A comparison of incompressible limits for resistive plasmas

The constraint of incompressibility is often used to simplify the magnetohydrodynamic (MHD) description of linearized plasma dynamics because it does not affect the ideal MHD marginal stability point. In this paper two methods for introducing incompressibility are compared in a cylindrical plasma model: In the first method, the limit $\gamma \to \infty$ is taken, where $\gamma$ is the ratio of specific heats; in the second, an anisotropic mass tensor $\mathbf{\rho}$ is used, with the component parallel to the magnetic field taken to vanish, $\rho_{\parallel} \to 0$. Use of resistive MHD reveals the nature of these two limits because the Alfv\'en and slow magnetosonic continua of ideal MHD are converted to point spectra and moved into the complex plane. Both limits profoundly change the slow-magnetosonic spectrum, but only the second limit faithfully reproduces the resistive Alfv\'en spectrum and its wavemodes. In ideal MHD, the slow magnetosonic continuum degenerates to the Alfv\'en continuum in the first method, while it is moved to infinity by the second. The degeneracy in the first is broken by finite resistivity. For numerical and semi-analytical study of these models, we choose plasma equilibria which cast light on puzzling aspects of results found in earlier literature.Comment: 14 pages, 10 figure

Credimus

We believe that economic design and computational complexity---while already important to each other---should become even more important to each other with each passing year. But for that to happen, experts in on the one hand such areas as social choice, economics, and political science and on the other hand computational complexity will have to better understand each other's worldviews. This article, written by two complexity theorists who also work in computational social choice theory, focuses on one direction of that process by presenting a brief overview of how most computational complexity theorists view the world. Although our immediate motivation is to make the lens through which complexity theorists see the world be better understood by those in the social sciences, we also feel that even within computer science it is very important for nontheoreticians to understand how theoreticians think, just as it is equally important within computer science for theoreticians to understand how nontheoreticians think

Comparison of two non-primitive methods for path integral simulations: Higher-order corrections vs. an effective propagator approach

Two methods are compared that are used in path integral simulations. Both methods aim to achieve faster convergence to the quantum limit than the so-called primitive algorithm (PA). One method, originally proposed by Takahashi and Imada, is based on a higher-order approximation (HOA) of the quantum mechanical density operator. The other method is based upon an effective propagator (EPr). This propagator is constructed such that it produces correctly one and two-particle imaginary time correlation functions in the limit of small densities even for finite Trotter numbers P. We discuss the conceptual differences between both methods and compare the convergence rate of both approaches. While the HOA method converges faster than the EPr approach, EPr gives surprisingly good estimates of thermal quantities already for P = 1. Despite a significant improvement with respect to PA, neither HOA nor EPr overcomes the need to increase P linearly with inverse temperature. We also derive the proper estimator for radial distribution functions for HOA based path integral simulations.Comment: 17 pages, latex, 6 postscript figure

Formation and Interaction of Membrane Tubes

We show that the formation of membrane tubes (or membrane tethers), which is a crucial step in many biological processes, is highly non-trivial and involves first order shape transitions. The force exerted by an emerging tube is a non-monotonic function of its length. We point out that tubes attract each other, which eventually leads to their coalescence. We also show that detached tubes behave like semiflexible filaments with a rather short persistence length. We suggest that these properties play an important role in the formation and structure of tubular organelles.Comment: 4 pages, 3 figure

Cisternal Organization of the Endoplasmic Reticulum during Mitosis

The endoplasmic reticulum (ER) of animal cells is a single, dynamic, and continuous membrane network of interconnected cisternae and tubules spread out throughout the cytosol in direct contact with the nuclear envelope. During mitosis, the nuclear envelope undergoes a major rearrangement, as it rapidly partitions its membrane-bound contents into the ER. It is therefore of great interest to determine whether any major transformation in the architecture of the ER also occurs during cell division. We present structural evidence, from rapid, live-cell, three-dimensional imaging with confirmation from high-resolution electron microscopy tomography of samples preserved by high-pressure freezing and freeze substitution, unambiguously showing that from prometaphase to telophase of mammalian cells, most of the ER is organized as extended cisternae, with a very small fraction remaining organized as tubules. In contrast, during interphase, the ER displays the familiar reticular network of convolved cisternae linked to tubules

Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage

Platy-1 elements are Platyrrhine-specific, short interspersed elements (SINEs) originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared to the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared to their respective consensus sequences, suggesting minimal ongoing retrotransposition in Aotus genus and no current activity in the Saimiri, Cebus and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes

A High-Resolution Multimode Digital Microscope System

In this chapter we describe the development of a high-resolution, multimode digital imaging system based on a wide-field epifluorescent and transmitted light microscope and a cooled charge-coupled device (CCD) camera. Taylor and colleagues (Farkas et al., 1993; Taylor et al., 1992) have reviewed the advantages of using multiple optical modes to obtain quantitative information about cellular processes and described instrumentation they have developed for multimode digital imaging. The instrument described here is somewhat specialized for our microtubule and mitosis studies, but it is also applicable to a variety of problems in cellular imaging including tracking proteins fused to the green fluorescent protein (GFP) in live cells (Cubitt et al., 1995; Heim and Tsien, 1996; Olson et al., 1995). For example, the instrument has been valuable for correlating the assembly dynamics of individual cytoplasmic microtubules (labeled by conjugating X-rhodamine to tubulin) with the dynamics of membranes of the endoplasmic reticulum (ER, labeled with DiOC6) and the dynamics of the cell cortex [by differential interference contrast (DIC)] in migrating vertebrate epithelial cells (Waterman-Storer and Salmon, 1997). The instrument has also been important in the analysis of mitotic mutants in the powerful yeast genetic system Saccharo-myces cerevisiae. Yeast cells are a major challenge for high-resolution imaging of nuclear or microtubule dynamics because the preanaphase nucleus is only about 2 μm wide in a cell about 6 μm wide. We have developed methods for visualizing nuclear and spindle dynamics during the cell cycle using high-resolution digitally enhanced DIC (DE-DIC) imaging (Yang et al., 1997; Yeh et al., 1995). Using genetic and molecular techniques. Bloom and coworkers (Shaw et al., 1997a,b) have been able to label the cytoplasmic astral microtubules in dividing yeast cells by expression of cytoplasmic dynein fused to GFP. Overlays of GFP and DIC images of dividing cells have provided the opportunity to see for the first time the dynamics of cytoplasmic microtubules in live yeast cells and how these dynamics and microtubule interactions with the cell cortex change with mitotic cell cycle events in wild-type and in mutant strains (Shaw et al., 1997a,b)

Metabolite profiles of medulloblastoma for rapid and non-invasive detection of molecular disease groups

\ua9 2024 The AuthorsBackground: The malignant childhood brain tumour, medulloblastoma, is classified clinically into molecular groups which guide therapy. DNA-methylation profiling is the current classification ‘gold-standard’, typically delivered 3–4 weeks post-surgery. Pre-surgery non-invasive diagnostics thus offer significant potential to improve early diagnosis and clinical management. Here, we determine tumour metabolite profiles of the four medulloblastoma groups, assess their diagnostic utility using tumour tissue and potential for non-invasive diagnosis using in vivo magnetic resonance spectroscopy (MRS). Methods: Metabolite profiles were acquired by high-resolution magic-angle spinning NMR spectroscopy (MAS) from 86 medulloblastomas (from 59 male and 27 female patients), previously classified by DNA-methylation array (WNT (n = 9), SHH (n = 22), Group3 (n = 21), Group4 (n = 34)); RNA-seq data was available for sixty. Unsupervised class-discovery was performed and a support vector machine (SVM) constructed to assess diagnostic performance. The SVM classifier was adapted to use only metabolites (n = 10) routinely quantified from in vivo MRS data, and re-tested. Glutamate was assessed as a predictor of overall survival. Findings: Group-specific metabolite profiles were identified; tumours clustered with good concordance to their reference molecular group (93%). GABA was only detected in WNT, taurine was low in SHH and lipids were high in Group3. The tissue-based metabolite SVM classifier had a cross-validated accuracy of 89% (100% for WNT) and, adapted to use metabolites routinely quantified in vivo, gave a combined classification accuracy of 90% for SHH, Group3 and Group4. Glutamate predicted survival after incorporating known risk-factors (HR = 3.39, 95% CI 1.4–8.1, p = 0.025). Interpretation: Tissue metabolite profiles characterise medulloblastoma molecular groups. Their combination with machine learning can aid rapid diagnosis from tissue and potentially in vivo. Specific metabolites provide important information; GABA identifying WNT and glutamate conferring poor prognosis. Funding: Children with Cancer UK, Cancer Research UK, Children\u27s Cancer North and a Newcastle University PhD studentship

Актуальність впровадження систем газового обліку в сучасних умовах

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.QC 20150505</p

Limits on the ultra-bright Fast Radio Burst population from the CHIME Pathfinder

We present results from a new incoherent-beam Fast Radio Burst (FRB) search on the Canadian Hydrogen Intensity Mapping Experiment (CHIME) Pathfinder. Its large instantaneous field of view (FoV) and relative thermal insensitivity allow us to probe the ultra-bright tail of the FRB distribution, and to test a recent claim that this distribution's slope, $\alpha\equiv-\frac{\partial \log N}{\partial \log S}$, is quite small. A 256-input incoherent beamformer was deployed on the CHIME Pathfinder for this purpose. If the FRB distribution were described by a single power-law with $\alpha=0.7$, we would expect an FRB detection every few days, making this the fastest survey on sky at present. We collected 1268 hours of data, amounting to one of the largest exposures of any FRB survey, with over 2.4\,$\times$\,10$^5$\,deg$^2$\,hrs. Having seen no bursts, we have constrained the rate of extremely bright events to $<\!13$\,sky$^{-1}$\,day$^{-1}$ above $\sim$\,220$\sqrt{(\tau/\rm ms)}$ Jy\,ms for $\tau$ between 1.3 and 100\,ms, at 400--800\,MHz. The non-detection also allows us to rule out $\alpha\lesssim0.9$ with 95$\%$ confidence, after marginalizing over uncertainties in the GBT rate at 700--900\,MHz, though we show that for a cosmological population and a large dynamic range in flux density, $\alpha$ is brightness-dependent. Since FRBs now extend to large enough distances that non-Euclidean effects are significant, there is still expected to be a dearth of faint events and relative excess of bright events. Nevertheless we have constrained the allowed number of ultra-intense FRBs. While this does not have significant implications for deeper, large-FoV surveys like full CHIME and APERTIF, it does have important consequences for other wide-field, small dish experiments