A microtubule RELION-based pipeline for cryo-EM image processing

Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins

Vacuum structure for expanding geometry

We consider gravitational wave modes in the FRW metrics in a de Sitter phase and show that the state space splits into many unitarily inequivalent representations of the canonical commutation relations. Non-unitary time evolution is described as a trajectory in the space of the representations. The generator of time evolution is related to the entropy operator. The thermodynamic arrow of time is shown to point in the same direction of the cosmological arrow of time. The vacuum is a two-mode SU(1,1) squeezed state of thermo field dynamics. The link between expanding geometry, squeezing and thermal properties is exhibited.Comment: Latex file, epsfig, 1 figure, 21 page

Prion propagation is dependent on key amino acids in Charge cluster 2 within the prion protein

To dissect the N-terminal residues within the cellular prion protein (PrPC) that are critical for efficient prion propagation, we generated a library of point, double, or triple alanine replacements within residues 23-111 of PrP, stably expressed them in cells silenced for endogenous mouse PrPC and challenged the reconstituted cells with four common but biologically diverse mouse prion strains. Amino acids (aa) 105-111 of Charge Cluster 2 (CC2), which is disordered in PrPC, were found to be required for propagation of all four prion strains; other residues had no effect or exhibited strain-specific effects. Replacements in CC2, including aa105-111, dominantly inhibited prion propagation in the presence of endogenous wild type PrPC whilst other changes were not inhibitory. Single alanine replacements within aa105-111 identified leucine 108 and valine 111 or the cluster of lysine 105, threonine 106 and asparagine 107 as critical for prion propagation. These residues mediate specific ordering of unstructured CC2 into β-sheets in the infectious prion fibrils from Rocky Mountain Laboratory (RML) and ME7 mouse prion strains

Narrow Spectral Feature In Resonance Fluorescence With A Single Monochromatic Laser Field

We describe the resonance fluorescence spectrum of an atomic three-level system where two of the states are coupled by a single monochromatic laser field. The influence of the third energy level, which interacts with the two laser-coupled states only via radiative decays, is studied in detail. For a suitable choice of parameters, this system gives rise to a very narrow structure at the laser frequency in the fluorescence spectrum which is not present in the spectrum of a two-level atom. We find those parameter ranges by a numerical analysis and use the results to derive analytical expressions for the additional narrow peak. We also derive an exact expression for the peak intensity under the assumption that a random telegraph model is applicable to the system. This model and a simple spring model are then used to describe the physical origins of the additional peak. Using these results, we explain the connection between our system, a three-level system in V-configuration where both transitions are laser driven, and a related experiment which was recently reported.Comment: 14 pages, 15 figures, extension of the spring mode

Quantum jumps induced by the center-of-mass motion of a trapped atom

We theoretically study the occurrence of quantum jumps in the resonance fluorescence of a trapped atom. Here, the atom is laser cooled in a configuration of level such that the occurrence of a quantum jump is associated to a change of the vibrational center-of-mass motion by one phonon. The statistics of the occurrence of the dark fluorescence period is studied as a function of the physical parameters and the corresponding features in the spectrum of resonance fluorescence are identified. We discuss the information which can be extracted on the atomic motion from the observation of a quantum jump in the considered setup

Line Graphs of Weighted Networks for Overlapping Communities

In this paper, we develop the idea to partition the edges of a weighted graph in order to uncover overlapping communities of its nodes. Our approach is based on the construction of different types of weighted line graphs, i.e. graphs whose nodes are the links of the original graph, that encapsulate differently the relations between the edges. Weighted line graphs are argued to provide an alternative, valuable representation of the system's topology, and are shown to have important applications in community detection, as the usual node partition of a line graph naturally leads to an edge partition of the original graph. This identification allows us to use traditional partitioning methods in order to address the long-standing problem of the detection of overlapping communities. We apply it to the analysis of different social and geographical networks.Comment: 8 Pages. New title and text revisions to emphasise differences from earlier paper

Role of electromagnetically induced transparency in resonant four-wave-mixing schemes.

Published versio

Cavity implementation of quantum interference in a Λ\Lambda-type atom

A scheme for engineering quantum interference in a $\Lambda$-type atom coupled to a frequency-tunable, single-mode cavity field with a pre-selected polarization at finite temperature is proposed. Interference-assisted population trapping, population inversions and probe gain at one sideband of the Autler-Townes spectrum are predicted for certain cavity resonant frequencies.Comment: 2 postscript figures are adde

Clinical quantitative cardiac imaging for the assessment of myocardial ischaemia

Cardiac imaging has a pivotal role in the prevention, diagnosis and treatment of ischaemic heart disease. SPECT is most commonly used for clinical myocardial perfusion imaging, whereas PET is the clinical reference standard for the quantification of myocardial perfusion. MRI does not involve exposure to ionizing radiation, similar to echocardiography, which can be performed at the bedside. CT perfusion imaging is not frequently used but CT offers coronary angiography data, and invasive catheter-based methods can measure coronary flow and pressure. Technical improvements to the quantification of pathophysiological parameters of myocardial ischaemia can be achieved. Clinical consensus recommendations on the appropriateness of each technique were derived following a European quantitative cardiac imaging meeting and using a real-time Delphi process. SPECT using new detectors allows the quantification of myocardial blood flow and is now also suited to patients with a high BMI. PET is well suited to patients with multivessel disease to confirm or exclude balanced ischaemia. MRI allows the evaluation of patients with complex disease who would benefit from imaging of function and fibrosis in addition to perfusion. Echocardiography remains the preferred technique for assessing ischaemia in bedside situations, whereas CT has the greatest value for combined quantification of stenosis and characterization of atherosclerosis in relation to myocardial ischaemia. In patients with a high probability of needing invasive treatment, invasive coronary flow and pressure measurement is well suited to guide treatment decisions. In this Consensus Statement, we summarize the strengths and weaknesses as well as the future technological potential of each imaging modality

Detection of a strongly negative surface potential at Saturn's moon Hyperion

On 26 September 2005, Cassini conducted its only close targeted flyby of Saturn's small, irregularly shaped moon Hyperion. Approximately 6 min before the closest approach, the electron spectrometer (ELS), part of the Cassini Plasma Spectrometer (CAPS) detected a field-aligned electron population originating from the direction of the moon's surface. Plasma wave activity detected by the Radio and Plasma Wave instrument suggests electron beam activity. A dropout in energetic electrons was observed by both CAPS-ELS and the Magnetospheric Imaging Instrument Low-Energy Magnetospheric Measurement System, indicating that the moon and the spacecraft were magnetically connected when the field-aligned electron population was observed. We show that this constitutes a remote detection of a strongly negative (~ −200 V) surface potential on Hyperion, consistent with the predicted surface potential in regions near the solar terminator