Steady-State Properties of Single-File Systems with Conversion

We have used Monte-Carlo methods and analytical techniques to investigate the influence of the characteristic parameters, such as pipe length, diffusion, adsorption, desorption and reaction rate constants on the steady-state properties of Single-File Systems with a reaction. We looked at cases when all the sites are reactive and when only some of them are reactive. Comparisons between Mean-Field predictions and Monte-Carlo simulations for the occupancy profiles and reactivity are made. Substantial differences between Mean-Field and the simulations are found when rates of diffusion are high. Mean-Field results only include Single-File behavior by changing the diffusion rate constant, but it effectively allows passing of particles. Reactivity converges to a limit value if more reactive sites are added: sites in the middle of the system have little or no effect on the kinetics. Occupancy profiles show approximately exponential behavior from the ends to the middle of the system.Comment: 15 pages, 20 figure

Identifying user preferences for a digital educational solution for young seniors with diabetes

The Eindhoven Diabetes Education Simulator project was initiated to develop an educational solution that helps diabetes patients understand and learn more about their diabetes. This article describes the identification of user preferences for the development of such solutions. Young seniors (aged 50-65 years) with type 2 diabetes were chosen as the target group because they are likely to have more affinity with digital devices than older people and because 88% of the Dutch diabetes population is > 50 years of age. Data about the target group were gathered through literature research and interviews. The literature research covered data about their device use and education preferences. To gain insight into the daily life of diabetes patients and current diabetes education processes, 20 diabetes patients and 10 medical experts were interviewed. The interviews were analyzed using affinity diagrams. Those diagrams, together with the literature data, formed the basis for two personas and corresponding customer journey maps. Literature showed that diabetes prevalence is inversely correlated to educational level. Computer and device use is relatively low within the target group, but is growing. The interviews showed that young seniors like to play board, card, and computer games, with others or alone. Family and loved ones play an important role in their lives. Medical experts are crucial in the diabetes education of young senior diabetes patients. These findings are translated into a list of design aspects that can be used for creating educational solutions

Applying habitat and population-density models to land-cover time series to inform IUCN Red List assessments

The IUCN (International Union for Conservation of Nature) Red List categories and criteria are the most widely used framework for assessing the relative extinction risk of species. The criteria are based on quantitative thresholds relating to the size, trends, and structure of species’ distributions and populations. However, data on these parameters are sparse and uncertain for many species and unavailable for others, potentially leading to their misclassification or classification as data deficient. We devised an approach that combines data on land-cover change, species-specific habitat preferences, population abundance, and dispersal distance to estimate key parameters (extent of occurrence, maximum area of occupancy, population size and trend, and degree of fragmentation) and hence predict IUCN Red List categories for species. We applied our approach to nonpelagic birds and terrestrial mammals globally (∼15,000 species). The predicted categories were fairly consistent with published IUCN Red List assessments, but more optimistic overall. We predicted 4.2% of species (467 birds and 143 mammals) to be more threatened than currently assessed and 20.2% of data deficient species (10 birds and 114 mammals) to be at risk of extinction. Incorporating the habitat fragmentation subcriterion reduced these predictions 1.5–2.3% and 6.4–14.9% (depending on the quantitative definition of fragmentation) for threatened and data deficient species, respectively, highlighting the need for improved guidance for IUCN Red List assessors on the application of this aspect of the IUCN Red List criteria. Our approach complements traditional methods of estimating parameters for IUCN Red List assessments. Furthermore, it readily provides an early-warning system to identify species potentially warranting changes in their extinction-risk category based on periodic updates of land-cover information. Given our method relies on optimistic assumptions about species distribution and abundance, all species predicted to be more at risk than currently evaluated should be prioritized for reassessment

Transient behavior in Single-File Systems

We have used Monte-Carlo methods and analytical techniques to investigate the influence of the characteristics, such as pipe length, diffusion, adsorption, desorption and reaction rates on the transient properties of Single-File Systems. The transient or the relaxation regime is the period in which the system is evolving to equilibrium. We have studied the system when all the sites are reactive and when only some of them are reactive. Comparisons between Mean-Field predictions, Cluster Approximation predictions, and Monte Carlo simulations for the relaxation time of the system are shown. We outline the cases where Mean-Field analysis gives good results compared to Dynamic Monte-Carlo results. For some specific cases we can analytically derive the relaxation time. Occupancy profiles for different distribution of the sites both for Mean-Field and simulations are compared. Different results for slow and fast reaction systems and different distribution of reactive sites are discussed.Comment: 18 pages, 19 figure

Reply to: Soils need to be considered when assessing the impacts of land-use change on carbon sequestration

Industrial Ecolog

Functional analysis of the SRV-1 RNA frameshifting pseudoknot

Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair pseudoknot. The solution structure of this pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109–1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base–base and base–sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for −1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter pseudoknots is discussed. Overall, the data emphasize the role of the triple helix in −1 frameshifting

A Bayesian approach to targeted experiment design

Motivation: Systems biology employs mathematical modelling to further our understanding of biochemical pathways. Since the amount of experimental data on which the models are parameterized is often limited, these models exhibit large uncertainty in both parameters and predictions. Statistical methods can be used to select experiments that will reduce such uncertainty in an optimal manner. However, existing methods for optimal experiment design (OED) rely on assumptions that are inappropriate when data are scarce considering model complexity

Projecting terrestrial biodiversity intactness with GLOBIO 4

Scenario-based biodiversity modelling is a powerful approach to evaluate how possible future socio-economic developments may affect biodiversity. Here, we evaluated the changes in terrestrial biodiversity intactness, expressed by the mean species abundance (MSA) metric, resulting from three of the shared socio-economic pathways (SSPs) combined with different levels of climate change (according to representative concentration pathways [RCPs]): a future oriented towards sustainability (SSP1xRCP2.6), a future determined by a politically divided world (SSP3xRCP6.0) and a future with continued global dependency on fossil fuels (SSP5xRCP8.5). To this end, we first updated the GLOBIO model, which now runs at a spatial resolution of 10 arc-seconds (~300 m), contains new modules for downscaling land use and for quantifying impacts of hunting in the tropics, and updated modules to quantify impacts of climate change, land use, habitat fragmentation and nitrogen pollution. We then used the updated model to project terrestrial biodiversity intactness from 2015 to 2050 as a function of land use and climate changes corresponding with the selected scenarios. We estimated a global area-weighted mean MSA of 0.56 for 2015. Biodiversity intactness declined in all three scenarios, yet the decline was smaller in the sustainability scenario (-0.02) than the regional rivalry and fossil-fuelled development scenarios (-0.06 and -0.05 respectively). We further found considerable variation in projected biodiversity change among different world regions, with large future losses particularly for sub-Saharan Africa. In some scenario-region combinations, we projected future biodiversity recovery due to reduced demands for agricultural land, yet this recovery was counteracted by increased impacts of other pressures (notably climate change and road disturbance). Effective measures to halt or reverse the decline of terrestrial biodiversity should not only reduce land demand (e.g. by increasing agricultural productivity and dietary changes) but also focus on reducing or mitigating the impacts of other pressures.Peer reviewe