Understanding preferences for tree attributes: the relative effects of socio-economic and local environmental factors

Urban plant biodiversity is influenced by both the physical environment and attitudes and preferences of urban residents for specific plant types. Urban residents are assumed to be disconnected from their immediate environment, and cultural and societal factors have been emphasized over environmental factors in studies of landscaping choices. However, we postulate that local climatic and environmental factors can also affect preferences for plant attributes. Therefore, spatial and temporal patterns in urban tree biodiversity may be driven not only by the direct effect of environmental variables on plant function, but also by the effect of environmental variables on attitudes toward trees and associated choices about which types of trees to plant. Here, we tested the relative effects of socio-economic and local environmental factors on preferences toward tree attributes in five counties in southern California in and surrounding Los Angeles, based on 1,029 household surveys. We found that local environmental factors have as strong an effect on preferences for tree attributes as socio-economic factors. Specifically, people located in hotter climates (average maximum temperature 25.1 °C) were more likely to value shade trees than those located in cooler regions (23.1 °C). Additionally, people located in desert areas were less likely to consider trees to be important in their city compared with people located in naturally forested areas. Overall, our research demonstrates the inherent connections between local environmental factors and perceptions of nature, even in large modern cities. Accounting for these factors can contribute to the growing interest in understanding patterns of urban biodiversity

Markov chain aggregation and its application to rule-based modelling

Rule-based modelling allows to represent molecular interactions in a compact and natural way. The underlying molecular dynamics, by the laws of stochastic chemical kinetics, behaves as a continuous-time Markov chain. However, this Markov chain enumerates all possible reaction mixtures, rendering the analysis of the chain computationally demanding and often prohibitive in practice. We here describe how it is possible to efficiently find a smaller, aggregate chain, which preserves certain properties of the original one. Formal methods and lumpability notions are used to define algorithms for automated and efficient construction of such smaller chains (without ever constructing the original ones). We here illustrate the method on an example and we discuss the applicability of the method in the context of modelling large signalling pathways

Climate tolerances and trait choices shape continental patterns of urban tree biodiversity

Aim: We propose and test a climate tolerance and trait choice hypothesis of urban macroecological variation in which strong filtering associated with low winter temperatures restricts urban biodiversity while weak filtering associated with warmer temperatures and irrigation allows dispersal of species from a global source pool, thereby increasing urban biodiversity. Location: Twenty cities across the USA and Canada. Methods: We examined variation in tree community taxonomic diversity, origins and production of an aesthetic ecosystem service trait in a cross-section of urban field surveys. We correlated urban tree community composition indicators with a key climate restriction, namely mean minimum winter temperature, and evaluated alternative possible drivers: precipitation, summer maximum temperature, population size and the percentage of adults with a college education. Results: Species accumulation curves differed substantially among cities, with observed richness varying from 22 to 122 species. Similarities in tree communities decreased exponentially with increases in climatic differences. Ordination of tree communities showed strong separation among cities with component axes correlated with minimum winter temperature and annual precipitation. Variation among urban tree communities in richness, origins and the provisioning of an aesthetic ecosystem service were all correlated with minimum winter temperature. Main conclusions: The urban climate tolerance and trait choice hypothesis provides a coherent mechanism to explain the large variation among urban tree communities resulting from an interacting environment, species and human decisions. Reconciling the feedbacks between human decision making and biophysical limitations provides a foundation for an urban ecological theory that can better understand and predict the dynamics of other linked biotic communities, associated ecosystem dynamics and resulting services provided to urban residents

Mothers’ self-focused reflective functioning interacts with childhood experiences of rejection to predict romantic relationship quality and insensitive parenting

Parents exposed to rejection in their childhood could experience bonding disturbances in their current relationships. Reflective functioning (RF), the capacity to understand one’s own and others’ behavior through the lens of underlying mental states (cognitions, emotions), has been identified as a potential protective process. The aim of this longitudinal study was to examine whether RF moderates the effect of parents’ experiences of rejection in childhood on later relationship functioning with partners and infants. Pregnant women with experiences of abuse and neglect were recruited and completed the Adult Attachment Interview, which was coded for RF and experiences of childhood rejection. During two follow‐up assessments, when their infants were 5 and 17 months old, the mothers in our sample who had partners reported on dyadic cohesion with these partners. Further, at 5 months postnatal, mothers completed interaction tasks with their infants, which were later assessed using observational measures (i.e., CARE‐Index). Results of mothers with partners (N = 93) indicated that RF moderated the relationship between dyadic cohesion with partners at 17 months only. Additionally, results with all mothers in the sample (N = 108) indicated that RF moderated the relationship between retrospectively reported experiences of rejection and controlling and unresponsive behaviors with infants. Adequate‐to‐high RF was associated with lower unresponsiveness and higher relationship satisfaction in the context of rejection, while being associated with higher levels of control. These findings have important clinical implications, as RF is amenable to change and can therefore be more prominently implemented within various interventions

Micro-costing the provision of emotional support and information in UK eye clinics

Sight loss has wide ranging implications for an individual in terms of education, employment, mobility and mental health. Therefore there is a need for information and support to be provided in eye clinics at the point of diagnosis of sight threatening conditions, but these aspects of care are often missing from clinics. To meet these needs, some clinics employ an Eye Clinic Liaison Officer (ECLO) but the position has yet to be widely implemented. The aims of this study were:(1) To evaluate the forms of advice and emotional support in eye clinics provided by ECLOs.(2) To determine the cost of the ECLO service per patient

Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BACKGROUND: Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. RESULTS: Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. CONCLUSION: The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself

Syntactic Markovian Bisimulation for Chemical Reaction Networks

In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in practice and represents the major bottleneck for the applicability of minimization techniques based, for instance, on lumpability. In this paper we present syntactic Markovian bisimulation (SMB), a notion of bisimulation developed in the Larsen-Skou style of probabilistic bisimulation, defined over the structure of a CRN rather than over its underlying CTMC. SMB identifies a lumpable partition of the CTMC state space a priori, in the sense that it is an equivalence relation over species implying that two CTMC states are lumpable when they are invariant with respect to the total population of species within the same equivalence class. We develop an efficient partition-refinement algorithm which computes the largest SMB of a CRN in polynomial time in the number of species and reactions. We also provide an algorithm for obtaining a quotient network from an SMB that induces the lumped CTMC directly, thus avoiding the generation of the state space of the original CRN altogether. In practice, we show that SMB allows significant reductions in a number of models from the literature. Finally, we study SMB with respect to the deterministic semantics of CRNs based on ordinary differential equations (ODEs), where each equation gives the time-course evolution of the concentration of a species. SMB implies forward CRN bisimulation, a recently developed behavioral notion of equivalence for the ODE semantics, in an analogous sense: it yields a smaller ODE system that keeps track of the sums of the solutions for equivalent species.Comment: Extended version (with proofs), of the corresponding paper published at KimFest 2017 (http://kimfest.cs.aau.dk/

Bridging Time Scales in Cellular Decision Making with a Stochastic Bistable Switch

Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene regulation, occuring on a time scale of minutes to hours. We show that a stochastic bistable switch forms a viable biochemical mechanism to implement decision processes on long time scales. As a case study, the mechanism is applied to model the initiation of follicle growth in mammalian ovaries, where the physiological time scale of follicle pool depletion is on the order of the organism's lifespan. We construct a simple mathematical model for this process based on experimental evidence for the involved genetic mechanisms. Despite the underlying stochasticity, the proposed mechanism turns out to yield reliable behavior in large populations of cells subject to the considered decision process. Our model explains how the physiological time constant may emerge from the intrinsic stochasticity of the underlying gene regulatory network. Apart from ovarian follicles, the proposed mechanism may also be of relevance for other physiological systems where cells take binary decisions over a long time scale.Comment: 14 pages, 4 figure