Beyond Word Frequency: Bursts,Lulls, and Scaling in the Temporal Distributions of Words

Background

Zipf''s discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication. More recent research has also identified scaling regularities in the dynamics underlying the successive occurrences of events, suggesting the possibility of similar findings for language as well.

Methodology/Principal Findings

By considering frequent words in USENET discussion groups and in disparate databases where the language has different levels of formality, here we show that the distributions of distances between successive occurrences of the same word display bursty deviations from a Poisson process and are well characterized by a stretched exponential (Weibull) scaling. The extent of this deviation depends strongly on semantic type – a measure of the logicality of each word – and less strongly on frequency. We develop a generative model of this behavior that fully determines the dynamics of word usage.

Conclusions/Significance

Recurrence patterns of words are well described by a stretched exponential distribution of recurrence times, an empirical scaling that cannot be anticipated from Zipf''s law. Because the use of words provides a uniquely precise and powerful lens on human thought and activity, our findings also have implications for other overt manifestations of collective human dynamics.     

Multidimensional Human Dynamics in Mobile Phone Communications

In today''s technology-assisted society, social interactions may be expressed through a variety of techno-communication channels, including online social networks, email and mobile phones (calls, text messages). Consequently, a clear grasp of human behavior through the diverse communication media is considered a key factor in understanding the formation of the today''s information society. So far, all previous research on user communication behavior has focused on a sole communication activity. In this paper we move forward another step on this research path by performing a multidimensional study of human sociality as an expression of the use of mobile phones. The paper focuses on user temporal communication behavior in the interplay between the two complementary communication media, text messages and phone calls, that represent the bi-dimensional scenario of analysis. Our study provides a theoretical framework for analyzing multidimensional bursts as the most general burst category, that includes one-dimensional bursts as the simplest case, and offers empirical evidence of their nature by following the combined phone call/text message communication patterns of approximately one million people over three-month period. This quantitative approach enables the design of a generative model rooted in the three most significant features of the multidimensional burst - the number of dimensions, prevalence and interleaving degree - able to reproduce the main media usage attitude. The other findings of the paper include a novel multidimensional burst detection algorithm and an insight analysis of the human media selection process.     

The Geospatial Characteristics of a Social Movement Communication Network

Social movements rely in large measure on networked communication technologies to organize and disseminate information relating to the movements’ objectives. In this work we seek to understand how the goals and needs of a protest movement are reflected in the geographic patterns of its communication network, and how these patterns differ from those of stable political communication. To this end, we examine an online communication network reconstructed from over 600,000 tweets from a thirty-six week period covering the birth and maturation of the American anticapitalist movement, Occupy Wall Street. We find that, compared to a network of stable domestic political communication, the Occupy Wall Street network exhibits higher levels of locality and a hub and spoke structure, in which the majority of non-local attention is allocated to high-profile locations such as New York, California, and Washington D.C. Moreover, we observe that information flows across state boundaries are more likely to contain framing language and references to the media, while communication among individuals in the same state is more likely to reference protest action and specific places and times. Tying these results to social movement theory, we propose that these features reflect the movement’s efforts to mobilize resources at the local level and to develop narrative frames that reinforce collective purpose at the national level.     

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes

To study the roles of translational accuracy, translational efficiency, and the Hill-Robertson effect in codon usage bias, we studied the intragenic spatial distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis, Sulfolobus tokodaii, and Thermotoga maritima) and two eukaryotic (Saccharomyces cerevisiae and Drosophila melanogaster) genomes. We generated supersequences at each codon position across genes in a genome and computed the overall bias at each codon position. By quantitatively evaluating the trend of spatial patterns using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias increases along translational direction, which is consistent with purifying selection against nonsense errors. Fruit fly genes show a nearly symmetric M-shaped spatial pattern of codon usage bias, with less bias in the middle and both ends. The low codon usage bias in the middle region is best explained by interference (the Hill-Robertson effect) between selections at different codon positions. In both yeast and fruit fly, spatial patterns of codon usage bias are characteristically different from patterns of GC-content variations. Effect of expression level on the strength of codon usage bias is more conspicuous than its effect on the shape of the spatial distribution.     

Gestural forms of communication in primates. II. The relation of gestures to acoustic signals and tool activities in primate phylogeny

The connection between the frequency of acoustic signals application, contact and gestural communication and the manipulation activity of Cercopithecidea and Anthropoidea have been examined. A scheme reflecting the changes of correlational behavioural systems at different periods of primate phylogenesis is proposed. The behavioural changes in the connections of gestures, vocalisation and manipulation activity during the process of their transition into the language and labour on the way to hominization are shown. On the basis of the exact data a possible role of gestural an acoustic signals in the origin of language is given.     

Synonymous codon usage is subject to selection in thermophilic bacteria

The patterns of synonymous codon usage, both within and among genomes, have been extensively studied over the past two decades. Despite the accumulating evidence that natural selection can shape codon usage, it has not been possible to link a particular pattern of codon usage to a specific external selective force. Here, we have analyzed the patterns of synonymous codon usage in 40 completely sequenced prokaryotic genomes. By combining the genes from several genomes (more than 80 000 genes in all) into a single dataset for this analysis, we were able to investigate variations in codon usage, both within and between genomes. The results show that synonymous codon usage is affected by two major factors: (i) the overall G+C content of the genome and (ii) growth at high temperature. This study focused on the relationship between synonymous codon usage and the ability to grow at high temperature. We have been able to eliminate both phylogenetic history and lateral gene transfer as possible explanations for the characteristic pattern of codon usage among the thermophiles. Thus, these results demonstrate a clear link between a particular pattern of codon usage and an external selective force.     

Analysis of the Relationship between Genomic GC Content and Patterns of Base Usage,Codon Usage and Amino Acid Usage in Prokaryotes: Similar GC Content Adopts Similar Compositional Frequencies Regardless of the Phylogenetic Lineages

The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a) base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b) the distance of each usage has a linear correlation with the GC content difference; and c) GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes.     

Comparative analysis of the base composition and codon usages in fourteen mycobacteriophage genomes

To study the possible codon usage and base composition variation in the bacteriophages, fourteen mycobacteriophages were used as a model system here and both the parameters in all these phages and their plating bacteria, M. smegmatis had been determined and compared. As all the organisms are GC-rich, the GC contents at third codon positions were found in fact higher than the second codon positions as well as the first + second codon positions in all the organisms indicating that directional mutational pressure is strongly operative at the synonymous third codon positions. Nc plot indicates that codon usage variation in all these organisms are governed by the forces other than compositional constraints. Correspondence analysis suggests that: (i) there are codon usage variation among the genes and genomes of the fourteen mycobacteriophages and M. smegmatis, i.e., codon usage patterns in the mycobacteriophages is phage-specific but not the M. smegmatis-specific; (ii) synonymous codon usage patterns of Barnyard, Che8, Che9d, and Omega are more similar than the rest mycobacteriophages and M. smegmatis; (iii) codon usage bias in the mycobacteriophages are mainly determined by mutational pressure; and (iv) the genes of comparatively GC rich genomes are more biased than the GC poor genomes. Translational selection in determining the codon usage variation in highly expressed genes can be invoked from the predominant occurrences of C ending codons in the highly expressed genes. Cluster analysis based on codon usage data also shows that there are two distinct branches for the fourteen mycobacteriophages and there is codon usage variation even among the phages of each branch.     

In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

ABSTRACT: BACKGROUND: Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. RESULTS: We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by dN/dS), nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3). CONCLUSIONS: Our results indicate that while the A. thaliana genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection.     

Maintenance of transmitter release from neuromuscular junctions with different patterns of usage ‘in vivo’

The basic mechanisms underlying chemically-mediated neurotransmission at synapses are well established. Synaptic vesicles release their contents of neurotransmitter by exocytosis, and are then recycled and refilled before re-priming for re-release. It is less clear, however, what determines the differences in the quantitative aspects of this process at synapses with different in vivo activity patterns, and the extent to which they can be adapted to changing patterns of usage. The neuromuscular junction is particularly suited to investigations of these issues, due to the presence of distinctive muscle fibre types, with well-differentiated physiological roles and hence, activity patterns. The relative accessibility of NMJs means that chronic recording and manipulation of in vivo activity patterns of single motor neurones are possible. Several laboratories around the world now examining how transmitter release at NMJs is adapted to maintain (or not) release under these identified activity patterns. This review will cover the current state of knowledge and briefly highlight areas where more research is required. For example, current knowledge is largely derived from invertebrate preparations, indicating a need for more detailed comparisons at mammalian NMJs with different activity patterns. Finally, it is not yet clear in any species whether adaptations observed with imposed activity can be driven to complete transformation, with appropriate stimulus regimes.     

Context, Structural Variability and Distinctiveness of California Towhee (Pipilo crissalis) Vocal Duets

Avian vocal duets occur when paired birds produce temporally and structurally coordinated vocalizations. Duets are given by members of many species from taxonomically distinct lineages and show great variety in form that often reflects function. By describing the structure of vocal duets we can learn about the diversity of communication signals present in nature and also gain insight into the evolution and operation of those signals. This study quantified the usage patterns and acoustic structure of California towhee duet vocalizations, and tested the distinctiveness of duets among different pairs. California towhee duets consist of a 'squeal' vocalization that is highly unlike the species-typical call note or male advertizement song. California towhees duet an average of three times per hour during the breeding season, and all duets are accompanied by an approach response that brings duetting partners into close spatial proximity. Males and females produce duet contributions with the same syllabic structure. Individual birds produce highly variable squeal vocalizations that are distinctive enough to signal identity. California towhee duet characteristics indicate that the squeal vocalization has evolved separately from other vocal traits in this species and was promoted by natural selection as a duet-specific vocalization. Duet usage patterns and structure suggest that these communication signals function in a cooperative context.     

Analysis of synonymous codon usage patterns in the genus Rhizobium

The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman’s rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.     

Analysis of the codon usage pattern in the Vibrio cholerae genome.

The codon usage in the Vibrio cholerae genome is analyzed in this paper. Although there are much more genes on the chromosome 1 than on chromosome 2, the codon usage patterns of genes on the two chromosomes are quite similar, indicating that the two chromosomes may have coexisted in the same cell for a very long history. Unlike the base frequency pattern observed in other genomes, the G+C content at the third codon position of the V. cholerae genome varies in a rather small interval. The most notable feature of codon usage of V. cholerae genome is that there is a fraction of genes show significant bias in base choice at the second codon position. The 2,006 known genes can be classified into two clusters according to the base frequencies at this position. The smaller cluster contains 227 genes, most of which code for proteins involved in transport and binding functions. The encoding products of these genes have significant bias in amino acids composition as compared with other genes. The codon usage patterns for the 1,836 function unknown ORFs are also analyzed, which is useful to study their functions.     

Collective response of human populations to large-scale emergencies

Despite recent advances in uncovering the quantitative features of stationary human activity patterns, many applications, from pandemic prediction to emergency response, require an understanding of how these patterns change when the population encounters unfamiliar conditions. To explore societal response to external perturbations we identified real-time changes in communication and mobility patterns in the vicinity of eight emergencies, such as bomb attacks and earthquakes, comparing these with eight non-emergencies, like concerts and sporting events. We find that communication spikes accompanying emergencies are both spatially and temporally localized, but information about emergencies spreads globally, resulting in communication avalanches that engage in a significant manner the social network of eyewitnesses. These results offer a quantitative view of behavioral changes in human activity under extreme conditions, with potential long-term impact on emergency detection and response.     

Introduction. The perception of speech: from sound to meaning

Spoken language communication is arguably the most important activity that distinguishes humans from non-human species. This paper provides an overview of the review papers that make up this theme issue on the processes underlying speech communication. The volume includes contributions from researchers who specialize in a wide range of topics within the general area of speech perception and language processing. It also includes contributions from key researchers in neuroanatomy and functional neuro-imaging, in an effort to cut across traditional disciplinary boundaries and foster cross-disciplinary interactions in this important and rapidly developing area of the biological and cognitive sciences.