Santa Fe Institute

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2014 Bibliography Entries

Althouse, B. M., Allem, J. P., Childers, M. A., Dredze, M., Ayers, J. W. (2014). "Population Health Concerns During the United States' Great Recession." American Journal of Preventive Medicine 46(2):166-170
Background: Associations between economic conditions and health are usually derived from costintensive surveys that are intermittently collected with nonspecific measures (i.e., self-rated health). Purpose: This study identified how precise health concerns changed during the U.S. Great Recession analyzing Google search ...   [More]
Ayers, J. W., Althouse, B. M., Noar, S. M., Cohen, J. E. (2014). "Do Celebrity Cancer Diagnoses Promote Primary Cancer Prevention?." Prevention Medicine 58:81-84
Objective. Celebrity cancer diagnoses generate considerable media coverage of and increase interest in cancer screening, but do they also promote primary cancer prevention? Methods. Daily trends for smoking cessation-related media (information-availability) and Google queries (information-seeking) around Brazilian President and smoker ...   [More]
Bowles, S., Loury, G. C., Sethi, R. (2014). "Group Inequality." Journal of the European Economic Association 12(1):129-152
We explore the combined effect of segregation in social networks, peer effects, and the relative size of a historically disadvantaged group on the incentives to invest in market-rewarded skills and the dynamics of inequality between social groups. We identify conditions ...   [More]
Braakman, R., Smith, E. (2014). "Metabolic Evolution of a Deep-Branching Hyperthermophilic Chemoautotrophic Bacterium." PLoS One 9(2)
Aquifex aeolicus is a deep-branching hyperthermophilic chemoautotrophic bacterium restricted to hydrothermal vents and hot springs. These characteristics make it an excellent model system for studying the early evolution of metabolism. Here we present the whole-genome metabolic network of this organism ...   [More]
Cirto, L. J. L., Assis, V. R. V., Tsallis, C. (2014). "Influence of the Interaction Range on the Thermostatistics of a Classical Many-Body System." Physica A - Statistical Mechanics and Its Applications 393:286-296
We numerically study a one-dimensional system of N classical localized planar rotators coupled through interactions which decay with distance as 1/r(alpha) (alpha >= 0). The approach is a first principle one (i.e., based on Newton's law), and yields the probability ...   [More]
Dell, A. I., Pawar, S., Savage, V. (2014). "Temperature Dependence of Trophic Interactions are Driven by Asymmetry of Species Responses and Foraging Strategy." Journal of Animal Ecology 83(1):70-84
Environmental temperature has systematic effects on rates of species interactions, primarily through its influence on organismal physiology. We present a mechanistic model for the thermal response of consumer-resource interactions. We focus on how temperature affects species interactions via key traits ...   [More]
Fitzpatrick, M. C., Hampson, K., Cleaveland, S., Mzimbiri, I., Lankester, F., Lembo, T., Meyers, L. A., Paltiel, D. A., Galvani, A. P. (2014). "Cost-Effectiveness of Canine Vaccination to Prevent Human Rabies in Rural Tanzania." Annals of Internal Medicine 160(2):92
Background: The annual mortality rate of human rabies in rural Africa is 3.6 deaths per 100 000 persons. Rabies can be prevented with prompt postexposure prophylaxis, but this is costly and often inaccessible in rural Africa. Because 99% of human ...   [More]
Fuentes, M. A., Robledo, A. (2014). "Sums of Variables at the Onset of Chaos." European Physical Journal B 87(2)
We explain how specific dynamical properties give rise to the limit distribution of sums of deterministic variables at the transition to chaos via the period-doubling route. We study the sums of successive positions generated by an ensemble of initial conditions ...   [More]
Glass, K., Girvan, M. (2014). "Annotation Enrichment Analysis: An Alternative Method for Evaluating the Functional Properties of Gene Sets." Scientific Reports 4
Gene annotation databases (compendiums maintained by the scientific community that describe the biological functions performed by individual genes) are commonly used to evaluate the functional properties of experimentally derived gene sets. Overlap statistics, such as Fishers Exact test (FET), are ...   [More]
Hellmuth, M., Leydold, J., Stadler, P. F. (2014). "Convex Cycle Bases." ARS Mathematica Contemporanea 7(1):123-140
Convex cycles play a role e.g. in the context of product graphs. We introduce convex cycle bases and describe a polynomial-time algorithm that recognizes whether a given graph has a convex cycle basis and provides an explicit construction in the ...   [More]
Hellmuth, M., Ostermeier, L., Stadler, P. F. (2014). "Unique Square Property, Equitable Partitions, and Product-Like Graphs." Discrete Mathematics 320:92-103
Equivalence relations on the edge set of a graph G that satisfy restrictive conditions on chordless squares play a crucial role in the theory of Cartesian graph products and graph bundles. We show here that such relations in a natural ...   [More]
Hoffman, L. R., Pope, C. E., Hayden, H. S., Heltshe, S., Levy, R., McNamara, S., Jacobs, M. A., Rohmer, L., Radey, M., Ramsey, B. W., Brittnacher, M. J., Borenstein, E., Miller, S. I. (2014). "Escherichia coli Dysbiosis Correlates With Gastrointestinal Dysfunction in Children With Cystic Fibrosis." Clinical Infectious Diseases 58(3):396-399
Cystic fibrosis gastrointestinal disease includes nutrient malabsorption and intestinal inflammation. We show that the abundances of Escherichia coli in fecal microbiota were significantly higher in young children with cystic fibrosis than in controls and correlated with fecal measures of nutrient ...   [More]
Kang, Y., Castillo-Chavez, C. (2014). "A Simple Epidemiological Model for Populations in the Wild with Allee Effects and Disease-Modified Fitness." Discrete and Continuous Dynamical Systems - Series B 19(1):899-130
In this work we assume that a population's survival is dependent on the existence of a critical mass of susceptible individuals. The implications of this Allee effect is considered within the context of a Susceptible-Infectious (SI) model where infection has ...   [More]
Kehr, S., Bartschat, S., Tafer, H., Stadler, P. F., Hertel, J. (2014). "Matching of Soulmates: Coevolution of snoRNAs and Their Targets." Molecular Biology and Evolution 31(2):455-467
Ribosomal and small nuclear RNAs (snRNAs) comprise numerous modified nucleotides. The modification patterns are retained during evolution, making it even possible to project them from yeast onto human. The stringent conservation of modification sites and the slow evolution of rRNAs ...   [More]
Kembel, S. W., Meadow, J. F., O'Connor, T. K., Mhuireach, G., Northcutt, D., Kline, J., Moriyama, M., Brown, G. Z., Bohannan, B. J. M., Green, J. L. (2014). "Architectural Design Drives the Biogeography of Indoor Bacterial Communities." PLoS One 9(1)
Background: Architectural design has the potential to influence the microbiology of the built environment, with implications for human health and well-being, but the impact of design on the microbial biogeography of buildings remains poorly understood. In this study we combined ...   [More]
Kintigh, K. W., Altschul, J. H., Beaudry, M. C., Drennan, R. D., Kinzig, A. P., Kohler, T. A., Limp, W. F., Maschner, H. D. G., Michener, W. K., Pauketat, T. R., Peregrine, P., Sabloff, J. A., Wilkinson, T. J., Wright, H. T., Zeder, M. A. (2014). "Grand challenges for archaeology." PNAS 111(3):879-880   [More]
Kintigh, K. W., Altschul, J. H., Beaudry, M. C., Drennan, R. D., Kinzig, A. P., Kohler, T. A., Limp, W. F., Maschner, H. D. G., Michener, W. K., Pauketat, T. R., Peregrine, P., Sabloff, J. A., Wilkinson, T. J., Wright, H. T., Zeder, M. A. (2014). "Grand Challenges for Archaeology." American Antiquity 79(1):5-24
This article represents a systematic effort to answer the question, What are archaeology's most important scientific challenges? Starting with a crowd-sourced query directed broadly to the professional community of archaeologists, the authors augmented, prioritized, and refined the responses during a ...   [More]
Ludescher, J., Gozolchiani, A., Bogachev, M. I., Bunde, A., Havlin, S., Schellnhuber, H. J. (2014). "Very early warning of next El Nino." PNAS 111(6):2064-2066
The most important driver of climate variability is the El Nino Southern Oscillation, which can trigger disasters in various parts of the globe. Despite its importance, conventional forecasting is still limited to 6 mo ahead. Recently, we developed an approach ...   [More]
Lunardi, J. T., Micciche, S., Lillo, F., Mantegna, R. N., Gallegati, M. (2014). "Do Firms Share the Same Functional Form of Their Growth Rate Distribution? A Statistical Test." Journal of Economic Dynamics & Control 39:140-164
We propose a hypothesis testing procedure to investigate whether the same growth rate distribution is shared by all the firms in a balanced panel or, more generally, whether they share the same functional form for this distribution, without necessarily sharing ...   [More]
Mandel, A., Gintis, H. (2014). "Stochastic Stability in the Scarf Economy." Mathematical Social Sciences 67:44-49
We present a mathematical model for the analysis of the bargaining games based on private prices used by Gintis to simulate the dynamics of prices in exchange economies in Gintis (2007). We then characterize, in the Scarf economy, a class ...   [More]
Ortman, S. G., Cabaniss, A. H. F., Sturm, J. O., Bettencourt, L. M. A. (2014). "The Pre-History of Urban Scaling." PLoS One 9(2)
Cities are increasingly the fundamental socio-economic units of human societies worldwide, but we still lack a unified characterization of urbanization that captures the social processes realized by cities across time and space. This is especially important for understanding the role ...   [More]
Payne, J. L., Wagner, A. (2014). "The Robustness and Evolvability of Transcription Factor Binding Sites." Science 343(6173):875-877
Robustness, the maintenance of a character in the presence of genetic change, can help preserve adaptive traits but also may hinder evolvability, the ability to bring forth novel adaptations. We used genotype networks to analyze the binding site repertoires of ...   [More]
Sherrington, D. (2014). "A Spin Glass Perspective on Ferroic Glasses." Physica Status Solidi B :1-15
A range of ferroic glasses, magnetic, polar, relaxor and strain glasses, are considered together from the perspective of spin glasses. Simple mathematical modelling is shown to provide a possible conceptual unification to back similarities of experimental observations, without considering all ...   [More]
Sherrington, D. (2014). "b(Mg1/3Nb2/3)O-3: A minimal induced-moment soft pseudospin glass perspective." Physical Review B 89(6):064105
An argument that relaxor ferroelectricity in the isovalent alloy Ba(Zr1-xTix)O-3 can be understood as an induced-moment soft pseudospin glass on the B ions of the ABO(3) matrix [Sherrington, Phys. Rev. Lett. 111, 227601 (2013)] is extended to the experimentally paradigmatic ...   [More]
Sunnaker, M., Zamora-Sillero, E., de Lomana, A. L. G., Rudroff, F., Sauer, U., Stelling, J., Wagner, A. (2014). "Topological Augmentation to Infer Hidden Processes in Biological Systems." Bioinformatics 30(2):221-227
Motivation: A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables-usually molecules and their interactions. Here we present a method called topological augmentation to infer this ...   [More]
Trancik, J. E., Chang, M. T., Karapataki, C., Stokes, L. C. (2014). "Effectiveness of a Segmental Approach to Climate Policy." Environmental Science & Technology 48(1):27-35
Resistance to adopting a cap on greenhouse gas emissions internationally, and across various national contexts, has encouraged alternative climate change mitigation proposals. These proposals include separately targeting clean energy uptake and demand-side efficiency in individual end-use sectors, an approach to ...   [More]
Wagner, A. (2014). "Mutational Robustness Accelerates the Origin of Novel RNA Phenotypes through Phenotypic Plasticity." Biophysical Journal 106(4):955-965
Novel phenotypes can originate either through mutations in existing genotypes or through phenotypic plasticity, the ability of one genotype to form multiple phenotypes. From molecules to organisms, plasticity is a ubiquitous feature of life, and a potential source of exaptations, ...   [More]
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