A unified framework for Schelling's model of segregation

Schelling's model of segregation is one of the first and most influential models in the field of social simulation. There are many variations of the model which have been proposed and simulated over the last forty years, though the present state of the literature on the subject is somewhat fragmented and lacking comprehensive analytical treatments. In this article a unified mathematical framework for Schelling's model and its many variants is developed. This methodology is useful in two regards: firstly, it provides a tool with which to understand the differences observed between models; secondly, phenomena which appear in several model variations may be understood in more depth through analytic studies of simpler versions.Comment: 21 pages, 3 figure

Empowering open science with reflexive and spatialised indicators

Bibliometrics have become commonplace and widely used by authors and journals to monitor, to evaluate and to identify their readership in an ever-increasingly publishing scientific world. This contribution introduces a multi-method corpus analysis tool, specifically conceived for scientific corpuses with spatialised content. We propose a dedicated interactive application that integrates three strategies for building semantic networks, using keywords (self-declared themes), citations (areas of research using the papers) and full-texts (themes derived from the words used in writing). The networks can be studied with respect to their temporal evolution as well as to their spatial expressions, by considering the countries studied in the papers under inquiry. The tool is applied as a proof-of-concept on the papers published in the online open access geography journal Cybergeo since its creation in 1996. Finally, we compare the three methods and conclude that their complementarity can help go beyond simple statistics to better understand the epistemological evolution of a scientific community and the readership target of the journal. Our tool can be applied by any journal on its own corpus, fostering thus open science and reflexivity

Dynamic modelling of the potential habitat loss of endangered species: the case of the Canarian houbara bustard (Chlamydotis undulata fuerteventurae)

In this work, we apply a dynamic modelling approach to analyse the habitat loss of the Canarian houbara bustard (Chlamydotis undulata fuerteventurae). This tool allows us to assess the effects of the socio-economic and environmental interactions on the factors threatening the habitat and to carry out a prospective analysis. The results show a potential habitat loss of around 13 % during the period 1996–2011, the land uptake and increase in new roads and tracks being the factors contributing most. After model testing, a set of scenarios was explored. Under the business as usual (BAU) scenario, around 20 % of the habitat would be lost by the end of the period considered (2012–2025). The impact of the economic growth scenario on the habitat would mean an additional loss of around 21 % with respect to BAU, whereas under the recession scenario, the loss might be around 6.5 % lower than BAU. The policy of restoration of gavias—traditional farming systems—would suppose an additional loss of almost 6 %, relative to BAU. If this policy took place under economic growth conditions, it might mean an additional loss of almost 28 % relative to BAU. These results point to the existence of a potential trade-off between the recuperation of ecosystem services offered by restored gavias and the conservation of the houbara habitat, which must be addressed within the management processes, as well as to the need for compensatory measures to guarantee the conservation goals

Monte Carlo Methods for Rough Free Energy Landscapes: Population Annealing and Parallel Tempering

Parallel tempering and population annealing are both effective methods for simulating equilibrium systems with rough free energy landscapes. Parallel tempering, also known as replica exchange Monte Carlo, is a Markov chain Monte Carlo method while population annealing is a sequential Monte Carlo method. Both methods overcome the exponential slowing associated with high free energy barriers. The convergence properties and efficiency of the two methods are compared. For large systems, population annealing initially converges to equilibrium more rapidly than parallel tempering for the same amount of computational work. However, parallel tempering converges exponentially and population annealing inversely in the computational work so that ultimately parallel tempering approaches equilibrium more rapidly than population annealing.Comment: 10 pages, 3 figure

Practical genetics: alpha-1-antitrypsin deficiency and the serpinopathies

Alpha-1-antitrypsin (alpha(1)-antitrypsin) is the archetypal member of the serine proteinase inhibitor or serpin superfamily. The most common severe deficiency variant is the Z allele, which results in the accumulation of mutant protein within hepatocytes. This 'protein overload' causes neonatal hepatitis, cirrhosis and hepatocellular carcinoma. The lack of circulating plasma alpha(1)-antitrypsin results in early-onset panlobular emphysema. The mechanism underlying the deficiency of Z alpha(1)-antitrypsin is due to an aberrant conformational transition within the protein and the formation of chains of polymers that tangle within the secretory pathway of hepatocytes. This mechanism also underlies the plasma deficiency of other members of the serpin superfamily to cause a class of diseases called the serpinopathies. Specifically mutant alleles of antithrombin, C1-inhibitor and alpha(1)-antichymotrypsin have been reported that favour the spontaneous formation of polymers and the retention of protein within hepatocytes. The consequent lack of plasma antithrombin, C1-inhibitor and alpha(1)-antichymotrypsin results in thrombosis, angio-oedema and emphysema, respectively. Moreover, the polymerisation of mutants of neuroserpin results in the retention of polymers within neurones to cause the inclusion body dementia, familial encephalopathy with neuroserpin inclusion bodies or FENIB. We review here the genetic and molecular basis and clinical features of alpha(1)-antitrypsin deficiency, and show how this provides a platform to understand the other serpinopathies

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition

Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular Graphic (InsP6) is involved in mRNA export and editing or chromatin remodeling among other events. InsP6 accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of InsP6 that, through chelation of metal ions, may have a detrimental effect on human health. Ins(1,3,4,5,6)P5 2-kinase (InsP5 2-kinase or Ipk1) catalyses the synthesis of InsP6 from InsP5 and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an InsP5 2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates

Exploring the Relationship Between the Acceptability of an Internet-Based Intervention for Depression in Primary Care and Clinical Outcomes: Secondary Analysis of a Randomized Controlled Trial

Background: Depression is one of the most prevalent psychological disorders worldwide. Although psychotherapy for depression is effective, there are barriers to its implementation in primary care in Spain. The use of the Internet has been shown to be a feasible solution. However, the acceptability of Internet-based interventions has not been studied sufficiently. Objective: To assess the acceptability of an Internet-based intervention (IBI) for depression in primary care, and explore the relationship between expectations and satisfaction and the improvement in the clinical variables in primary care patients receiving this intervention. Furthermore, it offers data about the effects of some sociodemographic characteristics on these acceptability variables and analyzes whether the expectations are related to finalizing the intervention. Methods: Data were based on depressive patients who were participants in a randomized controlled trial. In the present study, we present the data from all the participants in the Internet intervention groups (N = 198). All the participants filled out the expectation and satisfaction scales (six-item scales regarding treatment logic, satisfaction, recommending, usefulness for other disorders, usefulness for the patient, and unpleasantness), the Beck Depression Inventory-II, and the secondary outcome measures: depression and anxiety impairment, and positive and negative affect. Results: Results showed that participants'' expectations and satisfaction with the program were both high and differences in expectations and satisfaction depended on some sociodemographic variables (age: older people have higher expectations; sex: women have greater satisfaction). A positive relationship between these variables and intervention efficacy was found: expectations related to "usefulness for the patient" were a statistically related predictor to the results on the BDI-11 (Beta = 0.364), and the perception of how logical the treatment is (Beta = 0.528) was associated with change in the clinical variable. Furthermore, the higher the expectations, the higher the improvements exhibited by the patients in all measures evaluated during the ten intervention modules. High expectations were also directly related to finalizing the intervention. Conclusions: This is the first study in Spain to address this issue in the field of IBIs for depression in primary care. The IBI showed high acceptance related to the intervention''s efficacy and completion. Research on IBI acceptability could help to implement the treatment offered