition, morphological descriptors, land uses and water chemistry on THg and MeHg concentrations and the percentage of THg as MeHg (%MeHg) in 29 streams across Europe spanning from 41°N to 64 °N. THg concentrations (0.06-2.78 ng L-1) were highest in streams characterized by DOM with a high terrestrial soil signature and low nutrient content. MeHg concentrations (7.8-159 pg L-1) varied non-systematically across systems. Relationships between DOM bulk characteristics and THg and MeHg suggest that while soil derived DOM inputs control THg concentrations, autochthonous DOM (aquatically produced) and the availability of electron acceptors for Hg methylating microorganisms (e.g. sulfate) drive %MeHg and potentially MeHg concentration. Overall, these results highlight the large spatial variability in THg and MeHg concentrations at the European scale, and underscore the importance of DOM composition on mercury cycling in fluvial systems