Entropy Optimization of Scale-Free Networks Robustness to Random Failures

Many networks are characterized by highly heterogeneous distributions of links, which are called scale-free networks and the degree distributions follow $p(k)\sim ck^{-\alpha}$. We study the robustness of scale-free networks to random failures from the character of their heterogeneity. Entropy of the degree distribution can be an average measure of a network's heterogeneity. Optimization of scale-free network robustness to random failures with average connectivity constant is equivalent to maximize the entropy of the degree distribution. By examining the relationship of entropy of the degree distribution, scaling exponent and the minimal connectivity, we get the optimal design of scale-free network to random failures. We conclude that entropy of the degree distribution is an effective measure of network's resilience to random failures.Comment: 9 pages, 5 figures, accepted by Physica

Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates.

Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome's capacity to take up environmental DNA enables rapid adaptation to environmental stresses.IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments

Social networks: evolving graphs with memory dependent edges

The plethora, and mass take up, of digital communication tech- nologies has resulted in a wealth of interest in social network data collection and analysis in recent years. Within many such networks the interactions are transient: thus those networks evolve over time. In this paper we introduce a class of models for such networks using evolving graphs with memory dependent edges, which may appear and disappear according to their recent history. We consider time discrete and time continuous variants of the model. We consider the long term asymptotic behaviour as a function of parameters controlling the memory dependence. In particular we show that such networks may continue evolving forever, or else may quench and become static (containing immortal and/or extinct edges). This depends on the ex- istence or otherwise of certain infinite products and series involving age dependent model parameters. To test these ideas we show how model parameters may be calibrated based on limited samples of time dependent data, and we apply these concepts to three real networks: summary data on mobile phone use from a developing region; online social-business network data from China; and disaggregated mobile phone communications data from a reality mining experiment in the US. In each case we show that there is evidence for memory dependent dynamics, such as that embodied within the class of models proposed here

Sense of place and the city: the case of non-native residents in Lisbon

Tang, V., Acedo, A., & Painho, M. (2021). Sense of place and the city: the case of non-native residents in Lisbon. Journal of Spatial Information Science, Special Issue: Special Feature on Interdisciplinary Perspectives on Place(23), 125-155. https://doi.org/10.5311/JOSIS.2021.23.165 ------------------------------Funding Information: This work was supported by the Master of Science in Geospatial Technologies (Geotech), an Erasmus Mundus Joint Masters (EMJMD) consortium under the EU’s Erasmus+ program.When immigrants move to a new city, they tend to develop distinct relationships with the urban landscape, which in turn becomes the new setting of their routine-based activities that evolve over time. Previous works in environmental psychology have quantitatively examined non-native residents' development of sense of place towards their new environment. In this paper, we introduce the spatial perspective into studying the sense of place experienced by non-natives in an urban context. We study the person-place bonds, relationships, and feelings cultivated by non-native residents living in the city of Lisbon (Portugal) through an online map-based survey. Then, we carried out spatial analysis aimed at distinguishing and visualizing the different facets of sense of place developed by two participant groups: short-term residents and long-term residents. Results showed that while short-term residents reported bonds with places, long-term residents' senses of place were more intense and broader throughout the city. The correlations, associations, and relationships between participant groups and the dimensions of sense of place allowed us to observe features and patterns that were previously described in the literature, although adding the spatial lenses can potentially provide better insights for urban planning, community development, and inclusive policies.publishersversionpublishe

Quantization and holomorphic anomaly

We study wave functions of B-model on a Calabi-Yau threefold in various polarizations.Comment: 15 page

Rate of Memory Decline in AD Is Related to Education and Occupation: Cognitive Reserve?

Objective: To determine whether the rate of decline in performance on a memory test is more rapid in AD patients with higher versus lower educational and occupational attainment. Background: Epidemiologic and imaging studies have suggested that, given comparable clinical severity of dementia, AD pathology is more advanced in patients with higher educational and occupational attainment. Because educational and occupational attainment should not influence the progression of AD pathology, and because severe AD pathology will eventually produce a mortality-causing condition, people with higher attainment might experience clinical AD for a shorter time and have a more rapid clinical progression. Methods: A total of 177 AD patients were tested yearly for up to four study visits with the Selective Reminding Test (a memory test). Analysis of prospective change in the total recall score was performed by applying generalized estimating equations to regression analyses with repeated measures. Results: At the initial visit, scores were comparable in the high- and low-education and the high- and low-occupation groups. Overall, memory scores declined by approximately 1 point yearly (p < 0.01). There was a more rapid decline in memory scores in patients with higher educational (p < 0.057) and higher occupational attainment (p < 0.02). The authors then stratified patients based on their initial memory scores. The more rapid decline in memory scores associated with higher educational and occupational attainment was noted only in the group with low initial scores (p < 0.05 for both). The full group and stratified group analyses were also repeated controlling for other potentially relevant variables including age, gender, race, ethnicity, and the presence of extrapyramidal signs, stroke, or at least one apolipoprotein E-ε4 allele. The results remained unchanged. Conclusions: Memory declined more rapidly in AD patients with higher educational and occupational attainment. This adds support to the idea that the discontinuity between the degree of AD pathology and the observed clinical severity of AD is mediated through some form of reserve

Optimization of network structure to random failures

Network's resilience to the malfunction of its components has been of great concern. The goal of this work is to determine the network design guidelines, which maximizes the network efficiency while keeping the cost of the network (that is the average connectivity) constant. With a global optimization method, memory tabu search (MTS), we get the optimal network structure with the approximately best efficiency. We analyze the statistical characters of the network and find that a network with a small quantity of hub nodes, high degree of clustering may be much more resilient to perturbations than a random network and the optimal network is one kind of highly heterogeneous networks. The results strongly suggest that networks with higher efficiency are more robust to random failures. In addition, we propose a simple model to describe the statistical properties of the optimal network and investigate the synchronizability of this model.Comment: 11 pages, 6 figures, accepted by Physica