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2015 Bibliography Entries

Aktipis, C. A., Boddy, A. M., Jansen, G., Hibner, U., Hochberg, M. E., Maley, C. C., Wilkinson, G. S. (2015). "Cancer across the tree of life: cooperation and cheating in multicellularity." Philosophical Transactions of the Royal Society B - Biological Sciences 370(1673)
Multicellularity is characterized by cooperation among cells for the development, maintenance and reproduction of the multicellular organism. Cancer can be viewed as cheating within this cooperative multicellular system. Complex multicellularity, and the cooperation underlying it, has evolved independently multiple times. ...   [More]
Almberg, E. S., Cross, P. C., Dobson, A. P., Smith, D. W., Metz, M. C., Stahler, D. R., Hudson, P. J. (2015). "Social living mitigates the costs of a chronic illness in a cooperative carnivore." Ecology Letters 18(7):660-667
Infection risk is assumed to increase with social group size, and thus be a cost of group living. We assess infection risk and costs with respect to group size using data from an epidemic of sarcoptic mange (Sarcoptes scabiei) among ...   [More]
Althouse, B. M., Hanley, K. A. (2015). "The tortoise or the hare? Impacts of within-host dynamics on transmission success of arthropod-borne viruses." Philosophical Transactions of the Royal Society B - Biological Sciences 370(1675)
Arthropod-borne viruses (arboviruses) are maintained in a cycle of alternating transmission between vertebrate hosts and arthropod vectors. Arboviruses possess RNA genomes capable of rapid diversification and adaptation, and the between-host trade-offs inherent to host alternation impose well-documented constraints on arbovirus ...   [More]
Althouse, B. M., Scarpino, S. V. (2015). "Asymptomatic transmission and the resurgence of Bordetella pertussis." BMC Medicine 13
Background: The recent increase in whooping cough incidence (primarily caused by Bordetella pertussis) presents a challenge to both public health practitioners and scientists trying to understand the mechanisms behind its resurgence. Three main hypotheses have been proposed to explain the ...   [More]
Amos, M., Rasmussen, S., McCaskill, J., Dittrich, P. (2015). "Editorial." Artificial Life 21(2):193-194
Introductory Paragraph. We are pleased to present this special issue of Artificial Life, which is dedicated to articles arising from a workshop held on September 6, 2012, as part of the Unconventional Computation and Natural Computation (UCNC) conference in Orleans, ...   [More]
Andersen, J. L., Flamm, C., Merkle, D., Stadler, P. F. (2015). "In silico Support for Eschenmoser's Glyoxylate Scenario." Israel Journal of Chemistry 55(8):919-933
A core topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life, such as sugars, nucleotides, amino acids, and lipids to molecular food sources that were likely to have ...   [More]
Andris, C., Lee, D., Hamilton, M. J., Martino, M., Gunning, C. E., Selden, J. A. (2015). "The Rise of Partisanship and Super-Cooperators in the US House of Representatives." PLOS One 10(4)
It is widely reported that partisanship in the United States Congress is at an historic high. Given that individuals are persuaded to follow party lines while having the opportunity and incentives to collaborate with members of the opposite party, our ...   [More]
Andrist, R. S., Wootton, J. R., Katzgraber, H. G. (2015). "Error thresholds for Abelian quantum double models: Increasing the bit-flip stability of topological quantum memory." Physical Review A 91(4)
Current approaches for building quantum computing devices focus on two-level quantum systems which nicely mimic the concept of a classical bit, albeit enhanced with additional quantum properties. However, rather than artificially limiting the number of states to two, the use ...   [More]
Arcaute, E., Hatna, E., Ferguson, P., Youn, H., Johansson, A., Batty, M. (2015). "Constructing Cities, Deconstructing Scaling Laws." Journal of the Royal Society Interface 12(102)
Cities can be characterized and modelled through different urban measures. Consistency within these observables is crucial in order to advance towards a science of cities. Bettencourt et al. have proposed that many of these urban measures can be predicted through ...   [More]
Artzy-Randrup, Y., Dobson, A. P., Pascual, M. (2015). "Synergistic and antagonistic interactions between bednets and vaccines in the control of malaria." PNAS 112(10):3014-3019
It is extremely likely that the malaria vaccines currently in development will be used in conjunction with treated bednets and other forms of malaria control. The interaction of different intervention methods is at present poorly understood in a disease such ...   [More]
Avena-Koenigsberger, A., Goni, J., Sole, R., Sporns, O. (2015). "Network Morphospace." Journal of the Royal Society Interface 12(103)
The structure of complex networks has attracted much attention in recent years. It has been noted that many real-world examples of networked systems share a set of common architectural features. This raises important questions about their origin, for example whether ...   [More]
Ay, N. (2015). "Information Geometry on Complexity and Stochastic Interaction." Entropy 17(4):2432-2458
Interdependencies of stochastically interacting units are usually quantified by the Kullback-Leibler divergence of a stationary joint probability distribution on the set of all configurations from the corresponding factorized distribution. This is a spatial approach which does not describe the intrinsically ...   [More]
Ay, N., Jost, J., Le, H. V., Schwachhofer, L. (2015). "Information geometry and sufficient statistics." Probability Theory and Related Fields 162(1-2):327-364
Information geometry provides a geometric approach to families of statistical models. The key geometric structures are the Fisher quadratic form and the Amari-Chentsov tensor. In statistics, the notion of sufficient statistic expresses the criterion for passing from one model to ...   [More]
Ayers, J. W., Althouse, B. M., Emery, S. (2015). "Changes in Internet Searches Associated With the "Tips from Former Smokers" Campaign." American Journal of Preventive Medicine 48(6):E27-E29   [More]
Aymanns, C., Farmer, J. D. (2015). "The dynamics of the leverage cycle." Journal of Economic Dynamics & Control 50:155-179
We present a simple agent-based model of a financial system composed of leveraged investors such as banks that invest in stocks and manage their risk using a Value-at-Risk constraint, based on historical observations of asset prices. The Value-at-Risk constraint implies ...   [More]
Badano, E. I., Bustamante, R. O., Villarroel, E;., Marquet, P. A., Cavieres, L. A. (2015). "Facilitation by nurse plants regulates community invasibility in harsh environments." Journal of Vegetation Science 26(4):756-767
QuestionThe biotic resistance hypothesis states that species diversity is a barrier for plant biological invasions because alien species are more likely to find strong competitors as diversity of native plants increases. In stressful environments, however, these negative relationships could be ...   [More]
Bais, F. A., Haaker, S. M. (2015). "Topological symmetry breaking: Domain walls and partial instability of chiral edges." Physical Review B 92(7)
In two-dimensional topological systems chiral edges may exhibit a spectral change due to the formation of a Bose condensate and partial confinement in the bulk according to the topological symmetry breaking (TSB) mechanism. We analyze in detail what happens in ...   [More]
Baker, J., Meade, A., Pagel, M., Venditti, C. (2015). "Adaptive evolution toward larger size in mammals." PNAS 112(16):5093-5098
The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term ...   [More]
Balch, C., Arias-Pulido, H., Banerjee, S., Lancaster, A. K., Clark, K. B., Perilstein, M., Hawkins, B., Rhodes, J., Sliz, P., Wilkins, J. F., Chittenden, T. W. (2015). "Science and technology consortia in US biomedical research: A paradigm shift in response to unsustainable academic growth." BioEssays 37(2):119-122
Science and technology consortia provide a viable solution for the recent unsustainable academic growth in biomedical research.   [More]
Balch, C., Arias-Pulido, H., Banerjee, S., Lancaster, A. K., Clark, K. B., Perilstein, M., Hawkins, B., Rhodes, J., Sliz, P., Wilkins, J., Chittenden, T. W. (2015). "Science and technology consortia in U.S. biomedical research: a paradigm shift in response to unsustainable academic growth." BioEssays 37(2):119-122
Science and technology consortia provide a viable solution for the recent unsustainable academic growth in biomedical research.   [More]
Bargigli, L., Di Iasio, G., Infante, L., Lillo, F., Pierobon, F. (2015). "The multiplex structure of interbank networks." Quantitative Finance 15(4):673-691
The interbank market has a natural multiplex network representation. We employ a unique database of supervisory reports on Italian banks to the Banca d'Italia that includes all bilateral exposures broken down by maturity and by the secured and unsecured nature ...   [More]
Barnett, N; Crutchfield, JP (2015). "Computational Mechanics of Input-Output Processes: Structured Transformations and the is an element of-Transducer." Journal of Statistical Physics 161(2):404-451
Computational mechanics quantifies structure in a stochastic process via its causal states, leading to the process's minimal, optimal predictor-the . We extend computational mechanics to communication channels coupling two processes, obtaining an analogous optimal model-the -of the stochastic mapping between ...   [More]
Bech, M. L., Bergstrom, C. T., Rosvall, M., Garratt, R. J. (2015). "Mapping change in the overnight money market." Physica A - Statistical Mechanics and Its Applications 424:44-51
We use an information-theoretic approach to describe changes in lending relationships between financial institutions around the time of the Lehman Brothers failure. Unlike previous work that conducts maximum likelihood estimation on undirected networks our analysis distinguishes between borrowers and lenders ...   [More]
Bedhomme, S., Hillung, J., Elena, S. F. (2015). "Emerging viruses: why they are not jacks of all trades?." Current Opinion in Virrology 10:1-6
In order to limit the impact of the recent pandemics ignited by viral host jumps, it is necessary to better understand the ecological and evolutionary factors influencing the early steps of emergence and the interactions between them. Antagonistic pleiotropy, that ...   [More]
Bellafard, A., Chakravarty, S., Troyer, M., Katzgraber, H. G. (2015). "The effect of quenched bond disorder on first-order phase transitions." Annals of Physics 357:66-78
We investigate the effect of quenched bond disorder on the two-dimensional three-color Ashkin Teller model, which undergoes a first-order phase transition in the absence of impurities. This is one of the simplest and striking models in which quantitative numerical simulations ...   [More]
Bellan, S. E., Dushoff, J., Galvani, A. P., Meyers, L. A. (2015). "Reassessment of HIV-1 Acute Phase Infectivity: Accounting for Heterogeneity and Study Design with Simulated Cohorts." Plos Medicine 12(3)
Background The infectivity of the HIV-1 acute phase has been directly measured only once, from a retrospectively identified cohort of serodiscordant heterosexual couples in Rakai, Uganda. Analyses of this cohort underlie the widespread view that the acute phase is highly ...   [More]
Bellan, S. E., Pulliam, J. R. C., Pearson, C. A. B., Champredon, D., Fox, S. J., Skrip, L., Galvani, A. P., Gambhir, M., Lopman, B. A., Porco, T. C., Meyers, L. A., Dushoff, J. (2015). "Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis." Lancet Infectious Diseases 15(6):703-710
Background Safe and effective vaccines could help to end the ongoing Ebola virus disease epidemic in parts of west Africa, and mitigate future outbreaks of the virus. We assess the statistical validity and power of randomised controlled trial (RCT) and ...   [More]
Berdahl, A., Torney, C. J., Schertzer, E., Levin, S. A. (2015). "On the evolutionary interplay between dispersal and local adaptation in heterogeneous environments." Evolution 69(6):1390-1405
Dispersal, whether in the form of a dandelion seed drifting on the breeze, or a salmon migrating upstream to breed in a nonnatal stream, transports genes between locations. At these locations, local adaptation modifies the gene frequencies so their carriers ...   [More]
Bettencourt, L. M. A., Brelsford, C. (2015). "Industrial Ecology The View From Complex Systems." Journal of Industrial Ecology 19(2):195-197
Publisher's excerpt: . . . it is important to embrace all the circumstances where ‘simple’ engineering solutions are possible while at the same time being aware of conditions when they are not the best solution. Engineering solutions can fix problems ...   [More]
Bhat, U., Redner, S. (2015). "Intermediate-level crossings of a first-passage path." Journal of Statistical Mechanics — Theory and Experiment
We investigate some simple and surprising properties of a one-dimensional Brownian trajectory with diffusion coefficient D that starts at the origin and: (i) is at X at time T, or (ii) first reaches X at time T. We determine the ...   [More]
Blonder, B., Nogues-Bravo, D., Borregaard, M. K., Donoghue, J. C., Jorgensen, P. M., Kraft, N. J. B., Lessard, J. P., Morueta-Holme, N., Sandel, B., Svenning, J. C., Violle, C., Rahbek, C., Enquist, B. J. (2015). "Linking Environmental Filtering and Disequilibrium to Biogeography with a Community Climate Framework." Ecology 96(4):972-985
We present a framework to measure the strength of environmental filtering and disequilibrium of the species composition of a local community across time, relative to past, current, and future climates. We demonstrate the framework by measuring the impact of climate ...   [More]
Blonder, B., Vasseur, F., Violle, C., Shipley, B., Enquist, B. J., Vile, D. (2015). "Testing models for the leaf economics spectrum with leaf and whole-plant traits in Arabidopsis thaliana." AOB Plants 7
The leaf economics spectrum (LES) describes strong relationships between multiple functional leaf traits that determine resource fluxes in vascular plants. Five models have been proposed to explain these patterns: two based on patterns of structural allocation, two on venation networks ...   [More]
Blume, L. E., Brock, W. A., Durlauf, S. N., Jayaraman, R. (2015). "Linear Social Interactions Models." Journal of Political Economy 123(2):444-496
This paper provides a systematic analysis of identification in linear social interactions models. This is a theoretical and econometric exercise as the analysis is linked to a rigorously delineated model of interdependent decisions. We develop an incomplete information game for ...   [More]
Blume, L. E., Durlauf, S. N. (2015). "Capital in the Twenty-First Century: A Review Essay." Journal of Political Economy 123(4):749-777   [More]
Blume, L., Easley, D., Kleinberg, J., Kleinberg, R., Tardos, E. (2015). "Introduction to computer science and economic theory." JOURNAL OF ECONOMIC THEORY 156:1-13
This essay introduces the symposium on computer science and economic theory.   [More]
Borenstein, E. (2015). "Metagenomic Systems Biology: Metabolic Modeling and Multi-Meta-Omic Analysis of the Human Microbiome." FASEB JOURNAL 29(1)
The human microbiome represents a vastly complex ecosystem that is tightly linked to many host-related processes and that directly impact human health. To date, however, most studies have focused on characterizing the composition of the microbiome in health and in ...   [More]
Bormetti, G., Calcagnile, L. M., Treccani, M., Corsi, F., Marmi, S., Lillo, F. (2015). "Modelling systemic price cojumps with Hawkes factor models." Quantitative Finance 15(7):1137-1156
Instabilities in the price dynamics of a large number of financial assets are a clear sign of systemic events. By investigating portfolios of highly liquid stocks, we find that there are a large number of high-frequency cojumps. We show that ...   [More]
Bradley, E; Kantz, H (2015). "Nonlinear time-series analysis revisited." Chaos 25(9)
In 1980 and 1981, two pioneering papers laid the foundation for what became known as nonlinear time-series analysis: the analysis of observed data-typically univariate-via dynamical systems theory. Based on the concept of state-space reconstruction, this set of methods allows us ...   [More]
Bratulic, S; Gerber, F; Wagner, A (2015). "Mistranslation drives the evolution of robustness in TEM-1 beta-lactamase." PNAS 112(41):12758-12763
How biological systems such as proteins achieve robustness to ubiquitous perturbations is a fundamental biological question. Such perturbations include errors that introduce phenotypic mutations into nascent proteins during the translation of mRNA. These errors are remarkably frequent. They are also ...   [More]
Briggs, K; Deeds, EJ (2015). "Optimizing the Assembly of Stacked Rings." Biophysical Journal 108(2):220A-221A
Many macromolecular machines inside the cell exhibit a ‘‘stacked ring’’ architecture, with multiple uniform-length rings of protein subunits bound to one another. The majority of these machines must adopt their fully assembled quaternary structure in order to function, making the ...   [More]
Brocklebank, S., Pauls, S., Rockmore, D., Bates, T. C. (2015). "A spectral clustering approach to the structure of personality: Contrasting the FFM and HEXACO models." Journal of Research in Personality 57:100-109
Alternative analytic methods may help resolve the dimensionality of personality and the content of those dimensions. Here we tested the structure of personality using spectral clustering and conventional factor analysis. Study 1 analysed responses from 20,993 subjects taking the 300-item ...   [More]
Buhnerkempe, M. G., Roberts, M. G., Dobson, A. P., Heesterbeek, H., Hudson, P. J., Lloyd-Smith, J. O. (2015). "Eight challenges in modelling disease ecology in multi-host, multi-agent systems." Epidemiccs 10:26-30
Many disease systems exhibit complexities not captured by current theoretical and empirical work. In particular, systems with multiple host species and multiple infectious agents (i.e., multi-host, multi-agent systems) require novel methods to extend the wealth of knowledge acquired studying primarily ...   [More]
Caccioli, F., Farmer, J. D., Foti, N. J., Rockmore, D. (2015). "Overlapping portfolios, contagion, and financial stability." Journal of Economic Dynamics & Control 51:50-63
We study the problem of interacting channels of contagion in financial networks. The first channel of contagion is counterparty failure risk; this is captured empirically using data for the Austrian interbank network. The second channel of contagion is overlapping portfolio ...   [More]
Caceres, MO; Fuentes, MA (2015). "First-passage times for pattern formation in nonlocal partial differential equations." Physical Review E 92(4)
We describe the lifetimes associated with the stochastic evolution from an unstable uniform state to a patterned one when the time evolution of the field is controlled by a nonlocal Fisher equation. A small noise is added to the evolution ...   [More]
Cao, Y. D., Babbush, R., Biamonte, J., Kais, S. (2015). "Hamiltonian gadgets with reduced resource requirements." Physical Review A 91(1)
Application of the adiabatic model of quantum computation requires efficient encoding of the solution to computational problems into the lowest eigenstate of a Hamiltonian that supports universal adiabatic quantum computation. Experimental systems are typically limited to restricted forms of two-body ...   [More]
Carlson, K. M., Curran, L. M., Ponette-Gonzalez, A. G., Ratnasari, D., Ruspita,;, Lisnawati, N., Purwanto, Y., Brauman, K. A., Raymond, P. A. (2015). "Consistent results in stream hydrology across multiple watersheds: A reply to Chew and Goh REPLY." Journal of Geophysiccal Research - Biosciences 120(4):812-817   [More]
Castaneda, LE; Godoy, K; Manzano, M; Marquet, PA; Barbosa, O (2015). "Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile." Ecology and Evolution 5(18):3857-3868
Natural ecosystems provide services to agriculture such as pest control, soil nutrients, and key microbial components. These services and others in turn provide essential elements that fuel biomass productivity. Responsible agricultural management and conservation of natural habitats can enhance these ...   [More]
Chupeau, M., Benichou, O., Redner, S. (2015). "Optimal strategy to capture a skittish lamb wandering near a precipice." Journal of Statistical Mechanics — Theory and Experiment
We study the splitting probabilities for a one-dimensional Brownian motion in a cage whose two boundaries move at constant speeds c(1) and c(2). This configuration corresponds to the capture of a diffusing, but skittish lamb, with an approaching shepherd on ...   [More]
Clauset, A., Kogan, M., Redner, S. (2015). "Safe leads and lead changes in competitive team sports." Physical Review E 91(6)
We investigate the time evolution of lead changes within individual games of competitive team sports. Exploiting ideas from the theory of random walks, the number of lead changes within a single game follows a Gaussian distribution. We show that the ...   [More]
Corominas-Murtra, B., Hanel, R., Thurner, S. (2015). "Understanding scaling through history-dependent processes with collapsing sample space." PNAS 112(17):5348-5353
History-dependent processes are ubiquitous in natural and social systems. Many such stochastic processes, especially those that are associated with complex systems, become more constrained as they unfold, meaning that their sample space, or their set of possible outcomes, reduces as ...   [More]
Courchamp, F., Dunne, J. A., Le Maho, Y., May, R. M., Thebaud, C., Hochberg, M. E. (2015). "Fundamental ecology is fundamental." Trends in Ecology & Evolution 30(1):9-16
The primary reasons for conducting fundamental research are satisfying curiosity, acquiring knowledge, and achieving understanding. Here we develop why we believe it is essential to promote basic ecological research, despite increased impetus for ecologists to conduct and present their research ...   [More]
Courchamp, F., Dunne, J. A., Le Maho, Y., May, R. M., Thebaud, C., Hochberg, M. E. (2015). "Back to the fundamentals: a reply to Barot et al.." Trends in Ecology & Evolution 30(7):370-371
We appreciate that Barot and coworkers [1] recognize that our proposed model [2] advocates the end of the linear model of research. We indeed highlighted the importance of feedback mechanisms and multi-level integration in this model to illustrate the interdependency ...   [More]
Cuevas, J. M., Willemsen, A., Hillung, J., Zwart, M. P., Elena, S. F. (2015). "Temporal Dynamics of Intrahost Molecular Evolution for a Plant RNA Virus." Molecular Biology and Evolution 32(5):1132-1147
Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host ...   [More]
D'Souza, K; Epureanu, BI; Pascual, M (2015). "Forecasting Bifurcations from Large Perturbation Recoveries in Feedback Ecosystems." PLOS One 10(9)
Forecasting bifurcations such as critical transitions is an active research area of relevance to the management and preservation of ecological systems. In particular, anticipating the distance to critical transitions remains a challenge, together with predicting the state of the system ...   [More]
Daepp, M. I. G., Hamilton, M. J., West, G. B., Bettencourt, L. M. A. (2015). "The mortality of companies." Journal of the Royal Society Interface 12(106)
The firm is a fundamental economic unit of contemporary human societies. Studies on the general quantitative and statistical character of firms have produced mixed results regarding their lifespans and mortality. We examine a comprehensive database of more than 25 000 ...   [More]
Dall'Olio, G. M., Vahdati, A. R., Bertranpetit, J., Wagner, A., Laayouni, H. (2015). "VCF2Networks: applying genotype networks to single-nucleotide variants data." Bioinformatics 31(3):438-439
A wealth of large-scale genome sequencing projects opens the doors to new approaches to study the relationship between genotype and phenotype. One such opportunity is the possibility to apply genotype networks analysis to population genetics data. Genotype networks are a ...   [More]
Daniel B. Larremore, Sesh A. Sundararaman, Weimin Liu, William R. Proto, Aaron Clauset, Dorothy E. Loy, Sheri Speede, Lindsey J. Plenderleith, Paul M. Sharp, Beatrice H. Hahn, Julian C. Rayner & Caroline O. Buckee (2015). "Ape parasite origins of human malaria virulence genes." Nature Communications 6(8368)
Antigens encoded by the var gene family are major virulence factors of the human malaria parasite Plasmodium falciparum, exhibiting enormous intra- and interstrain diversity. Here we use network analysis to show that var architecture and mosaicism are conserved at multiple ...   [More]
Darmon, D.;, Girvan, M. (2015). "Complexity-Regularized Regression for Serially-Correlated Residuals with Applications to Stock Market Data." Entropy 17(1):1-27
A popular approach in the investigation of the short-term behavior of a non-stationary time series is to assume that the time series decomposes additively into a long-term trend and short-term fluctuations. A first step towards investigating the short-term behavior requires ...   [More]
Decelle, A., Zhang, P. (2015). "Inference of the sparse kinetic Ising model using the decimation method." Physical Review E 91(5)
In this paper we study the inference of the kinetic Ising model on sparse graphs by the decimation method. The decimation method, which was first proposed in Decelle and Ricci-Tersenghi [Phys. Rev. Lett. 112, 070603 (2014)] for the static inverse ...   [More]
DeLong, J. P., Gilbert, B., Shurin, J. B., Savage, V. M., Barton, B. T., Clements, C. F., Dell, A. I., Greig, H. S., Harley, C. D. G., Kratina, P., McCann, K. S., Tunney, T. D., Vasseur, D. A., O'Connor, M. I. (2015). "The Body Size Dependence of Trophic Cascades." American Naturalist 185(3):354-366
Trophic cascades are indirect positive effects of predators on resources via control of intermediate consumers. Larger-bodied predators appear to induce stronger trophic cascades (a greater rebound of resource density toward carrying capacity), but how this happens is unknown because we ...   [More]
di Iasio, G., Gallegati, M., Lillo, F., Mantegna, R. N. (2015). "Special issue of Quantitative Finance on 'Interlinkages and Systemic Risk' Foreword." Quantitative Finance 15(4):587-588   [More]
Duran-Nebreda, S., Sole, R. (2015). "Emergence of Multicellularity in a Model of Cell Growth, Death and Aggregation Under Size-Dependent Selection." Journal of the Royal Society Interface 12(102)
How multicellular life forms evolved from unicellular ones constitutes a major problem in our understanding of the evolution of our biosphere. A recent set of experiments involving yeast cell populations have shown that selection for faster sedimenting cells leads to ...   [More]
Einarsdottir, O; McDonald, W; Funatogawa, C; Szundi, I; Woodruff, WH; Dyer, RB (2015). "The pathway of O-2 to the active site in heme-copper oxidases." Biochimica et Biophysica Acta - Bioengeretics 1847(1):109-118
The route of O-2 to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (CO). Time-resolved and stationary infrared experiments in our laboratories of the fully reduced CO-bound enzymes, as well ...   [More]
Engelhardt, J., Stadler, P. F. (2015). "Evolution of the unspliced transcriptome." BMC Evolutionary Biology 15
Background: Despite their abundance, unspliced EST data have received little attention as a source of information on non-coding RNAs. Very little is know, therefore, about the genomic distribution of unspliced non-coding transcripts and their relationship with the much better studied ...   [More]
Erwin, D. H. (2015). "David M. Raup (1933-2015) OBITUARY." Nature 524(7563):36   [More]
Erwin, DH (2015). "Novelty and Innovation in the History of Life." Current Biology 25(19):R930-R940
The history of life as documented by the fossil record encompasses evolutionary diversifications at scales ranging from the Ediacaran-Cambrian explosion of animal life and the invasion of land by vascular plants, insects and vertebrates to the diversification of flowering plants ...   [More]
Farmer, J. D., Geanakoplos, J., Masoliver, J., Montero, M., Perello, J. (2015). "Value of the future: Discounting in random environments." Physical Review E 91(5)
We analyze how to value future costs and benefits when they must be discounted relative to the present. We introduce the subject for the nonspecialist and take into account the randomness of the economic evolution by studying the discount function ...   [More]
Farmer, JD; Hepburn, C; Mealy, P; Teytelboym, A (2015). "A Third Wave in the Economics of Climate Change." Environmental & Resource Economics 62(2):329-357
Modelling the economics of climate change is daunting. Many existing methodologies from social and physical sciences need to be deployed, and new modelling techniques and ideas still need to be developed. Existing bread-and-butter micro-and macroeconomic tools, such as the expected ...   [More]
Fochesato, M., Bowles, S. (2015). "Nordic exceptionalism? Social democratic egalitarianism in world-historic perspective." Journal of Public Economics 127:30-44
In what respect, if any, are the Nordic economies exceptionally egalitarian when viewed from a world historical perspective? Our answer is based on archaeological, historical and ethnographic as well as contemporary evidence over the past three thousand years. The countries ...   [More]
Gagnon, JS; Hochberg, D; Perez-Mercader, J (2015). "Small-scale properties of a stochastic cubic-autocatalytic reaction-diffusion model." Physical Review E 92(4)
We investigate the small-scale properties of a stochastic cubic-autocatalytic reaction-diffusion (CARD) model using renormalization techniques. We renormalize noise-induced ultraviolet divergences and obtain beta functions for the decay rate and coupling at one loop. Assuming colored (power-law) noise, our results show ...   [More]
Galetti, M., Guevara, R., Neves, C. L., Rodarte, R. R., Bovendorp, R. S., Moreira, M., Hopkins, J. B., Yeakel, J. D. (2015). "Defaunation affects the populations and diets of rodents in Neotropical rainforests." Biological Conservation 190:2-7
Most tropical rainforests have been defaunated of large-bodied mammals and the cascading effects of such extirpations have been poorly studied, particularly on other animals. We used a natural experiment in the Brazilian Atlantic rainforest to investigate the ecological responses of ...   [More]
Gallie, Jenna;, Libby, Eric;, Bertels, Frederic;, Remigi, Philippe;, Jendresen, Christian B.;, Ferguson, Gayle C.;, Desprat, Nicolas;, Buffing, Marieke F.;, Sauer, Uwe;, Beaumont, Hubertus J. E.;, Martinussen, Jan;, Kilstrup, Mogens;, Rainey, Paul B. (2015). "Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens." PLOS Biology 13(3)
Phenotype switching is commonly observed in nature. This prevalence has allowed the elucidation of a number of underlying molecular mechanisms. However, little is known about how phenotypic switches arise and function in their early evolutionary stages. The first opportunity to ...   [More]
Gardner, P. P., Fasold, M., Burge, S. W., Ninova, M., Hertel, J., Kehr, S., Steeves, T. E., Griffiths-Jones, S., Stadler, P. F. (2015). "Conservation and Losses of Non-Coding RNAs in Avian Genomes." PLOS One 10(3)
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We ...   [More]
Gintis, H. (2015). "SOCIOBIOLOGY Altruists together." Nature 517(7536):550-551
Book Reviews of: Does Altruism Exist?: Culture, Genes, and the Welfare of Others David Sloan Wilson Yale University Press 2015. ISBN: 9780300189490 and The Moral Arc: How Science and Reason Lead Humanity toward Truth, Justice, and Freedom Michael Shermer Henry ...   [More]
Gintis, H., van Schaik, C., Boehm, C. (2015). "Zoon Politikon: The Evolutionary Origins of Human Political Systems." Current Anthropology 56(3):327-353
We provide the most up-to-date evidence available in various behavioral fields in support of the hypothesis that the emergence of bipedalism and cooperative breeding in the hominin linetogether with environmental developments that made a diet of meat from large animals ...   [More]
Grady, J. M., Enquist, B. J., Dettweiler-Robinson, E., Wright, N. A., Smith, F. A. (2015). "Response to Comments on "Evidence for mesothermy in dinosaurs"." Science 348(6238)
D'Emic and Myhrvold raise a number of statistical and methodological issues with our recent analysis of dinosaur growth and energetics. However, their critiques and suggested improvements lack biological and statistical justification.   [More]
Greenblum, S., Carr, R., Borenstein, E. (2015). "Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species." Cell 160(4):583-594
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously ...   [More]
Grochow, J. A. (2015). "Unifying Known Lower Bounds via Geometric Complexity Theory." Computational Complexity(24):2
We show that most algebraic circuit lower bounds and relations between lower bounds naturally fit into the representation-theoretic framework suggested by geometric complexity theory (GCT), including: the partial derivatives technique (Nisan-Wigderson), the results of Razborov and Smolensky on AC (0)[p], ...   [More]
Grollemund, R; Branford, S; Bostoen, K; Meade, A; Venditti, C; Pagel, M (2015). "Bantu expansion shows that habitat alters the route and pace of human dispersals." PNAS 112(43):13296-13301
Unlike most other biological species, humans can use cultural innovations to occupy a range of environments, raising the intriguing question of whether human migrations move relatively independently of habitat or show preferences for familiar ones. The Bantu expansion that swept ...   [More]
Gurtner, G., Valori, L., Lillo, F. (2015). "Competitive allocation of resources on a network: an agent-based model of air companies competing for the best routes." Journal of Statistical Mechanics — Theory and Experiment
We present a stylized model of the allocation of resources on a network. By considering as a concrete example the network of sectors of the airspace, where each node is a sector characterized by a maximal number of simultaneously present ...   [More]
Gutfraind, A., Galvani, A. P., Meyers, L. A. (2015). "Efficacy and Optimization of Palivizumab Injection Regimens Against Respiratory Syncytial Virus Infection." JAMA Pediatrics 169(4):341-348
IMPORTANCE Infection with the respiratory syncytial virus (RSV) is the leading cause of hospitalizations in children, accounting for more than 90 000 hospitalizations every year in the United States. For children who are at risk for severe RSV infections, the ...   [More]
Gutfraind, A., Meyers, L. A. (2015). "Evaluating Large-scale Blood Transfusion Therapy for the Current Ebola Epidemic in Liberia." Journal of Infectious Diseases 211(8):1262-1267
Background. To combat the 2014-2015 Ebola virus disease (EVD) epidemic in West Africa, the World Health Organization urged the rapid evaluation of convalescent whole blood (CWB) and plasma (CP) transfusion therapy. However, the feasibility and likely impacts of broad implementation ...   [More]
Hayden, EJ; Bendixsen, DP; Wagner, A (2015). "Intramolecular phenotypic capacitance in a modular RNA molecule." PNAS 112(40):12444-12449
Phenotypic capacitance refers to the ability of a genome to accumulate mutations that are conditionally hidden and only reveal phenotype-altering effects after certain environmental or genetic changes. Capacitance has important implications for the evolution of novel forms and functions, but ...   [More]
Hebert-Dufresne, L., Althouse, B. M. (2015). "Complex dynamics of synergistic coinfections on realistically clustered networks." PNAS 112(33):10551-10556
We investigate the impact of contact structure clustering on the dynamics of multiple diseases interacting through coinfection of a single individual, two problems typically studied independently. We highlight how clustering, which is well known to hinder propagation of diseases, can ...   [More]
Hecker, J. P., Moses, M. E. (2015). "Beyond pheromones: evolving error-tolerant, flexible, and scalable ant-inspired robot swarms." Swarm Intelligence 9(1):43-70
For robot swarms to operate outside of the laboratory in complex real-world environments, they require the kind of error tolerance, flexibility, and scalability seen in living systems. While robot swarms are often designed to mimic some aspect of the behavior ...   [More]
Hellmuth, M., Wieseke, N., Lechner, M., Lenhof, H. P., Middendorf, M., Stadler, P. F. (2015). "Phylogenomics with paralogs." PNAS(112):7
Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data ...   [More]
Hillung, J., Cuevas, J. M., Elena, S. F. (2015). "Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host." Philosophical Transactions of the Royal Society B - Biological Sciences 370(1675)
The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance ...   [More]
Hobson, EA; Dedeo, S (2015). "Social Feedback and the Emergence of Rank in Animal Society." PLOS Computational Biology 11(9)
Dominance hierarchies are group-level properties that emerge from the aggression of individuals. Although individuals can gain critical benefits from their position in a hierarchy, we do not understand how real-world hierarchies form. Nor do we understand what signals and decision-rules ...   [More]
Hoen, A. G., Hladish, T. J., Eggo, R. M., Lenczner, M., Brownstein, J. S., Meyers, L. A. (2015). "Epidemic Wave Dynamics Attributable to Urban Community Structure: A Theoretical Characterization of Disease Transmission in a Large Network." Journal of Medical Internet Research 17(7)
Background: Multiple waves of transmission during infectious disease epidemics represent a major public health challenge, but the ecological and behavioral drivers of epidemic resurgence are poorly understood. In theory, community structure-aggregation into highly intraconnected and loosely interconnected social groups-within human ...   [More]
Hoffmann, S., Stadler, P. F., Strimmer, K. (2015). "A simple data-adaptive probabilistic variant calling model." Algorithms for Molecular Biology 10
Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing steps. In addition, the reference genome and the algorithms used for ...   [More]
Hooper, P. L., Gurven, M., Winking, J., Kaplan, H. S. (2015). "Inclusive fitness and differential productivity across the life course determine intergenerational transfers in a small-scale human society." Proceedings of the Royal Society B - Biological Sciences 282(1803)
Transfers of resources between generations are an essential element in current models of human life-history evolution accounting for prolonged development, extended lifespan and menopause. Integrating these models with Hamilton's theory of inclusive fitness, we predict that the interaction of biological ...   [More]
Hormozdiari, F., Penn, O., Borenstein, E., Eichler, E. E. (2015). "The discovery of integrated gene networks for autism and related disorders." Genome Research 25(1):142-154
Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously ...   [More]
Hosseini, SR; Barve, A; Wagner, A (2015). "Exhaustive Analysis of a Genotype Space Comprising 10(15) Central Carbon Metabolisms Reveals an Organization Conducive to Metabolic Innovation." PLOS Computational Biology 11(8)
All biological evolution takes place in a space of possible genotypes and their phenotypes. The structure of this space defines the evolutionary potential and limitations of an evolving system. Metabolism is one of the most ancient and fundamental evolving systems, ...   [More]
Hruschka, D. J., Branford, S., Smith, E. D., Wilkins, J. F., Meade, A., Pagel, M., Bhattacharya, T. (2015). "Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution." Current Biology 25(1):109
Background: Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon-a phenomenon ...   [More]
Janzac, B., Willemsen, A., Cuevas, J. M., Glais, L., Tribodet, M., Verrier, J. L., Elena, S. F., Jacquot, E. (2015). "Brazilian Potato virus Y isolates identified as members of a new clade facilitate the reconstruction of evolutionary traits within this species." Plant Pathology 64(4):799-807
Potato virus Y (PVY) is a plant virus distributed worldwide that causes damage to several species of the Solanaceae family. It was established long ago that groups of PVY isolates defined by phylogenetic analyses correlate strongly with those demarcated by ...   [More]
Jauregui, M., Tsallis, C. (2015). "Convergence of the probability of large deviations in a model of correlated random variables having compact-support Q-Gaussians as limiting distributions." Journal of Mathematical Physics 56(2)
We consider correlated random variables X-1,...,X-n taking values in {0,1} such that, for any permutation pi of {1,...,n}, the random vectors (X-1,...,X-n) and (X-pi(1),...,X-pi(n)) have the same distribution. This distribution, which was introduced by Rodriguez et al. [J. Stat. Mech. ...   [More]
Jauregui, M., Tsallis, C. (2015). "Paradoxical probabilistic behavior for strongly correlated many-body classical systems." Physics Letters A 379(32-33):1816-1820
Using a simple probabilistic model, we illustrate that a small part of a strongly correlated manybody classical system can show a paradoxical behavior, namely asymptotic stochastic independence. We consider a triangular array such that each row is a list of ...   [More]
Jesús Cuevas--Maraver · Panayotis G. Kevrekidis · Avadh Saxena · Fred Cooper · Avinash Khare · Andrew Comech · Carl M. Bender (2015). "Solitary waves of a PT-symmetric Nonlinear Dirac equation." IEEE Journal of Selected Topics in Quantum Electronics
In the present work, we consider a prototypical example of a PT-symmetric Dirac model. We discuss the underlying linear limit of the model and identify the threshold of the PT-phase transition in an analytical form. We then focu on the ...   [More]
Jo, C. L., Ayers, J. W., Althouse, B. M., Emery, S., Huang, J. D., Ribisl, K. M. (2015). "US consumer interest in non-cigarette tobacco products spikes around the 2009 federal tobacco tax increase." Tobacco Control 24(4):395-399
Objectives This quasi-experimental longitudinal study monitored aggregate Google search queries as a proxy for consumer interest in non-cigarette tobacco products (NTP) around the time of the 2009 US federal tobacco tax increase. Methods Query trends for searches mentioning common NTP ...   [More]
JY; Shattuck-Hufnagel, S; Demuth, K (2015). "Development of phonetic variants (allophones) in 2-year-olds learning American English: A study of alveolar stop/t, d/codas." JOURNAL OF PHONETICS 52(152-169)
This study examined the emergence of the phonetic variants (often called allophones) of alveolar phonemes in the speech production of 2-year-olds. Our specific question was: Does the child start by producing a "canonical' form of a phoneme (e.g., /t/ with ...   [More]
Kallus, Y. (2015). "Pessimal Packing Shapes." Geometry & Topology 19(1):343-363
We address the question of which convex shapes, when packed as densely as possible under certain restrictions, fill the least space and leave the most empty space. In each different dimension and under each different set of restrictions, this question ...   [More]
Kallus, Y. (2015). "When is the Ball a Local Pessimum for Covering?." Discrete and Computational Geometry 54(1):232-245
We consider the problem of identifying the worst point-symmetric shape for covering -dimensional Euclidean space with lattice translates. Here we focus on the dimensions where the thinnest lattice covering with balls is known and ask whether the ball is a ...   [More]
Karafet, T. M., Mendez, F. L., Sudoyo, H., Lansing, J. S., Hammer, M. F. (2015). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia." European Journal of Human Genetics 23(3):369-373
The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across ...   [More]
Katzgraber, H. G., Hamze, F., Zhu, Z., Ochoa, A. J., Munoz-Bauza, H. (2015). "Seeking Quantum Speedup Through Spin Glasses: The Good, the Bad, and the Ugly." Physical Review X 5(3)
There has been considerable progress in the design and construction of quantum annealing devices. However, a conclusive detection of quantum speedup over traditional silicon-based machines remains elusive, despite multiple careful studies. In this work we outline strategies to design hard ...   [More]
Kavlak, G., McNerney, J., Jaffe, R. L., Trancik, J. E. (2015). "Metal production requirements for rapid photovoltaics deployment." Energy & Environmental Science 8(6):1651-1659
As global photovoltaics (PV) deployment grows, the required input materials need to be supplied at an increasing rate. In this paper, we quantify the effect of PV deployment levels on the scale of metal production. For example, we find that ...   [More]
Kenneth O. Stanley; Joel Lehman. "Why greatness cannot be planned : the myth of the objective". Springer, 2015  [More]
Kevrekidis, PG; Cuevas-Maraver, J; Saxena, A; Cooper, F; Khare, A (2015). "Interplay between parity-time symmetry, supersymmetry, and nonlinearity: An analytically tractable case example." Physical Review E 92(4)
In the present work, we combine the notion of parity-time (PT) symmetry with that of supersymmetry (SUSY) for a prototypical case example with a complex potential that is related by SUSY to the so-called Poschl-Teller potential which is real. Not ...   [More]
Klimek, P., Kautzky-Willer, A., Chmiel, A., Schiller-Fruhwirth, I., Thurner, S. (2015). "Quantification of Diabetes Comorbidity Risks across Life Using Nation-Wide Big Claims Data." PLOS Computational Biology 11(4)
Despite substantial progress in the study of diabetes, important questions remain about its comorbidities and clinical heterogeneity. To explore these issues, we develop a framework allowing for the first time to quantify nation-wide risks and their age- and sex-dependence for ...   [More]
Klimek, P., Poledna, S., Farmer, J. D., Thurner, S. (2015). "To bail-out or to bail-in? Answers from an agent-based model." Journal of Economic Dynamics & Control 50:144-154
Since the beginning of the 2008 financial crisis almost half a trillion euros have been spent to financially assist EU member states in taxpayer-funded bail-outs. These crisis resolutions are often accompanied by austerity programs causing political and social friction on ...   [More]
Kokko, H., Hochberg, M. E. (2015). "Towards cancer-aware life-history modelling." Philosophical Transactions of the Royal Society B - Biological Sciences 370(1673)
Studies of body size evolution, and life-history theory in general, are conducted without taking into account cancer as a factor that can end an organism's reproductive lifespan. This reflects a tacit assumption that predation, parasitism and starvation are of overriding ...   [More]
Lachowiec, J., Lemus, T., Borenstein, E., Queitsch, C. (2015). "Hsp90 Promotes Kinase Evolution." Molecular Biology and Evolution 32(1):91-99
Heat-shock protein 90 (Hsp90) promotes the maturation and stability of its client proteins, including many kinases. In doing so, Hsp90may allow its clients to accumulatemutations as previously proposed by the capacitor hypothesis. If true, Hsp90 clients should show increased evolutionary ...   [More]
Lafferty, K. D., Deleo, G., Briggs, C. J., Dobson, A. P., Gross, T., Kuris, A. M. (2015). "A general consumer-resource population model." Science 349(6250):854-857
Food-web dynamics arise from predator-prey, parasite-host, and herbivore-plant interactions. Models for such interactions include up to three consumer activity states (questing, attacking, consuming) and up to four resource response states (susceptible, exposed, ingested, resistant). Articulating these states into a general ...   [More]
Laubichler, MD; Renn, J (2015). "Extended Evolution: A Conceptual Framework for Integrating Regulatory Networks and Niche Construction." Journal of Experimental Zoology Part B - Molecular and Developmental Evolution 324(7):565-577
This paper introduces a conceptual framework for the evolution of complex systems based on the integration of regulatory network and niche construction theories. It is designed to apply equally to cases of biological, social and cultural evolution. Within the conceptual ...   [More]
Letendre, K., Donnadieu, E., Moses, M. E., Cannon, J. L. (2015). "Bringing Statistics Up to Speed with Data in Analysis of Lymphocyte Motility." PLos One 10(5)
Two-photon (2P) microscopy provides immunologists with 3D video of the movement of lymphocytes in vivo. Motility parameters extracted from these videos allow detailed analysis of lymphocyte motility in lymph nodes and peripheral tissues. However, standard parametric statistical analyses such as ...   [More]
Levy, R., Carr, R., Kreimer, A., Freilich, S., Borenstein, E. (2015). "NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation." BMC Bioinformatics 16
Background: Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, ...   [More]
Lillo, F., Micciche, S., Tumminello, M., Piilo, J., Mantegna, R. N. (2015). "How news affects the trading behaviour of different categories of investors in a financial market." Quantitative Finance 15(2):213-229
We investigate the trading behaviour of a large set of single investors trading the highly liquid Nokia stock over the period 2003-2008 with the aim of determining the relative role of endogenous and exogenous factors that may affect their behaviour. ...   [More]
Lillo, F., Pirino, D. (2015). "The impact of systemic and illiquidity risk on financing with risky collateral." Journal of Economic Dynamics & Control 50:180202
Repurchase agreements (repos) are one of the most important sources of funding liquidity for many financial investors and intermediaries. In a repo, some assets are given by a borrower as collateral in exchange of funding. The capital given to the ...   [More]
Lin, S. S., Demuth, K. (2015). "Children's Acquisition of English Onset and Coda: Articulatory Evidence." Journal of Speech Language and Hearing Research 58(1):13-27
Purpose: The goal of this study was to better understand how and when onset l (leap) and coda l (peel) are acquired by children by examining both the articulations involved and adults' perceptions of the produced segments. Method: Twenty-five typically ...   [More]
Lovett, S., Moore, C., Russell, A. (2015). "Group representations that resist random sampling." Random Structures and Algorithms 47(3):605-614
We show that there exists a family of groups G(n) and nontrivial irreducible representations (n) such that, for any constant t, the average of rho(n) over t uniformly random elements g(1), ... , g(t) is an element of G(n) has ...   [More]
Mandel, A., Landini, S., Gallegati, M., Gintis, H. (2015). "Price dynamics, financial fragility and aggregate volatility." Journal of Economic Dynamics & Control 51:257-277
Within a general equilibrium framework a la (Long and Plosser, 1983), we investigate the dynamics emerging from the interactions of households and firms that are adaptive price setters and financially constrained. Adaptive price-setting behavior induces micro-founded out-of-equilibrium dynamics along which ...   [More]
Manor, O., Borenstein, E. (2015). "MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome." Genome Biology 16
Functional metagenomic analyses commonly involve a normalization step, where measured levels of genes or pathways are converted into relative abundances. Here, we demonstrate that this normalization scheme introduces marked biases both across and within human microbiome samples, and identify sample- ...   [More]
Marquet, P. A., Allen, A. P., Brown, J. H., Dunne, J. A., Enquist, B. J., Gillooly, J. F., Gowaty, P. A., Harte, J., Hubbell, S. P., Okie, J. G., Ostling, A., Ritchie, M., Storch, D., West, G. B. (2015). "On the Importance of First Principles in Ecological Theory Development." Bioscience 65(4):342-343
Letter, concluding paragraph: "We would like to end our letter by saying that, to a large extent, our article was motivated by the mounting dismissal of the value of theory in the biological sciences. This is particularly acute in systems ...   [More]
Mathew, S., Perreault, C. (2015). "Behavioural variation in 172 small-scale societies indicates that social learning is the main mode of human adaptation." Proceedings of the Royal Society B - Biological Sciences 2822(1810)
The behavioural variation among human societies is vast and unmatched in the animal world. It is unclear whether this variation is due to variation in the ecological environment or to differences in cultural traditions. Underlying this debate is a more ...   [More]
Meerson, B., Redner, S. (2015). "Mortality, Redundancy, and Diversity in Stochastic Search." Physical Review Letters 114(19)
We investigate a stochastic search process in one dimension under the competing roles of mortality, redundancy, and diversity of the searchers. This picture represents a toy model for the fertilization of an oocyte by sperm. A population of N independent ...   [More]
Mellor, A., Mobilia, M., Redner, S., Rucklidge, A. M., Ward, J. A. (2015). "Influence of Luddism on innovation diffusion." Physical Review E 92(1)
We generalize the classical Bass model of innovation diffusion to include a newclass of agents-Luddites-that oppose the spread of innovation. Our model also incorporates ignorants, susceptibles, and adopters. When an ignorant and a susceptible meet, the former is converted to ...   [More]
Mertens, S. (2015). "Stable roommates problem with random preferences." Journal of Statistical Mechanics — Theory and Experiment
The stable roommates problem with n agents has worst case complexity O(n(2)) in time and space. Random instances can be solved faster and with less memory, however. We introduce an algorithm that has average time and space complexity O(n 32) ...   [More]
Mertens, S. (2015). "Small random instances of the stable roommates problem." Journal of Statistical Mechanics — Theory and Experiment
Let p(n) denote the probability that a random instance of the stable roommates problem of size n admits a solution. We derive an explicit formula for pn and compute exact values of pn for n <= 12.   [More]
Minicka, J., Rymelska, N., Elena, S. F., Czerwoniec, A., Hasiow-Jaroszewska, B. (2015). "Molecular evolution of Pepino mosaic virus during long-term passaging in different hosts and its impact on virus virulence." Annals of Applied Biology 166(3):389-401
In this study the effect of host changes and multiple passages on Pepino mosaic virus (PepMV) evolution was analysed. A population of a mild isolate of PepMV was used to generate five independent evolution lineages on three tomato cultivars, which ...   [More]
Montufar, G; Ghazi-Zahedi, K; Ay, N (2015). "A Theory of Cheap Control in Embodied Systems." PLOS Computational Biology 11(9)
We present a framework for designing cheap control architectures of embodied agents. Our derivation is guided by the classical problem of universal approximation, whereby we explore the possibility of exploiting the agent's embodiment for a new and more efficient universal ...   [More]
Moore, C., Russell, A. (2015). "Approximate Representations, Approximate Homomorphisms, and Low-Dimensional Embeddings of Groups." SIAM Journal of Discrete Mathematics 29(1):182-197
Approximate algebraic structures play a defining role in additive number theory and have found remarkable applications to questions in theoretical computer science, including in pseudorandomness and probabilistically checkable proofs. Here we study approximate representations of finite groups: functions psi : ...   [More]
Mryglod, O., Fuchs, B., Szell, M., Holovatch, Y., Thurner, S. (2015). "Interevent time distributions of human multi-level activity in a virtual world." Physica A - Statistical Mechanics and Its Applications 419:681-690
Studying human behavior in virtual environments provides extraordinary opportunities for a quantitative analysis of social phenomena with levels of accuracy that approach those of the natural sciences. In this paper we use records of player activities in the massive multiplayer ...   [More]
Muneepeerakul, R., Castillo-Chavez, C. (2015). "Towards a Quantitative Science of Sustainability." Bulletin of Mathematical Biology 77(2):254-258
Introduction: The report Toward a Science of Sustainability (Clark and Levin 2010) states that “Building a science of sustainability...requires a truly multi-disciplinary approach that integrates practical experience with knowledge and know-how drawn from across the natural and social sciences, medicine ...   [More]
Mushegian, A. R., Elena, S. F. (2015). "Evolution of plant virus movement proteins from the 30K superfamily and of their homologs integrated in plant genomes." Virology 476:304-315
Homologs of Tobacco mosaic virus 30K cell-to-cell movement protein are encoded by diverse plant viruses. Mechanisms of action and evolutionary origins of these proteins remain obscure. We expand the picture of conservation and evolution of the 30K proteins, producing sequence ...   [More]
Newberry, MG; Ennis, DB; Savage, VM (2015). "Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks." PLOS Computational Biology 11(8)
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to capillaries and uses scaling ...   [More]
Newman, M. E. J., Peixoto, T. P. (2015). "Generalized Communities in Networks." Physical Review Letters 115(8)
A substantial volume of research is devoted to studies of community structure in networks, but communities are not the only possible form of large-scale network structure. Here, we describe a broad extension of community structure that encompasses traditional communities but ...   [More]
Nitsche, A., Rose, D., Fasold, M., Reiche, K., Stadler, P. F. (2015). "Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved." RNA - A Publication of the RNA Society 21(5):801-812
Large-scale RNA sequencing has revealed a large number of long mRNA-like transcripts (lncRNAs) that do not code for proteins. The evolutionary history of these lncRNAs has been notoriously hard to study systematically due to their low level of sequence conservation ...   [More]
Noar, SM; Althouse, BM; Ayers, JW; Francis, DB; Ribisl, KM (2015). "Cancer Information Seeking in the Digital Age: Effects of Angelina Jolie's Prophylactic Mastectomy Announcement." Medical Decision Making 35(1):16-21
Objective. This study used digital surveillance to examine the impact of Angelina Jolie's prophylactic mastectomy announcement on cancer information seeking. Methods. We analyzed 4 categories of breast cancer-related Internet search queries from 2010 to 2013 in the United States. Results. ...   [More]
Noble, A. E., Machta, J;., Hastings, A. (2015). "Emergent long-range synchronization of oscillating ecological populations without external forcing described by Ising universality." Nature Communications 6
Understanding the synchronization of oscillations across space is fundamentally important to many scientific disciplines. In ecology, long-range synchronization of oscillations in spatial populations may elevate extinction risk and signal an impending catastrophe. The prevailing assumption is that synchronization on distances ...   [More]
Noble, R., Kaltz, O., Hochberg, M. E. (2015). "Peto's paradox and human cancers." Philosophical Transactions of the Royal Society B - Biological Sciences 370(1673)
Peto's paradox is the lack of the expected trend in cancer incidence as a function of body size and lifespan across species. The leading hypothesis to explain this pattern is natural selection for differential cancer prevention in larger, longer lived ...   [More]
Norris, J. Q., Turcotte, D. L., Rundle, J. B. (2015). "Anisotropy in Fracking: A Percolation Model for Observed Microseismicity." Pure and Applied Geophysics 172(1):7-21
Hydraulic fracturing (fracking), using high pressures and a low viscosity fluid, allow the extraction of large quantiles of oil and gas from very low permeability shale formations. The initial production of oil and gas at depth leads to high pressures ...   [More]
Nunney, L., Maley, C. C., Breen, M., Hochberg, M. E., Schiffman, J. D. (2015). "Peto's paradox and the promise of comparative oncology." Philosophical Transactions of the Royal Society B - Biological Sciences 370(1673)
The past several decades have seen a paradigm shift with the integration of evolutionary thinking into studying cancer. The evolutionary lens is most commonly employed in understanding cancer emergence, tumour growth and metastasis, but there is an increasing realization that ...   [More]
Orr, Y; Lansing, JS; Dove, MR (2015). "Environmental Anthropology: Systemic Perspectives." Annual Review of Anthropology 44:153-168
Our brief overview of developments in environmental anthropology since 1980 and their antecedents is organized around three themes: systems ecology, political ecology, and cognitive science. In some areas, the context is familiar. As Latour recently observed, the intellectual themes captured ...   [More]
Ostermeier, L., Stadler, P. F. (2015). "The Grid Property and Product-Like Hypergraphs." Graphs and Combinatorics 31(3):757-770
Equivalence relations on the edge set of a hypergraph that satisfy the "grid property" (a certain restrictive condition on diagonal-free grids that can be seen as a generalization of the more familiar "square property" on graphs) play a crucial role ...   [More]
Otto, I. M., Biewald, A., Coumou, D., Feulner, G., Kohler, C., Nocke, T., Blok, A., Grober, A., Selchow, S., Tyfield, D., Volkmer, I., Schellnhuber, H. J., Beck, U. (2015). "COMMENTARY: Socio-economic data for global environmental change research." Nature Climate Change 5(6):503-506
Subnational socio-economic datasets are required if we are to assess the impacts of global environmental changes and to improve adaptation responses. Institutional and community efforts should concentrate on standardization of data collection methodologies, free public access, and geo-referencing.   [More]
Page, S. E. (2015). "What Sociologists Should Know About Complexity." Annual Review of Sociology 41(41):21-41
I discuss the concept of complexity and the burgeoning field of complex systems and their relevance to sociology. I begin by comparing and contrasting various definitions of complexity and then describe the attributes of systems capable of producing complexity: diversity, ...   [More]
Payne, J. L., Wagner, A. (2015). "Function does not follow form in gene regulatory circuits." Scientific Reports 5
Gene regulatory circuits are to the cell what arithmetic logic units are to the chip: fundamental components of information processing that map an input onto an output. Gene regulatory circuits come in many different forms, distinct structural configurations that determine ...   [More]
Poisot, T., Kefi, S., Morand, S., Stanko, M., Marquet, P. A., Hochberg, M. E. (2015). "A Continuum of Specialists and Generalists in Empirical Communities." PLOS One 10(5)
Understanding the persistence of specialists and generalists within ecological communities is a topical research question, with far-reaching consequences for the maintenance of functional diversity. Although theoretical studies indicate that restricted conditions may be necessary to achieve co-occurrence of specialists and ...   [More]
Poorter, L; van der Sande, MT; Thompson, J; Arets, EJMM; Alarcon, A; Alvarez-Sanchez, J; Ascarrunz, N; Balvanera, P; Barajas-Guzman, G; Boit, A; Bongers, F; Carvalho, FA; Casanoves, F; Cornejo-Tenorio, G; Costa, FRC; de Castilho, CV; Duivenvoorden, JF; Dutrieux, LP; Enquist, BJ; Fernandez-Mendez, F; Finegan, B; Gormley, LHL; Healey, JR; Hoosbeek, MR; Ibarra-Manriquez, G; Junqueira, AB; Levis, C; Licona, JC; Lisboa, LS; Magnusson, WE; Martinez-Ramos, M; Martinez-Yrizar, A; Martorano, LG; Maskell, LC; Mazzei, L; Meave, JA; Mora, F; Munoz, R; Nytch, C; Pansonato, MP; Parr, TW; Paz, H; Perez-Garcia, EA; Renteria, LY; Rodriguez-Velazquez, J; Rozendaal, DMA; Ruschel, AR; Sakschewski, B; Salgado-Negret, B; Schietti, J; Simoes, M; Sinclair, FL; Souza, PF; Souza, FC; Stropp, J; ter Steege, H; Swenson, NG; Thonicke, K; Toledo, M; Uriarte, M; van der Hout, P; Walker, P; Zamora, N; Pena-Claros, M (2015). "Diversity enhances carbon storage in tropical forests." Global Ecology and Biogeography 24(11):1314-1328
Aim Tropical forests store 25% of global carbon and harbour 96% of the world's tree species, but it is not clear whether this high biodiversity matters for carbon storage. Few studies have teased apart the relative importance of forest attributes ...   [More]
Pulliam, JRC; Bellan, SE; Gambhir, M; Meyers, LA; Dushoff, J (2015). "Evaluating Ebola vaccine trials: insights from simulation." Lancet Infectious Diseases 15(10):1134
Jolanta Piszczek and Eric Parlow1 outlined expected benefits of a stepped-wedge cluster trial (SWCT) design, with specific reference to the Sierra Leone Trial to Introduce a Vaccine against Ebola (STRIVE). STRIVE, however, is not an SWCT, but a phased-rollout trial ...   [More]
radley, E; Motter, AE; Pecora, LM (2015). "Introduction to Focus Issue: The 25th Anniversary of Chaos: Perspectives on Nonlinear Science-Past, Present, and Future." Chaos 25(9)
Excerpt from the introduction: Articles in this anniversary issue offer expert insights about the past, present, and future of nonlinear science. The authors of these invited papers were asked to share their personal opinions about interesting, important, and surprising developments ...   [More]
Rambaldi, M., Pennesi, P., Lillo, F. (2015). "Modeling foreign exchange market activity around macroeconomic news: Hawkes-process approach." Physical Review E 91(1)
We present a Hawkes-model approach to the foreign exchange market in which the high-frequency price dynamics is affected by a self-exciting mechanism and an exogenous component, generated by the pre-announced arrival of macroeconomic news. By focusing on time windows around ...   [More]
Ratcliff, W. C., Hawthorne, P., Libby, E. (2015). "Courting disaster: How diversification rate affects fitness under risk." Evolution 69(1):126-135
Life is full of risk. To deal with this uncertainty, many organisms have evolved bet-hedging strategies that spread risk through phenotypic diversification. These rates of diversification can vary by orders of magnitude in different species. Here we examine how key ...   [More]
Rodriguez-Sickert, C; Cosmelli, D; Claro, F; Fuentes, MA (2015). "The Underlying Social Dynamics of Paradigm Shifts." PLOS One 10(9)
We develop here a multi-agent model of the creation of knowledge (scientific progress or technological evolution) within a community of researchers devoted to such endeavors. In the proposed model, agents learn in a physical-technological landscape, and weight is attached to ...   [More]
Roodgar, M., Ross, C. T., Kenyon, N. J., Marcelino, G., Smith, D. G. (2015). "Inducible nitric oxide synthase (iNOS) regulatory region variation in non-human primates." Infection Genetics and Evolution 31:236-244
Inducible nitric oxide synthase (iNOS) is an enzyme that plays a key role in intracellular immune response against respiratory infections. Since various species of nonhuman primates exhibit different levels of susceptibility to infectious respiratory diseases, and since variation in regulatory ...   [More]
Roos, P., Orlando, P. A., Fagerstrom, R. M., Pepper, J. W. (2015). "In North America, Some Ovarian Cancers Express the Oncogenes of Preventable Human Papillomavirus HPV-18." Scientific Reports 5(8645)
Some researchers in other regions have recommended human papillomavirus (HPV) vaccination to reduce risk of ovarian cancer, but not in North America, where evidence has previously suggested no role for HPV in ovarian cancer. Here we use a large sample ...   [More]
Rowland, M. A., Harrison, B., Deeds, E. J. (2015). "Phosphatase Specificity and Pathway Insulation in Signaling Networks." Biophysical Journal 108(4):986-996
Phosphatases play an important role in cellular signaling networks by regulating the phosphorylation state of proteins. Phosphatases are classically considered to be promiscuous, acting on tens to hundreds of different substrates. We recently demonstrated that a shared phosphatase can couple ...   [More]
Ruggeri, A., Olsson, H., Katsikopoulos, K. V. (2015). "Opening the cuebox: The information children and young adults generate and rely on when making inferences from memory." British Journal of Developmental Psychology 33(3):355-374
We used a cue-generation and a cue-selection paradigm to investigate the cues children (9- to 12-year-olds) and young adults (17-year-olds) generate and select for a range of inferences from memory. We found that children generated more cues than young adults, ...   [More]
Ruiz, G., Tsallis, C. (2015). "Emergence of q-statistical functions in a generalized binomial distribution with strong correlations." Journal of Mathematical Physics 56(5)
We study a symmetric generalization p(k)((N)) (eta, alpha) of the binomial distribution recently introduced by Bergeron et al., where eta is an element of[0,1] denotes the win probability and alpha is a positive parameter. This generalization is based on q-exponential ...   [More]
Sabater-Munoz, B; Prats-Escriche, M; Montagud-Martinez, R; Lopez-Cerdan, A; Toft, C; Aguilar-Rodriguez, J; Wagner, A; Fares, MA (2015). "Fitness Trade-Offs Determine the Role of the Molecular Chaperonin GroEL in Buffering Mutations." Molecular Biology and Evolution 32(10):2681-2693
Molecular chaperones fold many proteins and their mutated versions in a cell and can sometimes buffer the phenotypic effect of mutations that affect protein folding. Unanswered questions about this buffering include the nature of its mechanism, its influence on the ...   [More]
Sadilek, M., Thurner, S. (2015). "Physiologically motivated multiplex Kuramoto model describes phase diagram of cortical activity." Scientific Reports 5
We derive a two-layer multiplex Kuramoto model from Wilson-Cowan type physiological equations that describe neural activity on a network of interconnected cortical regions. This is mathematically possible due to the existence of a unique, stable limit cycle, weak coupling, and ...   [More]
Sahyoun, AH; Holzer, M; Juhling, F; Siederdissen, CHZ; Al-Arab, M; Tout, K; Marz, M; Middendorf, M; Stadler, PF; Bernt, M (2015). "Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes." Nucleic Acids Research 43(16):8044-8056
Remolding of tRNAs is a well-documented process in mitochondrial genomes that changes the identity of a tRNA. It involves a duplication of a tRNA gene, a mutation that changes the anticodon and the loss of the ancestral tRNA gene. The ...   [More]
Salali, GD; Whitehouse, H; Hochberg, ME (2015). "A Life-Cycle Model of Human Social Groups Produces a U-Shaped Distribution in Group Size." PLOS One 10(9)
One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards ...   [More]
Salge, C; Ay, N; Polani, D; Prokopenko, M (2015). "Zipf's Law: Balancing Signal Usage Cost and Communication Efficiency." PLos One 1010
We propose a model that explains the reliable emergence of power laws (e.g., Zipf's law) during the development of different human languages. The model incorporates the principle of least effort in communications, minimizing a combination of the information-theoretic communication inefficiency ...   [More]
Scarpino, S. V., Iamarino, A., Wells, C., Dan, Y. M., Ndeffo-Mbah, M., Wenzel, N. S., Fox, S. J., Nyenswah, T., Altice, F. L., Galvani, A. P., Meyers, L. A., Townsend, J. P. (2015). "Epidemiological and Viral Genomic Sequence Analysis of the 2014 Ebola Outbreak Reveals Clustered Transmission." Clinical Infectious Diseases 60(7):1079-1082
Using Ebolavirus genomic and epidemiological data, we conducted the first joint analysis in which both data types were used to fit dynamic transmission models for an ongoing outbreak. Our results indicate that transmission is clustered, highlighting a potential bias in ...   [More]
Seoane, LF; Sole, R (2015). "Phase transitions in Pareto optimal complex networks." Physical Review E 92(3)
The organization of interactions in complex systems can be described by networks connecting different units. These graphs are useful representations of the local and global complexity of the underlying systems. The origin of their topological structure can be diverse, resulting ...   [More]
Sherrington, D. (2015). "Relaxors, spin, Stoner and cluster glasses." Phase Transitions 88(3):2020221
It is argued that the main characteristic features of displacive relaxor ferroelectrics of the form A(B, B ')O-3 with isovalent B, B ' can be explained and understood in terms of a soft pseudo-spin analogue of conventional spin glasses as ...   [More]
Shrestha, M., Scarpino, S. V., Moore, C. (2015). "Message-passing approach for recurrent-state epidemic models on networks." Physical Review E 92(2)
Epidemic processes are common out-of-equilibrium phenomena of broad interdisciplinary interest. Recently, dynamic message-passing (DMP) has been proposed as an efficient algorithm for simulating epidemic models on networks, and in particular for estimating the probability that a given node will become ...   [More]
Simova, I., Violle, C., Kraft, N. J. B., Storch, D., Svenning, J. C., Boyle, B., Donoghue, J. C., Jorgensen, P. M., McGill, B. J., Morueta-Holme, N., Piel, W. H., Peet, R. K., Regetz, J., Schildhauer, M., Spencer, N., Thiers, B., Wiser, S. K., Enquist, B. J. (2015). "Shifts in trait means and variances in North American tree assemblages: species richness patterns are loosely related to the functional space." Ecography 38(7):649-658
One of the key hypothesized drivers of gradients in species richness is environmental filtering, where environmental stress limits which species from a larger species pool gain membership in a local community owing to their traits. Whereas most studies focus on ...   [More]
Sloat, L. L., Henderson, A. N., Lamanna, C., Enquist, B. J. (2015). "The Effect of the Foresummer Drought on Carbon Exchange in Subalpine Meadows." Ecosystems 18(3):533-545
Climate in subalpine meadows of the Rocky Mountains can be characterized by an early (foresummer) drought that occurs after snowmelt (May) and lasts until the start of the summer monsoon season (July). Climate change models predict an increase in the ...   [More]
Smith, C., Pechuan, X., Puzio, R. S., Biro, D., Bergman, A. (2015). "Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures." Journal of the Royal Society Interface 12(108)
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary time scales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of biological networks is studied by considering a network ...   [More]
Sole, R. (2015). "Bioengineering the biosphere?." Ecological Complexity 22:40-49
Our planet is experiencing an accelerated process of change associated to a variety of anthropogenic phenomena. The future of this transformation is uncertain, but there is general agreement about its negative unfolding that might threaten our own survival. Furthermore, the ...   [More]
Sole, R. V., Montanez, R., Duran-Nebreda, S. (2015). "Synthetic circuit designs for earth terraformation." Biology Direct 10
Background: Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, ...   [More]
Sonay, TB; Koletou, M; Wagner, A (2015). "A survey of tandem repeat instabilities and associated gene expression changes in 35 colorectal cancers." BMC Genomics 16
Background: Colorectal cancer is a major contributor to cancer morbidity and mortality. Tandem repeat instability and its effect on cancer phenotypes remain so far poorly studied on a genome-wide scale. Results: Here we analyze the genomes of 35 colorectal tumors ...   [More]
Stark, S. C., Enquist, B. J., Saleska, S. R., Leitold, V., Schietti, J., Longo, M., Alves, L. F., Camargo, P. B., Oliveira, R. C. (2015). "Linking canopy leaf area and light environments with tree size distributions to explain Amazon forest demography." Ecology Letters 18(7):636-645
Forest biophysical structure - the arrangement and frequency of leaves and stems - emerges from growth, mortality and space filling dynamics, and may also influence those dynamics by structuring light environments. To investigate this interaction, we developed models that could ...   [More]
Steudel, B., Ay, N. (2015). "Information-Theoretic Inference of Common Ancestors." Entropy 17(4):2304-2327
A directed acyclic graph (DAG) partially represents the conditional independence structure among observations of a system if the local Markov condition holds, that is if every variable is independent of its non-descendants given its parents. In general, there is a ...   [More]
Strumsky, D., Lobo, J. (2015). "Identifying the sources of technological novelty in the process of invention." Research Policy 44(8):1445-1461
Much work on technological change agrees that the combination of new and existing technological capabilities is one of the principal sources of inventive novelty, and that there have been instances in history when new inventions appear with few antecedents. The ...   [More]
Szymanski, J. K., Temprano-Coleto, F., Perez-Mercader, J. (2015). "Unusual kinetics of poly(ethylene glycol) oxidation with cerium(IV) ions in sulfuric acid medium and implications for copolymer synthesis." Physical Chemistry Chemical Physics 17(10):6713-6717
The cerium(IV)-alcohol couple in an acidic medium is an example of a redox system capable of initiating free radical polymerization. When the alcohol has a polymeric nature, the outcome of such a process is a block copolymer, a member of ...   [More]
Thurner, S., Fuchs, B. (2015). "Physical Forces between Humans and How Humans Attract and Repel Each Other Based on Their Social Interactions in an Online World." PLOS One 10(7)
Physical interactions between particles are the result of the exchange of gauge bosons. Human interactions are mediated by the exchange of messages, goods, money, promises, hostilities, etc. While in the physical world interactions and their associated forces have immediate dynamical ...   [More]
Thurner, S., Hanel, R., Liu, B., Corominas-Murtra, B. (2015). "Understanding Zipf's law of word frequencies through sample-space collapse in sentence formation." Journal of the Royal Society Interface 12(108)
The formation of sentences is a highly structured and history-dependent process. The probability of using a specific word in a sentence strongly depends on the 'history' of word usage earlier in that sentence. We study a simple history-dependent model of ...   [More]
Toth, B., Palit, I., Lillo, F., Farmer, J. D. (2015). "Why is equity order flow so persistent?." Journal of Economic Dynamics & Control 51:218-239
Order flow in equity markets is remarkably persistent in the sense that order signs (to buy or sell) are positively autocorrelated out to time lags of tens of thousands of orders, corresponding to many days. Two possible explanations are herding, ...   [More]
Tsallis, C. (2015). "Thermodynamics and Statistical Mechanics for Complex Systems - Foundations and Applications." ACTA Physica Polonica B 46(6):1089-1101
The complexity (or simplicity) of a system can be characterized through very many paths. A quite interesting and operational one, which we follow here, consists in making use of entropic concepts. The thermodynamical and statistical-mechanical foundations of this approach, as ...   [More]
Tsallis, C. (2015). "Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems." Entropy 17(5):2853-2861
It is by now well known that the Boltzmann-Gibbs-von Neumann-Shannon logarithmic entropic functional (S-BG) is inadequate for wide classes of strongly correlated systems: see for instance the 2001 Brukner and Zeilinger's Conceptual inadequacy of the Shannon information in quantum measurements, ...   [More]
Tsallis, C., Haubold, H. J. (2015). "Boltzmann-Gibbs entropy is sufficient but not necessary for the likelihood factorization required by Einstein." EPL 110(3)
In 1910 Einstein published a work on a crucial aspect of his understanding of the Boltzmann entropy. He essentially argued that the likelihood function of any system composed by two probabilistically independent subsystems ought to be factorizable into the likelihood ...   [More]
Usher, T., Suter, E. (2015). "The Anim Languages of Southern New Guinea." Oceanic Linguistics 54(1):110-142
In this paper, we propose a new family of Papuan languages. The Anim languages are spread across the lowlands of south New Guinea on both sides of the border between Papua New Guinea and the Indonesian Province of Papua. They ...   [More]
Valverde, S., Sole, R. V. (2015). "Punctuated equilibrium in the large-scale evolution of programming languages." Journal of the Royal Society Interface 12(107)
The analogies and differences between biological and cultural evolution have been explored by evolutionary biologists, historians, engineers and linguists alike. Two well-known domains of cultural change are language and technology. Both share some traits relating the evolution of species, but ...   [More]
Varn, D. P., Crutchfield, J. P. (2015). "Chaotic crystallography: how the physics of information reveals structural order in materials." Current Opinion in Chemical Engineering 7:47-56
We review recent progress in applying information-theoretic and computation-theoretic measures to describe material structure that transcends previous methods based on exact geometric symmetries. We discuss the necessary theoretical background for this new toolset and show how the new techniques detect ...   [More]
Vijayaraghavan, VS; Noel, PA; Maoz, Z; D'Souza, RM (2015). "Quantifying dynamical spillover in co-evolving multiplex networks." Scientific Reports 5
Multiplex networks (a system of multiple networks that have different types of links but share a common set of nodes) arise naturally in a wide spectrum of fields. Theoretical studies show that in such multiplex networks, correlated edge dynamics between ...   [More]
Waagen, A., Verma, G., Chan, K., Swami, A., D'Souza, R. (2015). "Effect of zealotry in high-dimensional opinion dynamics models." Physical Review E 91(2)
Most of the work on opinion dynamics models focuses on the case of two or three opinion types. We consider the case of an arbitrary number of opinions in the mean field case of the naming game model in which ...   [More]
Wachsmuth, M., Domin, G., Lorenz, R., Serfling, R., Findeiss, S., Stadler, P. F., Morl, M. (2015). "Design criteria for synthetic riboswitches acting on transcription." RNA Biology 12(2):221-231
Riboswitches are RNA-based regulators of gene expression composed of a ligand-sensing aptamer domain followed by an overlapping expression platform. The regulation occurs at either the level of transcription (by formation of terminator or antiterminator structures) or translation (by presentation or ...   [More]
Wagner, A. (2015). "Causal Drift, Robust Signaling, and Complex Disease." PLOS One 10(3)
The phenotype of many regulatory circuits in which mutations can cause complex, polygenic diseases is to some extent robust to DNA mutations that affect circuit components. Here I demonstrate how such mutational robustness can prevent the discovery of genetic disease ...   [More]
Waldor, M. K., Tyson, G., Borenstein, E., Ochman, H., Moeller, A., Finlay, B. B., Kong, H. H., Gordon, J. I., Nelson, K. E., Dabbagh, K., Smith, H. (2015). "Where Next for Microbiome Research?." PLOS Biology 13(1)
The development of high-throughput sequencing technologies has transformed our capacity to investigate the composition and dynamics of the microbial communities that populate diverse habitats. Over the past decade, these advances have yielded an avalanche of metagenomic data. The current stage ...   [More]
Wang, W. L., Machta, J., Katzgraber, H. G. (2015). "Comparing Monte Carlo methods for finding ground states of Ising spin glasses: Population annealing, simulated annealing, and parallel tempering." Physical Review E 92(1)
Population annealing is a Monte Carlo algorithm that marries features from simulated-annealing and parallel-tempering Monte Carlo. As such, it is ideal to overcome large energy barriers in the free-energy landscape while minimizing a Hamiltonian. Thus, population-annealing Monte Carlo can be ...   [More]
Wang, WL; Machta, J; Katzgraber, HG (2015). "Chaos in spin glasses revealed through thermal boundary conditions." Physical Review B 92(9)
We study the fragility of spin glasses to small temperature perturbations numerically using population annealing Monte Carlo. We apply thermal boundary conditions to a three-dimensional Edwards-Anderson Ising spin glass. In thermal boundary conditions all eight combinations of periodic versus antiperiodic ...   [More]
Wani, P. S., Rowland, M. A., Ondracek, A;., Deeds, E. J., Roelofs, J. (2015). "Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association." Nature Communications 6
Proteasome assembly is a complex process, requiring 66 subunits distributed over several subcomplexes to associate in a coordinated fashion. Ten proteasome-specific chaperones have been identified that assist in this process. For two of these, the Pba1-Pba2 dimer, it is well ...   [More]
Warren, A. L., Bhat, U., Sattenspiel, L., Swedlund, A. C., Gumerman, G. J. (2015). "Exploring the effects of constant versus age-specific fertility rates on prehistoric population estimates." American Journal of Physical Anthropology 156(60):320
Summary: Many fundamental questions about the prehistory of the American Southwest require accurate estimates of population size and other demographic parameters in order to be investigated properly. The Artificial Anasazi model and its successor, Artificial Long House Valley, are agent-based ...   [More]
Weigel, M., Katzgraber, H. G., Machta, J., Hamze, F., Andrist, R. S. (2015). "Glassy Chimeras could be blind to quantum speedup: Designing better benchmarks for quantum annealing machines." Physical Review X 5(1)
Abstract to the working paper version: Recently, a programmable quantum annealing machine has been built that minimizes the cost function of hard optimization problems by adiabatically quenching quantum fluctuations. Tests performed by different research teams have shown that, indeed, the ...   [More]
Weis, S., Knauf, A., Ay, N., Zhao, M. J. (2015). "Maximizing the Divergence from a Hierarchical Model of Quantum States." Open Systems & Information Dynamics 22(1)
We study many-party correlations quantified in terms of the Umegaki relative entropy (divergence) from a Gibbs family known as a hierarchical model. We derive these quantities from the maximum-entropy principle which was used earlier to define the closely related irreducible ...   [More]
Wells, C., Yamin, D., Ndeffo-Mbah, M. L., Wenzel, N. S., Gaffney, S. G., Townsend, J. P., Meyers, L. A., Fallah, M., Nyenswah, T. G., Altice, F. L., Atkins, K. E., Galvani, A. P. (2015). "Harnessing Case Isolation and Ring Vaccination to Control Ebola." PLoS Neglected Tropical Diseases 9(5)
As a devastating Ebola outbreak in West Africa continues, non-pharmaceutical control measures including contact tracing, quarantine, and case isolation are being implemented. In addition, public health agencies are scaling up efforts to test and deploy candidate vaccines. Given the experimental ...   [More]
West, G. B.. "Theory of Everything". In This Idea Must Die: Scientific Theories That Are Blocking Progress, 1-4. Harper Perennial, 2015  [More]
Witt, K. E., Judd, K., Kitchen, A., Grier, C., Kohler, T. A., Ortman, S. G., Kemp, B. M., Malhi, R. S. (2015). "DNA analysis of ancient dogs of the Americas: Identifying possible founding haplotypes and reconstructing population histories." Journal of Human Evolution 79:105-118
As dogs have traveled with humans to every continent, they can potentially serve as an excellent proxy when studying human migration history. Past genetic studies into the origins of Native American dogs have used portions of the hypervariable region (HVR) ...   [More]
Wong, C. Y., Wilk, G., Cirto, L. J. L., Tsallis, C. (2015). "From QCD-based hard-scattering to nonextensive statistical mechanical descriptions of transverse momentum spectra in high-energy pp and p(p)over-bar collisions." Physical Review D 91(11)
Transverse spectra of both jets and hadrons obtained in high-energy pp and p (p) over bar collisions at central rapidity exhibit power-law behavior of 1/p(T)(n) at high p(T). The power index n is 4-5 for jet production and is 6-10 ...   [More]
Wood, SA; Russell, R; Hanson, D; Williams, RJ; Dunne, JA (2015). "Effects of spatial scale of sampling on food web structure." Ecology and Evolution 5(17):3769-3782
This study asks whether the spatial scale of sampling alters structural properties of food webs and whether any differences are attributable to changes in species richness and connectance with scale. Understanding how different aspects of sampling effort affect ecological network ...   [More]
Xu, C; Holmgren, M; Van Nes, EH; Maestre, FT; Soliveres, S; Berdugo, M; Kefi, S; Marquet, PA; Abades, S; Scheffer, M (2015). "Can we infer plant facilitation from remote sensing? a test across global drylands." Ecological Applications 25(6):1456-1462
Facilitation is a major force shaping the structure and diversity of plant communities in terrestrial ecosystems. Detecting positive plant-plant interactions relies on the combination of field experimentation and the demonstration of spatial association between neighboring plants. This has often restricted ...   [More]
Yeakel, J. D., Dunne, J. A. (2015). "Modern Lessons from Ancient Food Webs." American Scientist 103(3):188-195
Just as some bridges are "fracture critical," meaning the failure of one component can lead to the entire structure's collapse, some animal communities are more susceptible to mass extinction after losing a single or a few species. Yeakel and Dunne ...   [More]
Yeakel, J. D., Mangel, M. (2015). "A generalized perturbation approach for exploring stock recruitment relationships." Theoretical Ecology 8(1):1-13
Models of stock-recruitment relationships (SRRs) are often used to predict fish population dynamics. Commonly used SRRs include the Ricker, Beverton-Holt, and Cushing functional forms, which differ primarily by the degree of density-dependent effects (compensation). The degree of compensation determines whether ...   [More]
Yeakel, J. D., Pires, M. M., Rudolf, L., Dominy, N. J., Koch, P. L., Guimaraes, P. R., Grossc, T. (2015). "Reply to Evans and Bar-Oz et al.: Recovering ecological pattern and process in Ancient Egypt." PNAS 112(3):E240
Extract: Our recent paper used artistic depictions of animals and fossil evidence to examine the community-level effects of local extinction events over 6,000 y of Egyptian history (1). We found that local extinctions were nonrandom, that changes to community structure ...   [More]
Yoder, M. R., Rundle, J. B. (2015). "Record-Breaking Intervals: Detecting Trends in the Incidence of Self-Similar Earthquake Sequences." Pure and Applied Geophysics 172(8):2215-2235
We introduce a method of resolving temporal incidence trends in earthquake sequences. We have developed a catalog partitioning method based on canonical earthquake scaling relationships, and have further developed a metric based on record-breaking interval (RBI) statistics to resolve increasing ...   [More]
Yoder, M. R., Rundle, J. B., Glasscoe, M. T. (2015). "Near-Field ETAS Constraints and Applications to Seismic Hazard Assessment." Pure and Applied Geophysics 172(8):2277-2293
The epidemic type aftershock sequence (ETAS) statistical model of aftershock seismicity combines various earthquake scaling relations to produce synthetic earthquake catalogs, or estimates of aftershock seismicity rates, based on recent earthquake activity. One challenge to ETAS-based hazard assessment is the ...   [More]
Youn, H. J., Strumsky, D., Bettencourt, L. M. A., Lobo, J. (2015). "Invention as a combinatorial process: evidence from US patents." Journal of the Royal Society Interface 12(106)
Invention has been commonly conceptualized as a search over a space of combinatorial possibilities. Despite the existence of a rich literature, spanning a variety of disciplines, elaborating on the recombinant nature of invention, we lack a formal and quantitative characterization ...   [More]
Zhang, P. (2015). "Nonbacktracking Operator for the Ising Model and Its Applications in Systems with Multiple States." Physical Review 91(4)
The nonbacktracking operator for a graph is the adjacency matrix defined on directed edges of the graph. The operator was recently shown to perform optimally in spectral clustering in sparse synthetic graphs and have a deep connection to belief propagation ...   [More]
Zhu, Z., Ochoa, A. J., Katzgraber, H. G. (2015). "Efficient Cluster Algorithm for Spin Glasses in Any Space Dimension." Physical Review Letters 115(7)
Spin systems with frustration and disorder are notoriously difficult to study, both analytically and numerically. While the simulation of ferromagnetic statistical mechanical models benefits greatly from cluster algorithms, these accelerated dynamics methods remain elusive for generic spin-glass-like systems. Here, we ...   [More]
zu Siederdissen, C. H., Hofacker, I. L., Stadler, P. F. (2015). "Product Grammars for Alignment and Folding." IEEE-ACM Transactions on Computational Biology and Bioinformatics 12(3):507-519
We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple "atomic" grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search ...   [More]
Zwart, M. P., Elena, S. F. (2015). "Testing the Independent Action Hypothesis of Plant Pathogen Mode of Action: A Simple and Powerful New Approach." Phytopathology 105(1):18-25
The independent action hypothesis is a simple model of pathogen infection that can make many useful predictions on infection kinetics and, therefore, a number of different tests of independent action have been developed. However, some of these analyses are rather ...   [More]
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