Maximal entropy random walk in community finding

The aim of this paper is to check feasibility of using the maximal-entropy random walk in algorithms finding communities in complex networks. A number of such algorithms exploit an ordinary or a biased random walk for this purpose. Their key part is a (dis)similarity matrix, according to which nodes are grouped. This study encompasses the use of the stochastic matrix of a random walk, its mean first-passage time matrix, and a matrix of weighted paths count. We briefly indicate the connection between those quantities and propose substituting the maximal-entropy random walk for the previously chosen models. This unique random walk maximises the entropy of ensembles of paths of given length and endpoints, which results in equiprobability of those paths. We compare performance of the selected algorithms on LFR benchmark graphs. The results show that the change in performance depends very strongly on the particular algorithm, and can lead to slight improvements as well as significant deterioration.Comment: 7 pages, 4 figures, submitted to European Physical Journal Special Topics following the 4-th Conference on Statistical Physics: Modern Trends and Applications, July 3-6, 2012 Lviv, Ukrain

Nonlinear ion-acoustic (IA) waves driven in a cylindrically symmetric flow

By employing a self-similar, two-fluid MHD model in a cylindrical geometry, we study the features of nonlinear ion-acoustic (IA) waves which propagate in the direction of external magnetic field lines in space plasmas. Numerical calculations not only expose the well-known three shapes of nonlinear structures (sinusoidal, sawtooth, and spiky or bipolar) which are observed by numerous satellites and simulated by models in a Cartesian geometry, but also illustrate new results, such as, two reversely propagating nonlinear waves, density dips and humps, diverging and converging electric shocks, etc. A case study on Cluster satellite data is also introduced.Comment: accepted by AS

Mott Transition in An Anyon Gas

We introduce and analyze a lattice model of anyons in a periodic potential and an external magnetic field which exhibits a transition from a Mott insulator to a quantum Hall fluid. The transition is characterized by the anyon statistics, $\alpha$, which can vary between Fermions, $\alpha=0$, and Bosons, $\alpha=1$. For bosons the transition is in the universality class of the classical three-dimensional XY model. Near the Fermion limit, the transition is described by a massless $2+1$ Dirac theory coupled to a Chern-Simons gauge field. Analytic calculations perturbative in $\alpha$, and also a large N-expansion, show that due to gauge fluctuations, the critical properties of the transition are dependent on the anyon statistics. Comparison with previous calcualations at and near the Boson limit, strongly suggest that our lattice model exhibits a fixed line of critical points, with universal critical properties which vary continuosly and monotonically as one passes from Fermions to Bosons. Possible relevance to experiments on the transitions between plateaus in the fractional quantum Hall effect and the magnetic field-tuned superconductor-insulator transition are briefly discussed.Comment: text and figures in Latex, 41 pages, UBCTP-92-28, CTP\#215

Two-particle pairing and phase separation in a two-dimensional Bose-gas with one or two sorts of bosons

We present a phase diagram for a dilute two-dimensional Bose-gas on a lattice. For one sort of boson we consider a realistic case of the van der Waals interaction between particles with a strong hard-core repulsion $U$ and a van der Waals attractive tail $V$. For $V< 2 t$, $t$ being a hopping amplitude, the phase diagram of the system contains regions of the usual one-particle Bose-Einstein condensation (BEC). However for $V>2t$ we have total phase separation on a Mott-Hubbard Bose solid and a dilute Bose gas. For two sorts of structureless bosons described by the two band Hubbard model an s-wave pairing of the two bosons of different sort $\neq 0$ is possible. The results we obtained should be important for different Bose systems, including submonolayers of $^4$He, excitons in semiconductors, Schwinger bosons in magnetic systems and holons in HTSC. In the HTSC case a possibility of two-holon pairing in the slave-bosons theories of superconductivity can restore a required charge $2e$ of a Cooper pair.Comment: 10 pages, 2 figure

Phenomenological model for the Kbar N --> K Xi reaction

A phenomenological model for the Kbar N --> K Xi reaction is suggested. The model includes s and u channel exchanges by Lambda, Sigma, Sigma(1385), and Lambda(1520) and s channel exchanges by above-threshold hyperonic resonances. Explicit expression for the propagator for a particle with spin 7/2 is presented. High-mass and high-spin resonances play a significant role in the process. We deal with the whole set of existing experimental data on the cross sections and polarizations in the energy range from the threshold to 2.8 GeV in the center-of-mass system and reach a good agreement with experiments. Applications of the model to other elementary reactions of Xi production and to Xi hypernuclear spectroscopy are briefly discussed.Comment: Published version; minor change

Alterações na ultra-estrutura de genótipos de soja em resposta ao fornecimento de manganês em solução nutritiva

The deleterious effects of Mn stress on many species have been studied, mainly concerning biochemical, physiological and growth parameters of plants. However, there are few studies relating the anatomical and ultrastructural changes in response to manganese (Mn) nutritional disorders, This study examined the leaf ultrastructure of Mn-inefficient (IAC-15, Santa Rosa) and Mn-efficient (IAC-Foscarin 31) soybean (Glycine max L.) genotypes in response to three rates of Mn (0.5, 2 and 200 µmol L-1) in the nutrient solution. Symptoms of Mn deficiency developed 12 days after transplanting in IAC-15 and Santa Rosa, followed by IAC-Foscarin 31 on the 15th day. Only IAC-15 and Santa Rosa leaves showed symptoms of Mn toxicity. The Mn concentration in leaves ranged from 8.6 (deficiency) to 886.3 mg kg-1 d.w. (toxicity). There were no changes either in stomata length or stomata number per unit of leaf surface. Cytoplasm disorganization was observed in IAC-15 under Mn-excess. In this case, the cytoplasm was amorphous, densely stained and extensively disorganized, with increased vacuolation. Mn effects were not found in mitochondria and nucleus in any of the genotypes tested. Under all Mn concentrations, many lipid globules were observed in the IAC15 chloroplasts. There was an increase in the number of plastids as well as in the size of starch grains within IAC-Foscarin 31 chloroplasts as Mn concentration in the nutrient solution increased. Genotypes had marked differences in the ultrastructure organization, mainly in leaf chloroplasts grown under conditions of both Mn deficiency and toxicity (the most sensitive genotype was IAC-15).Os efeitos negativos provocados tanto pela deficiência quanto pela toxidez de manganês (Mn) no desenvolvimento das plantas têm sido avaliados, considerando-se os aspectos bioquímicos e produtivos da parte aérea, particularmente, onde os sintomas visuais são manifestados. Entretanto, há poucas informações na literatura abordando as alterações anatômicas e de ultra-estrutura, em relação ao suprimento de Mn. Os objetivos do presente estudo foram avaliar os efeitos do fornecimento de três doses de Mn (0,5; 2 e 200 µmol L-1), em solução nutritiva, nas ultra-estruturas de folhas de cultivares de soja Glycine max (L.): Santa Rosa, IAC-15 e IAC-Foscarin 31, contrastantes quanto à aquisição e ao uso do Mn. Os sintomas visuais de deficiência foram observados primeiramente em Santa Rosa e IAC-15 (ineficientes), os únicos a exibirem sintomas de toxidez. As concentrações de Mn nas folhas com sintomas variaram de 8,6 (deficiência) a 886,3 mg kg-1 (toxidez). Não houve alterações no comprimento e no número de estômatos nos limbos foliares. Em condição de toxidez, constatou-se no IAC-15, citoplasma desorganizado, vacuolado em excesso e denso evidenciando alterações nas membranas dos tilacóides. Não ocorreram alterações ultra-estruturais nas mitocôndrias e no núcleo das células dos três genótipos. Constatou-se presença de glóbulos de lipídios nos cloroplastos do cultivar IAC-15, em todas as condições de fornecimento de Mn. Houve aumento no número de plastídeos e grãos de amido, bem como no tamanho destes no IAC-Foscarin 31 com o suprimento de Mn. Os genótipos, tanto na condição de deficiência quanto de excesso, exibiram distintos graus de organização das ultraestruturas, notadamente, os cloroplastos. O IAC-15 exibiu maiores alterações das ultra-estruturas em função das desordens nutricionais em manganês

Plant-plant competition influences temporal dynamism of soil microbial enzyme activity.

Root-derived compounds can change rates of soil organic matter decomposition (rhizosphere priming effects) through microbial production of extracellular enzymes. Such soil priming can be affected by plant identity and soil nutrient status. However, the effect of plant-plant competition on the temporal dynamics of soil organic matter turnover processes is not well understood. This study used zymography to detect the spatial and temporal pattern of cellulase and leucine aminopeptidase activity, two enzyme classes involved in soil organic matter turnover. The effect of plant-plant competition on enzyme activity was examined using barley (Hordeum vulgare) plants grown in i) isolation, ii) intra- and iii) inter-cultivar competition. The enzyme activities of leucine aminopeptidase and cellulase were measured from portions of the root system at 18, 25 and 33 days after planting, both along the root axis and in the root associated area with detectable enzyme activity. The activities of cellulase and leucine aminopeptidase were both strongly associated with plant roots, and increased over time. An increase in the area of cellulase activity around roots was delayed when plants were in competition compared to in isolation. A similar response was found for leucine aminopeptidase activity, but only when in intra-cultivar competition, and not when in inter-cultivar competition. Therefore, plant-plant competition had a differential effect on enzyme classes, which was potentially mediated through root exudate composition. This study demonstrates the influence of plant-plant competition on soil microbial activity and provides a potential mechanism by which temporal dynamism in plant resource capture can be mediated

Feasibility of implementing the patient-reported outcomes version of the common terminology criteria for adverse events in a multicenter trial: NCCTG N1048

Purpose The US National Cancer Institute (NCI) Patient-Reported Outcomes version of the Common Terminology Criteria for Adverse Events (PRO-CTCAE) was developed to enable patient reporting of symptomatic adverse events in oncology clinical research. This study was designed to assess the feasibility and resource requirements associated with implementing PRO-CTCAE in a multicenter trial. Methods Patients with locally advanced rectal cancer enrolled in the National Cancer Institute-sponsored North Central Cancer Treatment Group (Alliance) Preoperative Radiation or Selective Preoperative Radiation and Evaluation before Chemotherapy and Total Mesorectal Excision trial were asked to self-report 30 PRO-CTCAE items weekly from home during preoperative therapy, and every 6 months after surgery, via either the Web or an automated telephone system. If participants did not self-report within 3 days, a central coordinator called them to complete the items. Compliance was defined as the proportion of participants who completed PRO-CTCAE assessments at expected time points. Results The prespecified PRO-CTCAE analysis was conducted after the 500th patient completed the 6-month follow-up (median age, 56 years; 33% female; 12% nonwhite; 43% high school education or less; 5% Spanish speaking), across 165 sites. PRO-CTCAE was reported by participants at 4,491 of 4,882 expected preoperative time points (92.0% compliance), of which 3,771 (77.2%) were selfreported by participants and 720 (14.7%) were collected via central coordinator backup. Compliance at 6-month post-treatment follow-up was 333 of 468 (71.2%), with 122 (26.1%) via backup. Site research associates spent a median of 15 minutes on PRO-CTCAE work for each patient visit. Work by a central coordinator required a 50% time commitment. Conclusion Home-based reporting of PRO-CTCAE in a multicenter trial is feasible, with high patient compliance and low site administrative requirements. PRO-CTCAE data capture is improved through centralized backup calls

Dynamic protein methylation in chromatin biology

Post-translational modification of chromatin is emerging as an increasingly important regulator of chromosomal processes. In particular, histone lysine and arginine methylation play important roles in regulating transcription, maintaining genomic integrity, and contributing to epigenetic memory. Recently, the use of new approaches to analyse histone methylation, the generation of genetic model systems, and the ability to interrogate genome wide histone modification profiles has aided in defining how histone methylation contributes to these processes. Here we focus on the recent advances in our understanding of the histone methylation system and examine how dynamic histone methylation contributes to normal cellular function in mammals