422 research outputs found
Swarming and complex pattern formation in <it>Paenibacillus vortex </it>studied by imaging and tracking cells
No full textAbstract Background Swarming motility allows microorganisms to move rapidly over surfaces. The Gram-positive bacterium Paenibacillus vortex exhibits advanced cooperative motility on agar plates resulting in intricate colonial patterns with geometries that are highly sensitive to the environment. The cellular mechanisms that underpin the complex multicellular organization of such a simple organism are not well understood. Results Swarming by P. vortex was studied by real-time light microscopy, by in situ scanning electron microscopy and by tracking the spread of antibiotic-resistant cells within antibiotic-sensitive colonies. When swarming, P. vortex was found to be peritrichously flagellated. Swarming by the curved cells of P. vortex occurred on an extremely wide range of media and agar concentrations (0.3 to 2.2% w/v). At high agar concentrations (> 1% w/v) rotating colonies formed that could be detached from the main mass of cells by withdrawal of cells into the latter. On lower percentage agars, cells moved in an extended network composed of interconnected "snakes" with short-term collision avoidance and sensitivity to extracts from swarming cells. P. vortex formed single Petri dish-wide "supercolonies" with a colony-wide exchange of motile cells. Swarming cells were coupled by rapidly forming, reversible and non-rigid connections to form a loose raft, apparently connected via flagella. Inhibitors of swarming (p-Nitrophenylglycerol and Congo Red) were identified. Mitomycin C was used to trigger filamentation without inhibiting growth or swarming; this facilitated dissection of the detail of swarming. Mitomycin C treatment resulted in malcoordinated swarming and abortive side branch formation and a strong tendency by a subpopulation of the cells to form minimal rotating aggregates of only a few cells. Conclusion P. vortex creates complex macroscopic colonies within which there is considerable reflux and movement and interaction of cells. Cell shape, flagellation, the aversion of cell masses to fuse and temporary connections between proximate cells to form rafts were all features of the swarming and rotation of cell aggregates. Vigorous vortex formation was social, i.e. required > 1 cell. This is the first detailed examination of the swarming behaviour of this bacterium at the cellular level.</p
Charging effects in mesoscopic tunnel junctions.
No full textIt is now possible to fabricate extremely small tunnel junctions with a capacitance C < 10\sp{-15}F. In such a case the charging energy e\sp2/2 can be larger than the thermal energy , and many novel effects are possible. We examine the theory of single tunnel junctions in the semiclassical and coherent limits, and determine the effect of the charging energy on junction dynamics in the two models. The predicted experimental signature of the two approaches, including I-V characteristics, hysterisis, effect of an alternating current, noise and power spectra, are discussed in detail. Understanding of the coherent model requires a detailed understanding of the dynamics of Zener tunnelling. We define a new quantity, the Zener time, which describes the time for a Zener transition, and calculate it in the sudden and adiabatic limits. We also derive expressions for the Zener tunnelling probability at finite times. We then look at two junction connected in series and driven by a voltage source in the semiclassical model. Using stochastic simulations and a master equation approach we show how such a system can have a staircase I-V characteristics. Relevant experiments are reviewed. We go on to show how this may be related to tunneling measurements on granular high T\sb{\rm c} superconductors. We discuss possible device applications, such as transistors and switches. We conclude with an effective equation approach for the semiclassical model, which gives the approximate dynamics of the stochastic process. This approach is then extended to a chain of junctions, and is used to demonstrate the possibility of a new collective excitation, the charge effect soliton. We discuss the soliton solution in detail, and consider its experimental consequences.PhDCondensed matter physicsElectromagneticsPure SciencesUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/128383/2/9001686.pd
Towards the "baby connectome": mapping the structural connectivity of the newborn brain.
No full textDefining the structural and functional connectivity of the human brain (the human "connectome") is a basic challenge in neuroscience. Recently, techniques for noninvasively characterizing structural connectivity networks in the adult brain have been developed using diffusion and high-resolution anatomic MRI. The purpose of this study was to establish a framework for assessing structural connectivity in the newborn brain at any stage of development and to show how network properties can be derived in a clinical cohort of six-month old infants sustaining perinatal hypoxic ischemic encephalopathy (HIE). Two different anatomically unconstrained parcellation schemes were proposed and the resulting network metrics were correlated with neurological outcome at 6 months. Elimination and correction of unreliable data, automated parcellation of the cortical surface, and assembling the large-scale baby connectome allowed an unbiased study of the network properties of the newborn brain using graph theoretic analysis. In the application to infants with HIE, a trend to declining brain network integration and segregation was observed with increasing neuromotor deficit scores
Encouraging expressions affect the brain and alter visual attention.
No full textBACKGROUND:Very often, encouraging or discouraging expressions are used in competitive contexts, such as sports practice, aiming at provoking an emotional reaction on the listener and, consequently, an effect on subsequent cognition and/or performance. However, the actual efficiency of these expressions has not been tested scientifically. METHODOLOGY/PRINCIPAL FINDINGS:To fill this gap, we studied the effects of encouraging, discouraging, and neutral expressions on event-related brain electrical activity during a visual selective attention task in which targets were determined by location, shape, and color. Although the expressions preceded the attentional task, both encouraging and discouraging messages elicited a similar long-lasting brain emotional response present during the visuospatial task. In addition, encouraging expressions were able to alter the customary working pattern of the visual attention system for shape selection in the attended location, increasing the P1 and the SP modulations while simultaneously fading away the SN. CONCLUSIONS/SIGNIFICANCE:This was interpreted as an enhancement of the attentional processes for shape in the attended location after an encouraging expression. It can be stated, therefore, that encouraging expressions, as those used in sport practice, as well as in many other contexts and situations, do seem to be efficient in exerting emotional reactions and measurable effects on cognition
Node Vulnerability under Finite Perturbations in Complex Networks
No full textA measure to quantify vulnerability under perturbations (attacks, failures, large fluctuations) in ensembles (networks) of coupled dynamical systems is proposed. Rather than addressing the issue of how the network properties change upon removal of elements of the graph (the strategy followed by most of the existing methods for studying the vulnerability of a network based on its topology), here a dynamical definition of vulnerability is introduced, referring to the robustness of a collective dynamical state to perturbing events occurring over a fixed topology. In particular, we study how the collective (synchronized) dynamics of a network of chaotic units is disrupted under the action of a finite size perturbation on one of its nodes. Illustrative examples are provided for three systems of identical chaotic oscillators coupled according to three distinct well-known network topologies. A quantitative comparison between the obtained vulnerability rankings and the classical connectivity/centrality rankings is made that yields conclusive results. Possible applications of the proposed strategy and conclusions are also discussed
The birth-death-mutation process: a new paradigm for fat tailed distributions.
No full textFat tailed statistics and power-laws are ubiquitous in many complex systems. Usually the appearance of of a few anomalously successful individuals (bio-species, investors, websites) is interpreted as reflecting some inherent "quality" (fitness, talent, giftedness) as in Darwin's theory of natural selection. Here we adopt the opposite, "neutral", outlook, suggesting that the main factor explaining success is merely luck. The statistics emerging from the neutral birth-death-mutation (BDM) process is shown to fit marvelously many empirical distributions. While previous neutral theories have focused on the power-law tail, our theory economically and accurately explains the entire distribution. We thus suggest the BDM distribution as a standard neutral model: effects of fitness and selection are to be identified by substantial deviations from it
Single electron effects and tunneling spectroscopy with a cryogenic scanning tunneling microscope.
No full textWe study experimentally tunnel junction systems that involve a very small conductive element (typical length scale of 100A). In these so-called mesoscopic tunnel junctions, the capacitive charging energy is larger than the thermal energy at the experimental temperatures (4.2K). Experimental problems realizing current-driven single junction charging effects motivate the consideration of two serially connected junctions driven by a voltage source. A brief theoretical treatment based on the semi-classical model for this system is presented, including details for an analytic solution for the calculation of current-voltage (I-V) characteristics. Basic physical assumptions used in the theoretical account are stated. A historical perspective on tunneling spectroscopy and single electron charging effects is taken for the introduction of these subjects. We describe an experiment where the STM probes an indium droplet (diameter 100A) that sits on an oxidized aluminum substrate. This system forms two mesoscopic tunnel junctions connected in series. Data in the form of a Coulomb staircase is of a quality that allows a detailed comparison to a theory based on the semi-classical model of mesoscopic tunnel junctions. The data shows that the typical capacitance associated with the droplets is 10\sp{-18}F. We conclude that the double junction system views the external circuit as an ideal voltage source (the effective source can respond during the time of tunneling), and that the electronic states of the droplet can be considered continuous. We examine single junctions formed with the STM and find that surface oxide effects of both the tip and sample can mask spectroscopic information of the underlying metals, such as a superconducting density of states. We present strong evidence that in some cases capacitive charging effects taking place within the oxides are responsible for the masking effect. The observation of Coulomb staircases in the I-V characteristics at some sites on bulk etched tungsten provide this evidence. These measurements lead to a much different interpretation of Coulomb blockade-like I-V characteristics measured with a cryogenic STM. Possible implications for other tunnel junction systems are discussed. Finally, we present a tunneling spectroscopy study of superconducting thin film YBa\sb2Cu\sb3O\sb7 (T\sb c \sim 85\rm K). Common in the data are Coulomb staircases, indicating charging effects taking place in the granular films. We fit an example of such an I-V characteristic. Our results provide a better understanding of what role charging effects play in the properties of high-T\sb c superconducting films. The most common type of I-V characteristic observed has a region of high conductance about zero bias. We present plausible explanations for this phenomena. We also present and discuss data showing negative differential resistance and BCS gap-like structure.PhDPhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/105471/1/9124138.pdfDescription of 9124138.pdf : Restricted to UM users only
Abstract 5568: Towards decoding the interplay between glycolysis and oxidative phosphorylation in cancer
No full textAbstract
Abnormal metabolism is a hallmark of cancer, yet its regulatory mechanism is poorly understood. Cancer cells were considered to mostly utilize glycolysis, referred to as the Warburg effect. However recent evidence suggests that oxidative phosphorylation also plays a crucial role during cancer progression. Here we utilized a systems biology approach to decipher the regulatory principle of glycolysis and oxidative phosphorylation. Integrating information from literature, we constructed a regulatory network of genes and metabolites, from which we extracted a core circuit containing HIF-1, AMPK and ROS. Our circuit analysis showed that while normal cells have an oxidative state and a glycolytic state, cancer cells can access an additional hybrid state with both metabolic modes coexisting, due to higher ROS production and/or oncogenic activation, such as RAS, MYC and c-SRC. The anti-correlation between AMPK and HIF-1 and the association of metabolic states with oncogenes were further confirmed using TCGA patient transcriptomics data of multiple cancer types and single-cell RNA-seq data of lung adenocarcinoma. We propose that the hybrid phenotype contributes to metabolic plasticity, allowing cancer cells to adapt to various microenvironments. Using model simulations, we predicted the efficacies of several metabolic cancer therapies based on their effectiveness in reducing metabolic plasticity. Our theoretical framework of metabolism can serve as a platform to decode cancer metabolic plasticity and design cancer therapies targeting metabolism.
Citation Format: Dongya Jia, Linglin Yu, Mingyang Lu, Eshel Ben-Jacob, Jianpeng Ma, Herbert Levine, Benny A. Kaipparettu, Jose Onuchic. Towards decoding the interplay between glycolysis and oxidative phosphorylation in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5568. doi:10.1158/1538-7445.AM2017-5568</jats:p
Finding Statistically Significant Communities in Networks
No full textCommunity structure is one of the main structural features of networks, revealing both their internal organization and the similarity of their elementary units. Despite the large variety of methods proposed to detect communities in graphs, there is a big need for multi-purpose techniques, able to handle different types of datasets and the subtleties of community structure. In this paper we present OSLOM (Order Statistics Local Optimization Method), the first method capable to detect clusters in networks accounting for edge directions, edge weights, overlapping communities, hierarchies and community dynamics. It is based on the local optimization of a fitness function expressing the statistical significance of clusters with respect to random fluctuations, which is estimated with tools of Extreme and Order Statistics. OSLOM can be used alone or as a refinement procedure of partitions/covers delivered by other techniques. We have also implemented sequential algorithms combining OSLOM with other fast techniques, so that the community structure of very large networks can be uncovered. Our method has a comparable performance as the best existing algorithms on artificial benchmark graphs. Several applications on real networks are shown as well. OSLOM is implemented in a freely available software (http://www.oslom.org), and we believe it will be a valuable tool in the analysis of networks.The project ICTeCollective acknowledges the financial support of the Future and Emerging
Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, under FET-Open grant number 238597. The
funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewe
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