Direct Distance Measurements Research Articles

Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis.

Ribonucleotide reductases (RNRs) catalyze conversion of ribonucleotides to deoxyribonucleotides in all organisms via a free-radical mechanism that is essentially conserved. In class I RNRs, the reaction is initiated and terminated by radical translocation (RT) between the α and β subunits. In the class Ic RNR from Chlamydia trachomatis (Ct RNR), the initiating event converts the active S = 1 Mn(IV)/Fe(III) cofactor to the S = 1/2 Mn(III)/Fe(III) "RT-product" form in the β subunit and generates a cysteinyl radical in the α active site. The radical can be trapped via the well-described decomposition reaction of the mechanism-based inactivator, 2'-azido-2'-deoxyuridine-5'-diphosphate, resulting in the generation of a long-lived, nitrogen-centered radical (N(•)) in α. In this work, we have determined the distance between the Mn(III)/Fe(III) cofactor in β and N(•) in α to be 43 ± 1 Å by using double electron-electron resonance experiments. This study provides the first structural data on the Ct RNR holoenzyme complex and the first direct experimental measurement of the inter-subunit RT distance in any class I RNR.

Time delay effect between long quasi-periodic oscillations of 37 GHz radio sources and the magnetic field of the nearest sunspots

Measurements and the interpretation of the time delay effect between long quasi-periodic oscillations of sunspot magnetic fields and nearby millimeter radio sources observed at 37 GHz were the main goals of this work. Ground-based radio telescope operated by Metsahovi Radio Observatory, Aalto University, Finland was used to obtain time series variations of radio intensity at 37 GHz frequency, as well as, the Helioseismic and Magnetic Imager instrument on-board the Solar Dynamics Observatory spacecraft was used to obtain the magnetic field time series variations. Lags (time delays) in the interval of 15–35 minutes were obtained by cross-correlation analysis of time series and by direct geometrical measurements of distances between the radio sources and nearby sunspots. These distances were in the interval of 11–24 Mm. Corresponding time delays were defined as the relation of these distances to the sound speed. Time delays obtained by two different independent methods turned to be very close. This fact confirms the interpretation of the phenomenon under the study as a process of propagation of disturbances from the slowly oscillating sunspot to the radio source with the sound speed.

OPTICAL MULTI-CHANNEL INTENSITY INTERFEROMETRY - OR: HOW TO RESOLVE O-STARS IN THE MAGELLANIC CLOUDS

Intensity interferometry, based on the Hanbury Brown-Twiss effect, is a simple and inexpensive method for optical interferometry at microarcsecond angular resolutions; its use in astronomy was abandoned in the 1970s because of low sensitivity. Motivated by recent technical developments, we argue that the sensitivity of large modern intensity interferometers can be improved by factors up to approximately 25,000, corresponding to 11 photometric magnitudes, compared to the pioneering Narrabri Stellar Interferometer. This is made possible by (i) using avalanche photodiodes (APD) as light detectors, (ii) distributing the light received from the source over multiple independent spectral channels, and (iii) use of arrays composed of multiple large light collectors. Our approach permits the construction of large (with baselines ranging from few kilometers to intercontinental distances) optical interferometers at the cost of (very) long-baseline radio interferometers. Realistic intensity interferometer designs are able to achieve limiting R-band magnitudes as good as ~14, sufficient for spatially resolved observations of main-sequence O-type stars in the Magellanic Clouds. Multi-channel intensity interferometers can address a wide variety of science cases: (i) linear radii, effective temperatures, and luminosities of stars; (ii) mass-radius relationships of compact stellar remnants; (iii) stellar rotation; (iv) stellar convection and the interaction of stellar photospheres and magnetic fields; (v) the structure and evolution of multiple stars; (vi) direct measurements of interstellar distances; (vii) the physics of gas accretion onto supermassive black holes; and (viii) calibration of amplitude interferometers by providing a sample of calibrator stars.

The enhanced Russell-based directional distance measure with undesirable outputs: Numerical example considering CO2 emissions

Following the spirit of the enhanced Russell graph measure, this paper proposes an enhanced Russell-based directional distance measure (ERBDDM) model for dealing with desirable and undesirable outputs in data envelopment analysis (DEA) and allowing some inputs and outputs to be zero. The proposed method is analogous to the output oriented slacks-based measure (OSBM) and directional output distance function approach because it allows the expansion of desirable outputs and the contraction of undesirable outputs. The ERBDDM is superior to the OSBM model and traditional approach since it is not only able to identify all the inefficiency slacks just as the latter, but also avoids the misperception and misspecification of the former, which fails to identify null-jointness production of goods and bads. The paper also imposes a strong complementary slackness condition on the ERBDDM model to deal with the occurrence of multiple projections. Furthermore, we use the Penn Table data to help us explore our new approach in the context of environmental policy evaluations and guidance for performance improvements in 111 countries.

Phase-slope and phase measurements of tunable CW-THz radiation with terahertz comb for wide-dynamic-range, high-resolution, distance measurement of optically rough object.

Phase measurement of continuous-wave terahertz (CW-THz) radiation is a potential tool for direct distance and imaging measurement of optically rough objects due to its high robustness to optical rough surfaces. However, the 2π phase ambiguity in the phase measurement of single-frequency CW-THz radiation limits the dynamic range of the measured distance to the order of the wavelength used. In this article, phase-slope measurement of tunable CW-THz radiation with a THz frequency comb was effectively used to extend the dynamic range up to 1.834 m while maintaining an error of a few tens µm in the distance measurement of an optically rough object. Furthermore, a combination of phase-slope measurement of tunable CW-THz radiation and phase measurement of single-frequency CW-THz radiation enhanced the distance error to a few µm within the dynamic range of 1.834 m without any influence from the 2π phase ambiguity. The proposed method will be a powerful tool for the construction and maintenance of large-scale structures covered with optically rough surfaces.

Enhanced Monocular Visual Odometry Integrated with Laser Distance Meter for Astronaut Navigation

Visual odometry provides astronauts with accurate knowledge of their position and orientation. Wearable astronaut navigation systems should be simple and compact. Therefore, monocular vision methods are preferred over stereo vision systems, commonly used in mobile robots. However, the projective nature of monocular visual odometry causes a scale ambiguity problem. In this paper, we focus on the integration of a monocular camera with a laser distance meter to solve this problem. The most remarkable advantage of the system is its ability to recover a global trajectory for monocular image sequences by incorporating direct distance measurements. First, we propose a robust and easy-to-use extrinsic calibration method between camera and laser distance meter. Second, we present a navigation scheme that fuses distance measurements with monocular sequences to correct the scale drift. In particular, we explain in detail how to match the projection of the invisible laser pointer on other frames. Our proposed integration architecture is examined using a live dataset collected in a simulated lunar surface environment. The experimental results demonstrate the feasibility and effectiveness of the proposed method.

Profiling the Dielectric Constant at the Membrane-Peptide Interface using Ionizable EPR Probes

Polarity, electric potentials, and hydration are the major physico-chemical characteristics of lipid membranes that govern membrane-protein and protein-protein interactions as well as small molecules transport. Insertion of transmembrane proteins perturbs membrane structure altering local dielectric environment and hydration at the membrane-protein interface. The significance of distorting local membrane structure at the lipid-protein interface for modulating protein-protein interactions should not be overlooked. In this work we report on employing pH-sensitive ionizable EPR labels to profile a heterogeneous dielectric environment along the α-helix of a WALP peptide integrated in a lipid bilayer. Labels were attached to two cysteine residues positioned equidistant from the center of the peptide so that the primary sequence of each peptide is palindromic, thus insuring symmetric location of the labels with respect to the bilayer center. The change in protonation state of the nitroxide was directly observed by EPR. Q-band double electron-electron resonance (DEER) experiments were carried out to determine the distance between spin labels when imbedded in lipid bilayers to provide information about the label location. Thus, for the first time measurements of local electrostatics at peptide-bilayer interface were based on direct distance measurements rather than on assumptions on the probe location. Two pH sensitive spin labels, methanethiosulfonic acid S-(1-oxyl-2,2,3,5,5-pentamethyl-imidazolidin-4-ylmethyl) ester (IMTSL) and S-4-(4-(dimethylamino)-2-ethyl-5,5-dimethyl-1-oxyl-2,5-dihydro-1H-imidazol-2-yl) benzylmethanethiosulfonate (IKMTSL), with intrinsic pKa's differing by approximately 2 pH units were used to expand the pH range of the titration experiments. This provided the opportunity to vary the lipid composition in order to investigate effect of the surface charge on dielectric profile at peptide-membrane interface. Water penetration at the peptide-membrane interface was assessed by hyperfine sublevel correlation spectroscopy (HYSCORE) experiment in which the hyperfine coupling between the nitroxide and hydrogen/deuterium atom of water is measured. Supported by NSF-0843632 to TIS.

A Fuzzy Directional Distance Measure

The measure of distance between two fuzzy sets is a fundamental tool within fuzzy set theory, however, distance measures currently within the literature use a crisp value to represent the distance between fuzzy sets. A real valued distance measure is developed into a fuzzy distance measure which better reflects the uncertainty inherent in fuzzy sets and a fuzzy directional distance measure is presented, which accounts for the direction of change between fuzzy sets. A multiplicative version is explored as a full maximal assignment is computationally intractable so an intermediate solution is offered.

Simulations of the Local Universe constrained by observational peculiar velocities

Peculiar velocities, obtained from direct distance measurements, are data of choice to achieve constrained simulations of the Local Universe reliable down to a scale of a few Megaparsecs. Unlike redshift surveys, peculiar velocities are direct tracers of the underlying gravitational field as they trace both baryonic and dark matter. This paper presents the first attempt to use solely observational peculiar velocities to constrain cosmological simulations of the nearby universe. In order to set up Initial Conditions, a Reverse Zel'dovich Approximation (RZA) is used to displace constraints from their positions at z=0 to their precursors' locations at higher redshifts. An additional new feature replaces original observed radial peculiar velocity vectors by their full 3D reconstructions provided by the Wiener-Filter (WF) estimator. Subsequently, the Constrained Realization of Gaussian fields technique (CR) is applied to build various realizations of the Initial Conditions. The WF/RZA/CR method is first tested on realistic mock catalogs built from a reference simulation similar to the Local Universe. These mocks include errors on peculiar velocities, on data-point positions and a large continuous zone devoid of data in order to mimic galactic extinction. Large scale structures are recovered with a typical accuracy of 5 Megaparsecs/h in position, the best realizations reaching a 2-3 Mpc/h precision, the limit imposed by the RZA linear theory. Then, the method is applied to the first observational radial peculiar velocity catalog of the project Cosmicflows. This paper is a proof of concept that the WF/RZA/CR method can be applied to observational peculiar velocities to successfully build constrained Initial Conditions.

Abstract 5: The Association between Patient Rural Status, Distance to Cath Lab, and Likelihood to Undergo Coronary Angiography: Insights from the VA CART Program

Background. Prior studies suggest rural patients are less likely to receive coronary procedures. This finding may represent the fact that rural patients live further than urban patients from the closest cath lab, but these studies failed to incorporate a direct measure of distance to cath lab. Accordingly, we incorporated patient distance to cath lab with rural location on the likelihood to undergo elective coronary angiography as a better explanation of this relationship. Methods. Using national data from the VA Clinical Assessment Reporting and Tracking (CART) Program, we evaluated all patients who underwent elective coronary angiography from October 2007 through September 2010. We calculated geodesic distance from patient home to cath. Patient rural status was determined using the VA Urban/Rural/Highly Rural (URH) system. Normal coronary angiography (an indirect measure of patient selection for elective coronary angiography) was defined as <20% stenosis in all vessels. Using generalized linear mixed modeling, we estimated the probability of angiographically normal coronaries as a function of distance to cath, modified by patient rural status. Results. Among 22,523 patients undergoing elective coronary angiography, 22.8% of patients had normal coronaries. Rural patients were more likely to have high Framingham risk (highly rural 44.2% vs. rural 39.8% vs. urban 36.9%, p<0.001). Rural patients who lived further from cath labs were associated with a lower probability of normal coronaries compared to rural patients closer to cath labs and urban patients across all distances(p=0.0014). For patients living within 50 miles of a cath lab, urban/rural status did not influence the probability of normal coronary angiography. From 50 to 150 miles, rural patients were less likely to have normal coronaries at angiography. (Figure 1). Conclusions. Among patients undergoing elective angiography in the VA, those who lived further from cath labs in rural locations were less likely to have normal coronaries. These findings suggest that patient location, rather than clinical factors, may affect the use of coronary procedures. Further study to understand the causes of this relationship, including potential for under- or over-use based on distance and rural status, may help optimize patient access for coronary procedures.

THE MEGAMASER COSMOLOGY PROJECT. V. AN ANGULAR-DIAMETER DISTANCE TO NGC 6264 AT 140 Mpc

We present the direct measurement of the Hubble constant, yielding the direct measurement of the angular-diameter distance to NGC 6264 using the H$_{2}$O megamaser technique. Our measurement is based on sensitive observations of the circumnuclear megamaser disk from four observations with the Very Long Baseline Array, the Green Bank Telescope and the Effelsberg Telescope. We also monitored the maser spectral profile for 2.3 years using the Green Bank Telescope to measure accelerations of maser lines by tracking their line-of-sight velocities as they change with time. The measured accelerations suggest that the systemic maser spots have a significantly wider radial distribution than in the archetypal megamaser in NGC 4258. We model the maser emission as arising from a circumnuclear disk with orbits dominated by the central black hole. The best fit of the data gives a Hubble constant of $H_{0} =$ 68$\pm$9 km s$^{-1}$ Mpc$^{-1}$, which corresponds to an angular-diameter distance of 144$\pm$19 Mpc. In addition, the fit also gives a mass of the central black hole of (3.09$\pm$0.42)$\times10^{7}$ $M_{\odot}$. The result demonstrates the feasibility of measuring distances to galaxies located well into the Hubble flow by using circumnuclear megamaser disks.

Direct distance measurements to SN 2009ip

Abstract We demonstrate the applicability of our new method (the Dense Shell Method or DSM) for the determination of astronomical distances by calculating the distance to SN 2009ip. The distance to this supernova has been accurately determined in the standard approach via the cosmic distance ladder and has been found to be 20.4 Mpc. Our direct method, assuming the most reasonable parameter values, gives a very close result, namely ≈20.1 ± 0.8 (68 per cent CL) Mpc to SN 2009ip.

Molecular pH Probes at a Protein-Lipid Interface: Assessment of Local Dielectric Environment for Transmembrane Peptide

Spin-labeling EPR spectroscopy has found many applications in studying structure and dynamics of proteins and biological membranes. Recently, there has been substantial interest in utilizing EPR to characterize local effects of polarity and hydrogen bonding in these systems. Here we report on employing an pH-sensitive EPR probe IMSTL (S-(1-oxyl-2,2,3,5,5-pentamethylimidazolidin-4-ylmethyl) ester) to profile heterogeneous dielectric environments along the α-helix of a WALP peptide integrated in a lipid bilayer. A series of symmetrically positioned double cysteine mutants were labeled with a pH-sensitive nitroxide and the protonation state of IMTSL was directly observed by EPR. Q-band DEER experiments with double-labeled WALPs were employed to derive nitroxide-nitroxide distances of nitroxides before and after the protonation and, therefore, the positions of pH probes with respect to lipid bialyer. Thus, for the first time measurements of local electrostatics at peptide-bilayer interface were based on direct distance measurements rather than on assumptions on the probe location. For double-labeled WALP consecutive protonation of symmetrically positioned nitroxide tags was observed. The difference in observable pKa values was interpreted in terms of electrostatic interaction energy between titratable probes allowing us to estimate effective dielectric constant. Supported by NSF-0843632 to TIS.

On measuring the absolute scale of baryon acoustic oscillations

The baryon acoustic oscillation (BAO) feature in the distribution of galaxies provides a fundamental standard ruler which is widely used to constrain cosmological parameters. In most analyses, the comoving length of the ruler is inferred from a combination of CMB observations and theory. However, this inferred length may be biased by various non-standard effects in early universe physics; this can lead to biased inferences of cosmological parameters such as H_0, \Omega_m and w, so it would be valuable to measure the absolute BAO length by combining a galaxy redshift survey and a suitable direct low-z distance measurement. One obstacle is that low-redshift BAO surveys mainly constrain the ratio r_S / D_V(z), where D_V is a dilation scale which is not directly observable by standard candles. Here, we find a new approximation D_V(z) \simeq (3/4) D_L(4z/3) (1+ 4z/3)^{-1} (1 - 0.02455 z^3 + 0.0105 z^4) which connects D_V to the standard luminosity distance D_L at a somewhat higher redshift; this is shown to be very accurate (relative error < 0.2 percent) for all WMAP-compatible Friedmann models at z < 0.4, with very weak dependence on cosmological parameters H_0, \Omega_m, \Omega_k, w. This provides a route to measure the absolute BAO length using only observations at z < 0.3, including type-Ia supernovae, and potentially future H_0-free physical distance indicators such as gravitational lenses or gravitational wave standard sirens. This would provide a zero-parameter check of the standard cosmology at 10^3 < z < 10^5, and can constrain the number of relativistic species N_{eff} with fewer degeneracies than the CMB.

Measuring the Hubble constant with observations of water-vapor megamasers

AbstractTo constrain models of dark energy, a precise measurement of the Hubble constant, H0, provides a powerful complement to observations of the cosmic microwave background. Recent, precise measurements of H0 have been based on the ‘extragalactic distance ladder,’ primarily using observations of Cepheid variables and Type Ia supernovae as standard candles. In the past, these methods have been limited by systematic errors, so independent methods of measuring H0 are of high value. Direct geometric distance measurements to circumnuclear H2O megamasers in the Hubble flow provide a promising new method to determine H0. The Megamaser Cosmology Project (MCP) is a systematic effort to discover suitable H2O megamasers and determine their distances, with the aim of measuring H0 to a few percent. Based on observations of megamasers in UGC 3789 and NGC 6264, and preliminary results from Mrk 1419, the MCP has so far measured H0 = 68.0 ± 4.8 km s−1 Mpc−1. This measurement will improve as distances to additional galaxies are incorporated. With the Green Bank Telescope, we recently discovered three more excellent candidates for distance measurements, and we are currently acquiring data to measure their distances.

Self-Association of the Histidine Kinase CheA as Studied by Pulsed Dipolar ESR Spectroscopy

Biologically important protein complexes often involve molecular interactions that are low affinity or transient. We apply pulsed dipolar electron spin resonance spectroscopy and site-directed spin labeling in what to our knowledge is a new approach to study aggregation and to identify regions on protein surfaces that participate in weak, but specific molecular interactions. As a test case, we have probed the self-association of the chemotaxis kinase CheA, which forms signaling clusters with chemoreceptors and the coupling protein CheW at the poles of bacterial cells. By measuring the intermolecular dipolar interactions sensed by spin-labels distributed over the protein surface, we show that the soluble CheA kinase aggregates to a small extent through interactions mediated by its regulatory (P5) domain. Direct dipolar distance measurements confirm that a hydrophobic surface at the periphery of P5 subdomain 2 associates CheA dimers in solution. This result is further supported by differential disulfide cross-linking from engineered cysteine reporter sites. We suggest that the periphery of P5 is an interaction site on CheA for other similar hydrophobic surfaces and plays an important role in structuring the signaling particle.

CHARACTERIZING THE COOL KOIs. II. THE M DWARF KOI-254 AND ITS HOT JUPITER

We report the confirmation and characterization of a transiting gas giant planet orbiting the M dwarf KOI-254 every 2.455239 days, which was originally discovered by the Kepler mission. We use radial velocity measurements, adaptive optics imaging and near infrared spectroscopy to confirm the planetary nature of the transit events. KOI-254b is the first hot Jupiter discovered around an M-type dwarf star. We also present a new model-independent method of using broadband photometry to estimate the mass and metallicity of an M dwarf without relying on a direct distance measurement. Included in this methodology is a new photometric metallicity calibration based on J-K colors. We use this technique to measure the physical properties of KOI-254 and its planet. We measure a planet mass of Mp = 0.505 Mjup, radius Rp = 0.96 Rjup and semimajor axis a = 0.03 AU, based on our measured stellar mass Mstar = 0.59 Msun and radius Rstar = 0.55 Rsun. We also find that the host star is metal-rich, which is consistent with the sample of M-type stars known to harbor giant planets.

Determination of the Distance between the Mo(V) and Fe(III) Heme Centers of Wild Type Human Sulfite Oxidase by Pulsed EPR Spectroscopy

Intramolecular electron transfer (IET) between the molybdenum and heme centers of vertebrate sulfite oxidase (SO) is proposed to be a key step in the catalytic cycle of the enzyme. However, the X-ray crystallographic distance between these centers, R(MoFe) = 32.3 Å, appears to be too long for the rapid IET rates observed in liquid solution. The Mo and heme domains are linked by a flexible tether, and it has been proposed that dynamic interdomain motion brings the two metal centers closer together and thereby facilitates rapid IET. To date, there have been no direct distance measurements for SO in solution that would support or contradict this model. In this work, pulsed electron-electron double resonance (ELDOR) and relaxation induced dipolar modulation enhancement (RIDME) techniques were used to obtain information about R(MoFe) in the Mo(V)Fe(III) state of wild type recombinant human SO in frozen glassy solution. Surprisingly, the data obtained suggest a fixed structure with R(MoFe) = 32 Å, similar to that determined by X-ray crystallography for chicken SO, although the orientation of the R(MoFe) radius-vector with respect to the heme center was found to be somewhat different. The implications of these findings for the flexible tether model are discussed.

Statistical analysis of signal measurement in time-of-flight cameras

Three-dimensional imaging systems have evolved significantly in the last two decades due to increase in demand for tasks in the field of close range photogrammetry. The fast and growing need of 3D imaging devices has given rise to range image technology, especially time-of-flight (TOF) cameras, that provide direct measurement of distance between the camera and the targeted surface. A significant advantage of TOF devices over traditional range data sensors is their capability to provide frame rate range data over a full image array. In phase shift TOF cameras, phase shift sampling of the received signal is used to measure amplitude, phase and the offset (intensity) of the received signal. As a result, the quality of the measurement of these sensors depends heavily on signal-to-noise (SNR) of the incoming signal and the subsequent processing algorithms. A detailed understanding of the statistical distributions of the measurement parameters is crucial for accurate distance measurement analysis especially in low SNR scenarios. In this paper, we provide explicit noise models for the three parameters of amplitude, phase and intensity. The proposed stochastic model helps in investigating the effect of noise on signal and classifying range data reliability in TOF cameras. The model is used for prediction of errors in a TOF camera under various SNR conditions. Experimental verification confirms the validity of the model using real data for range error classification under different noise conditions.

Spatial arrangement of macro-, midi-, and microchromosomes in transcriptionally active nuclei of growing oocytes in birds of the order galliformes

Three-dimensional genome organization in the cell nucleus reflects its functional state and is one of the regulatory levels of gene expression. Thus, a detailed exploration of the interrelations between the genome spatial organization and functioning is essential. In this work, three-dimensional genome organization in growing oocytes of Galliform birds, with giant transcriptionally active nucleus characterized by nearly absolute lack of structural constraints on chromosome decondensation, is analyzed in detail. Radial distribution of three groups of chromosomes with different size and gene density in the nuclei of chicken and Japanese quail oocytes was analyzed using confocal laser scanning microscopy followed by the 3D-reconstruction. The chromosome position relative to the nuclear center was estimated by analyzing its localization in the certain radial zones of the nucleus and direct distance measurements from the centre of the nucleus to the terminal regions and the center of gravity of the chromosome. It has been shown that, in the transcriptionally active nuclei of avian oocytes, chromosomes are located at a significant distance from the nuclear envelope and the gene-rich microchromosomes have no preferential location close to the center of the nucleus and are localized mainly at the periphery of the region occupied by the whole chromosome set. Therefore the radial distribution of lampbrush chromosomes in the oocyte nucleus does not obey the regularity of the spatial arrangement of chromosomes in the interphase nucleus according to which the gene-rich chromosome territories are located at the nuclear center and the gene-poor ones are at the nuclear periphery. With the help of visualization of 3D-preserved lampbrush chromosomes in the intact nucleus, we have confirmed the presence of the repulsion forces between the lateral loops of lampbrush half-bivalents and the lack of interactions between the heterochromatic segments of different bivalents at the lampbrush stage of oogenesis.