bluuebunny/crossref_metadata_2025 huggingface dataset:
Role of Reactive Oxygen Species and NFKB p65 in the Lupus Kidney
Authors: Nishikawa M , Igarashi R , Nakazawa T , Aikawa E
Published: July 2020

Reactive oxygen species (ROS) play an important role in lupus nephritis. It has been known that nuclear factor kB(NFkB) is activated by ROS, and binds to KB element in nucleus. Afterwards, inflammatory cytokines are translated and produced in lymphocytes, macrophages and glomerular cells in the kidney. In this study, we investigated the role of ROS and NFkB p65 in the pathogenesis of lupus nephritis (MRL lpr/lpr mice) by the histochemical and immuno-electron microscopic methods.

A modified Brigg’s method was used to determine the generation of H2O2 in the renal tissue of lupus mice. Tissue samples were incubate in 0.1 MTris maleate buffer (pH 7.4) with 7% sucrose, 1mM CeCl3 and 10 mM aminotriazole at 37 °C for 30 min. After completion of the cytochemical reaction, tissues were fixed in 2% w/v glutaraldehyde in 0.1 M cacodylate buffer (pH 7.4) at 4 °C for 60 min.
Microscopical Investigation of Cotton Chemically Modified to Accept Wool Dyes for Wool/Cotton Blend Textiles
Authors: Boylston Eileen K , Cardamone Jeanette M , Ingber Bruce F , Rice Trisha
Published: July 2020

Renewed interest in textile blends of wool and cotton has led to developments in union dyeing (same shade on both wool and cotton fibers) that has potential for increased markets for both fibers as trans-seasonal apparel. The difficulty of efficiently dyeing wool and cotton to the same shade has limited the availability of yarns and fabrics containing blends of both fibers. In fabrics containing blends of cellulosic cotton and proteinaceous wool, it is generally necessary to employ more than one class of dyes and the process involves several steps with adjustments of pH and temperature. The ARS process provides maximum effectiveness and efficiency for one-step union dyeing. It requires pretreatment before dyeing to impart cationic character to cellulosic cotton so that it can compete with protonated wool for a common anionic dye. Three pre-treatments have been applied.
TEM Sample Preparation for the Semiconductor Industry using the Allied High Tech Multiprep™ Polishing System in Conjunction with the Gat an Broad Beam Gun™ and Graphite Holder and Accessories
Authors: Dobbs Leah L , Ai Rebecca X
Published: July 2020

Due to the decreasing size of components in the semiconductor industry, TEM sample preparation grows increasingly difficult. And at the same time the customer need for TEM analysis increases, along with the urgency to report the data. We have found that TEM sample preparation has been greatly improved using the combination of the Allied High Tech MultiPrep™ System (Figure 1) in conjunction with the Gatan Broad Beam Guns™ with the Graphite Holder and accessories. The technique discussed in this paper will show that this procedure for sample preparation has decreased the time it takes to prepare the sample, decreased the number of failing samples and increased the ability to do high resolution imaging.

The MultiPrep™ is used when repeatability is critical for sample preparation and eliminates the function of holding the polisher by hand. When polishing by hand the amount of force placed on the sample while polishing is inconsistent.
Practical Aspects of FIB Milling: Understanding Ion Beam/Material Interactions
Authors: Prenitzer B I , Kempshall B W , Schwarz S M , Giannuzzi L A , Stevie F A
Published: July 2020

Nanometer scale, high resolution Ga+ ion probes, attainable in commercially available focused ion beam (FIB) instruments, allow imaging, sputtering and deposition operations to be performed with a high degree of spatial precision. Of particular interest is how this precision milling/deposition capability has enabled a wide range of site specific micromachining and microfabrication operations (e.g., TEM, SEM, SIMS, and AUGER specimen preparation and circuit modification). The applications of FIB instruments frequently involve the creation of high aspect ratio features (i.e., deep narrow trenches). Ideally, the sidewalls of an FIB milled feature should be vertical; however, it has been generally observed that the trenches tend to exhibit a gradual sloping. The observed deviation from vertical milling has been attributed to the redeposition of sputtered material, and is especially pervasive at high beam currents and confining trench geometries. A hole milled with an FIB tends to be widest at the top surface and taper down to a point at the bottom.
Focused Ion Beam (FIB): More than Just a Fancy Ion Beam Thinner
Authors: Dravid Vinayak P , Kim Steven , Brewer Luke N
Published: July 2020

The potential utility of FIB for routine (and novel) applications has come to forefront recently due to advances in ion optics which now allow formation of focused ion probe of better than ∼10-20 nm containing current density exceeding several A/cm2, with a liquid metal source (typically Gallium). The small ion probe size, coupled with shallow sputtering depth - yet high sputtering yield of ions, has opened several opportunities in machining, lithography and ion-assisted deposition[ 1-3] These developments, including automation, multi-specimen stages, cross-compatible specimen holders for FIB/TEM/SEM, use of in-situ electron beam (so-called dual beam), coupled with innovations such as the “lift-off process[4], have provided an invaluable set of tools for microelectronic defect characterization. However, re-deposition (contamination), ion implantation/damage especially for desirable thinner sections (<∼50 nm) remain major concerns for further applications.

While much of the excitement in TEM community for FIB is due to thin foil specimen preparation (especially in microelectronics),
The Application of SEM, FIB, LSM, AFM, and EDS Techniques During the Investigation of Failed Micromachined Elctronic Devices
Authors: Schaper Jake , Hopson Theresa , Brutcher Susan
Published: July 2020

Micromachined electronic devices present new challenges for established analytical tools in the semiconductor industry. These types of devices have moving components with spacing tolerances in the submicron domain. These spaces can be accumulation sites for mobile particles within the hermetically sealed device. Particles can then cause electrical malfunctions both random - for freely moving particles - and permanent - for entrapped particles. The problems for the failure analyst are: (1) a valid electrical test, (2) confirmation of the failure site without generating particles during the analysis; (3) the ability to locate and analyze known failure sites after the device is opened. A combination of several analytical tools are required for such tasks.

Surface micromachined devices are made by alternating layers of polysilicon and a sacrificial layer, such as oxide. To make a mechanical part from the deposited layer material, an underlying sacrificial layer is dissolved, thus freeing the element except where it is retained by an attachment to the silicon surface.
Cataract Formation in a Strain of Rats Selected for High Oxidative Stress
Authors: Costello M J , Marsili S , Lane C W , Salganik R I , Albright C D , Peiffer R L
Published: July 2020

The goals were to define the clinical and morphological characteristics of cataract formation in the OXYS strain of rats which are genetically susceptible to oxidative stress. The predominately inherited feature is the high cellular level of glucose uptake. The OXYS strain displays pathological changes in many tissues including blood vessels, liver and lung, which are consistent with increased oxidative damage. Early cataract formation is a prominent feature of this strain.

Rats were examined periodically from birth through the development of mature cataracts with slit lamp biomicroscopy. The morphology of selected stages of cataract development was studied using light and transmission electron microscopy (TEM) as well as immunohistochemical localization of lipid oxidation and DNA oxidation products. Lenses from normal rats of the same age were used as controls. OXYS rats developed cataracts as young as two weeks of age with progression to maturity by one year. Clinically, cataracts appeared initially as either nuclear or subcapsular cortical changes and developed into pronounced nuclear cataracts within months.
Decrease Tyrosine Phosphorylation of Stat3 in Human Myocardium with End-Stage Congestive Heart Failure
Authors: Bailey GW , McKernan S , Price RL , Walck SD , Charest P-M , Gauvin R , Wei C , McLaughlin J S
Published: July 2020

Recent study demonstrated that decrease signal transducer and activator of transcription-3 (STAT3) phosphorylation and increase apoptosis might be a critical point in the transition between compensatory cardiac hypertrophy and heart failure. To date, the protein expression of STAT3 in normal and failing human heart remains unclear. Therefore, the current study was designed to investigate the protein expression of STAT3 in human myocardium with end-stage congestive heart failure (CHF) and compared with that in normal human cardiac tissue.

Human cardiac atrial tissue was obtained from normal subjects (n=5) and end-stage CHF patients (n=5) during cardiac transplantation. To detect the DNA fragmentation, in situ terminal deoxymucleotidyl transferase dUTP nick end labeling (TUNEL) was performed. An average of 1000 nuclei was analyzed for TUNEL study. STAT3 protein expression and phosphorylation of STAT3 were determined by immunohistochemical staining (IHCS) with total STAT3 and phospho-specific STAT3 antibodies.
Secretion of Brain Natriuretic Peptide in Cultured Human Coronary Vascular Smooth Muscle Cells
Authors: Bailey GW , McKernan S , Price RL , Walck SD , Charest P-M , Gauvin R , Lin J , Wei C
Published: July 2020

Brain natriuretic peptide (BNP) is a peptide of cardiac origin which regulates plasma volume as well as vascular tone and growth. Recently, we have reported that brain natriuretic peptide is a potent inhibitor of endothelin-1-mediated proliferation in human coronary vascular smooth muscle cells (HCoVSMC). While brain natriuretic peptide has been reported to be produced and released from atrial and ventricular myocardium, we hypothesize that brain natriuretic peptide may be present and secreted from human coronary vascular smooth muscle cells.

Therefore, the present study was designed to investigate the secretion of brain natriuretic peptide in cultured human coronary vascular smooth muscle cells (HCoVSMC: Clonetics, San Diego, CA). The concentration of brain natriuretic peptide, and its second messenger cGMP, in culture media (48 hours) was determined by radioimmunoassay (Phoenix, Mountain View, CA). The presence of brain natriuretic peptide was determined by immunohistochemical staining using a human brain natriuretic peptide polyclonal antibody.
Expression of Angiotensin II Type 1 and Type 2 Receptor in Human Myocardium with Congestive Heart Failure
Authors: Lau P Y , Cardarelli M G , Wei C
Published: July 2020

Angiotensin II (AH) is a potent vasoconstrictor and mitogenic factor. AH receptors include type 1 (ATI) and type 2 (AT2) receptors. Recent studies demonstrated that both ATI and AT2 receptors expressed in human myocardium. Circulating and local tissue level of AH was increased in severe congestive heart failure (CHF). However, the expression of ATI and AT2 in cardiac tissue with CHF remains controversial. Therefore, the present study was designed to investigate the protein expression of ATI and AT2 receptors in normal human myocardium and in human cardiac tissue with mild and severe CHF.

Human atrial tissues from normal subjects and CHF patients with ischemic cardiomyopathy and dilated cardiomyopathy were obtained from open-heart surgery and cardiac transplantation. ATI and AT2 receptor expression was investigated by immunohistochemical staining (IHCS). The results of IHCS was evaluated by IHCS staining density scores (0, no staining; 1, minimal staining; 2, mild staining; 3, moderate staining; and 4, strong staining).
Increasing Apoptosis-Related Gene Expression in Human Myocardium with Congestive Heart Failure
Authors: Xie D , Wei C
Published: July 2020

Regulation of apoptosis involves a number of genes that can be classified into broad categories. These include genes that act as effectors of apoptosis, such as p53, c-myc, bax, p21- WAF, and genes that primarily suppress apoptosis, such as Bcl-2 gene family. These genes have been reported to be responsible for the modulation of certain stress induced apoptosis and cell cycle arrest.

It has also been reported that apoptosis involved in cardiovascular diseases such as myocardial infarction, reperfusion injury, left ventricular hypertrophy, and hypertension. However, the expression of apoptosis-related genes in human cardiomyocytes in normal subjects and in patients with congestive heart failure (CHF) remains unclear. Therefore, the present study was designed to determine the expression and localization of apoptosis-related genes in human heart.

Five normal subjects and five end-stage CHF human ventricular cardiac tissues were obtained from cardiac transplantation. The expression of p53, p21-WAF and Bcl-2 were determined by immunohistochemical staining (IHCS).
Angiotensin II Increases Apoptosis and Caspase-1 Expression in Human Myocardium
Authors: Song H , Downing S W , Wei C
Published: July 2020

Angiotensin II (AII) is a potent vasoconstrictor and mitogenic factor. The biological actions of All through AII receptors which include AT-1 and AT-2 receptors. However, the effects of AII on cardiomyocyte apoptosis and caspase expression remain controversial. Therefore, the current study was designed to investigate the actions of AII on human cardiomyocyte apoptosis and caspase-1 expression.

Human cardiac tissue was obtained from open-heart surgery (n=6). The cardiac tissue was minced and incubated in the special tissue culture system for 24 hours in the absence or presence of AII (10-7 M). These studies were repeated with losartan (10-6 M, AT-1 receptor antagonist) and PD123319 (PD, 10-6 M, AT-2 receptor antagonist). To detect the DNA fragmentation, TUNEL staining and DNA gel analyses were performed. The caspase-1 expression was determined by immunohistochemical staining (IHCS). An average of 1000 nuclei was analyzed for both TUNEL and caspase-1 IHCS studies.
Micro-Structural Analysis of Cyanobacterial Macro-Morphogenesis
Authors: Lazaroff Norman , Eichelberger Henry H
Published: July 2020

A seldom studied and poorly understood feature of cyanobacterial growth and development is the formation of ordered macroscopic structures from microscopic cells, trichomes, and filaments. The forms range from nostoc balls and layered mats of comparatively simple structure to more complex erect tree-like (dendroid) macro-structures. Using macrophotography, time lapse micro-cinematography, light and scanning electron microscopy of Nostoc species in pure culture, it has been possible to show how motility, adhesion and aggregation of photo-induced motile trichomes (hormogonia) result in the macro-morphogenesis of dendroid forms.

Nostocacean development proceeds by the differentiation of cells in a cyclic sequence of stages including: long chains of cells in heterocystous filaments, motile hormogonia, and large rounded cells termed the aseriate phase. When grown from localized inocula on solid media, sequential development recycles across the agar surface of the culture. Different strains and species vary in the form and duration of each stage and the photo-response of hormogonia.
Microbial Ecology of Extreme Environments: Automobile Air Conditioning Systems
Authors: Simmons RB , Rose LJ , Crow SA , Ahearn DG
Published: July 2020

Automobile air conditioning systems (ACS) might be considered an extreme environment for many microorganisms. Organisms surviving and proliferating in these systems may be presented with temperature changes ranging from subzero to over 140°F, water activity from saturation to dryness and a nutrient complexity including varying levels of hydrocarbons. Microbial communities develop in ACS and sometimes proliferate to the extent of massive colonization and production of objectionable odors.

In a few instances microorganisms emanating from ACS have been associated with hypersensitivity pneumonitis and other allergic reactions. Previously we demonstrated that foam insulation and glues, in particular, on ACS insulations were colonized by fungi such as Aspergillus, Aureobasidium, Cladosporium, and Penicillium. Such fungi often are implicated in colonization of similar substrates in buildings categorized with the sick building syndrome.

A total of 42 ACS from the United States, Europe and Central America have been examined by cabin air sampling culture swab, direct microscopy or a combination of these techniques.
Attachment and Invasion of Clostridium Difficile Endospores Incubated with CACO-2 Cells
Authors: Panessa-Warren BJ , Tortora GT , Warren JB
Published: July 2020

The small (0.5-0.75 um) Clostridial endospores are highly resistant to solvents, acids, bases, radiation, heat, cold, pressure, vacuum and most sporicides. C.difficile causes antibiotic induced pseudomembranous colitis, and is responsible for almost 20% of nosocomial diarrheas in todays hospitals. These endospores have been found on hospital floors, sheets and bedding, as well as on the hands and white coats of hospital personnel.

Our previous studies revealed that these endospores attach to agar by using a two phase attachment process. To examine if this mechanism for spore attachment is also responsible for C.difficile pathogenesis in the human colon, spore attachment and invasion of monolayers of human colon carcinoma cells (Caco-2 cells) using two strains of C.difficile,(ATCC 43594 an isolate from a patient with pseudomembranous colitis [FIG.1A] and ATCC 9689 a clinical microbology laboratory quality control strain) was studied. Cell monolayers grown on 6mm coverslips were inoculated with 10 ul of spore suspension (0.5 McFarland turbidity in sterile water),
An STM With A Time-Of-Flight Analyzer For Atomic Species Identification
Authors: Weierstall U , Spence JCH
Published: July 2020

The local chemistry of many surface reactions is unknown, since no techniques exist for identifying atom types at individual defect sites on extended crystal surfaces. An STM has therefore been constructed which allows atomic clusters of interest to be transferred into a time-of-flight spectrometer for species identification. Atoms are first transferred from the STM sample to the tip, using a small voltage pulse. The sample is then removed, and these atoms ejected into a time-of-flight (TOF) analyzer for mass identification. A 75mm flat Chevron MCP is used as TOF-detector. The output is led to a digital oscilloscope, whose trace is triggered by the tip pulse. Scope, triggering and high voltage are under Labview control, spectra are transferred into the PC and the mass to charge ratio of the ionized species is calculated. The STM has a vertical axis and is based on the Burleigh Inchworm with tube scanner for sample movement.
A Digital Readout Scheme for Arrays of Microcalorimeter X-Ray Detectors
Authors: Nam S , Wollman DA , Hilton GC , Chervenak J , Deiker S , Irwin KD , Martinis John M
Published: July 2020

While the performance of single-pixel microcalorimeter x-ray detectors has been shown to be very useful for microanalysis1, arrays of microcalorimeters will have a further impact on energy dispersive spectroscopy (EDS) by providing higher total count rates and larger effective areas. We are developing a system with a 32x32 pixel array with a total area of 40 mm2 and with a total count rate between 105 and 106 s-1. One of the challenges in constructing an array-based system will be the readout electronics.

In a typical microcalorimeter EDS setup, shown in Fig. 1, the microcalorimeter is readout using a cryogenic amplifier (SQUID system) and analog feedback electronics to control the SQUID. The signal from the room-temperature SQUID electronics is either attached to a spectroscopy-grade shaping amplifier and MCA for real-time analog signal processing or attached to a digitizer for optimal pulse processing.
Effects of Aged Conditions on the Fracture Surface Fractal Dimension and Mechanical Behavior of an Austenitic Stainless Steel
Authors: Hilders O A , Quintero A , Berrio L , Caballero R , Sáenz L , Peña N , Ramos M
Published: July 2020

There have been several attempts to find a relation between the fractal morphology of the fracture surfaces and the mechanical properties of engineering materials., although the current resuls are inconclusive. If there are correlations between the fractal dimension and such properties, this parameter could be very useful to predict them and to improve the resistance to fracture. The main part of the investigations concerned with the fractal geometry and fracture behavior concentrate on the relations between roughness and fracture toughness. In the present work, the effects of thermal aging at 850°C on the fracture topography developed during the rupture in tension at room temperature of a 304 type stainless steel and their relation with the strength and ductility, were studied using the fractal geometry approach.
SEM Evaluation of Chemically Finished Nonwoven Fabrics from Recycled Fibers
Authors: Bailey GW , McKernan S , Price RL , Walck SD , Charest P-M , Gauvin R , Goynes W R , Graves E E , Tao W , D'Anna G F , Day M P , Yachmenev V
Published: July 2020

The textile industry produces large quantities of waste and scrap materials. Most of this waste requires disposal. Both environmental and economic benefits could be derived by developing commercial products to use these materials. Environmentally acceptable textile products include those that utilize recycled materials, or materials that have not been chemically processed. Such products are often not economically profitable because of the added expense necessary for environmental protection. Development of such a cost-effective textile product requires use of low-cost materials, minimal cost production processes, and finishes that have already been developed and tested.

The objective of this research was to develop a semi-disposable, economical, light-weight, comfortable thermal blanket that would be both flame-resistant and antibacterial through a limited number of laundry cycles. Targeted uses would be in medical and health care facilities, disaster relief centers, short term and emergency housing needs, recreational areas such as camping, and in military maneuvers where environmental conditions could be harmful to long-term products.
On the Measurement of Total Elastic Cross-sections in the ESEM or VPSEM Using X-Ray Microanalysis
Authors: Gauvin Raynald , Joy David C
Published: July 2020

It is of paramount importance to know the total elastic-scattering cross sections of the gases which are present in the specimen chamber of the variable pressure scanning electron microscope (VP-SEM) or in the environmental SEM (ESEM) since these values are needed to compute the width of the beam broadening skirt by the use of Monte Carlo simulations. However, these values are not well known for even the most common gases because the vibrational modes of the molecules add another contribution to the usual value of the elastic scattering cross-section. To overcome this difficulty a method has been proposed to measure total elastic cross-sections which is based on a measurement on the unscattered beam current as a function of the chamber pressure using a Faraday cup. The total elastic cross-sections are then deduced using the well-known exponential decay law.
From the Scanning Electron Microscope to the Scanning Electron Macroscope with X-Ray Microanalysis in the ESEM
Authors: Gauvin Raynald
Published: July 2020

Recently, a new correction procedure has been proposed in order to perform X-Ray microanalysis in the ESEM or in the VP-SEM1. This new correction procedure is based on this equation:

where I is the measured intensity at a given pressure P, Ip is the intensity that would be generated without any gas in the microscope (the corrected intensity) and Im is the intensity with complete scattering of the electron beam. Im is therefore the contribution of the skirt on I. In equation (1), fp is the fraction of the incident beam, which is not scattered by the gas above the specimen, and it can be obtained from Monte Carlo simulations or from an analytical equation.
Rapid Automated 3-D Tracing of Neurons from Confocal Image Stacks
Authors: Al-Kofahi Khalid , Lasek Sharie , Turner James N , Roysam Badrinath
Published: July 2020

Automated, large-scale quantitative morphologic analysis of extended three-dimensional (3-D) branched structures such as neurons and vasculature is of broad interest to biomedicine, especially efforts such as the Human Brain Project, and angiogenesis. The present work has resulted in a key enabling technology for such studies - rapid, accurate fully-automatic 3-D tracing of such structures from confocal image stacks. The robustness and efficiency of the proposed method makes it attractive for large-scale applications such as high-throughput assays in the pharmaceutical industry, and initiatives such as the Human Brain Project. Also of interest are attempts to simulate computationally the electrochemical behavior of large collections of neurons for which actual, rather than simulated, neuro-anatomical data, would be valuable. Finally, of long-term interest are emerging studies of the development and growth of live neurons observed over time, for which the present method can provide a powerful morphometric tool.
Probing Biological Samples with Near-Field Optics
Authors: Vickery Sarah A , Hollars Christopher W , Dunn Robert C
Published: July 2020

Near-field scanning optical microscopy (NSOM) is an emerging optical technique capable of probing samples at the nanometric level. With the NSOM technique, high spatial resolution is achieved by scanning a small light source (or collector) close to a sample surface. The light source is usually formed with special fiber optic probes that funnel light down to an aperture that is smaller than the optical wavelength. By positioning the aperture close to a sample, the emerging radiation is forced to interact with the sample before diffracting out. Therefore, the spatial resolution in NSOM is only limited by the size of the aperture and its proximity to the sample, and not the wavelength of the light as in conventional optical microscopy.

Recently, we have been using the single molecule detection limits combined with the unique nature of the electric fields present near the NSOM tip aperture to probe molecular level structure in model lipid membranes.
Laser Capture Microdissection, Amplified Antisense Rna, and Highdensity Microarrays: The New Frontier for Gene Expression Profiling From Limited Amounts of Tissue
Authors: Madison, Ph.D. Roger D
Published: July 2020

Because the genes in all somatic cells of an individual are identical, it is the differential expression of the proteins encoded by particular genes that determines a cell's phenotype. There is now increasing interest in relating the simultaneous expression patterns of multiple proteins to complex biological processes. The goal is to develop ‘expression profiles’ of the proteins that are active within a cell or tissue during a particular condition. The ultimate control of functional protein expression is quite complex and may involve transcriptional, combinatorial, and postranslational mechanisms, as well as differences in protein degradation rates that vary under different conditions. Although mRNA levels do not always predict functional protein levels, they are a useful first step in determining the expression profile.

The evolution of three key technologies offers the promise of obtaining quantitative analysis of gene expression from restricted amounts of nervous system tissue. Laser capture microdissection can accomplish harvesting of identified cell populations from histologically processed tissue.
CRYO-Tem Measurements of Membrane Elasticity in Equilibrium Vesicle Systems: Two Distinct Mechanisms of Stability
Authors: Coldren B , Jung HT , Zasadzinski J
Published: July 2020

Aqueous mixtures of oppositely charged surfactants spontaneously form equilibrium phases of unilamellar vesicles.1 The wide variety of surfactants that display this behavior allows control over vesicle charge, size, and polydispersity. This may be useful for new applications in drug delivery, nanomaterials synthesis, and as tests of theoretical concepts of membrane organization and interactions.

A subtle competition between the entropy of mixing and the elastic properties of surfactant and lipid bilayers determines their phase behavior and morphology. The curvature energy per unit area of bilayer, fc, is

where R1 and R2 are the principle radii of curvature, K is the curvature modulus, and is the saddle-splay modulus. The spontaneous curvature, l/ro, is nonzero only if there is asymmetry between the two sides of the bilayer.
Single Molecule Detection of Fluorescently Labelled DNA Dendrimers
Authors: Nilsen TW , Getts R , Weinstein M
Published: July 2020

Single molecule detection has been achieved via many highly sophisticated microscopic techniques. Here we describe the detection of single molecules with conventional epifluorescent microscopy. The key to the technique is the use of DNA dendrimers DNA dendrimers have demonstrated utility in nucleic acid blots, Southerns, Northerns, etc. Typically DNA dendrimers yield 50-100 fold gain in signal over comparably labeled oligonucleotides. Immunodendrimers, DNA dendrimers conjugated to antibody molecules, have also been constructed and utilized in western blot assays. Individual, i.e. single molecule, 4- layer dendrimers, are readily detectable as point sources via conventional fluorescence microscopy and are useful for in situ hybridization and flow fluorescence quantitation.

Nucleic acid hybridization is the underlying principle behind DNA dendrimer assembly. The “monomer” of DNA dendrimers consists of partially double stranded heteroduplexed DNA. Each monomer has an approximately 50 base double stranded “waist” surrounded by four approximately 30 base single stranded “arms”.
Structural Analysis of Filaments Using the STEM
Authors: Simon M N , Lin B Y , Wall J S
Published: July 2020

The Scanning Transmission Electron Microscope (STEM) facility at BNL is an NIH Biotechnology Research Resource and as such is available to users with suitable projects, free of charge. Currently, many of our users' projects involve studying the structures of a variety of filaments. Most of these are of biological origin, although a couple involve conducting polymers. The STEM has a long history of being used to study different types of filaments and resolving controversies about their structure.

The mainstay of the STEM is mass analysis on unstained, isolated, freeze-dried samples. On these, the STEM can collect in-focus digital data directly. In a scan (8 sec. in real time) of a sample, at each of 512x512 picture elements (pixels), the number of electrons scattered into two annular detectors is recorded. For each pixel, the number of scattered electrons is directly proportional to the mass thickness in that pixel.
Characterization of Surface Roughness
Authors: Russ John C
Published: July 2020

Because of the session at this Microscopy and Microanalysis 2000 meeting concerned with the microanalysis of irregular surfaces, it seems appropriate to briefly review the methods used for the characterization of rough surfaces. This includes both mathematical tools for the concise description of surface roughness, and instruments used to acquire the necessary data. These methods are widely used in industry to characterize and specify the roughness of surfaces prepared by various machining, grinding, polishing, chemical etching, and physical and chemical deposition techniques, and to correlate the surface roughness with performance.

Historically, surface roughness has been measured by performing a linear traverse with a mechanical stylus that is sensitive to vertical displacements of nm but with a lateral resolution on the order of pm, which is quite similar to the dimensions of the region analyzed by X-ray microanalysis. Recently, more comprehensive characterizations have been obtained using a raster scan over surface areas.
Prospects for X-Ray Analysis of Rough Surfaces in the SEM
Authors: Statham PJ
Published: July 2020

Some of the key aspects affecting analysis of a rough surface are described in Fig. 1. If a hypothetical sample consisting of 96% Si, 1% O, 1% Na, 1% Al and 1% Fe is analysed at 20kV at constant beam current with an x-ray detector elevated at 30deg from horizontal then the measured intensities of the various characteristic lines will vary with tilt. While absorption of low energy x-rays is reduced as the sample tilts towards the detector, there is also a gradual loss of intensity due to increased backscatter. At the lower beam voltage of 5kV, absorption of x-rays at zero tilt is already small and Fig.2 shows that variation in intensity with positive tilts is substantially reduced, although absorption still becomes significant if the sample is tilted away from the detector.
An Electron Backscattered Diffraction Specimen Preparation Technique for High Resolution Serial Sectioning
Authors: Wall MA , Schwartz AJ , Nguyen L
Published: July 2020

A high-resolution serial sectioning specimen preparation technique is described for acquisition of electron backscattered diffraction orientation imaging microscopy (OIM) data. The primary objective is to develop a method to reproducibly remove a controlled thickness of material (a serial section) from a polycrystalline Ta sample while producing quality surfaces for OIM imaging. This is integrated with the ability to accurately measure the amount of material removed with each iteration and experimentally register the ensuing OIM scans.

A Si metrology device is fabricated by lithographic techniques to facilitate the measurement of the amount of material removed with each lapping iteration and the alignment of each serial section image. This metrology device contains a herringbone pattern with two orthogonal etched lines oriented at 45 degrees and one vertical line normal to the OIM surface. The metrology device is epoxied to a polished side surface of the Ta sample. Due to the orthogonality of the lines, the thickness of material removed equals one-half the total linear motion of the etched lines as seen in cross-section. To accurately measure the distance between the grooves after each lapping iteration, a high-resolution (0.1 μm) linear measuring system is attached to the table of a light metallograph.
Effects of Crystallographic Orientation Relatiotionships on the Propagation of Brittle Crack in Mn-Mo-Ni Low Alloy Steel
Authors: Oh Yong-Jun , Kim Min-Chul , Hong Jun-Hwa
Published: July 2020

Boundary properties between two adjacent grains with different crystallographic orientation relation are important factors in deciding the mechanical properties of materials. The concept of the geometric compatibility factor has been introduced in order to explain the relationship between transfer of deformation mode and crystal orientation. In the same manner, when the brittle crack propagates, grain boundary also obstructs crack propagation. Therefore it is also possible to introduce the concept of geometric compatibility considering the crystallographic orientation in analyzing the crack propagation.

In this study, the characteristics of the brittle crack propagation in bainitic low alloy steel with compositions shown in table 1 have been investigated using EBSD analysis. A 3-point bending test was performed at -100°C and the secondary crack below fracture surface was analyzed in relation to the crystallographic orientation. In order to explain the behavior of crack propagation, modified geometric compatibility factor, M was introduced considering loading axis and crystallographic orientation relationship.
Theoretical and Experimental Approaches to Identification of a Fiber Surface Cell Binding Domain in Collagen and its Application in Tissue Engineering.
Authors: Bhatnagar Rajendra S , Shattuck Mark B , Qian Jing Jing , Gough Craig A , Nicoll Steven B
Published: July 2020

Type I collagen comprises between 75-95% of the stationary extracellular matrix of most tissues, forming a continuum in which most of the static cells are anchored. Collagen serves as the track for haptotactic cell migration. The junction between collagen, its receptor integrins, and the cells’ cytoskeleton plays a crucial role in cell differentiation and morphogenesis by serving as the agent for transducing mechanical forces into chemical and biochemical work. The physiological, functional organization of collagen is the solid state in the form of a network of fibers. The only molecules available for engaging the receptors are those located on the fiber surface. Cryogenic scanning force microscopy (SFM) of single molecules of collagen allowed us to correlate surface features with known sequence and stereochemical markers within collagen. Theoretical conformational studies to locate markers for intermolecular recognition and allosteric binding showed that collagen a 1(1) chain residues 766GTPGPQGIAGQRGVV780 generate a distinctive conformation, characterized by a relatively stable (3-bend at the core (Fig. 1) within the triple helical polyproline II conformation extant in the rest of the molecule (1).
Detection of Early Cancers by Quantitative Cytology
Authors: Palcic B , Garner D , Sun XR
Published: July 2020

It has long been recognized that detecting cancers in their early, non-invasive stage is the best strategy to control malignant diseases. This has been best demonstrated by the example of cancer of the uterine cervix. Before screening for early signs of this malignancy, the prevalence of invasive cancer of the uterine cervix in the developed world was as high as 30 women per 100,000 and the mortality was 12-15 per 100,000 women per year, (all figures represent age standardized data). Since the introduction of cervical screening programs by Pap smears, the incidence of invasive cervical cancer and mortality due to this cancer has fallen dramatically. In British Columbia, for example, where population screening was introduced 50 years ago, the incidence and mortality have decreased several-fold and are at present below 6 and 3 per 100,000, respectively (1,2). It is believed that these figures could be even lower by encouraging more women into the program and by improving both sensitivity and specificity of the cytology.
7-Parameter Automated Measurement of the Shapes of Nanoscale Inclusion by TEM
Authors: Gabrisch H , Cong G , Parvin B , Kjeldgaard L , Johnson E , Dahmen U
Published: July 2020

The equilibrium shape of liquid inclusions in a crystalline matrix is a direct measure of the orientation dependence, or anisotropy, of the liquid/solid interfacial energy. In this work we have used diffraction contrast imaging in TEM to observe the shape of nanoscale liquid Pb inclusions in a solid Al matrix as a function of temperature. While a previous investigation reported a highly anisotropy equilibrium shape [1], more recent work showed that the inclusion shape depends on size, temperature and thermal history [2-4]. Here we report on a new method to make accurate automated measurements of these particle shapes during in-situ heating above the melting point of the inclusions.

Fig.l shows a typical bright field image of an array of liquid Pb inclusions in a solid Al matrix recorded at temperature during in-situ heating to 423°C. Under these two-beam diffraction conditions, particles are visible by absorption contrast and appear dark on a light background.
HRTEM Image Simulations of Structural Defects in Gate Oxides
Authors: Taylor S , Mardinly J , O'Keefe MA , Gronsky R
Published: July 2020

High-resolution transmission electron microscopy (HRTEM) is used extensively in the semiconductor industry for device characterization, and has become one of the highly favored techniques for characterizing the latest generation of ultra-thin gate oxides in MOSFET devices. However, relatively little is understood (either quantitatively or experimentally) about the limitations of HRTEM in detecting structural defects in gate oxides that could affect device performance. To investigate model defects experimentally, it would be necessary to construct “perfect” gate oxides, introduce defects with size and morphology known perfectly a priori, successfully make thin specimens that capture the defects, and then perform imaging experiments in the HRTEM. Since that task is virtually impossible, we have performed HRTEM image simulations to assess the visibility of various structural defects in gate oxides. The gate oxide was modeled as an amorphous silicon oxide 16.3Å-thick, sandwiched between a gate and substrate. The substrate was (100) silicon viewed along the [110] direction.
Diffusion of Ion Implanted Elements in Silicon by TEM And SIMS
Authors: Vanfleet RR , Francois-Saint-Cyr H , Stevie F , Giannuzzi L , Irwin R , Kempshell B , Shofner T
Published: July 2020

With the need to introduce new materials and processes to the semiconductor fabrication process, there is a great need to understand the diffusion of a large number of elements in silicon. To this end, a systematic SIMS study was done for implanted elements with subsequent annealing. There is a surprising lack of earlier work on many of the elements of the periodic table and the work that was done did not involve the additional effects of ion implantation.

The recent SIMS results allow the diffusion of the many elements to be categorized into several groups. These effects range from elements that do not appear to move substantially upon annealing, rapid diffusion to the surface, and formation of various peaks in the concentration profile.

Based on the SIMS results, we have used TEM to study the microstructure and composition of subset of the implants. The figure below shows the SIMS and TEM results for a Chromium implant.
Imaging Ionic Aggregates in Zn-Neutralized Sulfonated Polystyrene Ionomers: Shape and Spatial Heterogeneity
Authors: Kirkmeyer Brian P , Weiss Robert A , Winey Karen I
Published: July 2020

Ionomers are ionically-associating copolymers whose distinctive rheological and mechanical properties arise from the formation of ionic aggregates. The ionic aggregates form when dipoles of minority anionic polymer backbone segments and cationic neutralizing species locally associate and dissociate among each other. Specific ionomer properties depend upon the base copolymer, the minority constituent and the neutralizing agent. One system that has been studied extensively is sulfonated polystyrene ionomer neutralized with Zn (Zn-SPS). The most common technique to date for studying ionomer morphology is small-angle x-ray scattering (SAXS). This technique has provided quantitative information about the aggregate morphology by imposing morphology models that have not been independently confirmed.

In the present study, we demonstrate the capability to directly image the ionic aggregates of Zn-SPS ionomers using scanning transmission electron microscopy (STEM). This method will allow us to confirm or deny the competing morphological models applied to SAXS data. We have applied similar methods to polyethylene-based ionomers.
Development of a 1-MV Field-Emission Electron Microscope III. Electron Optical Design and Development of Field-Emission Electron Gun
Authors: Yoshida Takaho , Kawasaki Takeshi , Endo Junji , Furutsu Tadao , Matsui Isao , Matsuda Tsuyoshi , Osakabe Nobuyuki , Tonomura Akira , Kitazawa Koichi
Published: July 2020

Bright and coherent electron beams have been opening new frontiers in science and technology. So far, we have developed several field-emission transmission electron microscopes (FE-TEM) with increasing accelerating voltages to provide higher beam brightness. By using a 200-kV FE-TEM and electron holography techniques, we directly confirmed the Aharonov-Bohm effect. A 350-kV FE-TEM equipped with a low-temperature specimen stage enabled us to observe moving vortices in superconductors.2 Most Recently, we have developed a new 1-MV FE-TEM with a newly designed FE gun to obtain an even brighter and more coherent electron beam.

Electron beam brightness, Br, defined in Figure 1, is suitable for measuring the performance of electron guns, since both lens aberrations and mechanical/electrical vibrations contribute to a decrease in beam brightness, and beam coherency is proportional to (Br)1/2. Therefore, we optimized design of the illuminating system and its operation by maximizing the electron beam brightness.
Computer Controlled High-Throughput Integration System: FasTEM
Authors: Fukushima K , O'Donnell RM , Fujiwara K , Kai H , Okunishi E , Kawasaki M , Kersker M , Naruse M
Published: July 2020

Introduction

For the nano-area analysis of materials, it is necessary to evaluate all data obtained by HRTEM, EDS, EELS, and/or Energy Filter. Up till now, each analytical/imaging instrument required its original computer control system. Thus, the total operational environment for the nano-area analysis was not convenient for us. Recent progress of computer technology provides the ability to build a high performance environment for seamless operation by Client/Server design.

We have developed computer controlled high-throughput integration system based on PC, called FasTEM system, having seamless integration function and real-time remote control function of all instruments related to nano-area analysis. The FasTEM system is composed of Windows NT based Server PC System that is connected to the target TEM via RS232C for integrated operation, and Client PC SYSTEM connected to the Server PC via TCP/IP for remote operation (Fig.l).

Seamless Integration Function

All user interfaces of the analytical/imaging instruments, such as HRTEM, STEM BF/DF, EDS, PEELS and GIF can be seamlessly integrated into the Server PC.
Student Microscopes, A View from Down in the Trenches
Authors: Newberry S P
Published: July 2020

The use of microscopes in education has proved be a powerful tool in grades K through 12 for catching the student's interest in the sciences, the humanities and the arts. While the equipment and the approach varies with the grade level, the questions of availability, teacher training and cost are each important to obtaining full and successful use of microscopes in the classroom. The one item which is beyond the control of the school is the high cost of appropriate quality microscopes. A projection system capable of showing bacteria should be available to the teacher at all times and a number of microscopes which the students can use themselves should also be present Because of the cost, many schools, both public and private, have only one microscope room or share one set of microscopes for the entire school. The result is a study of the tool rather than using the tool to better appreciate history, ecology, high technology, medicine, and so forth.
Atom Probe Tomography: A Tutorial
Authors: Miller M K
Published: July 2020

Atom probe tomography (APT) is an ultrahigh resolution microanalytical technique that enables the spatial coordinates and elemental identities of the atoms in a small volume of material to be determined. The specimen volume that may be analyzed is typically ∼ 10 to 20 nm square by ∼ 100 to 250 nm deep, and contains up to ∼ 1 million atoms. The distribution of the solute atoms within this volume may then be reconstructed from these data. The compositions of small volumes are determined by simply counting the number of atoms of each type within that volume, and thus the technique provides a fundamental measure of local concentrations. Atom probe tomography requires that the specimen has some electrical conductivity and may be applied to almost all metals and alloys, many semiconductors, and some electrically conducting ceramics. The sharp needle-shaped specimens may be fabricated from bulk and thin film materials with the use of electropolishing, chemical or ion milling methods.