bluuebunny/crossref_metadata_2025_split huggingface dataset:
X-Ray Microscopy Developments at the ESRF
Authors: Kaulich B , Oestreich S , Barrett R , Susini J 
Published: July 2020

Abstract
The ESRF source properties offer the required coherence and brilliance to extend X-ray microscopy techniques, which have been extensively used in the soft X-ray region, to higher energies. This will enable new investigations such as the study of thicker specimens compared to the soft X-ray region, access to absorption edges of elements of major interest in the biological and materials sciences, in particular from Potassium to Chromium, the use of X-ray fluorescence for trace element mapping with high spatial resolution and the application of phase contrast.
Two microscopes are under development at the ESRF to cover a wide range of biological and material sciences applications:
A scanning transmission X-ray microscope (STXM) working in the photon energy range of 0.5-8keV. Whilst in its simplest form this might consist of taking multiple images of a single sample region at different incident energies, an interesting extension is to perform highly spatially resolved XAS scans on small regions of the sample.
High Resolution Transmission Electron Microscopy at Zero Cs
Authors: O'Keefe Michael A 
Published: July 2020

Abstract
Now that correctors for objective lens spherical aberration are becoming feasible, questions have been raised about the usefulness of high-resolution transmission electron microscopy at zero Cs and the possible difficulties of interpretation of such images. In general, high resolution TEM images are interpreted either by comparison with simulations from model structures or by contrast transfer functions (CTFs) to determine the weight (and sense) of spatial contributions to images from corresponding diffracted beams. At zero Cs, HREM image simulations will work, but a projected charge density theory should be used (instead of CTF theory) to interpret images. Both theories use approximations; CTF theory relies on kinematic scattering and PCD theory on zero Cs and limited defocus.
First Application of a Spherical-Aberration Corrected Microscope Material Science
Authors: Kabius B , Urban K , Haider M , Uhlemann S , Schwan E , Rose H 
Published: July 2020

Abstract
One of the most challenging tasks for high-resolution electron microscopy (HREM) is the atomistic investigation of defects and interfaces in thin films of semiconductors and ceramics. In particular, the application of these materials in electronic devices requires the understanding of the atomistic structure responsible for electronic and optical properties. The imaging of these structures requires a point resolution down to 0.1 nm. For example the smallest atomic spacing of GaAs in the (110) projection is 0.14 nm. According to Scherzer the point resolution of the TEM is proportional to spherical-aberration coefficient Cs1/4 and to the wave length λ3/4. Commercial medium-voltage microscopes up to 400 kV offer only a point resolution of 0.16 nm due to the high spherical-aberration constant Cs of the electromagnetic objective lens. Decreasing the wave length λ by increasing the electron energy improves the point resolution, but has the drawback of severe radiation damage and high costs.
Modification Of a Conventional TEM (CTEM) for Lorentz Microscopy
Authors: Wall M , Bajt S , Cerjan C 
Published: July 2020

Abstract
We have modified a CTEM in order to perform Lorentz microscopy experiments at high magnification and resolution on magnetic materials. The modification consists of the adaptation of a second side entry goniometer (SEG) to the CTEM (JEOL 200CX STEM) column above the objective lens, in a region of the column where the measured residual magnetic fields are &lt; 0.5 Gauss with the objective lens in a fully excited state (see Figure 1).
With the specimen positioned above the objective lens, it is necessary to increase the excitation of the lens by approximately 20% in order to bring the image into focus. This combination of a specimen positioned above the object pole piece, and the higher objective lens excitation, affects several changes in the optics. First, if a specimen is positioned within the pole piece gap and the objective lens is turned off for Lorentz microscopy purposes, the highest typical magnification achievable is approximately 1,000 X and the resolution is not much better than 0.1μm.
A New 200kv Energy Filter Field Emission Transmission Electron Microscope
Authors: Kaneyama T , Tsuno K , Honda T , Kersker M , Tsuda K , Terauchi M , Tanaka M 
Published: July 2020

Abstract
In the field of biological and materials sciences, the importance of energy filter transmission electron microscope(EF-TEM) is increasing. Because it is a powerful instrument for contrast enhancement and obtaining elemental mapping images. We have developed a 200kV EF-TEM equipped with a fieldemission gun and in-column spectrometer. The new EF-TEM JEM-2010FEF inherits the performance in high resolution imaging and analysis from field emission TEM. The outer view is shown in Fig.l.
Figure 2 shows the lens configuration of JEM-2010FEF. An in-column Q-type spectrometer is introduced within the imaging lens system. It was designed to have image distortion less than 1% and dispersion power 1.2p.m/eV for 200keV electrons. There is no need of compensating procedure of distortion. Imaging lens system consists of two objective lenses, three intermediate lenses and three projector lenses. The 8-stage imaging lens system enables wide range of imaging modes equal to conventional TEMs; energy spectroscopic image of magnification from ×200 to × 1,500,000, energy spectroscopic diffraction of camera length from 200mm to 2,000mm.
The CM120-Biofiiter: Digital Imaging Of Frozen Hydratedspecimens and Elemental Mapping
Authors: Lücken U , de Jong AF , Kundmann M , Chemy D , Leapman R 
Published: July 2020

Abstract
A new system for energy-filtered electron microscopy (EFTEM) has been developed, adapted for the study of life science specimens. Special attention has been given to integration, ease of use and the typical problems encountered while investigating unstained and cryo-specimens. Low-dose, cryocapabilities and a high-contrast objective lens have been combined with an imaging energy filter, digital image recording with phosphor scintillator and advanced image-processing capabilities. The CM120-BioFilter is an integration of the CM120-BioTWIN or the CM120TWIN with the Gatan postcolumn imaging filter GIF100. The BioTWIN objective lens (Cs=6.2 mm, f=5.9 mm) is optimized for high-contrast imaging. The TWIN lens(Cs=2mm,f=2.8mm) is optimized for high resolution in structural biology. The GIF 100 is a computer-controlled, second-order corrected energy filter with a cooled multiscan CCD for digital image recording. Improvement of the contrast can be achieved if inelastically scattered electrons are removed.
Quantitative Visible-Light and Electron Phase Microscopy
Authors: Barty A , Nugent KA , Paganin D , Roberts A 
Published: July 2020

Abstract
At the University of Melbourne we have been pursuing an ongoing program of investigation into the recovery of phase information from intensity measurements [1-9]. In this paper we consider the implications of this work in optical and electron microscopy.
Many objects of interest to biologists are phase objects which means that light is slowed and refracted in the object but not absorbed. Techniques such as phase-contrast microscopy and Nomarski differential interference contrast (DIC) microscopy are traditionally used to render the phase structure visible but do not directly map the phase distribution and are unable to produce quantitative data. These techniques also entangle the phase and amplitude information and so have limitations where both phase and amplitude information is required. In this paper, we demonstrate quantitative non-interferometric recovery of microscopic phase structure using incoherent illumination of the type commonly found in optical microscopes, and show that our results correlate with structure observed using Nomarski DIC techniques.
Isotopic Measurements of Inorganic Material by Time-Of-Flight SIMS
Authors: Fahey A J 
Published: July 2020

Abstract
Isotopic measurements via Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) have generally not been considered as practical because of the low duty cycle at which ToF-SIMS instruments operate and the corresponding low data rate. The recent discovery of pre-solar material in meteorites has shown that large variations in isotopic ratios (several orders of magnitude for some elements) exist in small (∼1 μm), refractory meteoritic grains. These grains are ideal candidates for ToF-SIMS, which consumes little sample material, compared to dynamic, magneticsector SIMS. ToF-SIMS also allows for parallel detection of all species present in the sample; thus, multiple isotopic systems can be studied in one measurement. As a prerequisite to studying the isotopic composition of meteoritic materials, preliminary determinations of ratios for a number of elements have been made on materials of known isotopic composition. This allows us to investigate problems that may be unique to ToF-SIMS for the measurement of isotopic ratios.
Visualizing Neuronal Sturcture by Combining GFP-Transfection With 2-Photon Microscopy In Living Brain Slices
Authors: Horch H L Wilson , Katz L C 
Published: July 2020

Abstract
Research in our lab is aimed at examining how signaling molecules affect the differentiation of neurons in the developing cortex. Most morphological studies rely on single time point images of cells within a population. It is obviously advantageous to examine changes in individual living cells over time. By combining 2-photon imaging with co-transfection of genes for green fluorescent protein (GFP) and neurotrophins in living neurons, we can asses the effects of these on individual living cells.
Individual neurons in brain slices from ferret visual cortex were transfected with GFP using particle mediated gene-transfer, or Biolistics. Using the Helios Gene Gun (Bio-Rad), DNA-coated gold particles are blasted into living brain slices. Neurons are transfected when a gold particle lands in the nucleus. Within 24 to 36 hours individual cells are well-filled with GFP allowing visualization of dendrites, spines, and axons.
Crista Junctions of Mitochondria Visualized by Electron Tomography
Authors: Perkins G A , Song J Y , Tarsa L , McCarty C , Deerinck T J , Ellisman M H , Frey T G 
Published: July 2020

Abstract
Electron microscope tomography is a useful method for deriving three-dimensional (3-D) structures from tilt series. We used an intermediate, high-voltage electron microscope operated at 400 kV to study the 3-D structure of selectively stained or labeled mitochondria from diverse sources. We have examined the structure of neuronal mitochondria and mitochondria from brown adipose tissue (BAT) employing either single-axis or double-axis techniques over a tilt range of ±60° with 1° or 2° angular increments (Fig. 1). Although BAT mitochondria contains only lamellar cristae with no tubular cristae as we have observed in neuronal mitochondria, we found that the inner membrane of BAT mitochondria invaginates to form cristae only through narrow, tubular openings or crista junctions (Fig. 2).
Recent interest in the possibility of structural artifacts in chemically fixed mitochondria imaged in situ motivated us to perform electron tomography on cryofixed brain and brown fat tissue.
Electron Microscopic Tomography of Cellular Organelles: Chemical Fixation Vs. Cryo-Substitution of Rat-Liver Mitochondria
Authors: Mannella CA , Buttle K , Tessitore K , Rath BK , Hsieh C , D'Arcangelis D , Marko M 
Published: July 2020

Abstract
Electron microscopic tomography is proving to be a valuable tool for investigating the 3D structure and organization of cellular organelles. Important progress is being made in the application of the technique to frozen-hydrated material, but it is likely that success with thick specimens will be limited by the low contrast and beam sensitivity of naked biological material. Thus, optimizing procedures for fixing, embedding, staining, and selectively labelling cells for 3D electron microscopy remains a priority.
Tomography of chemically fixed and plastic-embedded rat-liver tissue and isolated mitochondria has shown that the cristae (the invaginations of the mitochondrial inner membrane) are pleiomorphic and connected to each other and to the surface of the inner membrane by tubular regions 30-40 nm in diameter. This basic design feature has important implications for the microcompartmentation of ions and molecules within this organelle.
3d Structure Of Periodic Cubic-Phase Inner Membranes In Mitochondria of Chaos Carolinensis
Authors: Deng Y , Mieczkowski M , Marko M , Buttle K , Rath BK , Mannella CA 
Published: July 2020

Abstract
The mitochondrial inner membrane contains the machinery of oxidative phosphorylation. This membrane has invaginations called cristae which vary widely in shape between organisms and between tissues in the same organism. Electron microscopic tomography indicates that, despite this pleiomorphism, there is a common design feature, namely, the cristal membranes connect to each other and to the periphery of the inner membrane by tubular regions 30-40 nm in diameter. This finding has important implications for the internal diffusion of ions, metabolites and macromolecules within mitochondria.
In some types of mitochondria, the cristae exhibit periodicity.1 In the case of the amoeba Chaos carolinensis, detailed analysis and modeling of thin-section images of mitochondria in starved cells indicate that the highly curved cristae correspond to periodic cubic surfaces. We are undertaking electron microscopic tomographic and crystallographic approaches to more thoroughly characterize these membrane phases and, in particular, establish the continuity of the internal compartments which they define.
The Centrosome: Three-Dimensional Structure of a Cell Organelle at 40A Resolution Obtained by Electrontomography
Authors: Ruiz T , Radermacher M , Rath B , Rieder C , Bornens M 
Published: July 2020

Abstract
The organization of the microtubule network of eukariotic cells is controlled by the centrosome. This organelle which duplicates once during the cell cycle comprises two centrioles and a dense filamentous material called pericentriolar material. The centrioles are cylinders of ≈ 0.25 μm in diameter and ≈ 0.5μm in length and are composed of 9 microtubule triplets at the proximal end and 9 doublets at the distal end. For the last 50 years the centrosome and the centrioles in particular have been the object of many optical and electron microscopy studies. But, in spite of their highly symmetric organization, their fine structure is still not well understood. The reconstruction presented here is a substantial step forward towards a more detailed understanding of their structure.
Centrosomes were isolated from a human lymphoblastoma cell line (1). 10 nm gold particles were applied to formvar-carbon coated grids to provide markers for the alignment procedure (2,3). Centrosomes were centrifuged onto the grids and negatively stained.
Using Animation to Enhance 3D Visualization: A Strategy for a Production Environment
Authors: Dougherty M T , Chiu W 
Published: July 2020

Abstract
The use of animation can significantly enhance the visualization of three-dimensional (3D) structures. It can present a focused train of thought, or it can be used to systematically scan through previously unfathomable quantities of data to examine for unknown features and consistencies. In order to establish a modern animation facility requires a variety of technical, psychological and artistic skills, in addition to advanced computer graphics and related equipment. 3D graphics combined with animation has proven to be a very effective tool in storytelling. The dynamic visual image is uniquely suited for thought experiments, simulations and traversing vast quantities of data otherwise incomprehensible to the human mind. Sometimes animation is the only method that allows a clear presentation of complex empirical or theoretical information in many dimensions. Scientific visualization is by its nature an exploratory process. And frequently animations are iteratively refined and polished to enhance comprehensibility for the researchers and their peers.
Atomic Model of Tubulin by Electron Crystallography
Authors: Nogales Eva , Downing Kenneth H 
Published: July 2020

Abstract
The structure of tubulin, the major protein component of microtubules, has been obtained by electron crystallography of zinc-induced 2-D crystals. The atomic model of the tubulin dimer, built into a 3.7 Å density map, shows that α- and β-tubulin have basically identical structures. Each monomer is very compact and is formed by two interacting beta sheets surrounded by helices. The structure can be divided into three sequential domains that are functionally distinctive. The N-terminal domain forms a Rossmann fold that binds the nucleotide. Connected to the nucleotide-binding domain by the core helix is a second domain that in β-tubulin contains the binding site of taxol. The C-terminal region is formed by two long helices that constitute most of the interactive, outside surface of the microtubule. The nucleotide-binding and second domains are common with FtsZ, a bacterial homologue of tubulin essential for cell division. The bacterial protein, which lacks the C-terminal helices of tubulin, has generally shorter loops and contains an extra helix at the N-terminus.
Crystallographic Reconstruction of the Acrosomal Process from Limulus Polyphemus Sperm
Authors: Sherman M B , Jakana J , Sun S , Matsudaira P , Chiu W , Schmid M F 
Published: July 2020

Abstract
The acrosomal process is an intracellular quasi-crystalline organelle in the head of the sperm of the horseshoe crab Limulus polyphemus. It consists of 100 - 130 actin-scruin filaments packed together in a pseudo-hexagonal lattice2 and is up to 60 (im long with a diameter of 0.1 μm. Scruin-scruin interactions are responsible for cross-linking the actin filaments together in the bundle. The goal of the current study is to reveal interfilament interactions in the bundle. We have taken tilt series images in the electron microscope3 to reconstruct its three-dimensional structure without assuming helical symmetry.
The acrosomal process was purified as described.34 Bundles were embedded in vitreous ice over holes on a holey carbon film on copper grids. The specimen was kept at -167°C in a JEOL 4000EX electron microscope operating at 400 kV. Straight 6-10 (im long bundles were found using a TV-rate CCD camera in defocused diffraction mode.
Structure of a Recombinant Gap Junction Channel at 7Å Resolution
Authors: Unger VM , Entrikin D W , Guan X , Kumar NM , Gilula NB , Yeager M 
Published: July 2020

Abstract
Gap junction membrane channels mediate the electrical and metabolic coupling between cells. The channels are formed by the end-to-end docking of two hemichannels (connexons), each of which is formed by a hexameric cluster of protein subunits (connexins). The principal gap junction protein in the heart, α1 connexin (also designated Cx43), mediates action potential propagation between cells in order to synchronize cardiac contraction.
We recently utilized electron cryo-microscopy and image analysis to examine frozen-hydrated two-dimensional (2D) crystals of a recombinant, truncated α1- connexin (α1Cx263T). The projection map at 7Å resolution revealed that each 30kD connexin subunit has a transmembrane α-helix that lines the aqueous pore and a second α-helix in close contact with the membrane lipids [Nature Struct. Biol. 4: 39-43 (1997)]. The distribution of densities allowed us to propose a model in which the two apposing connexons that form the channel are staggered by ∼30°. Furthermore, apparent non-crystallographic twofold axes predicted that the two apposing connexons adopt identical conformations.
Electron Crystallography of a Prokaryotic Potassium Channel
Authors: Sui HX , Li HL , Ghanshani S , Lee S , Walian PJ , Wu CL , Chandy KG , Jap BK 
Published: July 2020

Abstract
Potassium channels are ubiquitous ion channel proteins which play a crucial role in a broad spectrum of important cell functions. KcsA is a potassium channel found in the bacterium, Streptomyces lividan, and is believed to have only two transmembrane helices.
The KcsA protein has been cloned, overexpressed and purified to homogeneity, and reconstituted with phospholipids to form two-dimensional (2-D) crystals. Crystal samples were embedded in trehalose and examined in a cryo-holder (-170 °C) using a JEOL 4000EX electron microscope operated at 400kV in low dose mode. Images were recorded in spot scan-mode at a magnification of 60,000X, then digitized on a Perkin Elmer PDS flat bed microdensitometer and processed by using the MRC program suite. Processed images were brought to a common phase origin, and the amplitudes and phases from individual images were vectorially combined.
User Access to Lorentz Microscopy at the NCEM, LBNL, Berkeley.
Authors: Verbist K , Nelson C , Krishnan K 
Published: July 2020

Abstract
A standard Philips CM200FEG electron microscope, without the special Lorentz lens, has been optimized for Lorentz imaging. The necessary field-free sample region is obtained by switching off the objective lens in the free lens mode. The limited range of magnification is compensated for by a post-column Gatan image filter (GIF) which magnifies by a factor of _ 20. Fresnel imaging is performed by defocusing with the diffraction lens. The use of low angle diffraction, in combination with the apertures located at the selected area aperture plane, allow Foucault imaging. The TEM analog of differential phase contrast (DPC) imaging has been implemented. This method makes it possible to obtain quantitave induction maps of the in-plane magnetization. TEM DPC is based on a series of Foucault images, recorded with different incremental beam tilts, which are processed to yield images equivalent to the quadrant signals obtained by the STEM DPC technique.
Analytical Light Microscopy: Examples of Practical Problemsolving and Efficiency in Pharmaceutical Quality Control and Formulation
Authors: Stoney D A , McCrone W C 
Published: July 2020

Abstract
Five applications of analytical light microscopy to problem-solving in the pharmaceutical industry are described and illustrated by case examples. Problems included are (1) the caking of pharmaceutical products, (2) chemical incompatibility, (3) nucleation and precipitation, (4) recognition of hydrates and polymorphs, and (5) identification and sourcing of contaminant particles.
Considerable effort goes into the sizing of solid pharmaceutical raw materials and products. In many instances, particle size is used to help control the rate and uniformity of dissolution, which in turn affects the kinetics of drug delivery. Caking is a macroscopic description of the change in a sample from a finely-divided powder to a single solid molded aggregate. Caking obviously has a severe impact on handling and dissolution characteristics.
Caking of a powder is almost always caused by moisture through the cyclical dissolution and precipitation on the surfaces of the particles. When exposed to sufficient vapor pressure, often through changes in humidity or temperature,