bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ reversed deformation of prefatigued aluminum single crystals in the HVEM
Authors: Wall M. A. , Kassner M. E. 
Published: June 2020

Utilizing a technique describe earlier by Wall et al., prefatigued aluminum single crystals oriented for single slip, were cyclically deformed in the HVEM operating at 1.5Mev by deforming in mutually perpendicular “X and Y” directions. Deforming in X and Y avoids foil buckling and allows for shear reversal (fatigue). Initial observations are reported here and will aid in the understanding of the micro-mechanisms of cyclic deformation.In situ specimens extracted from prefatigued single crystals (560 cycles, strain amplitude of 1.2 X 10−3at 77K) were oriented in such a manner as to facilitate imaging primary dislocations, b=[0,l,-1], on the primary (111) slip plane. The (111) plane is inclined 25° about the [0,1,-1] direction to increase the projected length of these dislocations for viewing on the TEM screen. The [0,1,-1] direction is also contained in the plane of the specimen foil and is 45° to the tensile axes. The specimens are then tilted to a [1,1,-1] diffracting condition. Nonperforated specimens were prepared by a technique described by Kassner Specimens were then alternately deformed along mutually perpendicular tensile axis in the HVEM.
Image analysis of fish stained specimens: A new diagnostic tool in genetics and oncology
Authors: Tanke H. J. , Vrolijk J. , Raap A. K. 
Published: June 2020

In situ hybridization allows the detection of specific nucleic acid sequences in morphologically intact cells and chromosomes. Presently, fluorescence in situ hybridization (FISH) has reached a high detection sensitivity (defined as the smallest DNA target detectable, high DNA resolution (defined as the smallest distance in kilobasepairs between two DNA targets that can be resolved microscopically and a high multiplicity (defined as the number of different probes that can be identified simultaneously. The current status of FISH methodology:*several direct and indirect nucleic acid modifications*sensitivity: unique DNA sequences 1-5 kb*DNA resolution: metaphase ~ > 1-3 Mbp (light microscopy) interphase ~50 kbp DNA halos ~ 1 kbp*multiplicity: at least 12Progress in in situ hybridization and related technology has caused molecular cytogenetics to become an established. In particular the ability of ISH techniques to detect chromosomes and/or chromosome parts in interphase nuclei (interphase cytogenetics) has significantly contributed to this acceptance of ISH, since this technique provides statistically reliable means to study the genetic composition of cells that can not, or only by complicated techniques, be brought in mitosis.
DNA sequence mapping in interphase and metaphase chromosomes by fluorescence in situ hybridization
Authors: Trask Barbara , Yokota Hiroki , Esposito Richard , Friedman Cynthia , Massa Hillary , van den Engh Ger 
Published: June 2020

By using FISH, the positions of DNA sequences can be discretely marked with a fluorescent spot. For this reason, FISH has proven useful in gene mapping, studying large-scale variation in the human genome, detecting chromosome rearrangements associated with disease, and in understanding the organization of the cell nucleus.The applications of FISH in gene mapping and cytogenetics requires a basic understanding of the organization of the interphase nucleus. These applications are constrained by the efficiency of hybridization, the spatial resolution of hybridization sites in nuclei, and the correlation (if any) between the separation of sequences in interphase chromatin and their separation on the linear DNA molecule.The efficiency of marking DNA sequences of the size cloned in cosmids is 90-95%, and the fluorescent spots produced after FISH are ∼0.3 μm in diameter. Sites of two sequences can be distinguished using two-color FISH. Different reporter molecules, such as biotin or digoxigenin, are incorporated into DNA sequence probes by nick translation. These reporter molecules are labeled after hybridization with different fluorochromes, e.g., FITC and Texas Red. The development of dual band pass filters (Chromatechnology) allows these fluorochromes to be photographed simultaneously without registration shift.
Digital imaging microscopy for molecular cytogenetics
Authors: Gray J. , Lockett S. , Mascio L. , Mullikin J. , Pinkel D. , Piper J. , Sudar D. , Thompson C. 
Published: June 2020

Digital imaging microscopy is an essential tool in molecular cytogenetics. We describe here, hardware and software for sensitive multi-color image acquisition and display, gene mapping, generation ofcopy number karyotypes using comparative genomic hybridization (CGH), and correlation between genotype and histology in three dimensions.(a) QUantitative Image Processing System (QUIPS):Hardware We have developed a QUIPS that is now in routine use. This system is built around a commercial fluorescence microscope equipped with computer-controlled stage, focus and fluorescence excitation filter selection. A high resolution cooled CCD camera and a video frame rate intensified CCD (ICCD) are attached to different ports on the microscope and light is split between them. The real time images of the ICCD are continuously displayed on a monitor and are used for visual scanning and focusing. The high resolution CCD is used for image acquisition. Images from the CCD are digitized at 12 bits per pixel resulting in high dynamic range and high precision. QUIPS employs a fluorescence filter package containing a beam splitter and emission filter that pass light in bands centered at approximately 440 nm (blue), 525 nm (green) and 600 nm (red).
Comparison of human normal and neoplastic prostate epithelial cells by TEM and quantitative image analysis and morphometry (QIAM)
Authors: Gau J. T. , Grove M. L. , Strom S. , Orsini R. , Song K. C. , Bahnson R. , Becich M. J. 
Published: June 2020

Prostate cancer is the most common tumor in men in the U.S.A. The regulation of growth control in normal prostate cells and its contribution to tumor progression is a subject of intense investigation.Recently our group developed culture techniques that allowed us to study normal and neoplastic human prostate epithelial cells from human prostatectomy specimens. Since quantitative evaluation of intracellular compartments will be critical to defining the role of membrane trafficking in the growth regulation, we used TEM and QIAM to characterize normal and neoplastic prostate epithelial cells invivo, as well as in vitro. This work will serve as a baseline to subsequent studies using perturbants of cell trafficking and conditions ;hat promote or block cellular growth, to investigate the role of growth factors and stromal/epithelial nteraction in prostate growth regulation.Normal and neoplastic tissues were sampled for ultrastructural examination from grid mapped radical prostatectomy specimens that were processed for whole mounts. The SV40 immortalized "normal" prostate cell line (P69) was provided by Dr. Strom.
Structure of frozen hydrated deoxy-sickle hemoglobin fibers
Authors: Lewis Michael R. , Josephs Robert 
Published: June 2020

Three-dimensional reconstruction of a helical particle can be accomplished from a single lateral view, but in practice the reconstruction procedure must be optimized to make the best use of the available projection data. This is especially true for unstained frozen hydrated (ice embedded) specimens, whose micrographs have a characteristically low signal to noise ratio. Deoxy-sickle hemoglobin (HbS) fibers present an additional difficulty as well because these particles have a variable pitch and may also have variation in their unit cell structure. We have carried out a three-dimensional reconstruction of an unstained frozen hydrated HbS fiber (Figs. 1 & 2) by convolution back projection. The procedures used to facilitate this three-dimensional reconstruction are described below.In this work especially close attention was paid to determining the image magnification in order that the reconstruction of this HbS fiber could be compared with previous HbS fiber models (Table 1) which are based on reconstructions of negatively stained HbS fibers. In order to determine the HbS fiber's dimensions accurately the particle (Fig. 1a) was reconstructed twice.
Bacteriophage HK97: Structural transitions along the capsid assembly pathway
Authors: Conway J. F. , Duda R. L. , Cheng N. , Hendrix R. W. , Steven A. C. 
Published: June 2020

The assembly pathway of the HK97 capsid passes through four stages, starting with the first complete precursor and ending with the mature head. The earliest particle, Prohead I, contains 415-420 copies of the major capsid protein (42kDa) arrayed in a T=7 icosahedral lattice. Proteolytic cleavage (42kDa → 31kDa) converts Prohead I into Prohead II. Expansion of Prohead II into Head I involves a major conformational change that is thought to be triggered in vivo by DNA packaging. The final transition to Head II involves the formation of covalent crosslinks between capsid protein subunits that confer additional stability. We have been examining the structural basis of these transitionsand describe here the Prohead II and Head II states.Highly purified preparations of capsids were prepared either from expression vectors of capsid proteins or from growing phage mutants in E. coli cells. Samples were prepared for electron microscopy in the frozen, hydrated, state, and imaged in a Philips EM400T operating at 100kV, using a Gatan 626 cryo-holder. Micrographs were digitized and three-dimensional density maps were calculated as described.
The automated interactive microscope (AIM) for investigating the functional dynamics of living cells: Status and vision
Authors: Harris Lowell D. , Deerfield David W. , Fahlman Scott E. , Gough Albert H. , Lanni Frederick , Farkas Daniel L. , Taylor D. Lansing 
Published: June 2020

The current status and future development plans for the Automated Interactive Microscope (AIM), to better define the mechanisms of the function of living cells, is described. The development of AIM is fueled by biologists need to spatially and temporally correlate biochemical, molecular and genetic patterns to study cell functions such as division, locomotion and endocytosis. AIM will allow the investigator to use the cell as a “living microcuvette”.AIM redefines the meaning of the term “microscope” to include the functional capability of the microscope system provided by computerization, in addition to the more classical definition which emphasizes the opto-mechanical hardware. AIM is an next generation electronic light microscope imaging system which has grown out of our work in the development of the multimode light microscope. New functionality includes new experiment control facilities as well as related multidimensional image processing, image analysis and interactive data visualization. AIM is built around microscope hardware with high precision motion controls and a powerful host workstation computer linked, via a very high speed data gateway, with the high performance computing and communication (HPCC) facilities of the Pittsburgh Supercomputing Center (PSC).
Progression of foam-cell formation in vitro in elicited macrophages after incubation with ox-LDL
Authors: Klinkner A.M. , Waites R. , Bugelski P. , Kerns W. D. 
Published: June 2020

Thioglycollate elicited mouse peritoneal macrophages incubated with copper-oxidized LDL(ox-LDL) developed foam cell morphology as observed by Nile red fluorescent staining for neutral lipids and by electron microscopic observations. Total cellular cholesterol content rose steadily over 168 hrs and esterified vs free cholesterol ratios also increased.Cultured macrophages were incubated with ox-LDL, fixed, and stained with Nile red or processed for electron microscopy. Macrophages stained with Nile red exhibited progressive accumulation of lipid over 24, 72 and 168 hrs (Fig. 1-3). The percentage of cells with lipid inclusions and the size and number of inclusions per cell increased progressively over 168 hrs. Control cells incubated without ox-LDL did not have staining indicative of foam cell formation.Transmission electron microscopy of cultured cells at 24, 72, and 168 hrs showed distinct ultrastructural changes (Fig. 4-6). Macrophages at 24 hrs possessed non-membrane bound lipid droplets. Following 72 hrs, lysosomes containing multilamellar lipoid structures were also present. Cells at 168 hrs had characteristics similar to those at 24 and 72 hrs with the addition of cholesterol crystal profiles.
High-speed brightfield 3-D imaging and 3-D image analysis of thick and overlapped cell clusters in cytological preparations
Authors: Mackin Robert W. 
Published: June 2020

This paper presents two advances towards the automated three-dimensional (3-D) analysis of thick and heavily-overlapped regions in cytological preparations such as cervical/vaginal smears. First, a high speed 3-D brightfield microscope has been developed, allowing the acquisition of image data at speeds approaching 30 optical slices per second. Second, algorithms have been developed to detect and segment nuclei in spite of the extremely high image variability and low contrast typical of such regions. The analysis of such regions is inherently a 3-D problem that cannot be solved reliably with conventional 2-D imaging and image analysis methods.High-Speed 3-D imaging of the specimen is accomplished by moving the specimen axially relative to the objective lens of a standard microscope (Zeiss) at a speed of 30 steps per second, where the stepsize is adjustable from 0.2 - 5μm. The specimen is mounted on a computer-controlled, piezoelectric microstage (Burleigh PZS-100, 68/μm displacement). At each step, an optical slice is acquired using a CCD camera (SONY XC-11/71 IP, Dalsa CA-D1-0256, and CA-D2-0512 have been used) connected to a 4-node array processor system based on the Intel i860 chip.
Low-light-level three-dimensional video microscope with long working distance objective lenses
Authors: Lin W. , Gregorio J. , Holmes T.J. , Szarowski D. H. , Turner J.N. 
Published: June 2020

A low-light level video microscope with long working distance objective lenses has been built as part of our integrated three-dimensional (3-D) light microscopy workstation (Fig. 1). It allows the observation of living specimens under sufficiently low light illumination that no significant photobleaching or alternation of specimen physiology is produced. The improved image quality, depth discrimination and 3-D reconstruction provides a versatile intermediate resolution system that replaces the commonly used dissection microscope for initial image recording and positioning of microelectrodes for neurobiology. A 3-D image is displayed on-line to guide the execution of complex experiments. An image composed of 40 optical sections requires 7 minutes to process and display a stereo pair.The low-light level video microscope utilizes long working distance objective lenses from Mitutoyo (10X, 0.28NA, 37 mm working distance; 20X, 0.42NA, 20 mm working distance; 50X, 0.42NA, 20 mm working distance). They provide enough working distance to allow the placement of microelectrodes in the specimen.
Real-time scanning-slit in vivo confocal microscope based on bilateral scanning which solves the problem of specimen motion blur: Applications to ocular neuroimaging
Authors: Masters Barry R. , Thaer Andreas A. 
Published: June 2020

The standard method to observe nerves in tissue is to use some agent such as silver or gold compounds which are localized in the nerve fibers and increase their contrast. These were the techniques developed by Camillo Golgi and Santiago Ramón y Cajal. Cajal’s work was published in a two-volume edition in French in 1909 with the title Histologie du Systéme Nerveux de l’ Homme et des Vertébrés. This work was republished in 1952-1955 as Histologie du Systéme Nerveux by L. Azoulay, Instituto Ramón y Cajal.Alternatively a fluorescent compound may be introduced near the cell bodies of the neurons and the compound diffuses along the lipid membranes of the nerve. Subsequent observations of the specimen in a fluorescent microscope provides the observer with a bright, high contrast image of the nerve and its branches and bifurcations.The standard instrument for the observation of the cornea is the slit-lamp. The slit-lamp was invented by Allvar Gullstrand. Gullstrand made major contributions to the theory of astigmatism and to the mechanism of accommodation of the eye.
Electron-Microscopic localization of biotinylated gastrin bound to eosinophils in the rat stomach
Authors: Miller Caroline A. , Nichols David H. , Murphy Richard F. 
Published: June 2020

Gastrin is a small peptide capable of both stimulating gastric acid secretion and acting as an enteric growth factor. Known functions of eosinophils in the rat stomach are related to immunological defense. Here we demonstrate the binding of biotinylated gastrin to rat stomach eosinophils in the electron microscope. Small pieces of stomach were fixed by immersion in 4% paraformaldehyde/0.1% glutaraldehyde in 0.1 M phosphate buffer, pH 7.4 for 1 hour. The tissue was then cryoprotected in 30% sucrose/0.1 M phosphate buffer, transferred to Tissue Tek OCT compound and frozen in isopentane cooled with liquid nitrogen. Transverse cryostat sections were cut at 25 μm, thawed in PBS and free floating sections exposed to 10−5 M biotinylated 1-17 gastrin (human sequence; Peninsula Labs) for 1 hour. Controls omitted the biotinylated gastrin from this step. Sections were then rinsed 3X in PBS and exposed to either:1).a 1:50 dilution of 10 nm Extravidin colloidal gold (Sigma) for 2 hours, or2).an avidin-biotin-alkaline phosphatase complex (ABC-AP;Vector) for 1 hour. A substrate solution containing cerium chloride was used to generate an electron dense reaction product.Sections from both procedures were postfixed in 1% OsO4 in 0.1 M phosphate buffer, rinsed and dehydrated. These were then flat embedded in EMbed 812 between two microscope slides coated with Liquid Release (both from Electron Microscopy Sciences).Polymerized sections were adhered to resin blocks using super glue, cut at 70-90 nm, stained with uranyl acetate/lead citrate and observed in a Philips CM-10 electron microscope.
A rapid phosphotungstic acid staining method on ultra-thin sections
Authors: Chien K. , Van de Velde R. L. , Heusser R.C. , Shiroishi H. , Cohen A.H. 
Published: June 2020

The Nail-Patella Syndrome (NPS) is an autosomal dominant hereditary disease in which about 60% of the patients have glomerular abnormalities. Phosphotungstic acid (PTA) has been used successfully to demonstrate the specific collagen fibrils of NPS within the glomerular basement membrane and/or mesangial matrix in ultra-thin sections. However, in our laboratory we had difficulty staining Eponate 12 sections with PTA. A modified staining procedure which makes use of the microwave has been developed as follows:1. Glutaraldehyde/osmium fixed kidney specimens were embedded in Eponate 12 and ultra-thin sections collected on Gilder 400 mesh copper grids. Grids were stained using a RTV 700 silicone rubber staining pad. This pad contains shallow, round wells (5mm in diameter and 2mm deep) with slots in the center bottom of each well. By bending the pad, the rim of a grid can be inserted into the slot. On release, the grids adhere securely to the wall of the slot.2. 10% aqueous phosphotungstic acid was dropped into the staining wells around each grid. The staining pad was then placed in a moisture chamber consisting of a pre-heated Petri dish containing wetted filter paper and placed in Pelco 3400 laboratory microwave oven for 110 seconds at 80% power. A Tripour beaker containing 200ml room temperature tap water was placed in the microwave oven as a heat sink.
SEM evaluation of acid-etched human dentin: Alternative techniques to critical-point drying
Authors: Perdigao Jorge , Lambrechts Paul , Van Meerbeek Bart , Vanherle Guido , Lopes Augusto L. B. 
Published: June 2020

Scanning electron microscopy (SEM) has become a useful tool in dentistry. During the late 1950's and yearly 1960's the primary use of SEM in dentistry was to study dentin and enamel ultrastructure. After the introduction of the acid-etch technique, SEM has also been extensively used to study the mechanisms of enamel bonding and dentin bonding.The mechanism of bonding of resin to enamel is the formation of resin tags into the microporesities created by the acid. Bonding to dentin is not as simple as bonding to enamel. Acidic agents demineralize dentin, expose lie collagen and increase the microporosity of the intertubular dentin. If this collagen is air-dried, it collapses over lie underlying unaffected dentin. If this collagen is air-dried, it collapses over the underlying unaffected dentin. In electron microscopy, this is called die “drying down” phenomenon. Criticalpoint drying (CPD) has been described as being essential for etched-dentin preservation and for resin-dentin interface observation.
New image-modeling software used for 3-D analysis of biological EM data on silicon graphics computers
Authors: Kremer James R. , Furcinitti Paul S. , Mcintosh J. Richard 
Published: June 2020

Since the early 1980’s, there have been several software packages available for no or low cost that have been developed for image processing of 3-dimensional (3-D) biological images as well as several viewing packages that can be used for viewing 3-D data sets. Work has been done to develop a modeling program that can make interactive 3-D models in stereo, but there is a present a gap between the image processing and model viewing steps for complex 3-D biological data. Although packages available for no or low cost have only rudimentary model building tools the biologist would like to have as accurate a 3-D model as possible. Here we describe a new image modeling software package for the 3-D analyses of biological EM data.We have developed a useful software package (IMOD, Image Modeler) that allows the user to draw two dimensional contours in 3-dimensional image data. The power of IMOD is the ability to see the 3-dimensional image data in several different views at the same time.
Corneal ultrastructure after excimer laser keratectomy
Authors: Nguyen H. , Eiferman R. S. , Nordquist R. E. 
Published: June 2020

The Argon fluoride excimer laser emits light at 193nm. At a fluence of 500mJ/CM2, one micron of organic tissue should be removed. This removal occurs by the disruption of chemical bonds rather than the normal heat vaporization seen with other types of lasers. These characteristics should allow the use of this laser in performing precise removal of superficial corneal scars and opacities as well as inducing changes in corneal curvature for refractive corrections. In our studies we will report the ultrastructural changes induced in both primates and man following excimer laser treatment.Following excimer laser treatment, the primates were followed for two years and the corneas removed for morphological studies. The human specimens were taken at various times after excimer treatment for clinical reasons, all having to do with unfavorable outcomes. All human specimens were taken at the time of transplantation of a new cornea to these eyes. The specimens were fixed with 2% paraformaldehyde and 2% gluderaldehyde in cacodylate buffer at pH 7.3. After fixation, these specimens were dehydrated, imbedded in Spurr epoxy resin, then sectioned and examined ultrastructurally.