Emergence,Evolution and Scaling of Online Social Networks

Online social networks have become increasingly ubiquitous and understanding their structural, dynamical, and scaling properties not only is of fundamental interest but also has a broad range of applications. Such networks can be extremely dynamic, generated almost instantaneously by, for example, breaking-news items. We investigate a common class of online social networks, the user-user retweeting networks, by analyzing the empirical data collected from Sina Weibo (a massive twitter-like microblogging social network in China) with respect to the topic of the 2011 Japan earthquake. We uncover a number of algebraic scaling relations governing the growth and structure of the network and develop a probabilistic model that captures the basic dynamical features of the system. The model is capable of reproducing all the empirical results. Our analysis not only reveals the basic mechanisms underlying the dynamics of the retweeting networks, but also provides general insights into the control of information spreading on such networks.     

The Stability of Cellulose: A Statistical Perspective from a Coarse-Grained Model of Hydrogen-Bond Networks

A critical roadblock to the production of biofuels from lignocellulosic biomass is the efficient degradation of crystalline microfibrils of cellulose to glucose. A microscopic understanding of how different physical conditions affect the overall stability of the crystalline structure of microfibrils could facilitate the design of more effective protocols for their degradation. One of the essential physical interactions that stabilizes microfibrils is a network of hydrogen (H) bonds: both intrachain H-bonds between neighboring monomers of a single cellulose polymer chain and interchain H-bonds between adjacent chains. We construct a statistical mechanical model of cellulose assembly at the resolution of explicit hydrogen-bond networks. Using the transfer matrix method, the partition function and the subsequent statistical properties are evaluated. With the help of this lattice-based model, we capture the plasticity of the H-bond network in cellulose due to frustration and redundancy in the placement of H-bonds. This plasticity is responsible for the stability of cellulose over a wide range of temperatures. Stable intrachain and interchain H-bonds are identified as a function of temperature that could possibly be manipulated toward rational destruction of crystalline cellulose.     

Expanding Metabolic Networks: Scopes of Compounds, Robustness, and Evolution

A new method for the mathematical analysis of large metabolic networks is presented. Based on the fact that the occurrence of a metabolic reaction generally requires the existence of other reactions providing its substrates, series of metabolic networks are constructed. In each step of the corresponding expansion process those reactions are incorporated whose substrates are made available by the networks of the previous generations. The method is applied to the set of all metabolic reactions included in the KEGG database. Starting with one or more seed compounds, the expansion results in a final network whose compounds define the scope of the seed. Scopes of all metabolic compounds are calculated and it is shown that large parts of cellular metabolism can be considered as the combined scope of simple building blocks. Analyses of various expansion processes reveal crucial metabolites whose incorporation allows for the increase in network complexity. Among these metabolites are common cofactors such as NAD⁺, ATP, and coenzyme A. We demonstrate that the outcome of network expansion is in general very robust against elimination of single or few reactions. There exist, however, crucial reactions whose elimination results in a dramatic reduction of scope sizes. It is hypothesized that the expansion process displays characteristics of the evolution of metabolism such as the temporal order of the emergence of metabolic pathways. [Reviewing Editor : Dr. David Pollock]     

Evolution of Diversity, Efficiency, and Community Stability

The response in species diversity associated with successionalchange in vegetation, or in a more general sense, species diversityas a function of time in any system of primary producers, hasbeen the subject of much speculation but little direct study.All evidence available shows that pioneer communities are lowin diversity, that in mesic environments the peak in diversityin forest communities can be expected 100-200 years after theinitiation of a secondary successional sequence (when elementsof both the pioneer and the stable communities are present),and that a downturn in both diversity and primary productiontakes place when the entire community is made up of the shade-tolerantclimax species. The natural tendency in forest systems toward periodic perturbation(at intervals of 50-200 years) recycles the system and maintainsa periodic wave of peak diversity. This wave is associated witha corresponding wave in peak primary production. Specializationfor the habitats in the early, middle, and later phases of thecycle has figured prominently in species-isolating mechanisms,giving rise to the diversity in each stage of the forest succession.It is concluded that any modifications of the system that precludeperiodic, random perturbation and recycling would be detrimentalto the system in the long run.     

Myelodysplasia: Problems of Long-Term Survival and Social Function

Problems of ninety-eight patients with myelodysplasia, ages 13 to 72, were reviewed. They were grouped as follows: Those having thoracic and high lumbar level (L₂↑) lesions and confined to wheel chairs, those with intermediate paralysis (L_3-5 nerve roots) as walking with aids and those with less paralysis (S₁↓) as fully ambulatory. Fifty-two percent of the L₂↑ and only 15 percent of of the less severely paralyzed patients were retarded below an IQ level 70 (P<0.01). Thirty-six patients (62 percent) were fully and 26 partially, but appropriately, self-sufficient. Thirty-six patients were found in some form of dependent care. Two of the 71 more paralyzed patients (L_3-5 and L₂↑) and five of the 28 S₁↓ patients were “naturally continent” but reported stress incontinence of urine. Thirteen of 23 female and five of 28 male patients between ages 16 and 72 years reported sexual activity and accounted for 17 normal offspring. All 23 retarded patients were in some form of custodial care. Dependency among the normal intellect patients could be attributed to neglect of physically deforming complications and emotional disorders, primarily low self-esteem centering around social and sexual identity problems associated with excrement soiling.     

Reproductive Flexibility: Genetic Variation,Genetic Costs and Long-Term Evolution in a Collembola

In a variable yet predictable world, organisms may use environmental cues to make adaptive adjustments to their phenotype. Such phenotypic flexibility is expected commonly to evolve in life history traits, which are closely tied to Darwinian fitness. Yet adaptive life history flexibility remains poorly documented. Here we introduce the collembolan Folsomia candida, a soil-dweller, parthenogenetic (all-female) microarthropod, as a model organism to study the phenotypic expression, genetic variation, fitness consequences and long-term evolution of life history flexibility. We demonstrate that collembola have a remarkable adaptive ability for adjusting their reproductive phenotype: when transferred from harsh to good conditions (in terms of food ration and crowding), a mother can fine-tune the number and the size of her eggs from one clutch to the next. The comparative analysis of eleven clonal populations of worldwide origins reveals (i) genetic variation in mean egg size under both good and bad conditions; (ii) no genetic variation in egg size flexibility, consistent with convergent evolution to a common physiological limit; (iii) genetic variation of both mean reproductive investment and reproductive investment flexibility, associated with a reversal of the genetic correlation between egg size and clutch size between environmental conditions ; (iv) a negative genetic correlation between reproductive investment flexibility and adult lifespan. Phylogenetic reconstruction shows that two life history strategies, called HIFLEX and LOFLEX, evolved early in evolutionary history. HIFLEX includes six of our 11 clones, and is characterized by large mean egg size and reproductive investment, high reproductive investment flexibility, and low adult survival. LOFLEX (the other five clones) has small mean egg size and low reproductive investment, low reproductive investment flexibility, and high adult survival. The divergence of HIFLEX and LOFLEX could represent different adaptations to environments differing in mean quality and variability, or indicate that a genetic polymorphism of reproductive investment reaction norms has evolved under a physiological tradeoff between reproductive investment flexibility and adult lifespan.     

The Evolution of Evolution: Reconciling the Problem of Stability

Evolutionary Science has, at least since the publication of Origin, been less concerned with the continuation of species in stable forms, than with the reconfiguration of forms into a host of varieties. So influential has this emphasis been that, over the years, “variation” has become a cardinal desideratum, even taking precedence over the macroevolutionary landscape. This orientation has made it much more difficult to objectively assess the meaning of non-change patterns such as periods of stasis, which appear to be widespread in most species. Yet, if stasis is an expectable outcome of evolutionary activity, this raises the possibility that there may be mechanisms and processes at many causal levels, acting on its behalf, without reference to the impetus toward persistent variation. Researchers have been reluctant to attribute stasis to a macroevolutionary tendency toward ‘stability’ despite the commonality of stasis in many species, and notwithstanding the many biological/behavioral processes that seem inclined to produce and maintain conformance, regulation and consistency. Speciation, paradoxically, is the best evidence for an overriding influence toward stability in that stability would seem to be a necessary condition prior to the development of isolating mechanisms. An alternative macroevolutionary model of biological activity is offered consisting of two tendencies, “variety” counterpoised with “stability” both acting in the service of the persistence of life.     

Statistical Mechanics and Thermodynamics of Viral Evolution

This paper uses methods drawn from physics to study the life cycle of viruses. The paper analyzes a model of viral infection and evolution using the "grand canonical ensemble" and formalisms from statistical mechanics and thermodynamics. Using this approach we enumerate all possible genetic states of a model virus and host as a function of two independent pressures–immune response and system temperature. We prove the system has a real thermodynamic temperature, and discover a new phase transition between a positive temperature regime of normal replication and a negative temperature “disordered” phase of the virus. We distinguish this from previous observations of a phase transition that arises as a function of mutation rate. From an evolutionary biology point of view, at steady state the viruses naturally evolve to distinct quasispecies. This paper also reveals a universal relationship that relates the order parameter (as a measure of mutational robustness) to evolvability in agreement with recent experimental and theoretical work. Given that real viruses have finite length RNA segments that encode proteins which determine virus fitness, the approach used here could be refined to apply to real biological systems, perhaps providing insight into immune escape, the emergence of novel pathogens and other results of viral evolution.     

The Structure and Evolution of Buyer-Supplier Networks

In this paper, we investigate the structure and evolution of customer-supplier networks in Japan using a unique dataset that contains information on customer and supplier linkages for more than 500,000 incorporated non-financial firms for the five years from 2008 to 2012. We find, first, that the number of customer links is unequal across firms; the customer link distribution has a power-law tail with an exponent of unity (i.e., it follows Zipf''s law). We interpret this as implying that competition among firms to acquire new customers yields winners with a large number of customers, as well as losers with fewer customers. We also show that the shortest path length for any pair of firms is, on average, 4.3 links. Second, we find that link switching is relatively rare. Our estimates indicate that the survival rate per year for customer links is 92 percent and for supplier links 93 percent. Third and finally, we find that firm growth rates tend to be more highly correlated the closer two firms are to each other in a customer-supplier network (i.e., the smaller is the shortest path length for the two firms). This suggests that a non-negligible portion of fluctuations in firm growth stems from the propagation of microeconomic shocks – shocks affecting only a particular firm – through customer-supplier chains.     

Opening the Gift: Social Inclusion, Professional Codes and Gift-Giving in Long-Term Mental Healthcare

Deinstitutionalisation has not only made the social inclusion of clients a key objective in long-term mental healthcare, it may also affect the role of the care professional. This article investigates whether the social inclusion objective clashes with other long-standing professional values, specifically when clients give gifts to care professionals. In making a typology of gifts, we compare the literature on gift-giving with professional codes for gifts and relate both to the objective of social inclusion of clients. Our typology draws on an analysis of ethnographic fieldwork carried out in 2007/2008 at a Dutch mental healthcare centre. We identify four types of gifts for professionals in long-term mental healthcare, each relating individually to professional codes and the objective of social inclusion of clients. Only the ‘personal gift’ directly supports social inclusion, by fostering personal relationships between professionals and clients. Acceptance of this type of gift is advocated only for long-term care professionals. We suggest that professional codes need to consider this typology of gifts, and we advocate promoting reflexivity as a means of accounting for professional behaviour in deinstitutionalised care settings.     

Long-Term Evolution of the Luteoviridae: Time Scale and Mode of Virus Speciation

Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic diversity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature.Although RNA viruses are the most common agents of emerging disease, key aspects of their evolution are still only partly understood. This is of both academic and practical importance, as virus evolution may compromise disease control strategies, including the rapid generation of genotypes that are able to evade host immune responses or of those that are resistant to antivirals or crop genetic resistance (20, 34, 47).Most of our knowledge of the rapidity of RNA virus evolution comes from the study of animal viruses, for which estimates of rates of nucleotide substitution normally fall within 1 order of magnitude of 1 × 10⁻³ nucleotide substitutions per site per year (subs/site/year) and largely reflect the background mutation rate (10, 13, 29, 37, 53). Equivalent studies on plant RNA viruses have reported more heterogeneous rates. Early studies suggested that some plant RNA viruses evolved more slowly than RNA viruses that infect animals. For example, estimates of the nucleotide substitution rate in the range of ∼1 × 10⁻⁶ to 1 × 10⁻⁸ subs/site/year have been obtained for Turnip yellow mosaic virus (4, 23) and some tobamoviruses (21, 25). In contrast, more recent estimates using Bayesian coalescent methods applied to sequences with known dates of sampling and allowing for rate variation among lineages have reported substitution rates in the same range as those of animal RNA viruses (22, 63) and therefore suggest relatively high rates of mutation, as expected, given the intrinsically error-prone nature of RNA replication (15, 65). As well as the differences in how these rates are estimated, a reasonable biological explanation for such a diversity of rate estimates is that they are increased in the short term due to the presence of mutational polymorphisms but lower in the long term because any such deleterious mutations would have then been removed by purifying selection (17, 22). In particular, severe population bottlenecks at transmission would allow deleterious mutations to rise to a high frequency due to strong genetic drift. Such effects make it dangerous to extrapolate long-term rates of evolutionary change from the analysis of intraspecific sequence data (31). Differences in the strength of adaptive evolution could also cause rate heterogeneity, including such processes as competition for susceptible individuals and the colonization of new host species (22, 65).Although there is a growing body of data on intraspecific evolutionary processes in plant RNA viruses, including rates of nucleotide substitution, there has been a general neglect of long-term evolutionary patterns, including the determinants of viral speciation. Exceptions are recent analyses of the Potyviridae and the Sobemovirus, which associated viral speciation with the development of agriculture (17, 24). Although RNA viruses reproduce asexually, it is informative to consider as analogies the two major forms of speciation used in studies of sexually reproducing eukaryotes: allopatric speciation, in which reproductive isolation follows geographic separation, and sympatric speciation, in which reproductive isolation occurs within an interbreeding population (67). In the context of RNA viruses, allopatric speciation can be thought of as the genetic diversification that occurs when viruses jump to new host species and thereafter evolve independently, as is commonly associated with the process of viral “emergence.” In contrast, sympatric speciation would occur when viruses diversify within a single host species, perhaps by exploiting different cell types (34). Despite the importance of these processes for our understanding of the macroevolution of RNA viruses, their respective roles are currently unknown.To better understand the nature of long-term evolutionary processes in plant RNA viruses, we undertook an extensive molecular evolutionary analysis of the family Luteoviridae, a heterogeneous family of plant viruses divided into three genera, Luteovirus, Polerovirus, and Enamovirus, containing five, nine, and one classified species, respectively, as well as a number of unclassified species (18). The Luteoviridae possess positive-sense single-stranded RNA genomes of 5,600 to 6,000 nucleotides (nt). These genomes can harbor five or six open reading frames (ORFs). 5′-proximal partially overlapping ORF1 and -2 encode proteins P1 and P2, which are involved in virus replication. Low-frequency −1 ribosomal frameshifting in the overlapping region results in the P1-P2 fusion RNA-dependent RNA polymerase protein (RdRp). ORF3 encodes the coat protein (CP) and completely contains ORF4, which is not found in Enamovirus and is needed for virus movement in the plant (the movement protein, MP). ORF5, which is necessary for aphid transmission (6, 27, 49) and is also involved in virus movement (57) and Luteoviridae phloem limitation (58), is translated through in-frame read-through of the ORF3 stop codon, existing as a read-through domain (RTD) fused to the CP. Members of the genus Polerovirus have an extra ORF0 in the 5′ end of the genome partially overlapping ORF1. Its translation product (P0) acts as a repressor of the RNA-silencing plant defense response (44, 59). Finally, some Luteovirus species have an additional ORF6 with an unknown function in the 3′ end of the genome (18, 48, 70). As a consequence of this particular genomic organization, approximately one-third of the Polerovirus genome, and a smaller fraction in the Luteovirus genome, is composed of overlapping regions.Due to their agronomic importance, gene sequence data, together with information on host range and geographical distribution, are available for a relatively large number of members of the family Luteoviridae. However, to date the only luteovirus for which rates of evolutionary change have been estimated is Barley yellow dwarf virus (BYDV). In this case, an analysis of substitution rates based on viral RNA extracted from herbarium specimens produced estimates of between 6.2 × 10⁻⁴ and 9.7 × 10⁻⁵ subs/site/year (43). Similarly, only one estimate of the point at which genetic diversity arose in the family Luteoviridae has been obtained, i.e., approximately 9,000 years ago, and therefore it is perhaps associated with the rise of agriculture (17). However, only a limited number of Luteoviridae species and sequences were included in this analysis. No studies have yet considered the mechanisms of speciation in the family Luteoviridae.The family Luteoviridae also represents a useful data set to study two other evolutionary phenomena: the pattern and determinants of recombination, which appears to be commonplace within the family Luteoviridae (26, 49, 51, 70, 71), and the differing evolutionary dynamics in genes with overlapping reading frames. There are contrasting hypotheses as to why overlapping reading frames are so commonly used in RNA viruses. According to one view, gene overlapping maximizes the genetic information in smaller genomes (1, 39). Alternatively, it has been suggested that gene overlap generates mutational robustness (i.e., the ability to preserve phenotypes despite the genomic mutational load) at the population level (2, 16, 42). Under the latter hypothesis, gene overlapping generates hypersensitivity to deleterious mutations, as these affect more than one gene. Although this hypersensitivity reduces the capacity of each individual to buffer mutation effects, it represents a selective advantage for wild-type genotypes, which then bolsters robustness at the population level (16, 42). As a consequence of this elevated burden of deleterious mutation, RNA viruses with larger proportions of their genomes present as overlapping reading frames are expected to exhibit lower rates of nucleotide substitution (41, 50). Such a rate reduction has been observed in many animal DNA and RNA viruses (for example, see references 35, 36, 55, 77, and 78), although only a few studies have considered plant RNA viruses in this context (28, 61).     

On Social and Cognitive Influences: Relating Adolescent Networks,Generalized Expectancies,and Adolescent Smoking

We examine the moderating role of friendship and school network characteristics in relationships between 1) youths’ friends smoking behavior and youths’ own generalized expectancies regarding risk and future orientation and 2) generalized expectancies of youths’ friends and youths’ own generalized expectancies. We then relate these constructs to smoking. Using a longitudinal sample from the National Longitudinal Study of Adolescent Health (N = 15,142), the relationship between friends’ generalized expectancies and youths’ expectancies is stronger for those more central in the network, with more reachability, or stronger network ties, and weaker for those with denser friendship networks. Risk expectancies exhibited an inverted U shaped relationship with smoking at the next time point, whereas future orientation expectancies displayed a nonlinear accelerating negative relationship. There was also a feedback effect in which smoking behavior led to higher risk expectancies and lower future orientation expectancies in instrumental variable analyses.     

Piecewise-linear Models of Genetic Regulatory Networks: Equilibria and their Stability

A formalism based on piecewise-linear (PL) differential equations, originally due to Glass and Kauffman, has been shown to be well-suited to modelling genetic regulatory networks. However, the discontinuous vector field inherent in the PL models raises some mathematical problems in defining solutions on the surfaces of discontinuity. To overcome these difficulties we use the approach of Filippov, which extends the vector field to a differential inclusion. We study the stability of equilibria (called singular equilibrium sets) that lie on the surfaces of discontinuity. We prove several theorems that characterize the stability of these singular equilibria directly from the state transition graph, which is a qualitative representation of the dynamics of the system. We also formulate a stronger conjecture on the stability of these singular equilibrium sets.     

Social Signals and Behaviors of Adult Alligators and Crocodiles

We compare and contrast the signalling systems and social behaviorsof Alligator mississippiensis, Crocodylus aculus, and Crocodylusmloticus. Our qualitative analysis focuses primarily on thebehaviors of adults during three phases of reproduction: I.Defense of Territory and Courtship, II. Nesting and Incubation,and III. Hatching and Post Hatching. Signals and signal elementsare very similar among the three species. For example, all havevocal, non-vocal acoustic, and visual signals, some transmittedthrough air or water and others through both media. In addition,each species' repertoire is composed of discrete, graded andcomplex signals. A few signals are unique to each species. However,their signalling systems differ in the temporal organizationof the behaviors, and in the relative frequency in which certainfunctional groups of signals occuror in which signals occurin a particular sensory mode. Apparently, the signalling systemsof C. acutus and C. niloticus are more similar to each otherthan either is to the signalling system of A. mississippiensis.The signalling systems of the crocodile species appear to beadapted to open water habitats in which visual signals are advantageousand to high density breeding groups and post-copulatory intersexualcontact. In contrast, the Alligatorsignalling system appearsadapted to a marsh habitat in which vocal signals are likelyfavored and to low density breeding groups.