bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote Control Scanning Electron Microscope with Web Operatoin Interface
Authors: Yamada Atsushi , Kobayashi Toshiharu , Negishi Tsutomu , Matsumoto Sunao , Handa Nobuo , Tsuchida Takayoshi , Sugano Naoki , Iwatsuki Masashi 
Published: July 2020

Abstract
Recently, SEM (Scanning Electron Microscope) and the other observation devices are coming to use a LAN (Local Area Network) to save the image in the database. We developed a remote control system in which SEM image and Control interface is indicated on the WEB Browser. in this system, SEM can be controlled by an external (client) PC installed in a general WEB Browser(Internet Explorer). Accordingly, operation interface can be indicated on the WEB browser.
A JSM-6700F is connected to a LAN, and so the microscope can be controlled by a client PC. Figure. 1 shows the block diagram of SEM remote control system. The JSM-6700F has two lines to the LAN for image transfer and communication with the SEM control. in order to transfer the image, the image size squeezes from 1280 × 1024-pixels (SEM image size) to 640 × 480-pixels for quick transfer. The image signal (640 × 480-pixels) is connected to the video server only, and then the image transfers to the client PC via LAN. The SEM control communicates with client PC for external command. On the other hand, the SEM control interface and the image are indicated on WEB Browser (Internet explorer) as shown Figure 2. The SEM control interface is composed of the SEM image area and the SEM control part. The SEM image indicates the 640×480-pixels live image. This pixel number was an image quality sufficient to adjust the focus. When a high quality image is necessary, the image of 1280 × 1024-pixels is saved on the the SEM(server) side by choosing the image save button.
Automated Very Low Magnification Imaging for TEM
Authors: Potter CS , Carragher B , Kriegman D , Pulokas J 
Published: July 2020

Abstract
A typical TEM specimen grid provides approximately a 2×2 mm area that is available for imaging. in order to identify and locate suitable targets on the grid the microscopist must usually inspect the grids at magnifications that allow for only a small area of the grid in the field of view at a time. Systematically searching the grid and mentally keeping track of relative locations presents a challenge for a microscopist especially as the image normally rotates as the magnification is changed. We present an automated technique that creates a very low magnification (VLM) image of the entire available imaging area on the grid. The VLM image can then be used as a reference map for searching the grid at high magnification.
VLM images were obtained at a nominal magnification of 57x using a Philips CM200 TEM equipped with a Gatan CCD camera. The VLM image of the entire 2 mm specimen grid can be created using a mosaic of 49 images, each 512×512 pixels in size. The sampling distance between the images in the 7×7 array is 300μm and the pixel size is 680nm. The images are then automatically tiled and re-sampled to form a final VLM matrix of 4K×4K with a pixel size of 730nm. The resampling factors for the tiling operation include the scale and the relative angle between the camera and goniometer axes. These factors are determined automatically from a calibration process that characterizes the goniometer.
Application of a SQL Database for Automated Image Acquisition and Analysis for CRYOEM
Authors: Fellmann D , Carragher B , Potter CS , Pulokas J 
Published: July 2020

Abstract
We have been developing a software system, called Leginon, for the control and acquisition of images from a transmission electron microscope. This software allows for the automatic acquisition of images under low dose conditions from a specimen embedded in vitreous ice. Thousands of images are collected during each session at the microscope. These images are collected at various magnifications and under a variety of conditions. For example, images are collected of the entire grid, individual grid squares, individual holes within the square, and several high magnification images are acquired for one to several targets within each hole (figure 1). in addition, for each identified hole an image is acquired at the low dose focus position. Power spectra are also calculated for each of the high magnification images as well as for the focus images. For managing these images we are using a relational database management system. We have also developed a bench of tools to store, access, and display the data as well as tools for extracting information from the database.
A database is a structured collection of data in which the information is classified by categories. Each category is then stored in a table and these tables are linked together by defined relations. Data may be combined from several tables on request. We have been using MySQL as our relational database management system. This allows us both to manage the images and to refer each image to its real context. in other words, through the database, we can keep track of information related to the microscope settings (e.g. defocus, electron dose, magnification, goniometer coordinates etc.), the type of image, and overall information about the specimen and the experiment.
Quantitating Calcium in Biological Specimens by Direct Fittingof X-ray Spectra
Authors: Ho R , Jia Z , Somlyo AP , Shao Z 
Published: July 2020

Abstract
Electron probe microanalysis has been a useful method for biological research for some years. Its advantages include the low background of x-ray spectra and range to include characteristic peaks of most biological elements. The traditional method of analyzing biological X-ray spectra filtering both the experimental and reference spectra with a top-hat filter, before performing a linear least squares fit, to remove the slowly varying background. We show that, as expected, this procedure introduces an additional error in the quantitation results, and reduces the sensitivity and precision of this method. Our experience with quantitating trace elements with EELS shows that direct fit of unfiltered spectra yields the highest sensitivity, when the data contain only statistical errors. Biological specimens usually contain high K and low Ca, and in X-ray spectra the K Kβ peak is overlapped with the Ca Kα peak. A small error in extracting the K signal will dramatically affect the quantitation of Ca. We demonstrate here the application of a direct fitting procedure, which focuses on the Ca and K region of the X-ray spectra (2800 ∼ 4900 eV), and yields smaller fitting uncertainties compared to the traditional filtered fit method in trace Ca quantitation.
Parallel Confocal Microscope using Vertical-Cavity Surface Emitting Laser Array
Authors: Fujita Motonobu , Naruse Makoto , Ishikawa Masatoshi 
Published: July 2020

Abstract
Here we show a confocal microscope system where a vertical-cavity surface-emitting laser (VCSEL) array is introduced for the parallel probing beams.
A VCSEL array is a semiconductor laser device that emits circular beams vertically to the surface of the chip, which can directly be used as confocal laser microscope applications. The VCSEL device itself can be the parallel beam source of the confocal laser system, whereas in conventional Nipkow disc-based system, several lenses are required to form probing beams. Figure 1 shows the basic structure of VCSEL-based confocal microscope systems. Since there is typically no correlation between individual channels of VCSEL, there are no interferences among dense parallel beam arrays. Additionally, in the case of Nipkow disc system, the signal to noise ratio of the detected light is another problem: some of the light from the source laser reflects at the surface of the disc, which eventually could be detected by the sensor as noise. in the proposed system no such problem occurs as shown in Fig. 2(a). in addition, “all” optical beam from VCSEL is used as probing beam whereas most of the power is lost at the disc as compared in Fig. 2(b). in addition, pixel parallel illumination control is also achievable by controlling each channel of the VCSEL so that the dynamic range of the detected signal is maximized.
The Use of Multidimensional Microscopy in the Characterization of Retinal Vascular Development in a Murine Model
Authors: Summers Robert G , Aguilar Edith , Leonard Marilyn , Friedlander Martin 
Published: July 2020

Abstract
The murine retinal vasculature develops in its entirety following birth through the process of angiogenesis. This developing system provides an extremely accessible model for investigation of angiogenic mechanisms in general and as they pertain to vascular diseases of the eye (e.g. diabetic retinopathy and macular degeneration). The model is particularly relevant clinically because the developmental events of retinal vascularization are nearly identical in mice and humans, although primate vessels develop in utero during the final trimester of pregnancy and are thus less accessible for experimental study. The model is also excellent for the testing of anti-angiogenic agents as potential treatments for vascular diseases. in this report we outline the use of confocal optical microscopy and multiphoton microscopy in the 3-dimensional characterization of retinal vascular development in the mouse.
We employed confocal microscopy to characterize the events of vascular development from postnatal days 0-56 (P0-P56). During this time the retinas are transformed from simple, thin bilaminar structures to more complex, functional, adult sensory organs. Retinal morphogenesis continues until P42. Retinas were dissected from eyes and vessels stained with collagen type-IV antibody (1) or Bandeiraea simplicifolia (Griffonia) lectin-dye conjugate (2) to outline the blood vessels. All patent vessels were stained by both techniques.
Enhancement of Reflection-Enhanced Backscatter Confocal Microscopy
Authors: Keith C H , Witek R 
Published: July 2020

Abstract
Tremendous advances have been made in the last twenty years in extending the usefulness of the light microscope in visualizing living biological specimens, and it is now possible to visualize most thin tissues in an unstained state at – or near – the limit of optical resolution. in general, however, these techniques have been used successfully on biological specimens in the transmitted light mode; unstained biological specimens generally do not have sufficient albedo or sufficient difference in refractive index from their surroundings to be efficiently visualized in epi-illumination. A number of applications, including studies of the growth of bacteria on metallic substrates, and studies of the studies of the formation of interfaces between living neurons and silicon chips, would benefit from being able to resolve living, unstained biological specimens growing on opaque substrates
We found that by imaging biological specimens on a reflective substrate in the reflection mode of the confocal microscope, we could get images that resemble transmission mode differential interference contrast images.
Angiotensin II Induces Translocation of Protein Kinase C α and ε in Neonatal Rat Cardiac Myocytes
Authors: Bullard Tara A , Goldsmith Edie , Price Robert L 
Published: July 2020

Abstract
Angiotensin II (Ang II) plays an important role in heart development and has been shown to stimulate the formation of premyofibrils and differentiation of cardiac myocytes. Ang II signaling occurs through two types of receptors, the AT1 and AT2 receptors, both of which appear to play a role in the development of the myocardium. Through the use of specific Ang II receptor blockers it as been shown that blocking the AT1 receptor with Losartan (Merck) inhibits the formation of premyofibrils and sarcomere formation and that blocking the AT2 receptor with PD123,319 (Parke-Davis) inhibits the formation of trabeculae in the developing heart.
In a number of cases it has been shown that signal transduction mechanisms operate through different growth factor receptors and elicit specific responses within a cell type. Protein kinase C (PKC) is a family of closely related signal transduction enzymes that phosphorylate proteins on serine or threonine residues.
Evaluation of Confocal Microscopy System Performance: Applications for Imaging Morphology and Death in Embryos and Rerpoductive Tissue/Organs
Authors: Zucker R M , Price OT 
Published: July 2020

Abstract
The confocal laser-scanning microscope (CLSM) has enormous potential in many biological fields. It is remarkable that procedures to test the performance of these machines are not done routinely by most investigators and thus many of the machines in operation are working at levels of sub optimal performance. When these machines are checked, it is usually a subjective assessment of performance accomplished by primarily evaluating the system using a specific test slide provided by each user’s laboratory. We have devised test methods on the Leica TCS-SP and TCS-4D systems to ensure that these machines were working properly and delivering their correct performance. Tests were derived or perfected that measure field illumination, lens clarity, laser power, laser stability, dichroic functionality, spectral registration, axial resolution, overall machine stability, and system noise. It is anticipated this type of data will help to set performance standards for confocal microscopes and eliminate the current subjectivity in evaluating the CLSM. These tests will also serve as a guide for other investigators to insure that their machines are working correctly and providing data that is accurate and having the necessary resolution, sensitivity and precision.
Non-linear Spectral Microscopy-Multi-Photon Fl, SHG and THG
Authors: Cheng Ping-chin , Sun Chi-Kuang , Kao Fu-Jen , Lin Bai-Ling 
Published: July 2020

Abstract
The non-linear nature of multi-photon fluorescence (FL) excitation, SHG and THG restricts the signal detecting volume to the vicinity of the focal point. As a result, the technology has intrinsic optical sectioning capability. The use of multi-photon fluorescence excitation also allows micro-fluorometry at high spatial resolution. Figure 1 shows a conventional optical micrograph of maize protoplasts, the time lapse fluorescence spectral change from a single chloroplast is shown in FIG 2. Under high intensity illumination, biological specimen not only emits fluorescence, but also generates harmonic emissions. in addition to the Ti-sapphire laser commonly used in multiphoton microscopy, the use of ultra-fast Cr-fosterite laser made simultaneous detecting two- and three-photon fluorescence, SHG and THG possible. in addition to the fluorescence signals generated by multi-photon excitation process, non-linear phenomena such as harmonic generation can also provide useful information about the structure and optical properties of a specimen (Kao et al., 2000). Simultaneous recording the spectral response in an image (x-y-λ) can provide insight about the nature of the signal.
What Can Epitope Specific Antibodies Tell us About the Organization of Caveolin in Cells?
Authors: Robinson JM 
Published: July 2020

Abstract
There are three members of the caveolin (CAV) gene family that give rise to four polypeptides. These polypeptides are CAV-1α, CAV-1β, CAV-2, and CAV-3. The CAV-1β isoform is a truncated form of CAV-1α that lacks 31 amino acids at the N-terminus of the molecule. The CAV- 1β molecule arises through an alternative splicing mechanism.
Caveolae are specialized plasma membrane microdomains that are expressed at high levels in some cell types (e.g., endothelium, adipocytes, fibroblasts). These specialized regions of the plasma membrane have a characteristic omega-shaped appearance with diameters ranging from 40-90 run. They are distinct from clathrin-coated pits since they lack the characteristic coated appearance in electron microscopy. Caveolae were among the first structures to be discovered by biological electron microscopy. However, biochemical characterization of these structures did not begin in earnest until a marker protein was identified. The initial marker was the 22-kDa protein known as caveolin.
Internalisation of CD46, Membrane Cofactor Protein, As Determinee By Light, Cofocal, and Electron Microscopy
Authors: Ellis Sarah , Crimeen Blessing , Farrelly Caroline , Russell Sarah 
Published: July 2020

Abstract
Human CD46 (membrane cofactor protein) is expressed on all nucleated human cells and is a cellsurface regulator of activated complement as well as a receptor for both the measles and herpes 6 viruses. CD46 is also expressed in particularly high levels on some tumor cell lines. Complement leads to the recognition of foreign material, targeting it for removal and immune cytolysis. The primary role of CD46 is to bind to one of the complement components, C3b, thereby protecting host cells from autologous complement attack. in addition to its role as a complement regulatory factor, CD46 acts as a measles virus (MV) receptor. Despite the development and use of an effective MV vaccine, at least one million deaths occur each year. MV infection leads to downregulation of cell surface CD46 and immunosupression. MV (and probably also C3b) is internalized shortly after complex formation with CD46, yet, despite much work in this area, precisely how MV enters cells is largely unclear.
A New Pre-Embedding Immunogold Method That Permits to Obtain a Very High Signal with a Very Good Ultrastucture
Authors: Grondin G , Bcaudoin AR 
Published: July 2020

Abstract
The ultimate goal of the immunocytochemistry is to get the best signal with the lowest background while preserving ultrastructure. Unfortunaly too often the experimentator faces a compromise between density of the signal and ultrastructure preservation (1). with the advent of hight resolution confocal light microscopy, two photon imaging and other new technologies there is a need to provide the best immunocytochemical complementary results with the high resolution of the electron microscope. But often for exemple the high level of labelling observed by immunofluorescence microscopy is not matched by immunocytochemistry (2). One approach to obtain comparable levels of labelling is to use comparable protocols. We propose here such a new immunogold method. to illustrate our point we used a very convenient biological material, the adherent cells grown on 35 mm plastic culture dishes. The following procedure was applied : Confluent endothelial cells were fixed in situ for 3 hours with the following freshly prepared and filtered solution : 1 % 1-lysine, 4% paraformaldehyde, 0.04% glutaraldehyde, 0.25% sodium metaperiodate in 0.04M sodium cacodylate buffer, pH 7.4.
In Situ Characterization of Dynamic Changes in the Microstructure and Chemistry of Catalysts
Authors: Crozier PA 
Published: July 2020

Abstract
Controlled atmosphere electron microscopy (CAEM) is a form of in situ microscopy in which the sample is exposed to a reactive gas during observation. This instrument essentially combines the nano-structural characterization features of a TEM with a microreactor and is ideal for studying gas/solid reactions in catalysts. Such in situ techniques can provide a link between surface studies performed under UHV conditions and catalytic reactions run in high-pressure reactors. with correctly designed experiments, CAEM is a powerful technique for correlating dynamic changes in microstructure with catalysis and can be used to provide insights on the location of active sites and mechanisms for catalysis. Baker and colleagues have worked for over thirty years on different heterogeneous catalysts using in situ electron microscopy (see [1] for example). Gai has also published many studies on the application of CAEM to oxide catalysts [2].
The technique usually relies on detecting a change in the heterogeneous catalyst during a catalytic reaction.
The Influence of Surface Termination and Domain Structure on the Photochemical Reactivity of SrTiO3 and BaTiO3
Authors: Giocondi Jennifer L , Rohrer Gregory S 
Published: July 2020

Abstract
The crystallographic orientation and atomic termination layer of oxide catalysts are known to influence their reactivity. The objective of this work was to measure how the relative photochemical reactivities of two ternary titanates vary with surface orientation and composition. The surface structure property relationships derived from these observations can be used to define optimized photocatalyst microstructures.
To measure the relative reactivity of surfaces with different orientations, crystallites (∽ 20 μm in diameter) in a polycrystalline ceramic were examined individually. First, polycrystalline specimens of BaTiO3 and SrTiO3 were synthesized using conventional ceramic processing. Surfaces for analysis were prepared by polishing and thermal etching in air. The surface orientations of selected grains in the sample were then determined from backscattered electron diffraction patterns recorded in a scanning electron microscope. to make a local measurement of the photochemical activity of each grain, we used a well established probe reaction (the reduction of aqueous Ag+ to Ag0) that deposits metallic silver on the surface as a reaction product.
Automated Imaging of Combinatorial Chemistry Synthesis Arrays in a Large Chamber Low Vacuum SEM
Authors: Schumacher Elaine F , Wendelbo Rune 
Published: July 2020

Abstract
In combinatorial chemistry, miniaturization and automation are used to carry out many experiments in a simultaneous array, as opposed to doing single experiments in sequence. This high throughput approach is widely used in the drug industry, and is now finding application in the development of novel materials for catalysis. Successful implementation of combinatorial methodology to speed discovery and commercialization of new materials requires that these techniques be applied to every step of the experimental process, from combination of reagents for synthesis through characterization and performance testing.
Arrays of catalyst precursors and molecular sieves synthesized by combinatorial methods must be rapidly screened for particle size distribution and morphology. Optimization of these characteristics is crucial for successful manufacture of formed products such as beads or extrudates on a commercial scale, and has traditionally been done by manual examination of dispersed powder samples in an SEM
Alloy Compositions in Model Bimetallic Catalysts
Authors: Tsen S-CY , Crozier P A , Liua J 
Published: July 2020

Abstract
For supported bimetallic catalysts it is important to know if the metal components are present in the form of ordered alloys or metal mixtures. For metals with similar crystal structure, Vegard's law predicts a simple relationship between alloy composition and lattice dimensions [1]. It is therefore possible to use high-resolution electron microscopy (HREM) to provide both structural and compositional information. in nanometer sized particles, accurate determination of the lattice spacing from fringes in an HREM image is difficult because of errors due to signal-to-noise, particle tilt and edge effects [2,3]. However, statistical distributions of fringe spacing can be used to determine the lattice spacing of particle ensembles to within 1.5% when measurements are carried out on at least 100 particles [2]. We extend this technique with model AuPd bimetallic catalysts and show that Vegard's law applies to nanometer-sized particles.
Model bimetallic catalysts were prepared by sputtering metal from AuPd alloy targets and/or a Pd target onto thin amorphous carbon substrates.