bluuebunny/crossref_metadata_2025_split huggingface dataset:
The development of an electronic microscopy journal on the world wide web
Authors: Mansfield John F. 
Published: June 2020

Developments in digital camera technology and digital data acquisition have allowed many of us to record most, if not all of our data entirely electronically. We are able to present this data at conferences and meetings direct from the desktop of a small personal computer. Why should we not think of publishing the data in the same manner? Indeed the assembly of the traditional scientific manuscript; printing out the text according to the journals strict format and printing and annotating the micrographs may really be thought of as a backward step. Frequently images, spectra and diffraction patterns appear much better on the screen of the computer than when they are printed out on paper. While this may be simply a limitation of developments in the printing technology lagging behind those in the display technology, why wait for the printing technology to catch up? We should publish electronically.Since it’s inception in 1989, The World Wide Web (typically shortened to the WWW or just The Web) has proved to be a tremendously popular system for the publication and dissemination of an incredibly broad spectrum of information.
Specimen preparation: the Achilles Heel of Microscopy
Authors: Kestel B. 
Published: June 2020

As the variety of microscopy techniques to reveal new information increases, the difficulty of preparing suitable specimens for examination has also grown. Some microscopy requires very uniform thickness, smooth surfaces, and minimal preparation induced damage or contamination. The variety of materials studied, their different physical properties, and the number of techniques available makes this process more troublesome than some project planners realize. New employees of an organization are often given this task, but their inexperience may compound the problem. A worker's success in this process may be increased by experience with tedious hobbies, teamwork events, or the need to record pertinent details of processes.A starting point for optical microscopy, mechanical dimpling before ion milling, and the making of thin slices or wedges is mechanical polishing. The relatively new tripod polishing technique is based on controlled mechanical polishing using very fine abrasives. Examples of modified equipment and simple fixtures which make surface polishing easier, faster, and of high quality with reduced labor will be shown.
Measuring intermolecular forces using thermal noise in an Atomic Force Microscope
Authors: Cleveland J.P. , Schaeffer T. , Hansma P.K. 
Published: June 2020

Understanding intermolecular forces in liquids at distances below a few nanometers is extremely important in many fields because forces on this length scale determine properties such as chemical bonding, wetting, and specific molecular recognition. However, it is difficult to measure forces over these length scales and perhaps even more difficult to understand them theoretically. The problem stems from the fact that it is hard to make simplifying approximations on these length scales. For example, continuum models usually break down because the finite size of the solvent molecules (typically several angstroms) can not be ignored. Molecular dynamics must often be used to study these systems, limiting the accessible time scales to, at most, many nanoseconds with current computing power.Atomic force microscopy (AFM) is a relatively new technique that is proving useful in the measurement of forces at these small length scales. Probably the oldest and most direct way to measure a force is through the deflection of a spring, and in many ways, the AFM is simply a much smaller version of more familiar spring based instruments that measure force such as a weight scale.
3-D reconstruction of paracrystalliné biological specimens by tomography
Authors: Taylor K. A. , Winkler H. 
Published: June 2020

The calculation of 3-D images of paracrystalline objects is often done using methods appropriate to 2-D crystals. However, this method leads to a loss of information about the structural variations within the paracrystal. Structural variations are often referred to as noise but may represent important features. In our own work with 3-D imaging of sectioned insect flight muscle (IFM) structural variations represent the adjustment in crossbridge form imposed by the filament lattice. In order to complement our averaged 3-D images obtained by 2-D crystal methods, we have experimented with performing essentially the same procedures using all the data, both sampled and continuous, to generate the 3-D image. While the method embodies no new principles, the combination of protocols appears to be unique.The procedure uses the following steps: (1) A uniaxis tilt series ranging to ±75° is recorded. The increment between tilt angles decreases as tilt angle increases and ranges from ˜8° at low angles to ˜2° at high tilts.
Tubulin structure at intermediate resolution
Authors: Downing K. H. , Wolf S. G. , Nogales E. 
Published: June 2020

Microtubules are involved in a host of critical cell activities, many of which involve transport of organelles through the cell. Different sets of microtubules appear to form during the cell cycle for different functions. Knowledge of the structure of tubulin will be necessary in order to understand the various functional mechanisms of microtubule assemble, disassembly, and interaction with other molecules, but tubulin has so far resisted crystallization for x-ray diffraction studies. Fortuitously, in the presence of zinc ions, tubulin also forms two-dimensional, crystalline sheets that are ideally suited for study by electron microscopy. We have refined procedures for forming the sheets and preparing them for EM, and have been able to obtain high-resolution structural data that sheds light on the formation and stabilization of microtubules, and even the interaction with a therapeutic drug.Tubulin sheets had been extensively studied in negative stain, demonstrating that the same protofilament structure was formed in the sheets and microtubules. For high resolution studies, we have found that the sheets embedded in either glucose or tannin diffract to around 3 Å.
How does lysozyme affect Escherichia coli: questions arising from impact frozen and freeze-substitutet bacteria
Authors: Gabrieli A. , Wild P. , Schraner E.M. , Pellegrini A. , von Fellenberg R. 
Published: June 2020

Since the discovery by Fleming in 1922 that lysozyme has the ability to lyse Grampositive bacteria but not Gram-negative bacteria the assumption was established that lysozyme per se cannot affect Gram-negative bacteria. One basis of this assumption is that lysozyme is an enzyme with muramidase activity acting on the peptidoglycan. In E. coli, the peptoglycan layer is protected by the outer membrane, and, thus lysozyme has no access to it unless the outer membrane is destroyed, e.g. by EDTA or complement1. Accidentally, Pellegrini et al. found that lysozyme kills but does not lyse E. coli. Electron microscopy of bacteria fixed with aldehydes revealed that affected E. coli were often enlarged, the cytoplasm destroyed to various extend, but the cell membranes seem to remain intact (Fig. 1).Chemical fixation is proved to induce dramatic changes in bacterial structure. Thus we immobilized bacteria after exposure to lysozyme at 37°C for 15 min by impact freezing on a liquid nitrogen cooled copper block.
Bismuth hematoxylin staining of nucleic acids
Authors: Smith A.A. 
Published: June 2020

Hematoxylin is readily oxidized to the blue pigment hematein. Hematein can complex with a wide variety of metal salts or mordants to form mordant dyes. These dyes stain various components of animal tissues. The component stained depends on the metal in the mordant dye.Alum hematoxylin uses trivalent aluminum ion as a mordant. At extreme dilution, requiring long staining times, alum hematoxylin is a specific stain for nucleic acids. As usually used, alum hematoxylin stains nucleoproteins, staining them nearly as well after the removal of the nucleic acids as before.Bismuth shows a high affinity for nucleic acids. Although all common bismuth salts are insoluble in water, sodium bismuthate reacts with an aqueous solution of hematoxylin to produce hematein and trivalent bismuth ions. The bismuth ions complex with the hematein to form a water-soluble “bismuth hematoxylin.” HEPES (N-[2-hydroxyethyl]piperazine- N'-2-ethanesulfonic acid), 8 mg/ml of solution, greatly increases the amount of bismuth hematoxylin formed. Glycerol, 1/8 v/v, improves the stability of the complex.
Different carbohydrate substrates affect cell wall adhesion in candida albicans
Authors: Browning Sara L. , Crang Richard F. E. , Burns Aaron D. , Vossbrinck Charles R. 
Published: June 2020

Candida albicans is an imperfect dimorphic yeast which is an opportunistic human pathogen that can cause diseases ranging from superficial to life-threatening systemic infections. Its ability to infect, however, depends upon its ability to adhere to host cells. A previous study has shown that adhesion of certain strains of C. albicans is made possible through a major cell wall antigen of approximately 49 kDa. This protein is also found to be associated with a carbohydrate (believed to be mannose), resulting in a glycoprotein. Growing the yeast in different carbon substrates has demonstrated differences in host cell adhesion.C. albicans (strain SC-5314) from the Bristol Myers Squibb Culture Collection (Wallingford, CT) was grown separately in media of several carbon substrates: sucrose, fructose, glucose, and mannose, at 37°C for 24 hr. Each group of cells were washed in phosphate-buffered saline and suspended in freshly isolated human buccal cells for 1 hr. During that time, counts were made every 10 min to determine an average number of adhered yeast cells/buccal cell based on counts of 100 buccal cells. Representative scanning electron micrographs were taken (Fig. 1).
Renal handling of native and glycated albumins by the normal mouse
Authors: Londoño I. , Bendayan M. 
Published: June 2020

One of the major pathophysiological sequela of long-term hyperglycemia is the increased glycation of proteins. The glycation reaction consists in the covalent attachment of glucose molecules to amino groups in proteins forming a stable product, the Amadori adduct. Albeit further transformations can occur, Amadori adducts constitute the predominant form of circulating glycated proteins in normal and diabetic subjects, and seem to be directly involved in the pathogenesis of diabetic nephropathy.In an attempt to determine the role of glycated proteins in glomerular hyperfiltration and proteinuria characteristics of diabetic nephropathy, we have evaluated the renal handling of glycated albumins by the normal mouse, at two levels: the glomerular filtration and the tubular epithelial reabsorption. Bovine serum albumin (BSA) was glycated in vitro within conditions allowing for the formation of Amadori products. Both native and glycated albumins were tagged to haptens and intravenously injected in mice. Upon 10 and 30 min of circulation, the renal cortex was fixed and processed for immunocytochemical labeling which combined anti-hapten antibodies and protein A-gold complexes.
Evaluation of the emerging coleorhiza and radicle of Bromus tectorum using SEM and light microscopy
Authors: Christensen Maren , Gardner John S. , Allen Phil S. 
Published: June 2020

The coleorhiza is a nonvascular sheath that encloses the embryonic radicle in Gramineae, and is generally the first tissue to emerge during germination. Coleorhiza cells develop extensions similar to root hairs, which are difficult to study quantitatively in situ because they are extremely sensitive to desiccation and breakage. Protective, absorptive and adhesive roles have been postulated for this tissue, but have received limited attention, This study used scanning electron microscopy (SEM) and light microscopy (LM) to characterize the coleorhiza and radicle during germination of Bromus tectorum, a species that often emerges from the soil surface in semiarid habitats.Caryopses (seeds) were imbibed at various water potentials over solutions of polyethylene glycol (PEG) or in soil until coleorhizae had emerged. For SEM, seeds imbibed over PEG were frozen in liquid freon and then freeze dried, Seeds imbibed in soil were frozen in liquid nitrogen and then freeze dried. For LM, seeds imbibed over PEG were subjected to freeze substitution in dry acetone with 1% OSO4 at -80°C for 19 days.
The use of Griffonia simplicifolia lectin, GSA-I-B-4, to determine the extent of neovascularity in murine neoplasms
Authors: Bucana C. D. , Reynolds D. , Dunner K. , Radinsky R. , Fidler I. J. 
Published: June 2020

Angiogenesis plays a critical role in many physiological and pathological processes and is measured by a vascularity index derived from quantification of newly formed blood vessels. Although the identification of human endothelial cells can be accomplished by binding of antibodies against Factor VIII or binding of Ulex europeaus I agglutinin (UEA-I), in murine tissues these markers produce poor results. Since the lectin (GSA-I-B4) from the seeds of Griffonia simplicifolia which binds to -D-galactose, has been shown to bind preferentially to murine endothelial and some epithelial cells,' we determined if binding of this lectin will identify mouse endothelial cells within and around tumors growing in different organs of the mouse such as lung, kidney, bladder, and subcutaneous space.Tumors were excised, fixed in 10% formalin and processed for histology. The original procedure was modified to include a microwave antigen retrieval procedure which appears to enhance the signal better than trypsin treatment of the deparaffinized sections (Fig. 1 and 2).
Proliferating cells in the vertebrate small intestine: an immunohistocheniical study
Authors: Kömüves Làszló G. 
Published: June 2020

In the small intestinal mucosa of healthy adult mammals proliferating cell are confined to the crypts of Lieberkiihn. Earlier radioautographic studies identified proliferative cells in the small intestine of several non-mammalian vertebrates. However, it is still not clear whether cell renewal is confined to proliferative compartment within the small intestinal mucosa in non-mammalian vertebrates. In the present study proliferative cells were identified using an immunological marker of cell proliferation, the proliferating cell nuclear antigen (PCNA) in the small intestine of several non-mammalian vertebrate species, including birds (zebrafinch, Poephila guttata), reptiles (green anole, Anolis carolinensis), amphibia (axolotl, Ambystoma mexicanum), and fishes (goldfish, Carassius auratus).Segments of the small intestine were fixed in 4% formaldehyde in 0.86 M phosphate buffer, pH=7.2 and embedded in paraffin. Deparaffinized and rehydrated sections were microwaved in citrate buffer. The immunohistochemical detection method used in this study based on the capillary action principle, as developed by Brigati.
Low temperature SEM comparisons of adjacent freeze-fractured and freeze-etched areas on frozen, hydrated samples
Authors: Wergin William P. , Erbe Eric F. , Yaklich Robert W. 
Published: June 2020

Most biological samples contain 70-95% water, consequently cryofixation and freeze-fracturing result in relatively smooth surfaces that exhibit few structural details. Freeze-etching, a technique that solved this problem, was initially developed for TEM observations of virus particles by Steere nearly 40 years ago. The technique, which sublimes water-ice from the surface of a fractured sample, produces surface topography that corresponds to the structural components on the freeze-etched face. This technique was further enhanced by recovering the complementary halves of a fractured sample, etching one of the surfaces and then comparing the complementary replicas from the freeze-fractured and freeze-etched faces. Recently, similar techniques were used on frozen, hydrated samples to examine complementary halves of freeze-fractured, freeze-etched specimens by low temperature SEM. Imaging complementary images of frozen, hydrated specimens in the SEM was faster than imaging complementary replicas in the TEM, however the procedure required specialized holders and was technically demanding.To simplify comparisons of freeze-fracture, freeze-etch images, samples were frozen, fractured and etched in the prechamber of an Oxford CT 1500 HF Cryotrans system that was attached to a Hitachi S-4100 FESEM.
Electron image conversion
Authors: Herrmann K.-H. 
Published: June 2020

Electronic image converters are installed in conventional transmission electron microscopes (CTEM) for several reasons depending on the field of application:1. Their real-time response permits immediate observation and evaluation of the image as required for both high precision adjustment of microscopes for atomic resolution in material science and minimum exposure technique in biology.2. Used as a fast interface to the computer, an electronic image converter allows on-line image processing for both automatic adjustment and low-dose techniques.
Correlation averaging of two-dimensional crystals: basic strategy and refinements
Authors: Baumeister W. , Rachel R. , Guckenberger R. , Hegerl R. 
Published: June 2020

IntroductionCorrelation averaging (CAV) is meanwhile an established technique in image processing of two-dimensional crystals /1,2/. The basic idea is to detect the real positions of unit cells in a crystalline array by means of correlation functions and to average them by real space superposition of the aligned motifs. The signal-to-noise ratio improves in proportion to the number of motifs included in the average. Unlike filtering in the Fourier domain, CAV corrects for lateral displacements of the unit cells; thus it avoids the loss of resolution entailed by these distortions in the conventional approach. Here we report on some variants of the method, aimed at retrieving a maximum of information from images with very low signal-to-noise ratios (low dose microscopy of unstained or lightly stained specimens) while keeping the procedure economical.
Inexact reconstruction with added noise
Authors: Mu C. , Shao Z. 
Published: June 2020

An inexact reconstruction technique (IRT) has recently been developed which allows a 3-D object to be reconstructed using a very limited number of views. The object is assumed to be adequately represented by a binary (Boolean) distribution of mass.This method has been successfully applied to a biological object using only three views at 45° intervals. The IRT method has been improved with regard to speed and accuracy and has been extended to the special case where three mutually orthogonal views can be obtained.
A multislice approach to the rheed and rem simulation
Authors: Peng L.M. , Cowley J.M. 
Published: June 2020

The multislice method of calculating dynamical diffraction is based on the physical optics theory of Cowley and Moodie, which has been shown is equivalent to the quantum theory, back scattering being neglected. This method is capable of the calculation of RHEED diffraction amplitudes and the REM image simulation provided that the surface structure and surface potential have been properly modeled.The procedure for RHEED and REM calculations used her,e is basically the same as the conventional multislice calculation. The periodic continuation assumption has been employed to include the desired model surface (Fig. 1). A large dimension normal to the surface must be used so that there is no interference between these extended unit cells. The choice of the specimen thickness depends on the competition between the requirements for short computing time and larger model surface required to simulate the real equilibrium diffraction processes.
TEM characterization of proton-exchanged LiNbO3 optical waveguides
Authors: Lee W. E. 
Published: June 2020

An optical waveguide consists of a several-micron wide channel with a slightly different index of refraction than the host substrate; light can be trapped in the channel by total internal reflection.Optical waveguides can be formed from single-crystal LiNbO3 using the proton exhange technique. In this technique, polished specimens are masked with polycrystal1ine chromium in such a way as to leave 3-13 μm wide channels. These are held in benzoic acid at 249°C for 5 minutes allowing protons to exchange for lithium ions within the channels causing an increase in the refractive index of the channel and creating the waveguide. Unfortunately, optical measurements often reveal a loss in waveguiding ability up to several weeks after exchange.
Microstructural investigation of temper embrittlement in 2.25% Cr-1%Mo steels with and without La additions
Authors: Burke M.G. , Garcia C. I. , DeArdo A. J. 
Published: June 2020

Lanthanide (rare earth) metal additions to 2.25% Cr-1% Mo steels have been found to alleviate the material's susceptibility to temper embrittlement. To elucidate the manner by which such additions impart immunity to temper embrittlement, analytical electron microscopy (AEM) and atom probe field-ion microscopy (APFIM) have been employed to study the microstructures of tempered 2.25% Cr-1% Mo steels containing tramp elements with and without lanthanum additions.Thin-foil and carbon extraction replica specimens were prepared from the heat-treated 2.25% Cr-1% Mo steels. These samples were examined in a JEOL 200CX Temscan at 200 kV. Alloy carbides were identified by electron diffraction and STEM qualitative energy dispersive x-ray analysis.
Improvements on the gaseous detector device
Authors: Danilatos G.D. 
Published: June 2020

The possibility of placing the specimen in a gaseous medium in the environmental SEM (ESEM) has created novel ways for detection of signals from the beam-specimen interactions. It was originally reported by Oanilatos that the ionization produced by certain signals inside the conditioning medium can be used to produce images. The aim of this report is to demonstrate some of the improvements on the system that have occurred thereafter.Two straight thin wires are aligned horizontally along a direction normal to the direction of the two scintillator backscattered electron (BSE) detectors reported elsewhere. The free end tips of the wires are about 5 mm apart halfway between the specimen and the pressure limiting aperture (specimen distance = 1.5 mm). The other end of each wire makes contact with the input of a separate preamplifier, two of which are built inside a shielding aluminum stub. With such a design, interference noise from the input cables is avoided.
Magnetic microstructure imaging by secondary electron spin polarization analysis
Authors: Hembree G. G. , Unguris J. , Celotta R. J. , Pierce D. T. 
Published: June 2020

Recent research has shown that the low energy secondary electrons generated from ferromagnetic material are spin polarized. The secondary electron polarization yields a signal which is directly proportional to the magnitude and direction of the magnetization within the volume of material in which the electrons were generated. This signal can be used in a scanning electron microscope to image the microstructure of magnetic domains on the surface of ferromagnetic materials.We have incorporated a new compact spin polarization analyzer into a commercial UHV SEM. A schematic diagram of the apparatus is shown in Fig. 1. The secondary electrons are extracted from the sample and are then focused into a hemispherical energy analyzer which filters out the high energy electrons.