bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular and Structural Studies on Dynein Associated Mutations in Chlamydomonas Flagella.
Authors: Porter ME , Myster S , Perrone C , O'Toole E
Published: July 2020

The dynein ATPases are a large family of motor enzymes that provide the driving force for flagellar motility and contribute to microtubule-based transport inside cells. The challenge for the field is to appreciate the functional significance of the multiple dynein motors, to determine how the cell assembles a motor complex and targets each motor to its appropriate location, and to understand how a cell regulates the activity of each motor to accomplish its specific task(s). In our laboratory, we have capitalized on the highly ordered structural organization of the flagellar axoneme and on the ease of genetic analysis in Chlamydomonas to ask how a single cell controls the assembly and activity of its multiple flagellar dyneins. In particular, we have focused our efforts on the inner dynein arms, which are both necessary and sufficient for normal flagellar motility. The significance of this work derives from the conservation of axoneme structure across species, as well as the numerous functional homologies between the flagellar and cytoplasmic dyneins.
Structure of Centrosomes and Chromosomes Through IVEM Tomography
Authors: Agard DA , Guenbaut Vincent , Moritz Michelle , Braunfeld MB , Zhang GuoFung , Sedat John W
Published: July 2020

Centrosome structure: The centrosome is the major microtubule-organizing center of animal cells - it initiates spindle formation at the onset of mitosis and plays an active role in chromosome segregation. At the most basic level, microtubule (MT) formation is regulated at least in part, through the functional availability of nucleation sites on the centrosome. Functional centrosomes can be isolated from Drosophila embryos. When visualized with IVEM Tomography (IVEM-T) ring complexes are visualized throughout the peri-centriolar material (PCM) (1). γ-tubulin has been implicated in MT nucleation. Through immuno-IVEM-T we have shown that the ring structures within the PCM, contain y-tubulin and further that the only place γ-tubulin is found is at the minus (nucleating) end of MTs (2). This strongly implicates these γ-tubulin containing ring structures in MT polymerization, until our studies there was no direct proof that γ-tubulin was located at the site of MT nucleation. Furthermore Zheng et al have been able to isolate similar ring structures that are soluble from both Xenopus and Drosophila embryos (3).
Automated Color Segmentation for Quantitative Microscopy
Authors: Gaddipati A , Vince DG , Cothren R M , Cornhill JF
Published: July 2020

Over the past decade, there has been increased interest in quantifying cell populations and morphological structures in tissue sections using image analysis systems. Automated analysis is now being used in limited pathological applications, such as PAP smear evaluation, with the dual aim of increasing the accuracy of diagnosis and reducing the review time. Applications such as these primarily use gray scale images and deal with cells that are well separated. Quantification of routinely stained tissue represents a more difficult problem in that objects can not be separated in gray scale and the images are more complex. Many of the existing semi-automated algorithms are specific to a particular application and are computationally expensive. Hence, we investigated general adaptive automated color segmentation approaches which alleviate these problems.

The first stage of this research concentrated on separating tissue color clusters in a color space histogram of the image.
Association of a Brush Border Myosin I-Like Protein with Vesicular Organelles of the Secretory Pathway in Chicken Enterocytes
Authors: Kömüves László G , Munson Scott , Bikle Daniel D
Published: July 2020

Brush border myosin I (BBMI) was first identified as a major constituent of the microvillus cytoskeleton, where it links the actin filaments of the microvillus core to the overlying plasma membrane. Recently, however, BBMI was also found on isolated Golgi membranes. This observation suggests that cytoplasmic BBMI might act as a molecular motor for apically targeted secretory vesicles.

In an earlier study from this laboratory a 105-110 kD protein was isolated from the chicken small intestine, which displayed several characteristics of the BBMI. Using an antibody against this BBMI- like protein (MLP), the protein was detected in the apical brush border of the enterocytes. The limited resolution of the light microscopic immunohistochemical techniques used in that investigation, however, did not provide information about the intracellular distribution of MLP in the enterocytes.

In this study the intracellular localization of MLP was characterized using post-embedding colloidal gold immunocytochemistry. Pieces of the jejunum from 6-week-old male White Leghorn chickens were fixed and embedded in LR Gold resin.
Morphometrical Ultrastructural Studies of the Rat's Hepatocytes Under Cooling
Authors: Kaprelyants AS , Kaprelyants AA , Reylan AN , Migunova RK
Published: July 2020

The aim of given investigation is to study the effect of cooling upon rat hepatocyte structure using transmission electron microscopic and computer morphometric methods. Ultrastructural and morphometrical characteristics of hepatocytes under liver cooling for various levels under in vivo and in vitro conditions were investigated. Vistar rats of 180-250 g were used in the experiment. Liver cooling (in vivo) was performed by means of original cryoapplicator with different probe temperature (1,2). Liver tissue for transmission electron microscopy was fixed in glutaraldehyde fixator on cocadylate buffer and OsO4. Dehydration was completed on acetone (3). Tissue embedding was done into the mixture of Epon/Araldite epoxy rasin. Ultrathin slices were contrasted by the method of Reinolds. Cell viewing and imaging were accomplished by electron microscope at accelerating power of 75kV.

Morphometrical and stereometrical analysis was performed using the “Morpho-Tools” original computer system (c) 1994-1996 A.S. Kaprelyants, A.A. Kaprelyants, A.N. Reylan.
Avian Extended Junctional SR: 3-D Geometry Rendered in Stereo
Authors: Sommer JR , High T , Ingram P , Kopf D , Nassar R , Taylor I
Published: July 2020

Extended junctional sarcoplasmic reticulum (EJSR) is an invariant differentiation of the sarcoplasmic reticulum (SR) in bird cardiac myocytes (CM) and central to excitation-contraction coupling (ECC). EJSR occurs as both continuous and discontinuous extensions of junctional sarcoplasmic reticulum (JSR), and surrounds and pervades the Z/I band as the “ EJSR Z-rete” whose geometry has mechanistic implications for the function of “couplings” in ECC, in general. “Peripheral coupling(s)” (PC) in birds, and the additional “interior coupling(s)” (IC) at transverse tubules (TT) in mammals, are formed by tight apposition to plasmalemma of JSR, a specialized calcium (Ca) store of the SR. Free SR (FSR; i.e. free of JSR/EJSR specializations) is the rest of the smooth, tubular SR network, which connects intercalated patches of EJSR forming the EJSR Z-retes and, elsewhere, displays both longitudinal and transverse geometries in surrounding the contractile material for the purpose of sequestering Ca after each muscle contraction. Except for EJSR having no plasmalemmal contact, morphologically, EJSR and JSR are homologues:1 both have similar sizes; are studded (approx. 32 nm center-to-center) with junctional processes (JP; ryanodine receptor (RyR)/-Ca-release channels);
EM Study of Gastric Tumor Microvasculature
Authors: Tonino P , Finol HJ , Sosa L , Hidalgo C , Salomón MC , Negri C , Godayol F
Published: July 2020

It has been considered that the behavior of tumors is consistent with the concept that tumor growth is angiogenesis dependent. However, additionally to the newly formed vessels other patterns of tumor capillaries have been described. Information concerning the ultrastructure of tumor blood vessels has been obtained mostly from experimental models. With regard to human tumors, since no systematic ultrastructural studies are available on the gastric tumor microvasculature, the aim of the present work was to characterize the vascular architecture of this type of tumor.

Surgically resected specimens were obtained in tumors from five patients (three males and two females) between 45 to 66 years of age (mean, 56.2 years), with a histopathological diagnosis of moderately differentiated gastric adenocarcinoma. Immediately after resection, tissue samples taken from areas of tumor center were processed by routine transmission electron microscopy techniques and observed in a Hitachi H-500 EM.

The microvasculature within gastric adenocarcinomas was characterized by newly formed capillaries with proliferative endothelial cytoplasm (Fig. 1).
Vacuolation in Renal Tubular Epithelium of Mice: an Incidental Lesion
Authors: Dovey-Hartman BJ , Johnson RC , Leach MW , Frank DW , Sinha D E , Mirro EJ , Little JM , Halliwell WH
Published: July 2020

Prominent cytoplasmic vacuoles in renal tubular epithelial cells of the outer medulla were observed in several kidneys from test article-dosed mice during routine light microscopic (LM) examination. Because the vacuolar change was seen infrequently by LM examination, and was not found in any control mice from that study, it was not clear whether the vacuolation represented a drug-induced change. To address this question, kidney sections from multiple unrelated mouse studies (214 control mice and 541 test article-dosed mice representing six different compounds) were examined by LM for similar vacuolar changes. Vacuolation was seen by LM in 2.3% of the control and 2.8% of the test article-dosed mice. Transmission electron microscopy (TEM) was performed on kidneys with prominent vacuoles seen by LM in 5 control mice and 2 test article-dosed mice to further characterize the vacuoles. Additionally, kidneys from 4 randomly selected control mice lacking vacuolation by LM were examined by TEM. Samples from the outer medulla of kidney that had been fixed by immersion in 10% formalin were post-fixed in 2.5% glutaraldehyde and 2% osmium tetroxide and processed routinely for TEM.
Tissue Response to Bone Substitute Materials
Authors: Krizan K E , Lew D , Farrell B B , Laffoon J E , Keller J C
Published: July 2020

The purpose of this study was to compare the biological response to two bone substitute materials, hydroxyapatite cement (HAC) and demineralized bone (DMB), when placed in canine cranial bone. The implants were surgically positioned in 15 mm diameter defects created in the parietal plate, harvested en bloc at 3 months (m) and 6m postop, and fixed in 70% ethyl alcohol to preserve the xylenol orange bone label. Half of each implant site was processed into paraffin and the other half into Spurr plastic resin. In order to evaluate the osseoinductive properties of DMB, implants were also surgically placed in the rectus femorous muscle, harvested en bloc at 3m post op, fixed in 0.1 M Na phosphate buffer, pH 7.2, decalcified in 5% EDTA, pH 7.2, and embedded in plastic. All implants were evaluated with light microscopy (LM), radiography, energy-dispersive spectroscopy (EDS), and transmission electron microscopy (TEM). Tissue for LM was routinely decalcified with SFFA, embedded in paraffin, sectioned, stained with hematoxylin/eosin, and viewed with a Zeiss transmitted-light photomicroscope [Figs. 1, 2, 5].
Highlights of Selected Microscopy Research Resource Activities at San Diego
Authors: Ellisman Mark H , Young Stephen J , Fan G Y , Perkins Guy , Lamont Steve , Martone Maryann E
Published: July 2020

The intermediate high-voltage electron microscope (IVEM) located at the National Center for Microscopy and Imaging Research at San Diego (NCMIR) can image relatively thick specimens that contain substantial three-dimensional (3-D) structure. Electron tomography is an important tool used at NCMIR for deriving 3-D cellular and subcellular structure from IVEM images. Reconstruction algorithms commonly used in electron tomography include weighted back projection, and iterative algebraic reconstruction techniques such as ART and SIRT. Improvements in reconstruction quality are possible using the iterative algorithms. Because these algorithms are computationally intensive, we have ported them to massively parallel computers at the San Diego Supercomputer Center, reducing the computation time over that required with workstation level machines.

The quality of tomographic data for the 3-D reconstruction of biological structures is also being enhanced by NCMIR projects to improve the microscope. We have designed and constructed special electron optics and microscope control systems for the JEOL 4000EX.
High-Resolution Analytical Microscopy in the Center for Materials Science and Engineering at MIT
Authors: Garratt-Reed Anthony J
Published: July 2020

The Center for Materials Science and Engineering at MIT, a Materials Research Science and Engineering Center sponsored by the National Science Foundation, maintains and supports, amongst others, an Electron Microscopy Shared Experimental Facility. The purpose of this paper is to highlight selected recent research results for high-resolution investigations performed in that facility.

The facility owns the first VG HB603 intermediate-voltage FEG-STEM, which operates at 250KeV and is equipped with a high-solid-angle x-ray detector and a Gatan Digi-Peels. It was intended to be, and has been, used for high sensitivity, high spatial resolution microanalysis. It is well-known that the “resolution” of an x-ray analysis is intimately (and inversely) related to its sensitivity; one extreme situation occurs when analyzing, for example, a diffusion profile, when the need is to determine the composition to the highest precision. An example of such an analysis is given in fig. 1. In this case, the sample is a 1.4Cr-0.8C pearlitic steel, and the chromium analysis is carried out across a cementite plate. During the growth of the pearlite, the chromium, which is not thermodynamically required to redistribute, nevertheless diffuses along the growth interface towards the cementite, resulting in a comparatively wide depletion profile in the ferrite, and a very narrow enrichment in the cementite.
Integrated Characterization at a Canadian National Facility
Authors: McMahon G , Wronski Z , Malis T
Published: July 2020

The pressure of shrinking budgets and downsizing has made it increasingly difficult to meet requests for comprehensive microstructural characterization. In many laboratories, especially those in industry, the expense of maintaining and staffing electron, X-ray and ion beam facilities has resulted in fewer analytical capabilities. At the same time, modern materials and products continue to diversify and increase in complexity, requiring increasingly sophisticated techniques. This growing paradox has increased the need for multiclient, shared-access ‘clusters’ of microanalytical instruments.

The above federal laboratory is mandated to serve both the Canadian public (in a broad sense) and Canadian industry (in the specific sense of collaborative and contract research projects). As a result, the Characterization Group has evolved into an integrated lab competency which compliments other competencies in materials processing (full-scale foundry, industrial rolling facility, Gleeble processing simulator) and mechanical behavior (fracture mechanics, stress and deformation modeling). Building on established expertise in metallography, microprobe, X-ray and TEM, the group has doubled in size (to 20 professionals and 10 major capabilities) and now includes SIMS and surface analysis (Table 1).
Capturing Developmental Events of the C. Elegans Embryo by High Pressure Freezing After Monitoring by a Multi-Photon Imaging System.
Authors: Lavin CA , Mohler W A , Keating H H , White JG
Published: July 2020

High pressure freezing enables the rapid arrest of developmental events without prefixation. Standard chemical fixation is a time dependent event and may cause artifacts in sensitive cytoskeletal components. We are studying two developmental events in embryonic Caenorhabditis elegans: that involve changes in the cytoskeleton: spindle alignment and membrane fusion. The mitotic spindle undergoes rapid rotational alignment prior to certain differentiative divisions. We are trying to capture these events by anticipation their timing and rapid freezing. Precursor hypodermal cells of embryonic C. elegans undergo a transition from individual cells to a syncytium at the onset of morphogenesis. In an effort to visualize the fusion events, embryos were stained with the vital probe FM4-64 to highlight cell membranes. Development was monitored by fluorescent microscopy using multiple-photon excitation imaging to minimize photobleaching while providing clear images of deep sections. Small cellulose capillary tubes, as described by Hohenberg for isolation and high pressure freezing of individual cells, were not of sufficient optical quality for monitoring by a laser-scanning microscope.
The National Nanofabrication Users Network (NNUN): Potential Applicability for Bio/Biomedical Science and Technology
Authors: Isaacson M S
Published: July 2020

For several decades the US scientific community has recognized the value of pooling specialized skills and equipment in centralized user facilities. Significant efficiencies are realized within the user community by avoiding unnecessary duplication and by moving projects more quickly to completion. The user facility concept served the nanofabrication community well for over two decades at the National Nanofabrication Facility (NNF) at Cornell. In 1994, the National Science Foundation expanded the concept by integrating NNF-Cornell (Now CNF) with several other nanofabrication programs throughout the country to form the National Nanofabrication Users Network (NNUN). Within this framework of a “users” network, scientists and engineers have access to state of the art equipment and expertise.

NNUN consists of two “full service” hub facilities at Cornell (the Cornell Nanofabrication Facility) and Stanford (the Stanford Nanofabrication Facility), in association with specialized facilities at Howard, Penn State and UC-Santa Barbara. The network is managed by the 5 site directors, who are responsible to NSF program management and to a Network Advisory Board.
High Resolution Magnetic Resonance Imaging of Resected Plaque
Authors: Saloner D
Published: July 2020

Atherosclerotic plaque at the carotid bifurcation is strongly correlated with the incidence of clinically significant events, such as transient ischemie attacks or stroke. Large multi-center trials have demonstrated that surgical removal of the atheroma is more effective in reducing these clinical events than is medical treatment alone. Patients are selected for surgery from an assessment of the severity of disease at the carotid bifurcation. The measure of disease severity is conventionally taken to be the degree of narrowing of the diseased vessel compared to a normal segment of vessel. However, using this criterion alone, many patients receive endarterectomy surgery who would probably not have progressed to other neurological events, while others are excluded who do progress to neurological events. For this reason, there is substantial interest in methods that could evaluate the composition of the atherosclerotic plaque in vivo, with the hope that this information would improve the predictive power of pre-surgical imaging of the diseased vessel.
Histologic Consequences of Endoluminal Coronary Artery Hydrogel Polymer Paving
Authors: Marijianowski MMH , Cipolla GD , Forestner DM , Campbell PK , Weselcouch EO , Slepian MJ , Apkarian RP , Robinson KA
Published: July 2020

Coronary artery balloon catheter angioplasty for the treatment of obstructive atherosclerosis has an unacceptably high restenosis rate of about 40% within 6 months. Local delivery of pharmaceuticals and nucleotide-based compounds is under investigation as one means to decrease recurrence. Labeled molecules, when delivered to arterial angioplasty sites in aqueous solution using porous balloon catheters, are quickly lost from the tissue. Alternative strategies include drug encapsulation in microparticles, and implantation of drug-containing polymers. We tested the feasibility of a catheter-based system to deposit a 70-μm thick layer of polyethylene glycol-lactate based hydrogel (polymerized by cross-linked end-terminal acrylate groups) onto the luminal surface of coronary arteries in pigs after balloon angioplasty, and examined the histologic consequences at one hour and seven days using light, scanning electron, and transmission electron microscopy.

At one hour the gel layer was readily visualized by all three microscopic techniques and appeared well adhered to and in intimate contact with the blood vessel surface (Figs. 1-2).
Quantitating Aortic Atherosclerosis in Rabbits and Mice
Authors: Bailey GW , Dimlich RVW , Alexander KB , McCarthy JJ , Pretlow TP , Sanan David A , Newland Dale L
Published: July 2020

Build-up of visible atherosclerotic plaque in the arteries is readily quantifiable. The mouse and the rabbit provide useful models for understanding the pathogenesis of atherosclerosis by investigating the effects of genetic and dietary perturbations.

Although the wild type mouse does not develop atherosclerosis, atherosclerosis susceptibility genes have been identified in some laboratory mouse strains which do. Furthermore, transgenic technology and gene targeting have produced genetically modified mice that express various apolipoproteins, enzymes and cofactors involved in human lipoprotein metabolism. Gene “knockout” technology allows transgene expression without interference from homologous genes. One notable “knockout” mouse, deficient in apolipoprotein E, develops spontaneous atherosclerosis on a normal chow diet. Transgenic modulations of the atherosclerotic responses of these highly susceptible mice are more pronounced and easily measured. Small, cheap and fast breeding, mice are convenient animal models. But to make mice susceptible to atherosclerosis, their genetic background has to be so drastically altered that the resulting lipoprotein metabolism may not model the human metabolism accurately enough.
A Cytochemical Study of NADH Oxidase and H2O2 in Developing Atheromas
Authors: Bailey GW , Dimlich RVW , Alexander KB , McCarthy JJ , Pretlow TP , Ann Ellis E , Bush David M , Wargovich Thomas J , Grant Maria B
Published: July 2020

Recent data suggests that reactive oxygen species (ROS) play a role in the progression of atherosclerosis. Superoxide (O2  ˙−) and its free radical metabolites can participate in the oxidation of LDLs, activation of proto-oncogenes and promotion of cellular growth. Endothelial and vascular smooth muscle cells are capable of producing O2  ˙− and other ROS. A major source of O2  ˙- and other reactive ROS in vascular tissues is a membrane associated NADH oxidase. This paper presents a study of NADH oxidase by cytochemical localization in developing atheromas in a rabbit model of diet-induced atherosclerosis.

NADH oxidase generates O2  ˙− which dismutates to hydrogen peroxide (H2O2). Cerium perhydroxide, an electron dense precipitate of cerium and H2O2, is the reaction product of NADH oxidase. Cytochemical localization of NADH oxidase was done by the cerium method in developing atheromas in abdominal aorta and iliac arteries of New Zealand rabbits made atherosclerotic by feeding a diet of 0.2% cholesterol/5% peanut oil over four months.
Fluorescence Intravital Microscopy of the Coronary Microvasculature
Authors: DeFily David V
Published: July 2020

Much of our knowledge of coronary blood flow regulation is based on global blood flow measurements or from studies of large epicardial coronary arteries. Those studies which have examined the coronary microcirculation, have often considered it as a single homogeneous vascular bed. However, regulation of coronary microvascular resistance is not distributed uniformly, but varies across different segments of the vasculature. Under normal conditions, a major portion of coronary vascular resistance is controlled by the coronary arterioles.

Studies of these vessels in vivo are difficult, due to problems associated with cardiac and ventilatory motion. To eliminate these problems, we have utilized a technique of fluorescent stroboscopic epi-illumination. Dogs (4-12 kg) were anesthetized with sodium pentobarbital, intubated, and ventilated with room air. A 24 gauge catheter was placed in the proximal left circumflex coronary artery for measurements of coronary artery pressure and administration of drugs. Following these procedures, the animal was ventilated on a high frequency jet ventilator synchronized to the cardiac cycle.
Use of Intra Vital Microscopy to Analyze Leukocyte Rolling and Adhesion In Vivo
Authors: Hickey Michael J , Kubes Paul
Published: July 2020

Inflammation is a vital process by which the body is able to fight infection and heal wounded tissue. However inappropriate control of inflammation is responsible for a wide range of pathologies (e.g. rheumatoid arthritis, inflammatory bowel disease). One of the hallmark features of inflammation, and one of the key pathogenic mechanisms in inflammatory disorders is leukocyte recruitment. Therefore understanding the molecular mechanisms by which leukocytes travel from the bloodstream to the extravascular tissue is of great importance.

Evidence suggests that there is a cascade of complex interactions between leukocytes and endothelium that to be fully understood must be studied on-line rather than using endpoint readouts such as tissue levels of leukocyte enzymes (myeloperoxidase) or histological techniques. A number of laboratories, including our own, have used a technique known as intravital microscopy to directly visualize leukocyte trafficking in individual vessels in a range of tissues, in an attempt to gain a better understanding of the mechanisms of leukocyte recruitment. Intravital microscopy entails microscopic examination of living tissues.
The Importance of Gamma Correction in the Acquisition, Display and Hardcoy of Digital Images
Authors: Mackenzie John M
Published: July 2020

Digital imaging is replacing conventional photography in many applications. As the quality of digital images improves, more applications for this technology will be found. This talk will examine the importance of gamma correction in digital imaging.

Although many researchers believe that digital imaging will soon replace photography, it is probably more correct to think of digital imaging as an enhancement to photography. The most critical problem with translating our knowledge of photography to digital imaging is that photography operates exclusively via logarithmic functions. The exposure versus density curves common to photography have an x axis that is logarithmic. The development curves for film and paper are also logarithmic. The slope of the log-linear portion of this curve is designated gamma. All operations normally performed in the darkroom whether processing film or prints manipulate the gamma functions to achieve the best recorded image. The first rule that should be obvious is that every image has a different optimal gamma and every different image medium (whether graded photographic paper or the density of print on a digital image printer) will change that optimal gamma.
Focused Ion Beam Milling for Site Specific Scanning and Transmission Electron Microscopy Specimen Preparation
Authors: Giannuzzi LA , Drownt JL , Brown SR , Irwin RB , Stevie FA
Published: July 2020

It has been shown that a focused ion beam (FIB) instrument may be used to prepare site specific cross-sectioned specimens to within < 0.1 μm for both scanning and transmission electron microscopy (SEM and TEM, respectively). FIB specimen preparation has been used almost exclusively in the microelectronics industry. Recently, FIB specimen preparation has been utilized for other materials systems and applications.

A cross-sectioned SEM specimen is produced by sputtering away a trench of material from near the region of interest. Large amounts of material are sputtered using large ion beam diameters (e.g., l00’s nm) and high beam current (e.g., l000’s pA), while the final sputtering operations are achieved using smaller beam diameters (e.g., < 10 nm) and lower beam current (e.g., 10’s of pA). The SEM specimen may then be etched to reveal particular microstructural features of interest. A low magnification SEM image of a multi-layered device prepared for cross-section analysis by the FIB method is shown in FIG. 1.
On holey polymer grids by condensation/dip-coating/draining/drying
Authors: Zheng Y , Li X , Vinson P K , Suszynski W , Davis H T , Scriven L E
Published: July 2020

Carbon-coated holey polymer film (HPF), or ‘holey carbon grid’ used to support fragile samples, is a crucial part of Cryo-TEM technique. A film with high porosity and uniform hole size as well as mechanical strength is needed. Efforts to develop a reliable preparation method date back to the 1950s. Today's favorite by far for routine application employs condensation, dip-coating, drainage and drying.it is not difficult, it affords control of hole size, and its yield is comparatively good. In this study, the mechanisms of hole generation and film formation were uncovered by means of in situ microscopy at medium working distance, super-VHS video recording and a high-speed motion analyzer, SEM and TEM.

Clean microscope slides were treated with Amine 105 (Kao-Atlas Co. Japan) to make the surface hydrophobic. A slide was then immersed in liquid nitrogen and exposed for 3 to 6 seconds to air with relative humidity of 30 to 60%.
Reduction of Charging in Biological Electron Cryomicroscopy
Authors: Sherman MB , Brink J , Chiu W
Published: July 2020

High resolution imaging in electron cryomicroscopy of biological macromolecules is strongly affected by beam-induced charging1. Charging is often expressed in frozen or glucose-embedded specimens as an increase in apparent mass-thickness of the irradiated area. Another obvious effect of charging is blurring of both the unscattered beam and reflections in electron diffraction patterns recorded from crystalline specimens. Coating of ice-embedded specimens with a carbon layer helps to improve the stability of the ice and probably reduce charging of the specimen. Coating in a Gatan ion-beam coater (model 681) of glucose-embedded specimens with thin layers of various conductive materials did reduce charging but the specimens were damaged by the high energy ions used for the coating. In general, coating resulted in much weaker reflections in electron diffraction patterns obtained from coated crystals and faster resolution fall-off.

We modified the Gatan coater by outfitting it with a new chamber that replaced the ion-beam deposition capability for thermal evaporation of carbon rods (Fig. 1).
Electron Microscopic Demonstration of the Photoconversion of a Fluorescent Label in Mixed Neuroglial Cultures
Authors: Ann Randall Kelly , Achim Cristian L , Wiley Clayton A , Dallasta Linda M
Published: July 2020

Endothelial cells (EC) possess receptors for and metabolize low-density lipoprotein (LDL); acetylation of LDL promotes EC metabolism and the intracellular deposition of its cholesteryl ester component. In turn, acetylated LDL linked to the fluorescent dye, Dil (Dil-Ac-LDL), has been used as a marker for endothelial cells, including cerebral microvascular endothelial cells (CEC). Due to the low electron density of fluorescent dyes, however, detection of this marker is not possible ultrastructurally. We demonstrate here the photo-conversion of the chromogen, 3,3'-diaminobenzidine tetrahydrochloride (DAB), into a stable, electron-dense reaction product in subcultured human fetal CEC containing the fluorescent marker, Dil-Ac-LDL, thus promoting identification of these cells via light and electron microscopy. This method, in turn, may be useful in identifying and tracking human fetal CEC grafted into SCID mice as a model for blood-brain barrier angiogenesis.

Isolated human fetal CEC were subcultured and labeled with Dil-Ac-LDL (10 ug/ml).
Light Microscopy Image Collection: Confocal, Widefield and Deconvolution
Authors: Turner J N , Szarowski D H , Roysam B , Holmes T J
Published: July 2020

Light microscopy instrumentation and biological applications continue to expand rapidly, and an important aspect of this expansion is three-dimensional (3-D) imaging and image analysis. For many biological specimens, optical sectioning, i.e. collecting images at a sequence of depths under controlled conditions, provides true 3-D data through the entire specimen. This is especially important for specimens whose thickness exceeds the depth-of-field of the microscope objective lens. This sequence of optical sections is the basis for 3-D image reconstruction providing information from all three specimen dimensions instead of just the traditional two in the image plane of the microscope. The analysis of images in 3-D provides insights into the structure and function of biological specimens that are not available through other means. However, 3-D microscopy also presents additional choices for image collection. The first of which is whether to use widefield or confocal microscopy and the second is whether to utilize digital deblurring or deconvolution methods.
Quantitative Three-Dimensional Image Analysis: Confocal and Widefield Light Microscopy
Authors: Roysam B , Holmes T J , Szarowski D H , Turner J N
Published: July 2020

Three-dimensional (3-D) light microscopy has been rapidly expanding for several years, both with respect to instrumentation, and biological applications. This new technology has transformed light microscopy from two-dimensional imaging of 3-D objects to a fully 3-D science. To date, qualitative analysis, reconstruction, and visualization has received far more attention compared to quantitative analysis. The motivations for 3-D image analysis are manifold, and include more accurate morphometry, separation of overlapping objects, and analysis of non-planar regions of interest and of thick specimens without the artifacts arising from physical sectioning. Furthermore, automating this analysis makes it fast, inexpensive, objective, and precise, and the results can be validated by manually confirming the analysis for any selected subset of 3-D images.

Increasingly, quantitative 3-D image analysis is emerging as an attractive technology for many applications. Studies include the testing of human-use products (shampoos, laxatives etc.), drug development, aging and development, cell loss/proliferation, fetal alcohol syndrome, and analysis of medical samples such as Pap smears, breast biopsies and a variety of cancers.
Atom-Bridge to Nano-Wire
Authors: Takayanagi K , Kondo Y , Ohnishi H , Ru Q , Kimata H
Published: July 2020

Nano-fabrications are now available for us to produce well-defined nano-structures showing quantum effects, quantized electron conductance at point contact, of phase interference of electron waves at quantum wires, and single electron tunneling at nano-capacitors. It seems near that we can fabricate even such nano-structures that Professor L.Feynman had described in his book “miniaturization”: the smallest memory unit(nano-particle), which contains 5x5x5 atoms. Such nano-particles are expected to have physical and chemical properties depending on their surface nature, since they have rather large volume of surface atoms compared with that of the core atoms. The surface atoms of such nano-particles might be reconstructed to a structure different from their bulk crystal structure, as well the surfaces of silicon and GaAs are reconstructed. It is, therefore, interesting to fablicate such nano-particles and to study their structures.

To study structure and properties of nano-particle surfaces, we developed a UHV high-resolution electron microscope equipped with a field-emission gun (UHV-FE-HR TEM: revised version of JEOL 2000V) at our ERATO project, as shown in fig. 1.
Mechanical Properties of Carbon Nanotubes Inferred from TEM
Authors: Treacy M M J , Ebbesen TW
Published: July 2020

The discovery of carbon nanotubes by Iijima has stimulated considerable research into their structural, chemical, electrical and mechanical properties. Apart from their intrinsic beauty as macromolecules, and their possibilities as one-dimensional conductors, researchers are stimulated by the notion that a structurally perfect nanotube may be one of the strongest known materials.

It is known that when nanotubes are bent through large angles, regions of high curvature buckle to develop crimps, similar to those observed when metal pipes are bent too much. Figure la shows a multi-walled nanotube that has one end embedded in a ceramic matrix. The other end is snagged so that the tube is bent. Several crimps are visible on the nanotube. Figure lb shows the same nanotube imaged a few moments later. Remarkably, the nanotube has sprung straight and the crimps have disappeared. This demonstrates that buckling in nanotubes does not involve plastic deformation, and that nanotubes can maintain their structural integrity even after severe deformation.
Three-Dimensional Hexagonal Close-Packed Superlattices of Passivated Ag Nanocrystals
Authors: Harfenist S A , Wang Z L , Whetten R L , Vezmar I , Alvarez M M , Salisbury B E
Published: July 2020

Silver nanocrystals passivated by dodecanethiol self-assembled monolayers were produced using an aerosol technique described in detail elsewhere [1]. Self-assembling passivated nanocrystal-superlattices (NCS's) involve self-organization into monolayers, thin films, and superlattices of size-selected nanoclusters encapsulated in a protective compact coating [2,3,4,5,6,7]. We report the preparation and structure characterization of three-dimensional (3-D) hexagonal close-packed Ag nanocrystal supercrystals from Ag nanocrystals of ˜4.5 nm in diameters. The crystallography of the superlattice and atomic core lattices were determined using transmission electron microscopy (TEM) and high-resolution TEM.

SEM was used to image the nanocrystal superlattices formed on an amorphous carbon film of an TEM specimen grid (fig. la). The superlattice films show well shaped, sharply faceted, triangular shaped sheets. Figure lb depicts numerous Ag nanocrystal aggregates uniformly distributed over the imaging region. Inset in this figure is an enlargement of the boxed region at the edge of a supercrystal typifying the ordered nanocrystal packing.
Electron Energy Loss Spectroscopy on Aggregated Fe-Cu-B Nanosized Particles
Authors: Duxin N , Brun N , Colliex C , Pileni M P
Published: July 2020

Nanostructured materials have attracted great attention because their physical and chemical properties may differ significantly from those of the bulk material. In the equilibrium state, the solid solubility between Fe and Cu is negligibly small. However by using methods as vapor quenching, ball milling or chemical reduction, a Fe-Cu solid solution can be formed. In the present work, colloidal solutions incorporating mixtures of iron (II) and copper (II) functionalized surfactants are used to obtain FexCu 1-x(B) alloys and composite. Different ranges of composition (x=0.3 and x=0.7) can be produced by varying the relative concentration of the surfactants.

The samples are characterized by different techniques, some of them such as X-ray diffraction, 57Fe Mössbauer spectroscopy, and magnetization measurements, provide an information averaged over the whole specimen. Transmission Electron Microscopy, together with electron diffraction and EDS analysis, constitutes a first step towards submicrometer analysis of the produced material available as aggregates of nanosized particles deposited on holey carbon films.
High Resolution Electron Microscopy of a Novel Zeolite
Authors: Crozier PA , Chan IY , Chen CY , Finger LW , Medrud RC , Harris TV
Published: July 2020

Low-dose high resolution electron microscopy (HREM) is a useful technique for elucidating the structure of zeolites. In recent years a number of zeolite structures have been solved using combinations of different characterization techniques including adsorption measurements, powder x-ray diffraction and low-dose high resolution electron microscopy (for example see ref. 2). We have used these techniques to study the structure of a novel zeolite material. However, great care must be exercised when interpreting data from these techniques in terms of crystal structural units. In this particular case, the structure was recently determined using single crystal x-ray diffraction and showed some surprises.

Details of the synthesis of this zeolite are given elsewhere. The high adsorption capacity suggested that this zeolite possessed two interpenetrating channels (either a 10 and a 12 ring or two 12 ring channels). X-ray powder diffraction showed the material to be monoclinic with a= 18.5Å, b= 13.4 Å, c= 7.6 Å β = 101.5°).
Microscopy as a Problem Solving Tool in Semiconductor Development and Manufacturing
Authors: Joseph TW
Published: July 2020

Problems in semiconductors and integrated circuits range from crystalline defects to contamination to misformed structures. They may be due to a single event (e.g. foreign particle) or a complex interaction between materials, processes, and environment. Many clues for the cause of these problems can be obtained from in-line measurements, such as electrical device behavior or layer thickness, but it is often not until after a defect or abnormal structure is seen that it is fully understood. The method of “seeing” must allow the normal to be distinguished from the abnormal and ultimately the reason for the difference to be determined. Vast amounts of data are often generated to electrically understand a defect or determine the reliability implications of a problem but it is often not until microscopic analysis is performed that the problem is fully revealed. It is not uncommon for just a small number of images bring to light the origin of a problem and lead to a solution.
Atomic Structure of Si-SiO2 Interface
Authors: Duscher G , Banhart F , Müllejans H , Pennycook SJ , Rühle M
Published: July 2020

Investigations of the atomic structure of Si-SiO2 interfaces have mostly been performed with high resolution transmission electron microscopy. However, the interpretation of the phase contrast in the amorphous phase at the interface is not unique. While Ourmazd et al. concluded on a crystalline phase at the Si-SiO2 interface, Akatsu and Ohdomari attributed the same contrast to an interface roughness parallel to the incident electrons.

We investigated the Si-SiO2 interface by studying the ELNES of the O-K edge with the spatial difference technique with a dedicated STEM with l00kV (VG HB501 UX). Also the interface was studied by Z-contrast imaging with a 300 kV dedicated STEM (VG HB603 U). Silicon wafers (110) were first thermally oxidised to produce a SiO2 layer. The thermally grown oxide was used as a substrate for liquid phase epitaxy of silicon, given two {111} Si-SiO2 interfaces in the sample grown by two different techniques (see fig. 1).
Applications of TEM for Analysis of Local Failures Occurring During Silicon Metallization Process
Authors: Lee Hoojeong , Sinclair Robert
Published: July 2020

As the size of integrated circuit devices continues to decrease, the ratio of interfacial area to volume increases and the dimension of thin films shrinks to the order of tens of nanometers. In such circumstances, the interfacial reactions, which are frequently accompanied with nanometer scale local failures, become a dominant mechanism for the breakdowns of the devices at high temperatures. This makes transmission electron microscopy (TEM) take a unique role in the research of Si metallization. In situ techniques have succeeded to reproduce and observe such real time reactions in the TEM. Moreover, after the introduction of the field emission gun systems(FEG), there have been enormous improvements in the spatial resolution and performance of x-ray energy dispersive spectroscopy (EDS) and electron microdiffraction. In the present work, two case studies of local failure were successfully investigated by combining these techniques: TiN diffusion barrier breakdown between Si and Al, and TiN electrodes on tantalum pentoxide (Ta2O5) capacitors for 1 Gigabit DRAM.
TEM Characterization of Arsenic and Phosphorus Implanted Silicon Devices
Authors: Tsung Lancy , Tsai Hun-Lian , Tsao Alwin , Takemura Makoto
Published: July 2020

Ion implantation of arsenic and phosphorus is a common practice in silicon devices for the formation of transistor source/drain regions. We used a TEM equipped with EDX capabilities to investigate effects of ion implantation in actual devices before and after annealing. A 200 kev field emission gun TEM was used in this study. Two implant cases were studied here. Both samples are p-type, (100) Si wafers.

Figure 1 shows the microstructure in a common source region of a silicon device after being implanted by phosphorus (4x1014 cm−2 at 30 kv, 0°), while Figure 2 shows a similar region for arsenic implantation (5x1015 cm−2 at 45 kv, 0°). No screen layer was used during implantation. The phosphorus implant results in a ˜0.05 μm amorphous layer sandwiched between heavily damaged crystalline silicon. High resolution images reveal a rough amorphous/damaged crystalline boundary and high density defects due to silicon lattice displacements.
Applications of High Spatial Resolution Analytical Electron Microscopy to the Process Development of Silicon Devices
Authors: Ameirhekmat B , Tsung LY , Tsai HL , Lu JP
Published: July 2020

Analytical transmission electron microscopy (AEM) equipped with a field emission gun has made it possible to analyze chemical information at local spots or interfaces with a very small electron probe. This technique has been applied to assist in process development and addressing certain reliability issues in silicon devices.

Figure 1 shows an example of applications of AEM to a 0.5 μm transistor. An oxide bump is found to be located in the middle of a transistor. A very thin layer (20 Å) is on the top of the oxide bump. Using EDS, the bump is determined to be a silicon oxide, but EDS failed to analyze the thin layer. Electron energy loss spectroscopy detects nitrogen in this residual layer (Fig. la), suggesting that the residue is a thin nitride. This residual nitride is caused by the incomplete removal of the nitride mask after field oxidation. This nitride residue blocks the subsequent removal of the buffer oxide between the nitride mask and the substrate.
In-Situ Transmission Elecron Microscopy (TEM) Study of the Nitridation of Basal Plane Sapphire by Reactive Molecular Beam Epitaxy (RMBE)
Authors: Yeadon M , Marshall MT , Gibson JM
Published: July 2020

Group III-nitride thin films are currently of great interest for use in wide-bandgap semiconductor applications including UV lasers and light emitting diodes (LEDs). Sapphire (a-Al2O3) is currently the substrate of choice for the growth of GaN despite a large lattice mismatch. Growth of high quality GaN epilayers typically involves the deposition of a buffer layer of either AIN or GaN at a temperature well below that used for the growth of the active GaN layer. It has been found empirically that nitridation of the sapphire surface with nascent nitrogen prior to growth of the buffer layer results in a substantial improvement in film quality. Using a novel ultra-high vacuum (UHV) in-situ TEM with in-situ RMBE, we have studied the nitridation of the (0001) sapphire surface using transmission and reflection electron microscopy (REM), reflection high energy electron diffraction (RHEED) and Auger electron spectroscopy (AES).

An electron-transparent sapphire TEM sample was annealed at 1400°C for 12 hours in flowing oxygen, to form atomically flat surfaces for our investigation.