Interactions In Space For Archaeological Models

In this article we examine a variety of quantitative models for describing archaeological networks, with particular emphasis on the maritime networks of the Aegean Middle Bronze Age. In particular, we discriminate between those gravitational networks that are most likely (maximum entropy) and most efficient (best cost/benefit outcomes).Comment: 21 pages, 6 figures, 2 tables. Contribution to special issue of Advances in Complex Systems from the conference `Cultural Evolution in Spatially Structured Populations', UCL, London, September 2010. To appear in Advances in Complex System

Gravity model in the Korean highway

We investigate the traffic flows of the Korean highway system, which contains both public and private transportation information. We find that the traffic flow T(ij) between city i and j forms a gravity model, the metaphor of physical gravity as described in Newton's law of gravity, P(i)P(j)/r(ij)^2, where P(i) represents the population of city i and r(ij) the distance between cities i and j. It is also shown that the highway network has a heavy tail even though the road network is a rather uniform and homogeneous one. Compared to the highway network, air and public ground transportation establish inhomogeneous systems and have power-law behaviors.Comment: 13 page

Randomly hyperbranched polymers

We describe a model for the structures of randomly hyperbranched polymers in solution, and find a logarithmic growth of radius with polymer mass. We include segmental overcrowding, which puts an upper limit on the density. The model is tested against simulations, against data on amylopectin, a major component of starch, on glycogen, and on polyglycerols. For samples of synthetic polyglycerol and glycogen, our model holds well for all the available data. The model reveals higher-level scaling structure in glycogen, related to the beta particles seen in electron microscopy

Spatial correlations in attribute communities

Community detection is an important tool for exploring and classifying the properties of large complex networks and should be of great help for spatial networks. Indeed, in addition to their location, nodes in spatial networks can have attributes such as the language for individuals, or any other socio-economical feature that we would like to identify in communities. We discuss in this paper a crucial aspect which was not considered in previous studies which is the possible existence of correlations between space and attributes. Introducing a simple toy model in which both space and node attributes are considered, we discuss the effect of space-attribute correlations on the results of various community detection methods proposed for spatial networks in this paper and in previous studies. When space is irrelevant, our model is equivalent to the stochastic block model which has been shown to display a detectability-non detectability transition. In the regime where space dominates the link formation process, most methods can fail to recover the communities, an effect which is particularly marked when space-attributes correlations are strong. In this latter case, community detection methods which remove the spatial component of the network can miss a large part of the community structure and can lead to incorrect results.Comment: 10 pages and 7 figure

A universal model for mobility and migration patterns

Introduced in its contemporary form by George Kingsley Zipf in 1946, but with roots that go back to the work of Gaspard Monge in the 18th century, the gravity law is the prevailing framework to predict population movement, cargo shipping volume, inter-city phone calls, as well as bilateral trade flows between nations. Despite its widespread use, it relies on adjustable parameters that vary from region to region and suffers from known analytic inconsistencies. Here we introduce a stochastic process capturing local mobility decisions that helps us analytically derive commuting and mobility fluxes that require as input only information on the population distribution. The resulting radiation model predicts mobility patterns in good agreement with mobility and transport patterns observed in a wide range of phenomena, from long-term migration patterns to communication volume between different regions. Given its parameter-free nature, the model can be applied in areas where we lack previous mobility measurements, significantly improving the predictive accuracy of most of phenomena affected by mobility and transport processes.Comment: Main text and supplementary informatio

Genetically altered AMPA-type glutamate receptor kinetics in interneurons disrupt long-range synchrony of gamma oscillation

Gamma oscillations synchronized between distant neuronal populations may be critical for binding together brain regions devoted to common processing tasks. Network modeling predicts that such synchrony depends in part on the fast time course of excitatory postsynaptic potentials (EPSPs) in interneurons, and that even moderate slowing of this time course will disrupt synchrony. We generated mice with slowed interneuron EPSPs by gene targeting, in which the gene encoding the 67-kDa form of glutamic acid decarboxylase (GAD67) was altered to drive expression of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate receptor subunit GluR-B. GluR-B is a determinant of the relatively slow EPSPs in excitatory neurons and is normally expressed at low levels in γ-aminobutyric acid (GABA)ergic interneurons, but at high levels in the GAD-GluR-B mice. In both wild-type and GAD-GluR-B mice, tetanic stimuli evoked gamma oscillations that were indistinguishable in local field potential recordings. Remarkably, however, oscillation synchrony between spatially separated sites was severely disrupted in the mutant, in association with changes in interneuron firing patterns. The congruence between mouse and model suggests that the rapid time course of AMPA receptor-mediated EPSPs in interneurons might serve to allow gamma oscillations to synchronize over distance

Homozygosity for a missense mutation in the 67 kDa isoform of glutamate decarboxylase in a family with autosomal recessive spastic cerebral palsy: parallels with Stiff-Person Syndrome and other movement disorders

Background Cerebral palsy (CP) is an heterogeneous group of neurological disorders of movement and/or posture, with an estimated incidence of 1 in 1000 live births. Non-progressive forms of symmetrical, spastic CP have been identified, which show a Mendelian autosomal recessive pattern of inheritance. We recently described the mapping of a recessive spastic CP locus to a 5 cM chromosomal region located at 2q24-31.1, in rare consanguineous families. Methods Here we present data that refine this locus to a 0.5 cM region, flanked by the microsatellite markers D2S2345 and D2S326. The minimal region contains the candidate gene GAD1, which encodes a glutamate decarboxylase isoform (GAD67), involved in conversion of the amino acid and excitatory neurotransmitter glutamate to the inhibitory neurotransmitter γ-aminobutyric acid (GABA). Results A novel amino acid mis-sense mutation in GAD67 was detected, which segregated with CP in affected individuals. Conclusions This result is interesting because auto-antibodies to GAD67 and the more widely studied GAD65 homologue encoded by the GAD2 gene, are described in patients with Stiff-Person Syndrome (SPS), epilepsy, cerebellar ataxia and Batten disease. Further investigation seems merited of the possibility that variation in the GAD1 sequence, potentially affecting glutamate/GABA ratios, may underlie this form of spastic CP, given the presence of anti-GAD antibodies in SPS and the recognised excitotoxicity of glutamate in various contexts

Mutation-enrichment next-generation sequencing for quantitative detection of KRAS mutations in urine cell-free DNA from patients with advanced cancers

Purpose: Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers noninvasive biological material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of KRASExperimental Design: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA was developed, and results were compared with clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer.Results: With 90 to 110 mL of urine, the KRASG12/G13 cfDNA test had an analytical sensitivity of 0.002% to 0.006% mutant copies in wild-type background. In 71 patients, the concordance between urine cfDNA and tumor was 73% (sensitivity, 63%; specificity, 96%) for all patients and 89% (sensitivity, 80%; specificity, 100%) for patients with urine samples of 90 to 110 mL. Patients had significantly fewer KRASG12/G13 copies in urine cfDNA during systemic therapy than at baseline or disease progression (P = 0.002). Compared with no changes or increases in urine cfDNA KRASG12/G13 copies during therapy, decreases in these measures were associated with longer median time to treatment failure (P = 0.03).Conclusions: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA had good concordance with testing of archival tumor tissue. Changes in mutated urine cfDNA were associated with time to treatment failure

Patient allocations in general practice in case of patients' preferences for gender of doctor and their unavailability

<p>Abstract</p> <p>Background</p> <p>In some countries every citizen has the right to obtain a designated general practitioner. However, each individual may have preferences that cannot be fulfilled due to shortages of some kind. The questions raised in this paper are: To what extent can we expect that preferences are fulfilled when the patients "compete" for entry on the lists of practitioners? What changes can we expect under changing conditions? A particular issue explored in the paper is when the majority of women prefer a female doctor and there is a shortage of female doctors.</p> <p>Findings</p> <p>The analysis is done on the macro level by the so called gravity model and on the micro level by recent theories of benefit efficient population behaviour, partly developed by two of the authors. A major finding is that the number of patients wanting a doctor of the underrepresented gender is less important than the strength of their preferences as determining factor for the benefit efficient allocation.</p> <p>Conclusions</p> <p>We were able to generate valuable insights to the questions asked and to the dynamics of benefit efficient allocations. The approach is quite general and can be applied in a variety of contexts.</p