Community Structure in Time-Dependent, Multiscale, and Multiplex Networks

Network science is an interdisciplinary endeavor, with methods and applications drawn from across the natural, social, and information sciences. A prominent problem in network science is the algorithmic detection of tightly-connected groups of nodes known as communities. We developed a generalized framework of network quality functions that allowed us to study the community structure of arbitrary multislice networks, which are combinations of individual networks coupled through links that connect each node in one network slice to itself in other slices. This framework allows one to study community structure in a very general setting encompassing networks that evolve over time, have multiple types of links (multiplexity), and have multiple scales.Comment: 31 pages, 3 figures, 1 table. Includes main text and supporting material. This is the accepted version of the manuscript (the definitive version appeared in Science), with typographical corrections included her

Reactions in Crystalline Lattices: Chemistry of Lower Valence States of Lanthanides

Reduction of rare-earth (RE) ions to lower valence states in ionic crystals is described in terms of the equilibrium distribution theory for the (alkali halide):RE2+ and (alkaline-earth halide):RE3+ systems. Thermoluminescence glow curves of radiation-reduced CaF2:RE3+ systems reveal that the reoxidation of the divalent ions apparently occurs through thermal excitation of an f electron to the d bands. The additive reduction of RE2+ to the monovalent state in alkali halides yields striking results: While Sm1+ ions in KCl obtained by gamma radiation give rise to broad-band optical spectra which were attributed to 4f66s1 --> 4f56s2 transitions, those obtained through high-temperature additive treatment with liquid K give rise to narrow-line spectra that are not easily interpreted. These results illustrate well the major differences between the radiation reduction and additive reduction processes

Improving signal-to-noise resolution in single molecule experiments using molecular constructs with short handles

We investigate unfolding/folding force kinetics in DNA hairpins exhibiting two and three states with newly designed short dsDNA handles (29 bp) using optical tweezers. We show how the higher stiffness of the molecular setup moderately enhances the signal-to-noise ratio (SNR) in hopping experiments as compared to conventional long handles constructs (approximately 700 bp). The shorter construct results in a signal of higher SNR and slower folding/unfolding kinetics, thereby facilitating the detection of otherwise fast structural transitions. A novel analysis of the elastic properties of the molecular setup, based on high-bandwidth measurements of force fluctuations along the folded branch, reveals that the highest SNR that can be achieved with short handles is potentially limited by the marked reduction of the effective persistence length and stretch modulus of the short linker complex.Comment: Main paper: 20 pages and 6 figures. Supplementary Material: 25 page

Force-Velocity Relations of a Two-State Crossbridge Model for Molecular Motors

We discuss the force-velocity relations obtained in a two-state crossbridge model for molecular motors. They can be calculated analytically in two limiting cases: for a large number and for one pair of motors. The effect of the strain-dependent detachment rate on the motor characteristics is studied. It can lead to linear, myosin-like, kinesin-like and anomalous curves. In particular, we specify the conditions under which oscillatory behavior may be found.Comment: 5 pages, 4 figures, REVTeX; thoroughly revised version; also available at http://www.physik.tu-muenchen.de/~frey

Neoplastic transformation of mouse C3H 10T1/2 and Syrian hamster embryo cells by heavy ions

C3H 10T1/2 mouse-embryo fibroblasts were used for transformation experiments to study the effectiveness of various heavy ions with energies up to 20 MeV/u and LET values from 170 to 16.000 keV/μm. The transformation frequency per unit absorbed dose decreased with increasing ionization density; at the highest values of LET we found a decrease even of the transformation efficiency per unit fluence. Uranium ions at energies of 5, 9, and 16.3 MeV/u did not induced any transformation. In additional studies piimary Syrian hamster embryo cells (SHE) were exposed to heavy ions in order to characterize cytological and molecular changes which may be correlated with neoplastic transformation. Growth behaviour, chromosomal status, tumorigenicity in nude mice, and expression of oncogenes of transformed cell lines were examined

Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei

Background: Trypanosomes undergo extensive developmental changes during their complex life cycle. Crucial among these is the transition between slender and stumpy bloodstream forms and, thereafter, the differentiation from stumpy to tsetse-midgut procyclic forms. These developmental events are highly regulated, temporally reproducible and accompanied by expression changes mediated almost exclusively at the post-transcriptional level. Results: In this study we have examined, by whole-genome microarray analysis, the mRNA abundance of genes in slender and stumpy forms of T. brucei AnTat1.1 cells, and also during their synchronous differentiation to procyclic forms. In total, five biological replicates representing the differentiation of matched parasite populations derived from five individual mouse infections were assayed, with RNAs being derived at key biological time points during the time course of their synchronous differentiation to procyclic forms. Importantly, the biological context of these mRNA profiles was established by assaying the coincident cellular events in each population (surface antigen exchange, morphological restructuring, cell cycle re-entry), thereby linking the observed gene expression changes to the well-established framework of trypanosome differentiation. Conclusion: Using stringent statistical analysis and validation of the derived profiles against experimentally-predicted gene expression and phenotypic changes, we have established the profile of regulated gene expression during these important life-cycle transitions. The highly synchronous nature of differentiation between stumpy and procyclic forms also means that these studies of mRNA profiles are directly relevant to the changes in mRNA abundance within individual cells during this well-characterised developmental transition.Publisher PDFPeer reviewe