“An ethnographic seduction”: how qualitative research and Agent-based models can benefit each other

We provide a general analytical framework for empirically informed agent-based simulations. This methodology provides present-day agent-based models with a sound and proper insight as to the behavior of social agents — an insight that statistical data often fall short of providing at least at a micro level and for hidden and sensitive populations. In the other direction, simulations can provide qualitative researchers in sociology, anthropology and other fields with valuable tools for: (a) testing the consistency and pushing the boundaries, of specific theoretical frameworks; (b) replicating and generalizing results; (c) providing a platform for cross-disciplinary validation of results

Power Law of Customers' Expenditures in Convenience Stores

In a convenience store chain, a tail of the cumulative density function of the expenditure of a person during a single shopping trip follows a power law with an exponent of -2.5. The exponent is independent of the location of the store, the shopper's age, the day of week, and the time of day.Comment: 9 pages, 5 figures. Accepted for publication in Journal of the Physical Society of Japan Vol.77No.

How to Choose a Champion

League competition is investigated using random processes and scaling techniques. In our model, a weak team can upset a strong team with a fixed probability. Teams play an equal number of head-to-head matches and the team with the largest number of wins is declared to be the champion. The total number of games needed for the best team to win the championship with high certainty, T, grows as the cube of the number of teams, N, i.e., T ~ N^3. This number can be substantially reduced using preliminary rounds where teams play a small number of games and subsequently, only the top teams advance to the next round. When there are k rounds, the total number of games needed for the best team to emerge as champion, T_k, scales as follows, T_k ~N^(\gamma_k) with gamma_k=1/[1-(2/3)^(k+1)]. For example, gamma_k=9/5,27/19,81/65 for k=1,2,3. These results suggest an algorithm for how to infer the best team using a schedule that is linear in N. We conclude that league format is an ineffective method of determining the best team, and that sequential elimination from the bottom up is fair and efficient.Comment: 6 pages, 3 figure

Comparative analysis of miRNAs and their targets across four plant species

BACKGROUND: MicroRNA (miRNA) mediated regulation of gene expression has been recognized as a major posttranscriptional regulatory mechanism also in plants. We performed a comparative analysis of miRNAs and their respective gene targets across four plant species: Arabidopsis thaliana (Ath), Medicago truncatula(Mtr), Brassica napus (Bna), and Chlamydomonas reinhardtii (Cre). RESULTS: miRNAs were obtained from mirBase with 218 miRNAs for Ath, 375 for Mtr, 46 for Bna, and 73 for Cre, annotated for each species respectively. miRNA targets were obtained from available database annotations, bioinformatic predictions using RNAhybrid as well as predicted from an analysis of mRNA degradation products (degradome sequencing) aimed at identifying miRNA cleavage products. On average, and considering both experimental and bioinformatic predictions together, every miRNA was associated with about 46 unique gene transcripts with considerably variation across species. We observed a positive and linear correlation between the number miRNAs and the total number of transcripts across different plant species suggesting that the repertoire of miRNAs correlates with the size of the transcriptome of an organism. Conserved miRNA-target pairs were found to be associated with developmental processes and transcriptional regulation, while species-specific (in particular, Ath) pairs are involved in signal transduction and response to stress processes. Conserved miRNAs have more targets and higher expression values than non-conserved miRNAs. We found evidence for a conservation of not only the sequence of miRNAs, but their expression levels as well. CONCLUSIONS: Our results support the notion of a high birth and death rate of miRNAs and that miRNAs serve many species specific functions, while conserved miRNA are related mainly to developmental processes and transcriptional regulation with conservation operating at both the sequence and expression level

Field dependent thermodynamics and Quantum Critical Phenomena in the dimerized spin system Cu2(C5H12N2)2Cl4

Experimental data for the uniform susceptibility, magnetization and specific heat for the material Cu2(C5H12N2)2Cl4 (abbreviated CuHpCl) as a function of temperature and external field are compared with those of three different dimerized spin models: alternating spin-chains, spin-ladders and the bilayer Heisenberg model. It is shown that because this material consists of weakly coupled spin-dimers, much of the data is insensitive to how the dimers are coupled together and what the effective dimensionality of the system is. When such a system is tuned to the quantum critical point by application of a field, the dimensionality shows up in the power-law dependences of thermodynamic quantities on temperature. We discuss the temperature window for such a quantum critical behavior in CuHpCl.Comment: Revtex, 5 pages, 4 figures (postscript

Functional Specialization of the Plant miR396 Regulatory Network through Distinct MicroRNA–Target Interactions

MicroRNAs (miRNAs) are ∼21 nt small RNAs that regulate gene expression in animals and plants. They can be grouped into families comprising different genes encoding similar or identical mature miRNAs. Several miRNA families are deeply conserved in plant lineages and regulate key aspects of plant development, hormone signaling, and stress response. The ancient miRNA miR396 regulates conserved targets belonging to the GROWTH-REGULATING FACTOR (GRF) family of transcription factors, which are known to control cell proliferation in Arabidopsis leaves. In this work, we characterized the regulation of an additional target for miR396, the transcription factor bHLH74, that is necessary for Arabidopsis normal development. bHLH74 homologs with a miR396 target site could only be detected in the sister families Brassicaceae and Cleomaceae. Still, bHLH74 repression by miR396 is required for margin and vein pattern formation of Arabidopsis leaves. MiR396 contributes to the spatio-temporal regulation of GRF and bHLH74 expression during leaf development. Furthermore, a survey of miR396 sequences in different species showed variations in the 5′ portion of the miRNA, a region known to be important for miRNA activity. Analysis of different miR396 variants in Arabidopsis thaliana revealed that they have an enhanced activity toward GRF transcription factors. The interaction between the GRF target site and miR396 has a bulge between positions 7 and 8 of the miRNA. Our data indicate that such bulge modulates the strength of the miR396-mediated repression and that this modulation is essential to shape the precise spatio-temporal pattern of GRF2 expression. The results show that ancient miRNAs can regulate conserved targets with varied efficiency in different species, and we further propose that they could acquire new targets whose control might also be biologically relevant

Spinons in a Crossed-Chains Model of a 2D Spin Liquid

Using Random Phase Approximation, we show that a crossed-chains model of a spin-1/2 Heisenberg spins, with frustrated interchain couplings, has a non-dimerized spin-liquid ground state in 2D, with deconfined spinons as the elementary excitations. The results are confirmed by a bosonization study, which shows that the system is an example of a `sliding Luttinger liquid'. In an external field, the system develops an incommensurate field-induced long range order with a finite transition temperature.Comment: 4 pages, 3 figures; added references; scaling analysis, preserving spin rotational invariance, is extended to finite temperatur

Spatial interactions in agent-based modeling

Agent Based Modeling (ABM) has become a widespread approach to model complex interactions. In this chapter after briefly summarizing some features of ABM the different approaches in modeling spatial interactions are discussed. It is stressed that agents can interact either indirectly through a shared environment and/or directly with each other. In such an approach, higher-order variables such as commodity prices, population dynamics or even institutions, are not exogenously specified but instead are seen as the results of interactions. It is highlighted in the chapter that the understanding of patterns emerging from such spatial interaction between agents is a key problem as much as their description through analytical or simulation means. The chapter reviews different approaches for modeling agents' behavior, taking into account either explicit spatial (lattice based) structures or networks. Some emphasis is placed on recent ABM as applied to the description of the dynamics of the geographical distribution of economic activities, - out of equilibrium. The Eurace@Unibi Model, an agent-based macroeconomic model with spatial structure, is used to illustrate the potential of such an approach for spatial policy analysis.Comment: 26 pages, 5 figures, 105 references; a chapter prepared for the book "Complexity and Geographical Economics - Topics and Tools", P. Commendatore, S.S. Kayam and I. Kubin, Eds. (Springer, in press, 2014

Dynamical Properties of One-Dimensional Multicomponent Quantum Liquids in Metallic Phase

We investigate low-energy dynamical properties of one-dimensional multicomponent quantum liquids with the short-range interaction as well as the $1/x$-type long-range interaction. By calculating the single-particle spectrum and the dynamical spin susceptibility by means of the bosonization method, we discuss how the orbital degeneracy and the band splitting affect the dynamical response functions. The effect of the long-range interaction is also addressed. Although the long-range interaction suppresses charge fluctuations, it effectively enhances spin fluctuations via the formation of the Wigner crystal.Comment: 17 pages, 8 figure

Deep Annotation of Populus trichocarpa microRNAs from Diverse Tissue Sets

Populus trichocarpa is an important woody model organism whose entire genome has been sequenced. This resource has facilitated the annotation of microRNAs (miRNAs), which are short non-coding RNAs with critical regulatory functions. However, despite their developmental importance, P. trichocarpa miRNAs have yet to be annotated from numerous important tissues. Here we significantly expand the breadth of tissue sampling and sequencing depth for miRNA annotation in P. trichocarpa using high-throughput smallRNA (sRNA) sequencing. miRNA annotation was performed using three individual next-generation sRNA sequencing runs from separate leaves, xylem, and mechanically treated xylem, as well as a fourth run using a pooled sample containing vegetative apices, male flowers, female flowers, female apical buds, and male apical and lateral buds. A total of 276 miRNAs were identified from these datasets, including 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Importantly, we identified several xylem-enriched miRNAs predicted to target genes known to be important in secondary growth, including the critical reaction wood enzyme xyloglucan endo-transglycosylase/hydrolase and vascular-related transcription factors. This study provides a thorough genome-wide annotation of miRNAs in P. trichocarpa through deep sRNA sequencing from diverse tissue sets. Our data significantly expands the P. trichocarpa miRNA repertoire, which will facilitate a broad range of research in this major model system