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Synthetic biological networks

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics.

 

Synthetic biological networks

Eric Archer and Gürol M Süel 2013 Rep. Prog. Phys. 76 096602

http://dx.doi.org/10.1088/0034-4885/76/9/096602

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The Rise and Fall of R&D Networks

Drawing on a large database of publicly announced R&D alliances, we track the evolution of R&D networks in a large number of economic sectors over a long time period (1986-2009). Our main goal is to evaluate temporal and sectoral robustness of the main statistical properties of empirical R&D networks. By studying a large set of indicators, we provide a more complete description of these networks with respect to the existing literature. We find that most network properties are invariant across sectors. In addition, they do not change when alliances are considered independently of the sectors to which partners belong. Moreover, we find that many properties of R&D networks are characterized by a rise-and-fall dynamics with a peak in the mid-nineties. Finally, we show that such properties of empirical R&D networks support predictions of the recent theoretical literature on R&D network formation.

 

The Rise and Fall of R&D Networks
Mario Vincenzo Tomasello, Mauro Napoletano, Antonios Garas, Frank Schweitzer

http://arxiv.org/abs/1304.3623

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The Social Life of Genes: Shaping Your Molecular Composition

The Social Life of Genes: Shaping Your Molecular Composition | Papers | Scoop.it

Your DNA is not a blueprint. Day by day, week by week, your genes are in a conversation with your surroundings. Your neighbors, your family, your feelings of loneliness: They don’t just get under your skin, they get into the control rooms of your cells. Inside the new social science of genetics.

 

http://www.psmag.com/health/the-social-life-of-genes-64616/

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The role of information diffusion in the evolution of social networks

Every day millions of users are connected through online social networks, generating a rich trove of data that allows us to study the mechanisms behind human interactions. Triadic closure has been treated as the major mechanism for creating social links: if Alice follows Bob and Bob follows Charlie, Alice will follow Charlie. Here we present an analysis of longitudinal micro-blogging data, revealing a more nuanced view of the strategies employed by users when expanding their social circles. While the network structure affects the spread of information among users, the network is in turn shaped by this communication activity. This suggests a link creation mechanism whereby Alice is more likely to follow Charlie after seeing many messages by Charlie. We characterize users with a set of parameters associated with different link creation strategies, estimated by a Maximum-Likelihood approach. Triadic closure does have a strong effect on link formation, but shortcuts based on traffic are another key factor in interpreting network evolution. However, individual strategies for following other users are highly heterogeneous. Link creation behaviors can be summarized by classifying users in different categories with distinct structural and behavioral characteristics. Users who are popular, active, and influential tend to create traffic-based shortcuts, making the information diffusion process more efficient in the network.

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A new fast algorithm for solving the minimum spanning tree problem based on DNA molecules computation

In this paper, we present a new fast DNA algorithm for solving the minimum spanning tree problem using DNA molecular operations.

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Consciousness in humans and non-human animals: Recent advances and future directions

This joint article reflects the authors’ personal views regarding noteworthy advances in the neuroscience of consciousness in the last ten years, and suggests what we feel may be promising future directions. (...) we summarize recent advances in our understanding of subjectivity in humans and other animals, including empirical, applied, technical and conceptual insights. These include the evidence for the importance of fronto-parietal connectivity and of feedback processes, both of which enable information to travel across distant cortical areas effectively, as well as numerous dissociations between consciousness and cognitive functions, such as attention, in humans. In addition, we describe the development of mental imagery paradigms, which made it possible to identify covert awareness in non-responsive subjects. Non-human animal consciousness research has also witnessed substantial advances on the specific role of cortical areas and higher order thalamus for consciousness, thanks to important technological advances. In addition, much progress has been made in the understanding of non-vertebrate cognition relevant to possible conscious states. Finally, major advances have been made in theories of consciousness, and also in their comparison with the available evidence. Along with reviewing these findings, each author suggests future avenues for research in their field of investigation.

 

Consciousness in humans and non-human animals: Recent advances and future directions.
Melanie Boly, Anil K. Seth, Melanie Wilke, Paul Ingmundson, Bernard Baars, Steven Laureys, David Edelman and Naotsugu Tsuchiya

Front. Psychol. | http://dx.doi.org/10.3389/fpsyg.2013.00625

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Miguel Garcia's curator insight, August 30, 2013 11:14 AM

I like the development of mental imagery paradigms as a key to subjectivity. 

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Joys of Noise

Joys of Noise | Papers | Scoop.it

In engineering, uncertainty is usually as welcome as sand in a salad. The development of digital technologies, from the alphabet to the DVD, has been driven in large part by the desire to eliminate random fluctuations, or noise, inherent in analog systems like speech or VHS tapes. But randomness also has a special ability to make some systems work better. Here are five cases where a little chaos is a critical part of the plan (...)

 

http://nautil.us/issue/2/uncertainty/joys-of-noise

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ECAL '93 Proceedings online (2nd European Conference on Artificial Life)

ECAL '93 Proceedings online (2nd European Conference on Artificial Life) | Papers | Scoop.it

Proceedings first published on the web in August, 2013. The original proceedings of the conference were distributed in hard-copy to attendees but were not published more widely. The proceedings published on the web comprise scanned copies of the original hard-copy papers. Thanks to Barry McMullin for providing a copy of the original proceedings for scanning. The scanning was performed by Tim Taylor in July 2013.

 

http://alife.org/ecal93/proceedings

Complexity Digest's insight:

Several interesting "early" papers by Bedau, Bonabeau, Camazine, Floreano, Franks, Huberman, Ikegami, Luisi, Matarić, McMullin, Merelo, Millonas, Miramontes, Nolfi, Nowak, Pfeifer, Thornton, Todd, Webb, Weisbuch, Wuensche, and many more.

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Sentiment in New York City: A High Resolution Spatial and Temporal View

Sentiment in New York City: A High Resolution Spatial and Temporal View | Papers | Scoop.it

Measuring public sentiment is a key task for researchers and policymakers alike. The explosion of available social media data allows for a more time-sensitive and geographically specific analysis than ever before. In this paper we analyze data from the micro-blogging site Twitter and generate a sentiment map of New York City. We develop a classifier specifically tuned for 140-character Twitter messages, or tweets, using key words, phrases and emoticons to determine the mood of each tweet. This method, combined with geotagging provided by users, enables us to gauge public sentiment on extremely fine-grained spatial and temporal scales. We find that public mood is generally highest in public parks and lowest at transportation hubs, and locate other areas of extreme sentiment such as cemeteries, medical centers, a jail, and a sewage facility. Sentiment progressively improves with proximity to Times Square. Periodic patterns of sentiment fluctuate on both a daily and a weekly scale: more positive tweets are posted on weekends than on weekdays, with a daily peak in sentiment around midnight and a nadir between 9:00 a.m. and noon.

 

K.Z. Bertrand, M. Bialik, K. Virdee, A. Gros, Y. Bar-Yam, Sentiment in New York City: A High Resolution Spatial and Temporal View. NECSI Report 2013-08-01 (08/20/2013).

http://necsi.edu/research/social/newyork/

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Emergence of structural and dynamical properties of ecological mutualistic networks

Cooperation among species tends to result in mutualistic networks with a nested structure, which is thought to increase biodiversity and persistence but may be less stable than unstructured networks: here nested networks are shown to result from a mechanism that maximizes species abundances in mutualistic communities, and the abundance of nested species is found to be directly linked to the resilience of the community.

 

Emergence of structural and dynamical properties of ecological mutualistic networks
Samir Suweis, Filippo Simini, Jayanth R. Banavar & Amos Maritan

Nature 500, 449–452 (22 August 2013) http://dx.doi.org/10.1038/nature12438

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Mom Knows Best: The Universality of Maternal Microbial Transmission

Mom Knows Best: The Universality of Maternal Microbial Transmission | Papers | Scoop.it

The sterile womb paradigm is an enduring premise in biology that human infants are born sterile. Recent studies suggest that infants incorporate an initial microbiome before birth and receive copious supplementation of maternal microbes through birth and breastfeeding. Moreover, evidence for microbial maternal transmission is increasingly widespread across animals. This collective knowledge compels a paradigm shift—one in which maternal transmission of microbes advances from a taxonomically specialized phenomenon to a universal one in animals. It also engenders fresh views on the assembly of the microbiome, its role in animal evolution, and applications to human health and disease.

 

Funkhouser LJ, Bordenstein SR (2013) Mom Knows Best: The Universality of Maternal Microbial Transmission. PLoS Biol 11(8): e1001631. http://dx.doi.org/10.1371/journal.pbio.1001631

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International Co-authorship Relations in the Social Science Citation Index: Is Internationalization Leading the Network?

We analyze international co-authorship relations in the Social Science Citation Index 2011 using all citable items in the DVD-version of this index. Network statistics indicate four groups of nations: (i) an Asian-Pacific one to which all Anglo-Saxon nations (including the UK and Ireland) are attributed; (ii) a continental European one including also the Latin-American countries; (iii) the Scandinavian nations; and (iv) a community of African nations. Within the EU-28 (including Croatia), eleven of the EU-15 states have dominant positions. Collapsing the EU-28 into a single node leads to a bi-polar structure between the US and EU-28; China is part of the US-pole. We develop an information-theoretical test to distinguish whether international collaborations or domestic collaborations prevail; the results are mixed, but the international dimension is more important than the national one in the aggregated sets (this was found in both SSCI and SCI). In France, however, the national distribution is more important than the international one, while the reverse is true for most European nations in the core group (UK, Germany, the Netherlands, etc.). Decomposition of the USA in terms of states shows a similarly mixed result; more US states are domestically oriented in SSCI, whereas more internationally in SCI. The international networks have grown during the last decades in addition to the national ones, but not by replacing them.

 

International Co-authorship Relations in the Social Science Citation Index: Is Internationalization Leading the Network?
Loet Leydesdorff, Han Woo Park, Caroline Wagner

http://arxiv.org/abs/1305.4242

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Estimating the tolerance of species to the effects of global environmental change

Global environmental change is affecting species distribution and their interactions with other species. In particular, the main drivers of environmental change strongly affect the strength of interspecific interactions with considerable consequences to biodiversity. However, extrapolating the effects observed on pair-wise interactions to entire ecological networks is challenging. Here we propose a framework to estimate the tolerance to changes in the strength of mutualistic interaction that species in mutualistic networks can sustain before becoming extinct. We identify the scenarios where generalist species can be the least tolerant. We show that the least tolerant species across different scenarios do not appear to have uniquely common characteristics. Species tolerance is extremely sensitive to the direction of change in the strength of mutualistic interaction, as well as to the observed mutualistic trade-offs between the number of partners and the strength of the interactions.

 

Estimating the tolerance of species to the effects of global environmental change
Serguei Saavedra, Rudolf P. Rohr, Vasilis Dakos, Jordi Bascompte

http://arxiv.org/abs/1308.3584

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Is the Voter Model a model for voters?

The voter model has been studied extensively as a paradigmatic opinion dynamics' model. However, its ability for modeling real opinion dynamics has not been addressed. We introduce a noisy voter model (accounting for social influence) with agents' recurrent mobility (as a proxy for social context), where the spatial and population diversity are taken as inputs to the model. We show that the dynamics can be described as a noisy diffusive process that contains the proper anysotropic coupling topology given by population and mobility heterogeneity. The model captures statistical features of the US presidential elections as the stationary vote-share fluctuations across counties, and the long-range spatial correlations that decay logarithmically with the distance. Furthermore, it recovers the behavior of these properties when a real-space renormalization is performed by coarse-graining the geographical scale from county level through congressional districts and up to states. Finally, we analyze the role of the mobility range and the randomness in decision making which are consistent with the empirical observations.

 

Is the Voter Model a model for voters?
Juan Fernández-Gracia, Krzysztof Suchecki, José J. Ramasco, Maxi San Miguel, Víctor M. Eguíluz

http://arxiv.org/abs/1309.1131

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Using a complex system approach to address world challenges in Food and Agriculture

World food supply is crucial to the well-being of every human on the planet in the basic sense that we need food to live. It also has a profound impact on the world economy, international trade and global political stability. Furthermore, consumption of certain types and amounts foods can affect health, and the choice of livestock and plants for food production can impact sustainable use of global resources. There are communities where insufficient food causes nutritional deficiencies, and at the same time other communities eating too much food leading to obesity and accompanying diseases. These aspects reflect the utmost importance of agricultural production and conversion of commodities to food products. Moreover, all factors contributing to the food supply are interdependent, and they are an integrative part of the continuously changing, adaptive and interdependent systems in the world around us. The properties of such interdependent systems usually cannot be inferred from the properties of its parts. In addressing current challenges, like the apparent incongruences of obesity and hunger, we have to account for the complex interdependencies among areas such as physics and sociology. This is possible using the complex system approach. It encompasses an integrative multi-scale and inter-disciplinary approach. Using a complex system approach that accounts for the needs of stakeholders in the agriculture and food domain, and determines which research programs will enable these stakeholders to better anticipate emerging developments in the world around them, will enable them to determine effective intervention strategies to simultaneously optimise and safeguard their interests and the interests of the environment.

 

Using a complex system approach to address world challenges in Food and Agriculture
H.G.J. van Mil, E.A. Foegeding, E.J. Windhab, N. Perrot, E. van der Linden

http://arxiv.org/abs/1309.0614

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Virality Prediction and Community Structure in Social Networks

Virality Prediction and Community Structure in Social Networks | Papers | Scoop.it
How does network structure affect diffusion? Recent studies suggest that the answer depends on the type of contagion. Complex contagions, unlike infectious diseases (simple contagions), are affected by social reinforcement and homophily.
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The evolution of genetic architectures underlying quantitative traits

In the classic view introduced by R. A. Fisher, a quantitative trait is encoded by many loci with small, additive effects. Recent advances in quantitative trait loci mapping have begun to elucidate the genetic architectures underlying vast numbers of phenotypes across diverse taxa, producing observations that sometimes contrast with Fisher's blueprint.

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From the digital divide to inclusive innovation

In this report, the authors investigate one of the radical and rapid transformations in the commercial world: the rise of digital money. As well as highlighting the profound changes already wrought, their analysis paves the way for a future in which digital money could be used to address some of the most severe marginalisation and deprivation that exists within the global economy.

 

http://www.thersa.org/action-research-centre/enterprise-and-design/enterprise/reports/from-the-digital-divide-to-inclusive-innovation

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How big data is changing the world

How big data is changing the world | Papers | Scoop.it

You may not be that bothered about the idea of living in a smart city but I bet you'd love to live in one that was happy.

 

Tomorrow's cities: How big data is changing the world
By Jane Wakefield

http://www.bbc.co.uk/news/technology-23253949

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The Simple Rules of Social Contagion

It is commonly believed that information spreads between individuals like a pathogen, with each exposure by an informed friend potentially resulting in a naive individual becoming infected. However, empirical studies of social media suggest that individual response to repeated exposure to information is significantly more complex than the prediction of the pathogen model. As a proxy for intervention experiments, we compare user responses to multiple exposures on two different social media sites, Twitter and Digg. We show that the position of the exposing messages on the user-interface strongly affects social contagion. Accounting for this visibility significantly simplifies the dynamics of social contagion. The likelihood an individual will spread information increases monotonically with exposure, while explicit feedback about how many friends have previously spread it increases the likelihood of a response. We apply our model to real-time forecasting of user behavior.

 

The Simple Rules of Social Contagion
Nathan O. Hodas, Kristina Lerman

http://arxiv.org/abs/1308.5015

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António F Fonseca's curator insight, December 23, 2013 7:12 AM

Another paper about information propagation. A study on the user interface of two social sites, mainly the problem of limited attention and attention managment.

Claude Emond's curator insight, September 23, 3:52 PM

A contagious feel-good-ness :)

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The Man Who Invented Modern Probability

The Man Who Invented Modern Probability | Papers | Scoop.it

For Kolmogorov, his ideas neither eliminated chance, nor affirmed a fundamental uncertainty about our world; they simply provided a rigorous language to talk about what cannot be known for certain. The notion of “absolute randomness” made no more sense than “absolute determinism,” he once remarked, concluding, “We can’t have positive knowledge of the existence of the unknowable.” Thanks to Kolmogorov, though, we can explain when and why we don’t.

 

http://nautil.us/issue/4/the-unlikely/the-man-who-invented-modern-probability

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Understanding metropolitan patterns of daily encounters

Understanding of the mechanisms driving our daily face-to-face encounters is still limited; the field lacks large-scale datasets describing both individual behaviors and their collective interactions. However, here, with the help of travel smart card data, we uncover such encounter mechanisms and structures by constructing a time-resolved in-vehicle social encounter network on public buses in a city (about 5 million residents). Using a population scale dataset, we find physical encounters display reproducible temporal patterns, indicating that repeated encounters are regular and identical. On an individual scale, we find that collective regularities dominate distinct encounters’ bounded nature. An individual’s encounter capability is rooted in his/her daily behavioral regularity, explaining the emergence of “familiar strangers” in daily life. Strikingly, we find individuals with repeated encounters are not grouped into small communities, but become strongly connected over time, resulting in a large, but imperceptible, small-world contact network or “structure of co-presence” across the whole metropolitan area. Revealing the encounter pattern and identifying this large-scale contact network are crucial to understanding the dynamics in patterns of social acquaintances, collective human behaviors, and—particularly—disclosing the impact of human behavior on various diffusion/spreading processes.

 

Understanding metropolitan patterns of daily encounters
Lijun Sun, Kay W. Axhausen, Der-Horng Lee, and Xianfeng Huang

http://dx.doi.org/10.1073/pnas.1306440110
PNAS August 20, 2013 vol. 110 no. 34 13774-13779

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The Health Risk of Obesity—Better Metrics Imperative

Obesity has increased worldwide; is a major risk factor for diabetes, cardiovascular disease, cancer, sleep apnea, nonalcoholic fatty liver disease, osteoarthritis, and other ailments; and has been associated with disability, mortality, and enormous health costs (1, 2). Despite these clear adverse consequences of obesity, some studies have suggested that obesity as defined by body mass index (BMI) improves survival under certain conditions (3–8). Here, we discuss the controversies surrounding the “obesity-mortality paradox” and offer potential mechanisms to explain the effects of obesity on health.

 

The Health Risk of Obesity—Better Metrics Imperative
Rexford S. Ahima, Mitchell A. Lazar

Science 23 August 2013:
Vol. 341 no. 6148 pp. 856-858
http://dx.doi.org/10.1126/science.1241244

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The relationship between obesity and disease is clearly nonlinear: there are healthy overweight people and also ill people with a normal weight.

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A place-focused model for social networks in cities

The focused organization theory of social ties proposes that the structure of human social networks can be arranged around extra-network foci, which can include shared physical spaces such as homes, workplaces, restaurants, and so on. Until now, this has been difficult to investigate on a large scale, but the huge volume of data available from online location-based social services now makes it possible to examine the friendships and mobility of many thousands of people, and to investigate the relationship between meetings at places and the structure of the social network. In this paper, we analyze a large dataset from Foursquare, the most popular online location-based social network. We examine the properties of city-based social networks, finding that they have common structural properties, and that the category of place where two people meet has very strong influence on the likelihood of their being friends. Inspired by these observations in combination with the focused organization theory, we then present a model to generate city-level social networks, and show that it produces networks with the structural properties seen in empirical data.

 

A place-focused model for social networks in cities
Chloë Brown, Anastasios Noulas, Cecilia Mascolo, Vincent Blondel

http://arxiv.org/abs/1308.2565

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The Limits of Phenomenology: From Behaviorism to Drug Testing and Engineering Design

It is widely believed that theory is useful in physics because it describes simple systems and that strictly empirical phenomenological approaches are necessary for complex biological and social systems. Here we prove based upon an analysis of the information that can be obtained from experimental observations that theory is even more essential in the understanding of complex systems. Implications of this proof revise the general understanding of how we can understand complex systems including the behaviorist approach to human behavior, problems with testing engineered systems, and medical experimentation for evaluating treatments and the FDA approval of medications. Each of these approaches are inherently limited in their ability to characterize real world systems due to the large number of conditions that can affect their behavior. Models are necessary as they can help to characterize behavior without requiring observations for all possible conditions. The testing of models by empirical observations enhances the utility of those observations. For systems for which adequate models have not been developed, or are not practical, the limitations of empirical testing lead to uncertainty in our knowledge and risks in individual, organizational and social policy decisions. These risks should be recognized and inform our decisions.

 

The Limits of Phenomenology: From Behaviorism to Drug Testing and Engineering Design
Yaneer Bar-Yam

http://arxiv.org/abs/1308.3094

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