The map equation

Many real-world networks are so large that we must simplify their structure before we can extract useful information about the systems they represent. As the tools for doing these simplifications proliferate within the network literature, researchers would benefit from some guidelines about which of the so-called community detection algorithms are most appropriate for the structures they are studying and the questions they are asking. Here we show that different methods highlight different aspects of a network's structure and that the the sort of information that we seek to extract about the system must guide us in our decision. For example, many community detection algorithms, including the popular modularity maximization approach, infer module assignments from an underlying model of the network formation process. However, we are not always as interested in how a system's network structure was formed, as we are in how a network's extant structure influences the system's behavior. To see how structure influences current behavior, we will recognize that links in a network induce movement across the network and result in system-wide interdependence. In doing so, we explicitly acknowledge that most networks carry flow. To highlight and simplify the network structure with respect to this flow, we use the map equation. We present an intuitive derivation of this flow-based and information-theoretic method and provide an interactive on-line application that anyone can use to explore the mechanics of the map equation. We also describe an algorithm and provide source code to efficiently decompose large weighted and directed networks based on the map equation.Comment: 9 pages and 3 figures, corrected typos. For associated Flash application, see http://www.tp.umu.se/~rosvall/livemod/mapequation

Warped and eccentric discs around black holes

Accretion discs around black holes in X-ray binary stars are warped if the spin axis of the black hole is not perpendicular to the binary orbital plane. They can also become eccentric through an instability involving a resonance with the binary orbit. Depending on the thickness of the disc and the efficiency of dissipative processes, these global deformations may be able to propagate into the innermost part of the disc in the form of stationary bending or density waves. We describe the solutions in the linear regime and discuss the conditions under which a warp or eccentricity is likely to produce significant activity in the inner region, which may include the excitation of quasi-periodic oscillations.Comment: 6 pages, 3 figures; accepted for inclusion in the proceedings of "Cool Discs, Hot Flows: The Varying Faces of Accreting Compact Objects," ed. M. Axelsson (New York: AIP

A trait-based plant economic framework can help increase the value of reforestation for conservation

While reforestation is gaining momentum to moderate climate change via carbon sequestration, there is also an opportunity to use tree planting to confront declining global biodiversity. Where tree species vary in support of diversity, selecting appropriate species for planting could increase conservation effectiveness. We used a common garden experiment in Borneo using 24 native tree species to examine how variation among tree species in their support of beetle diversity is predicted by plant traits associated with "acquisitive" and "conservative" resource acquisition strategies. We evaluate three hypotheses: (1) beetle communities show fidelity to host identity as indicated by variation in abundance and diversity among tree species, (2) the leaf economic spectrum partially explains this variation as shown by beetle preferences for plant species that are predicted by plant traits, and (3) a small number of selected tree species can capture higher beetle species richness than a random tree species community. We found high variation among tree species in supporting three highly intercorrelated metrics of beetle communities: abundance, richness, and Shannon diversity. Variation in support of beetle communities was predicted by plant traits and varied by plant functional groups; within the dipterocarp family, high beetle diversity was predicted by conservative traits such as high wood density and slow growth, and in non-dipterocarps by the acquisitive traits of high foliar K and rapid growth. Using species accumulation curves and extrapolation to twice the original sample size, we show that 48 tree species were not enough to reach asymptote levels of beetle richness. Nevertheless, species accumulation curves of the six tree species with the highest richness had steeper slopes and supported 33% higher richness than a random community of tree species. Reforestation projects concerned about conservation can benefit by identifying tree species with a disproportional capacity to support biodiversity based on plant traits

A pre-adaptive approach for tropical forest restoration during climate change using naturally occurring genetic variation in response to water limitation

Effective reforestation of degraded tropical forests depends on selecting planting material suited to the stressful environments typical at restoration sites that can be exacerbated by increased duration and intensity of dry spells expected with climate change. While reforestation efforts in nontropical systems are incorporating drought-adapted genotypes into restoration programs to cope with drier conditions, such approaches have not been tested or implemented in tropical forests. As the first effort to examine genetic variation in plant response to drought in a tropical wet forest, we established a watering experiment using five replicated maternal lines (i.e. seedlings from different maternal trees) of five dipterocarp species native to Borneo. Apart from the expected species level variation in growth and herbivory (3-fold variation in both cases), we also found intraspecific variation so that growth in some cases varied 2-fold, and herbivory 3-fold, among genetically different maternal lines. In two species we found that among-maternal line variation in growth rate was negatively correlated with tolerance to water limitation, that is, the maternal lines that performed the best in the high water treatment lost proportionally more of their growth during water limitation. We argue that selection for tolerance to future drier conditions is not only likely to impact population genetics of entire forests, but likely extends from forest trees to the communities of canopy arthropods associated with these trees. In tropical reforestation efforts where increased drought is predicted from climate change, including plant material resilient to drier conditions may improve restoration effectiveness

Cerebrospinal fluid biomarkers as a measure of disease activity and treatment efficacy in relapsing-remitting multiple sclerosis

Cerebrospinal fluid (CSF) biomarkers can reflect different aspects of the pathophysiology of relapsing-remitting multiple sclerosis (RRMS). Understanding the impact of different disease modifying therapies on the CSF biomarker profile may increase their implementation in clinical practice and their appropriateness for monitoring treatment efficacy. This study investigated the influence of first-line (interferon beta) and second-line (natalizumab) therapies on seven CSF biomarkers in RRMS and their correlation with clinical and radiological outcomes. We included 59 RRMS patients and 39 healthy controls. The concentrations of C-X-C motif chemokine 13 (CXCL13), C-C motif chemokine ligand 2 (CCL2), chitinase-3-like protein 1 (CHI3L1), glial fibrillary acidic protein, neurofilament light protein (NFL), and neurogranin were determined by ELISA, and chitotriosidase (CHIT1) was analyzed by spectrofluorometry. RRMS patients had higher levels of NFL, CXCL13, CHI3L1, and CHIT1 than controls (p < 0.001). Subgroup analysis revealed higher NFL, CXCL13 and CHIT1 levels in patients treated with first-line therapy compared to second-line therapy (p = 0.008, p = 0.001 and p = 0.026, respectively). NFL and CHIT1 levels correlated with relapse status, and NFL and CXCL13 levels correlated with the formation of new magnetic resonance imaging lesions. Furthermore, we found an association between inflammatory and degenerative biomarkers. The results indicate that CSF levels of NFL, CXCL13, CHI3L1, and CHIT1 correlate with the clinical and/or radiological disease activity, providing additional dimensions in the assessment of treatment efficacy

Fluorescence diffuse optical tomography using upconverting nanoparticles

Fluorescence diffuse optical tomography (FDOT) can provide important information in biomedical studies. In this ill-posed problem, suppression of background tissue autofluorescence is of utmost importance. We report a method for autofluorescence-insensitive FDOT using nonlinear upconverting nanoparticles (NaYF4:Yb3+/Tm3+) in a tissue phantom under excitation intensities well below tissue-damage thresholds. Even with the intrinsic autofluorescence from the phantom only, the reconstruction of the nanoparticles is of much better quality than the reconstruction of a Stokes-shifting dye. In addition, the nonlinear power dependence leads to more confined reconstructions and may increase the resolution in FDOT