bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods to Monitor and Improve the Performance of Specimen Holders for Transmission Electron Cryomicroscopy
Authors: Armbruster B. L. , Kraus B. , Pan M. 
Published: June 2020

One goal in electron microscopy of biological specimens is to improve the quality of data to equal the resolution capabilities of modem transmission electron microscopes. Radiation damage and beam- induced movement caused by charging of the sample, low image contrast at high resolution, and sensitivity to external vibration and drift in side entry specimen holders limit the effective resolution one can achieve. Several methods have been developed to address these limitations: cryomethods are widely employed to preserve and stabilize specimens against some of the adverse effects of the vacuum and electron beam irradiation, spot-scan imaging reduces charging and associated beam-induced movement, and energy-filtered imaging removes the “fog” caused by inelastic scattering of electrons which is particularly pronounced in thick specimens.Although most cryoholders can easily achieve a 3.4Å resolution specification, information perpendicular to the goniometer axis may be degraded due to vibration. Absolute drift after mechanical and thermal equilibration as well as drift after movement of a holder may cause loss of resolution in any direction.
Improving x-ray map resolution with image restoration techniques
Authors: Mott Richard B. , Friel John J. , Waldman Charles G. 
Published: June 2020

X-rays are emitted from a relatively large volume in bulk samples, limiting the smallest features which are visible in X-ray maps. Beam spreading also hampers attempts to make geometric measurements of features based on their boundaries in X-ray maps. This has prompted recent interest in using low voltages, and consequently mapping L or M lines, in order to minimize the blurring of the maps.An alternative strategy draws on the extensive work in image restoration (deblurring) developed in space science and astronomy since the 1960s. A recent example is the restoration of images from the Hubble Space Telescope prior to its new optics. Extensive literature exists on the theory of image restoration. The simplest case and its correspondence with X-ray mapping parameters is shown in Figures 1 and 2.Using pixels much smaller than the X-ray volume, a small object of differing composition from the matrix generates a broad, low response. This shape corresponds to the point spread function (PSF). The observed X-ray map can be modeled as an “ideal” map, with an X-ray volume of zero, convolved with the PSF. Figure 2a shows the 1-dimensional case of a line profile across a thin layer. Figure 2b shows an idealized noise-free profile which is then convolved with the PSF to give the blurred profile of Figure 2c.
Methods and morality of digital manipulation of microscopic images
Authors: Kinnamon J. C. , Sherman-Crosby Terri A. 
Published: June 2020

In recent years dramatic increases in both the computational power of personal computers and the ability of image enhancement software to “retouch” acquired images have provided the structural biologist with capabilities that were undreamed of less than a decade ago. Possessing the power to manipulate acquired images, however, does not necessarily mean that it is appropriate to do so. The goals of this presentation are: 1) to describe how images can be enhanced using commonly available software (e.g., Adobe Photoshop) and 2) to present some of the ethical issues related to the manipulation of microscopic images.First of all, it should be stated that manipulating images did not begin with the introduction of the computer. The ability to adjust the appearance of microscopic images has been around as long as the darkroom. Several options for image manipulation were available to the skilled darkroom technician. One could adjust the contrast level by using different grades of paper, or increase the contrast level and sharpness or “snap” by using a point source illumination instead of an opal light source. A scratch on a negative might be covered by retouching the print using Spotone. Dodging and burning were used to even out poorly exposed images.
Unix-based workstations for digital image processing and analysis
Authors: Prestridge Eddie B. 
Published: June 2020

The modern workstation, with its inherent high speed and massive memory, allows the use of complicated image analysis and processing algorithms and artificial intelligence programs not available to current PCs and mini-computers.There is no single feature that differentiates the UNIX based workstation from a PC. Rather, it is its fundamental design that gives the workstation superior performance. This superiority in no small part is the result of the UNIX operating system. UNIX is a word that sometimes strikes fear into the hearts of mortal men! There is no reason to fear, however. Users of UNIX-based systems have no more interaction with the operating system than say users of WordPerfect running on a MS-DOS or MAC OS machine.UNIX is the only operating system that runs on a wide range of systems from laptops to mainframes. It is unique in at least five areas: 1) massive data sets handling, 2) multitasking, 3) multi-user, 4) security, and 5) networking. Let me give you what I think are usable descriptions for these five areas.
The IBM-PC in electron microscopy
Authors: Mancuso James F. 
Published: June 2020

IBM PC compatible computers are widely used in microscopy for applications ranging from control to image acquisition and analysis. The choice of IBM-PC based systems over competing computer platforms can be based on technical merit alone or on a number of factors relating to economics, availability of peripherals, management dictum, or simple personal preference.IBM-PC got a strong “head start” by first dominating clerical, document processing and financial applications. The use of these computers spilled into the laboratory where the DOS based IBM-PC replaced mini-computers. Compared to minicomputer, the PC provided a more for cost-effective platform for applications in numerical analysis, engineering and design, instrument control, image acquisition and image processing. In addition, the sitewide use of a common PC platform could reduce the cost of training and support services relative to cases where many different computer platforms were used. This could be especially true for the microscopists who must use computers in both the laboratory and the office.
The role of mixed cubic/hexagonal nucleation layers on threading dislocation reduction in epitaxial GaN films
Authors: Wu X. H. , Brown L. M. , Kapolnek D. , Kellert S. , Kellert B. , DenBaars S.P. , Speck J.S. 
Published: June 2020

The defect density and their configuration in epitaxial GaN films on sapphire are strongly related to the optical and electrical properties of the films. The crystalline quality of GaN on sapphire can be greatly improved by introducing a low temperature GaN buffer layer. However, recent studies in our group demonstrate that the pre-growth substrate treatment can significantly change the defects structure and electron properties of the films. In this paper, we present our results on studies of the film microstructures and their corresponding nucleation layers. We propose a novel mechanism for dislocation reduction for GaN on sapphire.The growths for this study were achieved in a horizontal flow reactor operating at atmospheric pressure. Basal plane AI2O3 (Union Carbide) substrates were first cleaned in solvents and then heated in flowing H2 at 1050°C. Sample A was exposed to an ammonia flow of 3 1/min for 60s, sample B for 400s before the temperature was then reduced to 600°C and a nominal 190 Å thick GaN layer was grown.
HRTEM Study of Zircon from Eliseev Anorthosite Complex, Antarctica
Authors: Wirth R. , Kämpf H. , Höhndorf A. 
Published: June 2020

Zircon is a common accessory mineral in magmatic, metamorphic and sedimentary rocks. The crystal structure is tetragonal with space group I41/amd. Zircon contains minor amounts of U and Th and can be dated by a variety of techniques yielding ages of crystallization, cooling, and redistribution of radioactive isotopes and their daughter products. The precision of the radiogenic age determination strongly depends on the ability of zircon to retain the daughter products which were produced by the radiogenic decay of U and Th.Zircon-bearing rocks of this study are metamorphic oxide-apatite gabbronorites (OAGN) from the Eliseev Anorthosite Complex, Wohlthat-Massif, East Antarctica (Kampf et al., 1995). These unusual rocks are strongly enriched in accessory minerals (apatite: < 10 vol.%; zircon: < 1 vol.%, Owens & Dymek, 1992). Three steps in the evolution of these rocks are distinguished: a magmatic formation, followed by a granulite facies metamorphism and finally a tectonomagmatic overprint. The zircon crystals of this study are brown colored, up to 12 mm in length and up to 3 mm wide (Fig.1). Petrological investigations show that zircon has formed during the granulite facies event. Optical microscopy and cathodoluminiscence microscopy reveal a rhythmic zoning and many microcracks. The concentrations of uranium and thorium are low (U: 34-89 ppm and Th: 3-9 ppm). The radiation damage by radioactive decay of U and Th is expected to be minor due to the low uranium and thorium content.
Electron-microscopy studies of grain boundary phases and fracture in yttria-zirconia ceramics
Authors: Lash S.E. , Pham H. , Cooper A. , Mecartney M.L. 
Published: June 2020

Trace amounts of intergranular silicate phases in zirconia ceramics are known to be significant factors in modifying the ionic conductivity of cubic yttria stabilized zirconia and in enhancing high temperature superplastic deformation behavior of tetragonal yttria stabilized zirconia. This work studies how the composition and distribution of the intergranular phase affect fracture.Samples were prepared of yttria stabilized zirconia ceramics with 3 mol% yttria (3Y-TZP, metastable tetragonal zirconia) and 8 mol% yttria (8Y-FSZ, fully stabilized cubic zirconia). Additions of 1 wt.% of a barium silicate glass or a borosilicate glass were made prior to sintering so that different intergranular phases could be formed. Samples were sintered at 1400-1600°C for 2-21 h. SEM images of fracture surfaces were digitized and analyzed using Adobe Photoshop and Prismview programs.Figure la shows the SEM analysis of a fracture surface of a 3Y-TZP sample sintered 1500°C for 10 hours. Transgranular fracture is indicated by the rough and wavy surfaces. Approximately 30% of the fracture is transgranular fracture.
Electron diffraction from anthracene
Authors: Tivol W. F. , Kim J. H. 
Published: June 2020

Collection of a three-dimensional data set from anthracene illustrates some of the difficulties which can be encountered. Since the crystals are grown from solution their orientation is not certain, and the crystals are very bendy, so a range of orientations is encountered at a given tilt setting. Anthracene is moderately labile to irradiation, so care must be taken to avoid radiation damage during data collection. Anthracene will sublime at room temperature under vacuum, so the data must be collected at reduced temperature. Flat, well-ordered areas of the crystals are rare, so collection of high-resolution data is time-consuming. The thickness of the crystals is difficult to control, so finding areas which have minimal multiple scattering is also formidable.The structure of anthracene is already known, so simulations of the diffraction patterns along various zone axes can be made. Cerius 2.0® was used to produce simulated zone axis patterns for all combinations of indices whose absolute values were 3 or less. The preferred orientation for the untilted grid is [102]. Scans of several preparations resulted in patterns which matched the simulation for [102]. The angles for each of the Miller planes with respect to [102] were calculated from the formula given by Dorset.
Decomposition of an Al-Cu-Ru quasi-crystal at 1420 K
Authors: Kitano Y. , Fujikawa Y. , Watanabe T. 
Published: June 2020

Quasi–crystals of Al65Cu20RU15 alloy are known to be an icosahedral— phase (I— phase) of the F–type. This state has been confirmed to be stable near 1100 K, but perhaps not at temperatures higher than around 1300 K. In this paper we report high temperature behavior of this alloy. We have found that the stable I-phase would decompose into three or four phases at 1420 K, one of which is an I–phase having a different composition. We denote the lower temperature I–phase, I–phase(L), and this high temperature one, I–phase(H).5N Al and Cu and 3N Ru were arc-melted in Ar. The nominal composition of the alloy was 65A1, 20Cu and 15Ru. In order to obtain homogeneous materials, the ingot was annealed at 1020 K for 100 hours. The X-ray powder diffraction pattern confirmed that the heat-treated ingot was only I-phase(L). This is the starting material in this study. DTA and EPMA analysis, and SEM and TEM observations were carried out in order to investigate subsequence thermal reaction. Experimental results with brief discussion are as follows.
Distensibility and wall composition of rat cerebral arterioles in hypertension induced by chronic blockade of nitric oxide synthase
Authors: Ghoneim S. M. , Chillon J. M. , Baumbach G.L. 
Published: June 2020

We have previously reported that, during chronic hypertension, cerebral arterioles undergo hypertrophy of the vessel wall, accompanied by a paradoxical increase in passive distensibility. We have proposed that this increase may be due to a reduction in the proportion of nondistensible (collagen and basement membrane) to the distensible (smooth muscle, elastin and endothelium) components of the vessel wall. We have recently observed in stroke-prone spontaneously hypertensive rats(SHRSP), that an endothelium derived factor, endothelin, may contribute to hypertrophy, but not to increases in passive ditensibility, of cerebral arterioles vessel wall.The goal of this study was to examine wall mass, composition and passive ditensibility of cerebral arterioles in chronic hypertension induced by decreased availability of another endothelium derived factor, nitric oxide (NO).Four weeks old male Sprague-Dawley rats were treated with LG-nitro-L-arginine methyl ester (LNAME; 10 mg /kg/day) in the drinking water. We examined distensibility of maximally dilated cerebral arterioles in 4 months old Sprague-Dawley rats. Arterioles were then fixed at physiological pressure (2.25% gluterladehyde in 0.10 mol/L cacodylate buffer), the arteriolar segment used for distensibility measurements was removed then immerse fixed, rinsed briefly in 0.1 M cacodylate buffer, osmicated and processed routinely for electron microscopy (TEM).
Activation of isolated heterophils from chicks stimulated in vivo with salmonella enteritidis-immune lymphokines
Authors: Moyes R. B. , Droleskey R. E. , Kogut M. H. , DeLoach J. R. 
Published: June 2020

Salmonella enteritidis (SE) is of great concern to the poultry industry due to the organism's ability to penetrate the intestinal mucosa of the laying hen and subsequently colonize the ovaries and yolk membrane. The resultant subclinical infection can lead to SE infection of raw eggs and egg products. Interference with the ability of the organism to invade has been linked to the activation and recruitment of inflammatory polymorphonuclear cells, heterophils, to the lamina propria of the intestinal tract.Recently it has been established that heterophil activation and increased resistance to SE organ invasion can be accomplished by the administration of SE-immune lymphokines (SE-ILK) obtained from supernatants of concanavalin-A stimulated SE immune T lymphocytes from SE hyperimmunized hens. Invasion of SE into the lamina propria provides a secondary signal for directing activated heterophils to the site of SE invasion.
Cyprinella lutrensis gill lesions after exposure to terbufos
Authors: Messaad Ibrahim A. , Peters Edward J. 
Published: June 2020

Terbufos (O, O-diethyl, S-(((1, 1-dimethylethyl)thio)methyl) phosphorodithioate), purity 98% acts as anticholinestrase. Commercial formulations are applied to soil as an insecticide-nematicide throughout the United States to control com root-worm larvae and other pests, preventing an economical loss to producers Terbufos is highly toxic to fish species (e.g., fathead minnows 96 hr's LC50 is 150 μg L−1) and toxicity increases as temperature increase. There have been no reports on its effects on fish gills.Red shiners (Cyprinella lutrensis) were collected from the Platte River, Nebraska using a seine and maintained in 30-L glass aquaria (10 fish /tank) for a 14-d acclimation period at 22°C on a 12:12 photoperiod and fed a commercial fish food once daily except for 24-h before and at the beginning of bioassays. During the 14-d bioassay, fish were exposed to terbufos concentrations of 0, 1, 10, and 100μg L−1. At the conclusion of the bioassay, fish were fixed in 3% glutaraldehyde with 0.1 M phosphate buffer. Gills were removed, washed in 0.1 M phosphate buffer and post-fixed in 1% OsO4 for 2-h, gills were rinsed in water and dehydrated in a graded ethanol series. After critical point drying using liquid CO2, gill tissues were mounted on stubs, coated with gold-palladium and examined using a Cambridge S-90 stereoscan at 15 kV
Identification of a baculovirus polyhedron formation mutant with a novel phenotype
Authors: Slavicek James M. , Mercer Melissa J. , Kelly Mary Ellen 
Published: June 2020

Nucleopolyhedroviruses (NPV, family Baculoviridae) produce two morphological forms, a budded virus form and a viral form that is occluded into a paracrystalline protein matrix. This structure is termed a polyhedron and is composed primarily of the protein polyhedrin. Insects are infected by NPVs after ingestion of the polyhedron and release of the occluded virions through dissolution of the polyhedron in the alkaline environment of the insect midgut. Early after infection the budded virus form is produced. It buds through the plasma membrane and then infects other cells. Later in the infection cycle the occluded form of the virus is generated (reviewed by Blissard and Rohrmann, 1990).The processes of polyhedron formation and virion occlusion are likely to involve a number of viral gene products. However, only two genes, the polyhedrin gene and 25K FP gene, have been identified to date that are necessary for the wild type number of polyhedra to be formed and viral particles occluded.
Internal organisation of the nuclear pore complex by surface imaging with field emission in lens SEM (FEISEM)
Authors: Allen T.D. , Kiseleva E.V. , Goldberg M.W. 
Published: June 2020

We have been working towards a 3 dimensional structural understanding of the Nuclear Pore Complex (NPC) with a view to investigating structural alterations associated with the molecular mechanism of transport across the nuclear envelope. FEISEM allows direct visualisation of changes in individual NPCs which will complement information from TEM 3D reconstructions. FEISEM has produced significant new information on the more peripheral elements of the NPC, most notably the nuclear pore basket or ‘fishtrap’ and the nuclear envelope lattice. NPC baskets have been recognised in both avian and insect species as well as amphibia and are likely to be evolutionarily conserved. In the salivary gland nuclei ofChironomusdifferent configurations of basket structure have been recognised undergoing interaction with Balbiani Ring particles during mRNA export. (Fig 1).The ability to observe and directly compare large numbers of NPCs on isolated NEs from either the cytoplasmic or nucleoplasmicface, at equivalent biological resolution to TEM has enabled us to access internal NPC organisation by surface imaging.
Problems in observation of natural biological surfaces with high-resolution scanning electron microscopy
Authors: Hermann René , Müller Martin 
Published: June 2020

High resolution scanning electron microscopy can contribute a lot to the understanding of events occurring on biological surfaces even at a molecular level (either natural or artificially produced surfaces, e.g. by freeze-fracturing). In order to reach this goal, significant structural elements, down to dimensions of 2 - 4 nm have to be preserved as a function of the physiological state. Cryotechniques are important tools to fulfil this task.A natural biological surface is often not easily accessible to scanning electron microscopic observation. The surface is the part of the specimen where an exchange with the surroundings takes place. Removal or replacement of the surrounding medium can strongly influence the surface structure. Surrounding fluids normally contain non volatile components (only a few organsisms, e.g. yeasts, survive in distilled water without damage). Drying procedures - out of the native milieu - therefore result in deposition of solutes onto the specimen surface, sometimes mimiking natural biological structures.
Surface photoelectrochemistry using near-field scanning optical microscopy (NSOM)
Authors: Moyer Patrick J. 
Published: June 2020

Near-field scanning optical microscopy (NSOM) has been used to characterize and modify surfaces with lateral spatial resolution as high as 50 nm. Some of these experiments were performed under electrochemical conditions. Progress towards this goal involved several important steps. They include proving adequate operation of the shear force feedback mechanism in liquids and fabrication of appropriate NSOM fiber probes.With regards to shear force feedback, which is used to maintain the fiber probe within the near field of the sample, there has been ample discussion regarding the physics of the tip-sample interaction. It is important for biological and photoelectrochemical applications that the feedback mechanism operates successfully in liquid environments. Our results indicate that shear force operation in water allows for high spatial resolution NSOM characterization while providing high force sensitivity. When comparing the frequency spectra of the probe resonances in air and water, the water resonance is broadened. The broadened resonance peak when completely immersing the probe in water indicates an increase in damping.
Magnetic resonance investigations of blood: From hemoglobin to lymphocyte migration
Authors: Ho C. 
Published: June 2020

We have applied various nuclear magnetic resonance (NMR) techniques, from high-resolution solution-state NMR spectroscopy to magnetic resonance imaging MRI), to investigate blood components such as hemoglobin and T-cells. We are interested in the structure-function relationship in human normal adult hemoglobin (Hb A) and in tracking the movement of T-cells in live rats. In this presentation, we shall give a brief summary of our approach and recent experimental results.We have recently developed an expression system to produce authentic Hb A in Escherichia coli. With our Hb A expression plasmid (pHE2) (Fig. 1), we are in a position to produce any desired hemoglobin in E. coli. We are carrying out a study to learn the rules governing oxygen affinity and cooperativity of the oxygen binding process in hemoglobin. We have constructed several recombinant hemoglobins which exhibit varying degrees of oxygen affinity and cooperativity (as measured by the Hill coefficient).