Improving resolution in multidimensional NMR using random quadrature detection with compressed sensing reconstruction.

NMR spectroscopy is central to atomic resolution studies in biology and chemistry. Key to this approach are multidimensional experiments. Obtaining such experiments with sufficient resolution, however, is a slow process, in part since each time increment in every indirect dimension needs to be recorded twice, in quadrature. We introduce a modified compressed sensing (CS) algorithm enabling reconstruction of data acquired with random acquisition of quadrature components in gradient-selection NMR. We name this approach random quadrature detection (RQD). Gradient-selection experiments are essential to the success of modern NMR and with RQD, a 50 % reduction in the number of data points per indirect dimension is possible, by only acquiring one quadrature component per time point. Using our algorithm (CSRQD), high quality reconstructions are achieved. RQD is modular and combined with non-uniform sampling we show that this provides increased flexibility in designing sampling schedules leading to improved resolution with increasing benefits as dimensionality of experiments increases, with particular advantages for 4- and higher dimensional experiments.Part of this work was performed using the Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and funding from the Science and Technology Facilities Council.This is the final version of the article. It first appeared from Springer via https://doi.org/10.1007/s10858-016-0062-

Accommodation to hyperpolarization of human axons assessed in the frequency domain

Human axonsin vivowere subjected to subthreshold currents with a threshold-"ZAP" profile (Impedance [ Z: ] A: mplitude P: rofile) to allow the use of frequency domain techniques to determine the propensity for resonant behavior, and to clarify the relative contributions of different ion channels to their low-frequency responsiveness. Twenty-four studies were performed on the motor and sensory axons in 6 subjects. The response to oscillatory currents was tested between 'DC' and 16 Hz. A resonant peak at ~2 to 2.5 Hz was found in the response of hyperpolarized axons, but there was only a small broad response in axons at resting membrane potential (RMP). A mathematical model of axonal excitability developed using DC pulses provided a good fit to the frequency response for human axons, and indicated that the hyperpolarization-activated currentIh, and the slow potassium currentIKsare principally responsible for the resonance. However the results indicate that if axons are hyperpolarized more than -60% of resting threshold, the only conductances that are appreciably active areIhand the leak conductance - i.e., that the activity of these conductances can be studiedin vivovirtually in isolation at hyperpolarized membrane potentials. Given that the leak conductance dampens resonance it is suggested that the -60% hyperpolarization used here is optimal forIh As expected differences between the frequency responses of motor and sensory axons were present and best explained by reduced GKs, up-modulation ofIhand increased persistent Na(+)current,INaP(due to depolarization of RMP) in sensory axons

Peacock Bundles: Bundle Coloring for Graphs with Globality-Locality Trade-off

Bundling of graph edges (node-to-node connections) is a common technique to enhance visibility of overall trends in the edge structure of a large graph layout, and a large variety of bundling algorithms have been proposed. However, with strong bundling, it becomes hard to identify origins and destinations of individual edges. We propose a solution: we optimize edge coloring to differentiate bundled edges. We quantify strength of bundling in a flexible pairwise fashion between edges, and among bundled edges, we quantify how dissimilar their colors should be by dissimilarity of their origins and destinations. We solve the resulting nonlinear optimization, which is also interpretable as a novel dimensionality reduction task. In large graphs the necessary compromise is whether to differentiate colors sharply between locally occurring strongly bundled edges ("local bundles"), or also between the weakly bundled edges occurring globally over the graph ("global bundles"); we allow a user-set global-local tradeoff. We call the technique "peacock bundles". Experiments show the coloring clearly enhances comprehensibility of graph layouts with edge bundling.Comment: Appears in the Proceedings of the 24th International Symposium on Graph Drawing and Network Visualization (GD 2016

In vivo assessment of muscle membrane properties in myotonic dystrophy

INTRODUCTION: Myotonia in myotonic dystrophy types 1 (DM1) and 2 (DM2) is generally attributed to reduced chloride channel conductance. We used muscle velocity recovery cycles (MVRCs) to investigate muscle membrane properties in DM1 and DM2, with comparisons with myotonia congenita (MC). METHODS: MVRCs and responses to repetitive stimulation were compared between patients with DM1 (n=18), DM2 (n=5), MC (n=18), and normal controls (n=20). RESULTS: Both DM1 and DM2 showed enhanced late supernormality after multiple conditioning stimuli, indicating delayed repolarization as in MC. Contrary to MC, however, DM1 showed reduced early supernormality after multiple conditioning stimuli, and weak DM1 patients also showed abnormally slow latency recovery after repetitive stimulation. DISCUSSION: These findings support impaired chloride conductance in both DM1 and DM2. The early supernormality changes indicate that sodium currents were reduced in DM1, while the weakness-associated slow recovery after repetitive stimulation may provide an indication of reduced Na(+) /K(+) -ATPase activation

Coccolithophore biodiversity controls carbonate export in the Southern Ocean

Southern Ocean waters are projected to undergo profound changes in their physical and chemical properties in the coming decades. Coccolithophore blooms in the Southern Ocean are thought to account for a major fraction of the global marine calcium carbonate (CaCO3) production and export to the deep sea. Therefore, changes in the composition and abundance of Southern Ocean coccolithophore populations are likely to alter the marine carbon cycle, with feedbacks to the rate of global climate change. However, the contribution of coccolithophores to CaCO3 export in the Southern Ocean is uncertain, particularly in the circumpolar subantarctic zone that represents about half of the areal extent of the Southern Ocean and where coccolithophores are most abundant. Here, we present measurements of annual CaCO3 flux and quantitatively partition them amongst coccolithophore species and heterotrophic calcifiers at two sites representative of a large portion of the subantarctic zone. We find that coccolithophores account for a major fraction of the annual CaCO3 export, with the highest contributions in waters with low algal biomass accumulations. Notably, our analysis reveals that although Emiliania huxleyi is an important vector for CaCO3 export to the deep sea, less abundant but larger species account for most of the annual coccolithophore CaCO3 flux. This observation contrasts with the generally accepted notion that high particulate inorganic carbon accumulations during the austral summer in the subantarctic Southern Ocean are mainly caused by E. huxleyi blooms. It appears likely that the climate-induced migration of oceanic fronts will initially result in the poleward expansion of large coccolithophore species increasing CaCO3 production. However, subantarctic coccolithophore populations will eventually diminish as acidification overwhelms those changes. Overall, our analysis emphasizes the need for species-centred studies to improve our ability to project future changes in phytoplankton communities and their influence on marine biogeochemical cycles.info:eu-repo/semantics/publishedVersio

Structural insights into the mechanism of negative regulation of single-box high mobility group proteins by the acidic tail domain.

The Drosophila and plant (maize) functional counterparts of the abundant vertebrate chromosomal protein HMGB1 (HMG-D and ZmHMGB1, respectively) differ from HMGB1 in having a single HMG box, as well as basic and acidic flanking regions that vary greatly in length and charge. We show that despite these variations, HMG-D and ZmHMGB1 exist in dynamic assemblies in which the basic HMG boxes and linkers associate with their intrinsically disordered, predominantly acidic, tails in a manner analogous to that observed previously for HMGB1. The DNA-binding surfaces of the boxes and linkers are occluded in "auto-inhibited" forms of the protein, which are in equilibrium with transient, more open structures that are "binding-competent." This strongly suggests that the mechanism of auto-inhibition may be a general one. HMG-D and ZmHMGB1 differ from HMGB1 in having phosphorylation sites in their tail and linker regions. In both cases, in vitro phosphorylation of serine residues within the acidic tail stabilizes the assembled form, suggesting another level of regulation for interaction with DNA, chromatin, and other proteins that is not possible for the uniformly acidic (hence unphosphorylatable) tail of HMGB1.This work was supported by the Biotechnology and Biological Sciences Research Council through the award of Grant BB/D002257/1 (to J. O. T.) and a grant from the Deutsche Forschungsgemeinschaft (DFG) (to K. D. G.).This is the final published version. It first appeared at http://www.jbc.org/content/289/43/29817.long

The Gregory-Laflamme instability for the D2-D0 bound state

The D2-D0 bound state exhibits a Gregory-Laflamme instability when it is sufficiently non-extremal. If there are no D0-branes, the requisite non-extremality is finite. When most of the extremal mass comes from D0-branes, the requisite non-extremality is very small. The location of the threshhold for the instability is determined using a local thermodynamic analysis which is then checked against a numerical analysis of the linearized equations of motion. The thermodynamic analysis reveals an instability of non-commutative field theory at finite temperature, which may occur only at very long wavelengths as the decoupling limit is approached.Comment: 19 pages, Latex2e. v2: two refs added. v3: clearer exposition in section

Array-conditioned deconvolution of multiple component teleseismic recordings

We investigate the applicability of an array-conditioned deconvolution technique, developed for analyzing borehole seismic exploration data, to teleseismic receiver functions and data preprocessing steps for scattered wavefield imaging. This multichannel deconvolution technique constructs an approximate inverse filter to the estimated source signature by solving an overdetermined set of deconvolution equations, using an array of receivers detecting a common source. We find that this technique improves the efficiency and automation of receiverfunction calculation and data preprocessing workflow. We apply this technique to synthetic experiments and to teleseismic data recorded in a dense array in northern Canada. Our results show that this optimal deconvolution automatically determines and subsequently attenuates the noise from data, enhancing P-to-S converted phases in seismograms with various noise levels. In this context, the array-conditioned deconvolution presents a new, effective and automatic means for processing large amounts of array data, as it does not require any ad-hoc regularization; the regularization is achieved naturally by using the noise present in the array itself

Conceptually driven and visually rich tasks in texts and teaching practice: the case of infinite series

The study we report here examines parts of what Chevallard calls the institutional dimension of the students’ learning experience of a relatively under-researched, yet crucial, concept in Analysis, the concept of infinite series. In particular, we examine how the concept is introduced to students in texts and in teaching practice. To this purpose, we employ Duval's Theory of Registers of Semiotic Representation towards the analysis of 22 texts used in Canada and UK post-compulsory courses. We also draw on interviews with in-service teachers and university lecturers in order to discuss briefly teaching practice and some of their teaching suggestions. Our analysis of the texts highlights that the presentation of the concept is largely a-historical, with few graphical representations, few opportunities to work across different registers (algebraic, graphical, verbal), few applications or intra-mathematical references to the concept's significance and few conceptually driven tasks that go beyond practising with the application of convergence tests and prepare students for the complex topics in which the concept of series is implicated. Our preliminary analysis of the teacher interviews suggests that pedagogical practice often reflects the tendencies in the texts. Furthermore, the interviews with the university lecturers point at the pedagogical potential of: illustrative examples and evocative visual representations in teaching; and, student engagement with systematic guesswork and writing explanatory accounts of their choices and applications of convergence tests