bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of antibody and lectin-colloidal gold conjugates to detect surface and extracellular glycoproteins produced in vivo by the Lyme disease spirochete Borrelia bergdorferi
Authors: Dorward David W. , Garon Claude F. 
Published: June 2020

Despite the often serious pathological ramifications of Lyme disease, Borrelia burgdorferi, the causative agent, is rarely demonstrated in nor isolated from naturally-infected mammalian hosts. This dilemma has led to suggestions that a limited number of spirochetes expel extracellular bioproducts that may contribute to the clinical symptoms. Currently, no mammalian toxins have been attributed to B. burgdorferi, however, the production of extracellular vesicles by this bacterium was recently described. In order to assay the possible presence of such extracellular material in infected hosts, we developed a sensitive electron microscopic assay to detect and characterize B. burgdorferi products in biological samples.Polyclonal rabbit serum was raised against purified B. burgdorferi vesicles and against an electrophoretically-purified 83 kilodalton (kDa) vesicle-associated protein. After purification of IgG from the sera, anti-vesicle F(ab’)2 fragments were produced and used to “activate” parlodion-coated grids. Such grids were incubated with cultured spirochetes, or with fluids and tissues from infected and non-infected mammals and ticks. Captured antigens were then labeled with anti-83 kDa IgG and Protein A-colloidal gold conjugates, and/or lectin-colloidal gold conjugates, then examined and characterized by electron microscopy.
Quantitative immunocytochemical localization of four immunodominant antigens of Toxoplasma gondii
Authors: Bonhomme A. , Boulanger F. , Lebonvallet S. , Bonnet N. , Bharadwaj L.M. , Pinon J.M. 
Published: June 2020

Four immunodominant antigens frequently observed in congenital, acquired and reactivated toxoplasmosis have been localized on Toxoplasma gondii ultrathin sections using four monoclonal antibodies (Mab GII9, IV47, IE10 II38) which detect membrane and cytoplasmic antigens. Thin sections as well as the whole surface of RH tachyzoïtes of Toxoplasma gondii are immunolabeled with the different Mab and Biotin-streptavidin-colloïdal gold complex. The quantitative analysis of immunogold labeling was performed with the help of a semi-automatic procedure developped by us, using a digital image analysis system (Bio 500-BIOCOM, les Ullis, FRANCE). The number of gold particles per unit surface are quantified inside three cellular compartments defined on the video screen : surface membrane, submembrane area and rhoptries.On the whole cell surface, proteins of 30 kDa (P30) detected with Mab GII9 were the major surface protein (Fig 1). By quantitative evaluation, they were 50 fold more abundant than P45-50kDa (recognized by Mab II38) proteins and 7 fold more abundant than P66-70kDa (recognized by Mab IE10) proteins. For the proteins of 28 kDa detected with Mab IV47 the labeling was very intensive in the submembrane area (Fig 3).
A description of the phospholipid arrangement in DOPE:DOPC mixture and its modification by trehalose as studied by freeze-fracture
Authors: Mariana Tihova 
Published: June 2020

The effect of trehalose on the lamellar/HII phase transition in hydrated dioleoylphosphatidylethanolamine:dioleoylphosphatidylcholin mixtures as a function of temperature (t°) was investigated.DOPE:DOPC/3:I or DOPE only (at concentrations 60wt%)(Avanti Pol.Lip.) were hydrated in 1.8M trehalose solution at t°>TH and shaken 5-10 times on a vortex mixer ai this t° by the technique of exhaustively cycling the t° through TH. Suspensions were equilibrated at the t° desired and quenching was achieved by liquid nitrogen jet freezing.A gradual transition of HII phase into a new type of bilayer - sinusoidal ripple phase in the lipid mixture quenched from 22°C is shown in fig.1. The HII phase exhibits unusual appearance presented by bent cylinders situated at an angle to each other. The sinusoidal ripples described as a stable intermediate structure between Lα and HII phases is different from Pβ’ripple phase in saturated lipid-water systems. Upon cooling the ripple bilayers transform at 0°C into smooth lamellae (figs.2a,2b) with non typical fracture face.
Molecular and Microscopic Analysis of Altered Gene Expression in Transgenic and Gene Targeted Mice
Authors: Jones W. K. , Robbins J. 
Published: June 2020

Two myosin heavy chains (MyHC) are expressed in the mammalian heart and are differentially regulated during development. In the mouse, the α-MyHC is expressed constitutively in the atrium. At birth, the β-MyHC is downregulated and replaced by the α-MyHC, which is the sole cardiac MyHC isoform in the adult heart. We have employed transgenic and gene-targeting methodologies to study the regulation of cardiac MyHC gene expression and the functional and developmental consequences of alteredα-MyHCexpression in the mouse.We previously characterized an α-MyHC promoter capable of driving tissue-specific and developmentally correct expression of a CAT (chloramphenicol acetyltransferase) marker in the mouse. Tissue surveys detected a small amount of CAT activity in the lung (Fig. 1a). The results ofin situhybridization analyses indicated that the pattern of CAT transcript in the adult heart (Fig. 1b, top panel) is the same as that ofα-MyHC(Fig. 1b, lower panel). The α-MyHC gene is expressed in a layer of cardiac muscle (pulmonary myocardium) associated with the pulmonary veins (Fig. 1c). These studies extend our understanding ofα-MyHCexpression and delimit a third cardiac compartment.
Phosphorus-mapping of isolated viruses by energy spectroscopic imaging (ESI): an experimental approach to discriminate mass-effects from the element signal
Authors: Richter K. , Tröster H. , Haking A. , Schultz P. , Oudet P. , Witz J. , Probst W. , Spiess E. , Spring H. , Trendelenburg M. 
Published: June 2020

ESI uses the fact that the probability of an electron beam loosing a certain amount of energy by inelastic scattering is a function of the elemental composition of the specimen. However, to extract precise information about the elemental distribution from the specimen, the background intensity at the element sensitive energy-loss must be known. Since background increases with mass-thickness, adequate background-estimation is a crucial prerequisite for element mapping in isolated particles as otherwise the element signal conflicts with the contrast in mass-thickness.To control the mass effect, a double layer of carbon film is used as an internal probe for phosphorus detection of the RNA in TYMV (turnip yellow mosaic virus). Phosphorus detection was performed at the P-L23-edge above 132 eV (energy-windows: 155/120/90 eV; window-size dE=15eV; irradiation dose per image approx. 105 e/nm2 EM Leo 912; detection device slow-scan ccd 14 bit). Virus particles (diameter 25 nm, ratio Protein/RNA 3/2; 6000 bases; ca. 20 P-atoms/pixel) and carbon film (thickness 10 nm) have about the same mass thickness. A second set of images taken before the P-edge (120/100/75 eV) was acquired as a negative-control for phosphorus. ESI-signals calculated from this set of images are interpreted as mass-thickness.
Characterization of Aluminum Bonding Pad Corrosion by Electron Microscopy
Authors: Klein J.E. 
Published: June 2020

One leading factor of integrated circuit (IC) reliability today deals with the identification and prevention of aluminum bonding pad corrosion. Using three common IC industry conductors, namely aluminum (99.999%), aluminum-copper(0.5%) and aluminum-silicon(l .0%), samples were fabricated and analyzed by FE-SEM/EDS after various IC processing steps.Samples consisted of boron doped (P type) <100> silicon wafers which were processed according to a standard fabrication procedure. Metal deposition was performed using a metal sputter system with an RF field and heated stage. To examine deposition temperature effects, stage temperature was varied from 200 to 300°C for each conductor type. Wafers were processed through normal fabrication with one wafer from each deposition temperature and metal type being examined after various processing steps. In addition, samples were also subjected to accelerated testing by exposure to a Pressure Cooker Test (PCT) at 120°C, 1.5 atm for 24 hours. In order to characterize the effects of oxide growth of the different metals, sputter deposited samples of each conductor as processed earlier but at one stage temperature, were microsectioned and examined by TEM.
Blind Deconvolution to Aid Morphometrics of 3D Light Micrographs
Authors: Holmes T.J. , O’Connor N.J. , Szarowski D. , Bhattacharyya S. , Ancin H. , Holmes M. , Marko M. , Roysam B. , Turner J.N. 
Published: June 2020

We are developing novel deconvolution algorithms for 3D light microscopy that include the widefield fluorescence, transmitted light brightfield and confocal fluorescence modalities. The main novelties that we have introduced are (1), the usage of maximum likelihood estimation as a mathematical optimization criterion and (2), incorporation of blind deconvolution such that the optical point spread function does not need to be measured (see references in 1,2).Our recent research has included evaluations of performance. This includes validating the images, using artificial test objects of (reasonably) “known” geometry and evaluating the accuracy of morphometries that are aided by deconvolution. Test objects include microspheres and specially drawn, fluorescent filled micropipette tips. The performance measures are comparisons of various morphometries against chosen benchmarks Rat hippocampal neurons filled with lucifer yellow were used in evaluating performance with a biological sample. Morphometries obtained from nondeblurred and deblurred data sets, by way of automatic segmentation, were compared against benchmark measurements. The benchmarks, in these cases, were measurements obtained by way of the Stereocon software. The Stereocon software uses operator judgement to segment the object, and, in our case, uses the assumption that the dendrites have circular cross sections. This assumption provides a realistic benchmark measurement because it ensures that the thickness of the dendrites, on average, is isotropic. Some of these benchmark comparisons, with confocal fluorescence, are summarized in Table 1. Fig. 1 shows projectional images of the data sets from which some of these measurements were obtained. These data imply that incorporation of deconvolution methods will improve the accuracy of absolute morphometric measurements whenever automated segmentation schemes are embedded within the measurement process.
3D Microscopy: Confocal, Deconvolution or Both?
Authors: Pawley J. B. , Czymmek K. 
Published: June 2020

Over the past 20 years great improvements have been made in the techniques available for doing 3D fluorescent microscopy on living cells. The first approach, generally referred to as image deconvolution, treats the stack of 2D widefield (WF) image data as merely the sum of a number of discrete point-spread functions (PSF) and uses the computer to find the array of emitters that, when blurred by the PSF, best fits the stored data. If the PSF is known, only presence of statistical and electronic noise in the data, prevents this best-fit set of emitters from being a perfect image of the dye distribution in the specimen. The crucial role played by noise can be appreciated by comparing images from the Hubbell space telescope in its original condition, even after deconvolution, with images taken after the optics had been repaired.The second approach to 3D microscopy requires the introduction of a confocal aperture in front of the photodetector of a scanning laser microscope so that only the fluorescent signal emitted from the plane-offocus is recorded. As a result the image formed represents an “optical section” and a stack of such sections
can be recorded at different focus heights to produce a 3D data set.
Comparison of Techniques for EELS Mapping in Biology
Authors: Leapman R.D. , Andrews S.B. 
Published: June 2020

Elemental mapping of biological specimens by electron energy loss spectroscopy (EELS) can be carried out both in the scanning transmission electron microscope (STEM), and in the energy-filtering transmission electron microscope (EFTEM). Choosing between these two approaches is complicated by the variety of specimens that are encountered (e.g., cells or macromolecules; cryosections, plastic sections or thin films) and by the range of elemental concentrations that occur (from a few percent down to a few parts per million). Our aim here is to consider the strengths of each technique for determining elemental distributions in these different types of specimen.On one hand, it is desirable to collect a parallel EELS spectrum at each point in the specimen using the ‘spectrum-imaging’ technique in the STEM. This minimizes the electron dose and retains as much quantitative information as possible about the inelastic scattering processes in the specimen. On the other hand, collection times in the STEM are often limited by the detector read-out and by available probe current. For example, a 256 x 256 pixel image in the STEM takes at least 30 minutes to acquire with read-out time of 25 ms. The EFTEM is able to collect parallel image data using slow-scan CCD array detectors from as many as 1024 x 1024 pixels with integration times of a few seconds. Furthermore, the EFTEM has an available beam current in the µA range compared with just a few nA in the STEM. Indeed, for some applications this can result in a factor of ~100 shorter acquisition time for the EFTEM relative to the STEM. However, the EFTEM provides much less spectral information, so that the technique of choice ultimately depends on requirements for processing the spectrum at each pixel (viz., isolated edges vs. overlapping edges, uniform thickness vs. non-uniform thickness, molar vs. millimolar concentrations).
A Simple Correlative Technique for Morphologic and Energy-Dispersive Analysis of Glass-Mounted Paraffin Sections
Authors: Baker K. W. , King L. , Walker R. , Piscopo I. , Smith A. 
Published: June 2020

Tissue sections, smears, and many other varied types of specimen are often mounted on glass slides for light microscopic (LM) evaluation and analysis. These same preparations’ using gold/palladiumcoated glass slides as specimen mounts, are also well suited to correlative scanning electron microscopy (SEM) and, energy dispersive X-ray analysis (SEM/EDX). The following short note describes a procedure for glass-mounted specimens that provides slides suitable for combined LM, SEM and SEM/EDX characterization. In addition, the method establishes a specimen-based reference point for the empirical determination of optimum electron probe depth and accelerating voltage for SEM/EDX analysis.For illustrative purposes we used sections of mammalian kidney cortex known to be heavily laden with crystalline deposits of unknown structure and composition.In each sample, birefringent crystalline material was initially observed in hematoxylin and eosinstained paraffin sections using bright field polarized light microscopy (Fig. 1).
Orientation Imaging of A Nb-Ti-Si Directionally Solidified In-Situ Composite
Authors: Sutliff J. A. , Bewlay B. P. 
Published: June 2020

In this paper we report on the microstructural characterization of a directionally solidified (DS) Nb-Ti-Si alloy. The solidified ingot had a nominal composition of Nb-33 at%Ti-16 at% Si and was grown using the Czochralski technique with growth rate of 5 mm/min. The as-solidified ingot was approximately 50 mm long with a 10 mm diameter. The microstructure was examined using backscatter electron imaging and the microtexture of each of the phases was determined using the Electron BackScattering Pattern (EBSP) technique for electron diffraction in the scanning electron microscope. The details of the experiments are similar to those we have reported previously. Automated EBSP scans were acquired in order to map the local texture (microtexture) over most of a transverse cross-section through the ingot.Figure 1 is a backscattered electron image (BEI) of a transverse section of the as-solidified microstructure. In this image, the bcc-Nb phase is the lighter gray phase and has a dendritic structure. The dark gray phase is (Nb,Ti)3Si having a Ti3P crystal structure. The silicide phase appears as both multiply-faceted dendrites and irregularly bounded grains. A pattern of shading, due to Ti segregation, can be seen in figure 1 and suggests a cellular solidification structure. Figure 2 is a BEI taken at higher magnification to show a region that was analyzed by automated-EBSP. Figure 3 contains orientation images generated from the automated-EBSP data set. In Figure 3a, the color black signifies positions for which no Nb diffraction patterns could be indexed and other shades of gray signify specific Nb orientations, as described by a set of Euler angles. A similarly generated orientation image for the silicide phase is shown in Figure 3b. The greyscale image presented here is actually a rendering of a truecolor image based on a RGB triplet using the Euler angles.
High-Temperature Instability of A Cr2Nb-Nb(Cr) Microlaminate Composite
Authors: Larsen M. , Rowe R.G. , Skelly D.W. 
Published: June 2020

Microlaminate composites consisting of alternating layers of a high temperature intermetallic compound for elevated temperature strength and a ductile refractory metal for toughening may have uses in aircraft engine turbines. Microstructural stability at elevated temperatures is a crucial requirement for these composites. A microlaminate composite consisting of alternating layers of Cr2Nb and Nb(Cr) was produced by vapor phase deposition. The stability of the layers at elevated temperatures was investigated by cross-sectional TEM.The as-deposited composite consists of layers of a Nb(Cr) solid solution with a composition in atomic percent of 91% Nb and 9% Cr. It has a bcc structure with highly elongated grains. Alternating with this Nb(Cr) layer is the Cr2Nb layer. However, this layer has deposited as a fine grain Cr(Nb) solid solution with a metastable bcc structure and a lattice parameter about half way between that of pure Nb and pure Cr. The atomic composition of this layer is 60% Cr and 40% Nb. The interface between the layers in the as-deposited condition appears very flat (figure 1). After a two hour, 1200 °C heat treatment, the metastable Cr(Nb) layer transforms to the Cr2Nb phase with the C15 cubic structure. Grain coarsening occurs in the Nb(Cr) layer and the interface between the layers roughen. The roughening of the interface is a prelude to an instability of the interface at higher heat treatment temperatures with perturbations of the Cr2Nb grains penetrating into the Nb(Cr) layer.
The Instructional SEM Laboratory at Iowa State University
Authors: Chumbley L. S. , Meyer M. , Fredrickson K. , Laabs F.C. 
Published: June 2020

The Materials Science Department at Iowa State University has developed a laboratory designed to improve instruction in the use of the scanning electron microscope (SEM). The laboratory makes use of a computer network and a series of remote workstations in a classroom setting to provide students with increased hands-on access to the SEM. The laboratory has also been equipped such that distance learning via the internet can be achieved.A view of the laboratory is shown in Figure 1. The laboratory consists of a JEOL 6100 SEM, a Macintosh Quadra computer that acts as a server for the network and controls the energy dispersive spectrometer (EDS), four Macintosh computers that act as remote workstations, and a fifth Macintosh that acts as an internet server. A schematic layout of the classroom is shown in Figure 2. The workstations are connected directly to the SEM to allow joystick and computer control of the microscope. An ethernet connection between the Quadra and the workstations allows students seated there to operate the EDS. Control of the microscope and joystick is passed between the workstations by a switch-box assembly that resides at the microscope console. When the switch-box assembly is activated a direct serial line is established between the specified workstation and the microscope via the SEM’s RS-232.
Remote Operation of a Scanning Electron Microscope (SEM) from Distant Classrooms
Authors: Smith N. R. , Tullis R. E. , Fegan N. , Morgan C. L. 
Published: June 2020

California State University, Hayward (CSUH) has successfully demonstrated remote operation of a scanning electron microscope (SEM) using several networking interfaces. One of these methods is the use of highbandwidth asynchronous transfer mode (ATM). The different networking schemes have made it possible for instructors and researchers to access and control the Cal State Hayward SEM from classrooms located within the same building housing the microscope. In addition, the microscope has been remotely operated from across campus, from the local community college, and from San Jose State University.The development of digital imaging technology provides opportunities of developing networking schemes for access and control of scientific instrumentation. The ability to network microscopes offers the capability of teaching microscopy methods to a large number of students at the same time. The traditional microscopy class includes the instructor training one student at a time while other students observe the operator of the instrument. Remote shared access to scientific instrumentation provides the advantages of a wider variety of resources and pooling of knowledge by a larger community.
SmartTilt: The Sensible Way of Tilting
Authors: Otten Max T. 
Published: June 2020

Tilting a crystalline material in the Transmission Electron Microscope to bring it to a particular crystallographic orientation can be an experience that varies from the almost trivial (e.g. in the case of a large single-crystal piece of silicon in a semiconductor specimen) to something that frustrates even the most experienced operator (e.g. in the case of nanometre-sized crystals in a polycrystalline matrix). The problems encountered during such tilting experiments have to do mostly with the following characteristics of the double-tilt holder and goniometer of the microscope:•the second tilt is not eucentric•the mechanical characteristics of the goniometer and specimen holder are such that the forces applied by the tilt drive mechanism can lead to displacements ranging from a few to hundreds of nanometres•the tilt required commonly involves a combination of α and β tilts.Normally the operator has to juggle to keep the crystal within the beam (by applying corrections to the x and/or z goniometer axes), set or adjust the tilt speeds for the α and β tilts, judge how much to tilt with α and β, and assess the result on the diffraction pattern. As a consequence, the whole procedure is normally done in increments, with many intermediate steps, corrections for overshoots, and so on. The time taken to tilt a particular crystal is inversely related to its size. For an experienced operator who knows the relative orientations of the diffraction pattern and the tilt direction, tilting a very small crystal sometimes can take up to tens of minutes. For an inexperienced operator, the procedure commonly results in losing track of the crystal and having to start over with another one.