bluuebunny/crossref_metadata_2025_split huggingface dataset:
Image Recovery Using Set-Theoretic Methods
Authors: Sezan Ibrahim 
Published: June 2020

Recently, there is some interest in the application of set-theoretic methods to the solution of the image recovery problem in electron microscopy. Several current studies have reported promising results.The purpose of this paper is to introduce set-theoretic methods to the electron microscopy community.In electron microscopy, the image recovery problem refers to obtaining an estimate of the ideal three-dimensional (3-D) image distribution from its incomplete and possibly noisy Fourier transform data.In the spatial domain, the recovery problem is stated on the basis of theobservation equation:where vectorsg, fandn∈ RNdenote the lexicographical ordering of the (N-voxel) measured (degraded) image distribution, the ideal image distribution and the noise processes, respectively. The operatorD: RN→ RNdenotes the degradation operator that effectively limits the data to the “data cone” in the frequency domain. The degradation operator can be adequately modeled by a space-invariant (convolutional) operator, and thereforeDhas a block-Toeplitz structure.
Three-Dimensional Reconstruction of Native Androctonus Australis Hemocyanin
Authors: Boisset Nicolas , Taveau Jean-Christophe , Lamy Jean , Wagenknecht Terence , Radermacher Michael , Frank Joachim 
Published: June 2020

Hemocyanin, the respiratory pigment of the scorpion Androctonus australis is composed of 24 kidney shaped subunits. A model of architecture supported by many indirect arguments has been deduced from electron microscopy (EM) and immuno-EM. To ascertain, the disposition of the subunits within the oligomer, the 24mer was submitted to three-dimensional reconstruction by the method of single-exposure random-conical tilt series.A sample of native hemocyanin, prepared with the double layer negative staining technique, was observed by transmisson electron microscopy under low-dose conditions. Six 3D-reconstructions were carried out indenpendently from top, side and 45°views. The results are composed of solid-body surface representations, and slices extracted from the reconstruction volume.The main two characters of the molecule previously reported by Van Heel and Frank, were constantly found in the solid-body surface representations. These features are the presence of two different faces called flip and flop and a rocking of the molecule around an axis passing through diagonnally opposed hexamers. Furthermore, in the solid-body surface of the top view reconstruction, the positions and orientations of the bridges connecting the half molecules were found in excellent agreement with those predicted by the model.
Time-Resolved Cryo-Electron Microscopy of Oscillating Microtubules
Authors: Mandelkow Eva-Maria , Milligan Ron 
Published: June 2020

Microtubules form part of the cytoskeleton of eukaryotic cells. They are hollow libers of about 25 nm diameter made up of 13 protofilaments, each of which consists of a chain of heterodimers of α-and β-tubulin. Microtubules can be assembled in vitro at 37°C in the presence of GTP which is hydrolyzed during the reaction, and they are disassembled at 4°C. In contrast to most other polymers microtubules show the behavior of “dynamic instability”, i.e. they can switch between phases of growth and phases of shrinkage, even at an overall steady state [1]. In certain conditions an entire solution can be synchronized, leading to autonomous oscillations in the degree of assembly which can be observed by X-ray scattering (Fig. 1), light scattering, or electron microscopy [2-5]. In addition such solutions are capable of generating spontaneous spatial patterns [6].In an earlier study we have analyzed the structure of microtubules and their cold-induced disassembly by cryo-EM [7]. One result was that disassembly takes place by loss of protofilament fragments (tubulin oligomers) which fray apart at the microtubule ends. We also looked at microtubule oscillations by time-resolved X-ray scattering and proposed a reaction scheme [4] which involves a cyclic interconversion of tubulin, microtubules, and oligomers (Fig. 2). The present study was undertaken to answer two questions: (a) What is the nature of the oscillations as seen by time-resolved cryo-EM? (b) Do microtubules disassemble by fraying protofilament fragments during oscillations at 37°C?
Electron-Spectroscopic Imaging (Esi) of Frozen-Hydrated Lipid Vesicles and Membrane Proteins: A Comparison With Tem
Authors: Lücken Uwe 
Published: June 2020

Imaging of frozen-hydrated lipid vesicles was carried out in TEM by Lepault et al. and Talmon et al. . It was concluded that the bilayer profile is independent of the lipid composition but depends upon the phase transition of the lipids forming the bilayer. Toyoshima et al. reported that the bilayer dimension depends upon the lipid composition. They found 4 nm for a cholesterine-rich membrane part in the surrounding area of the acetylcholine receptor.Lipid vesicles of homogeneous size were prepared by sonication, dialysis and ultrafiltration with 200nm-pore membrane filter. Proteins were reconstituted into these vesicles by conventional methods.Depending on the lipid-acid composition, the bilayer width varies between 3 and 6 nm; this width could be used as a standard provided it remains unaltered during preparation for electron microscopy. Embedment in ice should preserve the native dimension. The goal of this study is to confirm this contention. Therefore, we addressed the following questions:Does the choice of focus influence the image dimension of the bilayer?Does ESI provide advantages over regular cryomicroscopy?
Tomographic Three-Dimensional Reconstruction of Patch-Clamped Membranes Imaged With The High-Voltage Electron Microscope
Authors: McEwen B.F. , Song M.J. , Ruknudin A. , Barnard D.P. , Frank J. , Sachs F. 
Published: June 2020

Patch-clamped membranes have revolutionized the field of cellular electrophysiology, but nothing was known about their ultrastructure until they were imaged using the high-voltage electron microscope (HVEM). In present study we compute a tomographic three-dimensional (3D) reconstruction ofpatch-clamped membranes made from a Xenopus oocyte according to standard techniques. The sample was prepared for viewing in the HVEM according to the dry-mounting technique previously described. A tilt series was collected with a 2° angular interval and an angular range from -64° to 66°. All micrographs were recorded at 1 MV (Fig. 1). Our alignment procedure was hampered by the lack of good fiduciary markers and the presence of the wall of the micropipette, however, we were able to compute a preliminary reconstruction of reasonable quality using the weighted back projection method.Tomograms from the 3D reconstruction demonstrate that the cylindrical axis of the micropipette was not coaxial with the tilt axis of the HVEM state (Fig. 2). The reconstruction was rotated until it was coaxial with the y-axis of the reconstruction volume and a series of cylindrical projections were computed (Fig. 3). The projections from the inner radii show the thin profile of the disk which spans the micropipette, while the projections at larger radii show the distribution of features along the wall or the micropipette. The blurred area in the middle (and at the ends) of each cylindrical projection is caused by the missing angular range, while the blank area in the longest projection is a result of the slightly elliptical cross-section of the micropipette. A small 3D volume containing the pipette-spanning disk was extracted from the reconstruction volume (Fig. 4); the fibrous nature of the disk is evident. A different view of the disk is presented by removing tomograms which contain interfering features from the front and back walls of micropipette from the reconstruction in its original orientation (Fig. 5).
Principles and Practice of On-Line Data Acquisition For Transmission Electron Microscopy
Authors: Tietz R. 
Published: June 2020

For about 15 years now TV-camera based image acquisition systems have been used in many laboratories. These TV-systems facilitate focusing and stigmating of the instrument at low beam currents and the recording of dynamic events in the microscope with a video-tape recorder. Recently, digital image processing systems have become available which make image accumulation or averaging possible, or which can correct for uneven illumination conditions. This simple image processing is the basis for further image analysis (Automatic control of TEM parameters or real analysis of the specimen).The bottle neck in on-line data acquisition for a TEM is the image pick-up system. Compared to a photographic plate, which has about 10.000 by 10.000 resolved pixels, the resolution of commercial, TV-based camera systems is very poor, in the best case about 500 by 500 pixels. The poor resolution of TV-systems restricts the use of image analysis to objects which do not need large image fields.Fig. 1 illustrates the principles of TV-based image pick-up systems.
Analytical Electron Microscopy of Extraterrestrial Ice Analogs
Authors: Blake D.F. , Allamandola LJ. , Palmer G. , Pohorille A. 
Published: June 2020

The natural history of the biogenic elements H, C, N, O, P and S in the cosmos is of great interest because it is these elements which comprise all life. Material ejected from stars (or pre-existing in the interstellar medium) is thought to condense into diffuse bodies of gravitationally bound gas and dust called cold interstellar molecular clouds. Current theories predict that within these clouds, at temperatures of 10-100° K, gases (primarily H2O, but including CO, CO2, CH3OH, NH3, and others) condense onto submicron silicate grains to form icy grain mantles. This interstellar ice represents the earliest and most primitive association of the biogenic elements. Within these multicomponent icy mantles, pre-biotic organic compounds are formed during exposure to UV radiation. It is thought that icy planetesimals (such as comets) within our solar system contain some pristine interstellar material, including ices, and may have (during the early bombardment of the solar system, ∼4 Ga) carried this material to Earth.Despite the widespread occurrence of astrophysical ices and their importance to pre-biotic organic evolution, few experimental data exist which address the relevant phase equilibria and possible structural states. A knowledge of the petrology of astrophysical ice analogs will allow scientists to more confidently interpret astronomical IR observations. Furthermore, the development and refinement of procedures for analyzing ices and other materials at cryogenic temperatures is critical to the study of materials returned from the proposed Rosetta comet nucleus and Mars sample return missions.
Fsem: Fast Scanning Electron Microscopy
Authors: Fishbine Brian H. , Macy Robert J. 
Published: June 2020

Commercially available SEM‘s offer a maximum “TV” framing rate of ∼30 Hz. We have obtained a digitally-acquired framing rate of 381 Hz with submicron resolution [1]. This is at a 25 MHz pixel rate, compared with the ≤4 MHz video bandwidth of TV-rate machines. We have also performed analog-acquired experiments at effective framing rates of 4.9 kHz and effective pixel rates of >50 MHz. Our present detection and recording system is capable of 200 MHz pixel rates, with reduced contrast range at higher rates. Extrapolating current technology suggests that GHz pixel rates with useable final image signal-to-noise ratios are possible [2].In large part, the success of electron microscopy is due to: the high resolution possible with the small de Broglie wavelength of even keV electrons, small effective electron source diameters, and small optical aberrations of well-designed electron optics. With this resolution, SEM also attains large depth of focus with scanned, narrow electron beams. SEM micrographs are generally noted for exceptional sharpness and large depth of focus. The highest quality micrographs require scan times of tens of seconds or more.
Investigation of central electrode artefacts of ionisation chamber effect on dose calculation using advanced calculation algorithms AAA and Acuros XB
Authors: Shaiju V. S. , Kumar Rajesh , Rajasekhar K. V. , Zacharia George , Phani Debjani , Bhasi Saju , Nair Raghuram K 
Published: June 2020

AbstractAim:To investigate the central electrode artefact effect of different ion chambers in the verification phantom using the dose calculation algorithms Analytical Anisotropic Algorithm (AAA) and Acuros XB.Materials and methods:The dosimetric study was conducted using an in-house fabricated polymethyl methacrylate head phantom. The treatment planning system (TPS)-calculated doses in the phantom with detectors were compared against the dummy detector fillets using AAA and Acuros XB algorithm. The planned and measured doses were compared for the study.Results:The mean percentage variation in volumetric-modulated arc therapy plans using Acuros XB and the measurement in the head phantom are statistically significant (p-value = 0.001) for FC65 and CC13 chambers. In small volume chambers (A14SL and CC01), the measured and TPS-calculated dose shows a good agreement.Findings:The study confirmed the CT set of the phantom with detectors (FC65 and CC13) give more artefacts/heterogeneity caused a significant variation in dose calculation using Acuros XB. Therefore, the study suggests a method of using phantom CT set with the dummy detector for mean dose calculation for the Acuros XB algorithm.
3‐D Intrinsic and Scattering Seismic Attenuation Structures Beneath Kyushu, Japan
Authors: Shito A. , Matsumoto S. , Ohkura T. , Shimizu H. , Sakai S. , Iio Y. , Takahashi H. , Yakiwara H. , Watanabe T. , Kosuga M. , Okada T. , Yoshimi M. , Asano Y. 
Published: June 2020

AbstractThe attenuation of seismic wave energy is caused by intrinsic absorption and scattering. The former involves the conversion of seismic wave energy to heat energy via internal friction due to the anelasticity of the medium, whereas the latter involves the scattering of seismic wave energy due to random elastic heterogeneities in the medium. Quantifying both intrinsic (
) and scattering (
) attenuation is therefore important for understanding the physical properties of the Earth's interior and predicting seismic wave propagation. Here we develop a new procedure to separately map three‐dimensional (3‐D)
and
structures. The path‐averaged
and
values are obtained via an envelope‐fitting approach that employs a multiple‐scattering model. The path‐averaged
and
structures are then mapped into 3‐D space using a tomographic inversion technique based on sensitivity kernels, which are calculated from a Monte Carlo simulation of the radiative transfer equations. We apply this method to map the crustal structure beneath Kyushu, Japan, and obtain 3‐D
and
structures for the 1–2, 2–4, and 4–8 Hz frequency bands. The spatial attenuation patterns are similar for each of the analyzed frequency bands, with the spatial variability in
being more pronounced than that in
. The high‐
and
regions correspond to the locations of active volcanoes. Conversely, the northern Kyushu area possesses low‐
and
zones that correspond to low heat flow and Cretaceous granite, respectively. The overall
and
distributions correlate with thermal and geological structures, respectively.
Changes in Tropical Precipitation Intensity With El Niño Warming
Authors: Sullivan Sylvia C. , Schiro Kathleen A. , Yin Jiabo , Gentine Pierre 
Published: June 2020

AbstractMesoscale convection generates the majority of extreme precipitation in tropical regions. Changes to these precipitation intensities, P, with long‐term modes of climate variability have been hard to assess because they are not well represented in current climate models. Here we stratify a satellite climatology of convective systems by El Niño phase and cloud top temperature. We find that gains (losses) in high precipitation intensity (
10 mm hr−1) are largest for the deepest (least deep) systems during El Niño relative to La Niña. The surface temperature and wind changes that define El Niño manifest as surface flux changes but are not sufficient to explain these
trends. We explore also the dynamical component of precipitation generation with a vertical momentum budget. Midtropospheric drying in the vicinity of the deepest systems boosts instability and ascent rates during El Niño, while the strengthened large‐scale ascent minimizes the drag force on their updrafts.
Does Ring Current Heating Generate the Observed O+ Shell?
Authors: Krall J. , Huba J. D. , Fok M.‐C. 
Published: June 2020

AbstractThe Naval Research Laboratory (NRL) Sami3 is Also a Model of the Ionosphere (SAMI3) ionosphere/plasmasphere code is used to examine the effect of ring current heating during a storm. With a ring current heating function added to SAMI3, a cold thermal (<1 eV) oxygen ion outflow is produced, with O+ density and location similar to observations of the so‐called “oxygen torus.” The ring current heating function is based on a Comprehensive Inner Magnetosphere‐Ionosphere (CIMI) model simulation of the 7 October 2015 storm. We find that the ring current can heat plasmasphere electrons, subsequently heating plasmasphere H+, and ionosphere O+. The resulting O+ outflows resemble observed O+ enhancements in the inner magnetosphere.
Using polygenic scores for identifying individuals at increased risk of substance use disorders in clinical and population samples
Authors: Barr Peter B. , Ksinan Albert , Su Jinni , Johnson Emma C. , Meyers Jacquelyn L. , Wetherill Leah , Latvala Antti , Aliev Fazil , Chan Grace , Kuperman Samuel , Nurnberger John , Kamarajan Chella , Anokhin Andrey , Agrawal Arpana , Rose Richard J. , Edenberg Howard J. , Schuckit Marc , Kaprio Jaakko , Dick Danielle M. 
Published: June 2020

AbstractGenome-wide, polygenic risk scores (PRS) have emerged as a useful way to characterize genetic liability. There is growing evidence that PRS may prove useful for early identification of those at increased risk for certain diseases. The current potential of PRS for alcohol use disorders (AUD) remains an open question. Using data from both a population-based sample [the FinnTwin12 (FT12) study] and a high-risk sample [the Collaborative Study on the Genetics of Alcoholism (COGA)], we examined the association between PRSs derived from genome-wide association studies (GWASs) of (1) alcohol dependence/alcohol problems, (2) alcohol consumption, and (3) risky behaviors with AUD and other substance use disorder (SUD) criteria. These PRSs explain ~2.5–3.5% of the variance in AUD (across FT12 and COGA) when all PRSs are included in the same model. Calculations of area under the curve (AUC) show PRS provide only a slight improvement over a model with age, sex, and ancestral principal components as covariates. While individuals in the top 20, 10, and 5% of the PRS distribution had greater odds of having an AUD compared to the lower end of the continuum in both COGA and FT12, the point estimates at each threshold were statistically indistinguishable. Those in the top 5% reported greater levels of licit (alcohol and nicotine) and illicit (cannabis and opioid) SUD criteria. PRSs are associated with risk for SUD in independent samples. However, usefulness for identifying those at increased risk in their current form is modest, at best. Improvement in predictive ability will likely be dependent on increasing the size of well-phenotyped discovery samples.
The phosphodiesterase-4 and glycine transporter-1 inhibitors enhance in vivo hippocampal theta network connectivity and synaptic plasticity, whereas D-serine does not
Authors: Ahnaou A. , Broadbelt T. , Biermans R. , Huysmans H. , Manyakov N. V. , Drinkenburg W. H. I. M. 
Published: June 2020

AbstractDysfunctional N-methyl-D-aspartate receptors (NMDARs) and cyclic adenosine monophosphate (cAMP) have been associated with deficits in synaptic plasticity and cognition found in neurodegenerative and neuropsychiatric disorders such as Alzheimer’s disease (AD) and schizophrenia. Therapeutic approaches that indirectly enhance NMDAR function through increases in glycine and/or D-serine levels as well as inhibition of phosphodiesterases that reduces degradation of cAMP, are expected to enhance synaptic strength, connectivity and to potentially impact cognition processes. The present in vivo study investigated effects of subcutaneous administration of D-serine, the glycine transporter 1 (GlyT1) inhibitor SSR504734 and the PDE4 inhibitor rolipram, on network oscillations, connectivity and long-term potentiation (LTP) at the hippocampi circuits in Sprague-Dawley rats. In conscious animals, multichannel EEG recordings assessed network oscillations and connectivity at frontal and hippocampal CA1–CA3 circuits. Under urethane anaesthesia, field excitatory postsynaptic potentials (fEPSPs) were measured in the CA1 subfield of the hippocampus after high-frequency stimulation (HFS) of the Schaffer collateral-CA1 (SC) pathway. SSR504734 and rolipram significantly increased slow theta oscillations (4–6.5 Hz) at the CA1–CA3, slow gamma oscillations (30–50 Hz) in the frontal areas and enhanced coherence in the CA1–CA3 network, which were dissociated from motor behaviour. SSR504734 enhanced short-term potentiation (STP) and fEPSP responses were extended into LTP response, whereas the potentiation of EPSP slope was short-lived to STP with rolipram. Unlike glycine, increased levels of D-serine had no effect on network oscillations and limits the LTP induction and expression. The present data support a facilitating role of glycine and cAMP on network oscillations and synaptic efficacy at the CA3–CA1 circuit in rats, whereas raising endogenous D-serine levels had no such beneficial effects.