bluuebunny/crossref_metadata_2025_split huggingface dataset:
A System for Computer-based Reconstruction of 3-Dimensional Structures from Serial Tissue Sections: an Application to the Study of Normal and Neoplastic Mammary Gland Biology
Authors: Fernandez-Gonzalez Rodrigo , Jones Arthur , Garcia-Rodriguez Enrique , Knowles Davis , Sudar Damir , Ortiz de Solorzano Carlos 
Published: July 2020

Abstract
Tissue heterogeneity and three-dimensionality are generally neglected by most traditional analytical microscopy methods in Biology. These often disregard contextual information important for understanding most biological systems. in breast cancer, which is a tissue level disease, heterogeneity and three dimensionality are at the very base of cancer initiation and clonal progression. Thus, a three dimensional quantitative system that allows low resolution virtual reconstruction of the mammary gland from serial sections, followed by high resolution cell-level reconstruction and quantitative analysis of the ductal epithelium emerges as an essential tool in studying the disease. We present here a distributed microscopic imaging system which allows acquiring and registering low magnification (1 pixel = 5 μm) conventional (bright field or fluorescence) images of entire tissue sections; then it allows tracing (in 3D) the ducts of the mammary gland from adjacent sections, to create a 3D virtual reconstruction of the gland; finally it allows revisiting areas of interest for high resolution (1 pixel = 0.5 μm) imaging and automatic analysis. We illustrate the use of the system for the reconstruction of a small volume of breast tissue.
Automation for Cryo-TEM: from Specimen Grid to 3D Map
Authors: Carragher B , Fellmann D , Kisseberth N , Milligan RA , Potter CS , Pulokas J , Zhu Y 
Published: July 2020

Abstract
Cryo-electron microscopy is becoming an increasingly powerful tool for solving the structure of protein complexes and has the potential to address problems that cannot be solved using other methods. The field however suffers from several major disadvantages related to the time required to acquire, process and analyze the data and the tedium of using the current prevailing methods. We have for some time been working towards the goal of developing a system that will result in a 3D map of a macromolecular structure automatically and within hours of inserting a specimen into a transmission electron microscope. We propose that these automated methods for data collection and analysis will have a significant impact in transferring the cryo-electron microscopy technology to the general biological community as well as in increasing the volume of data that can be collected during a single session at the microscope.
The Leginon system that we have developed is designed to emulate all of the decisions and actions of a highly trained microscopist in collecting data from a vitreous ice specimen. These include identifying suitable areas of vitreous ice at low magnification, determining the presence and location of specimen on the grid, automatically adjusting imaging parameters (focus, astigmatism) under low dose conditions and acquiring images at high magnification to either film or a digital camera.
Automated Data Collection with a Tecnai 12 Electron Microscope for Applications in Structural Biology
Authors: Zhang Peijun , Beatty Alexis , Milne Jacqueline LS , Subramaniam Sriram 
Published: July 2020

Abstract
In high-resolution biological electron microscopy, the speed of collection of large numbers of micrographs of the required quality is a rate-limiting step in the overall process of structure determination. Approaches to speed up data collection can be very useful especially in “single molecule” microscopy of large multi-protein and protein-nucleic acid complexes, where many thousands of individual molecular images need to be averaged to determine the threedimensional structure.
Here, we report the development of an automated low-dose image acquisition procedure on a Tecnai 12 electron microscope using the scripting functionality available on the microscope computer. The program that we have developed and implemented, AutoEM, is presently aimed at providing automation capabilities for the user familiar with normal operation of the microscope. However, the user’s participation is relatively minimal, and involves the following steps. After preparing a specimen grid and inserting it into the microscope as is normal for a cryo transfer session, the user simply downloads a Low-Dose alignment file that contains information on the relative beam shifts between the Search, Focus and Exposure modes that would normally be employed in a manual low-dose data collection experiment.
Automatic Page-Layout Scripts for Gatan Digital Micrograph®
Authors: Hou Vincent D-H 
Published: July 2020

Abstract
The software DigitalMicrograph (DM) by Gatan, Inc., is a popular software platform for digital imaging in microscopy. in a service-oriented microscopy laboratory, a large number of images from many different samples are generated each day. It is critical that each printed image is properly labeled with sample identification and a description before printing. with DM, a script language is provided: from this, various analyses can be designed or customized and repetitive tasks can be automated. This paper presents the procedures and DM scripts needed to perform these tasks. Due to the major software architecture change between version 2.5x and version 3.5x, each will be discussed separately.
DM Version 2.5.8 (on Macintosh®)A “Data Bar” mechanism is provided in this version of DM. Using the “Edit→Data Bar→Define and Add Data Bar...“ menu command specifies data bar items (e.g., scale bar, microscope operator) to be included in the image. in addition, other annotations (text, line, rectangle, and oval) can be included as part of “Data Bar.” This is done by first selecting the desired annotation on the image and then using the “Edit→Data Bar→use AS Default Data Bar...” menu command. After defining data bar items, executing the menu command adds these data bar items to the image.
Automated Determination of Tc for a High Tc Superconductor During Electron Irradiation Experiments in the Argonne HVEM
Authors: Ockers Stanley T , Ryan Edward A 
Published: July 2020

Abstract
Over the more than twenty years of operation of the 1.2 MeV AEI/Kratos HVEM at Argonne (Fig 1.), the primary emphasis by the user community has been on a wide variety of in situ irradiation effects studies involving both electrons and ions. in many cases it has been essential for the success of experiments for the professional technical staff of the Facility to develop specialty devices and techniques. This contribution deals with one such system which we have developed, namely, the design, assembly and operation of a system for in situ automated measurement of specimen electrical resistivity as a function of temperature in the range 15-135 K. A major problem is associated with this situation, which involves a small gauge-section conductor, requiring stable amplification and measurement of very minute electrical signals. The specific set of experiments for which this application was developed involved determining the effect of electron irradiation on the superconducting transition temperature Tc of YBaCuprate (YBCO) in order to distinguish between two possible theories of the conduction mechanism. in this type of experiment the critical temperature Tc is determined from a plot of electrical resistivity as a function of temperature following irradiation at 100 K at zero applied magnetic field to preclude the Meissner Effect. in these experiments Tc is 89 K prior to electron irradiation and drops to &lt;15 K with increasing electron fluence. The analysis also revealed an oxygen-disorder-induced superconductor to normal-metal transition after sufficient electron fluence. Fig. 2 shows typical measurement results for two temperature ramps. The detailed results of these experiments are described elsewhere by Giapintzakis et al.
Eliminating effects of biprism drift in electron holography
Authors: Kahl F , Voelkl E 
Published: July 2020

Abstract
Reconstruction of phase images from off-axis electron holograms recorded in a field-emission TEM was for many years a tedious and time-consuming process. The advent of digital imaging systems and ever-faster desktop computers has recently resulted in processing times of a few seconds for a useful phase reconstruction. However, a goal of the “holographer” has been to view the phase images essentially in “live-time”, that is, at least at a few frames per second. This enables effective observation of phase change, through “a window to the phase world,” while the sample is being searched. Chen et al. used a mixture of digital and analog techniques to obtain phase images at nearly TV scan rates. Because optical lens systems provide the fast Fourier processing required for phase reconstructions, their geometry allows phase images to be displayed while the sample is being moved and/or timedependent specimen changes are occurring. Voelkl et al. have described a purely digital system for phase reconstructions from electron holograms that provides several phase images per second, and has several advantages over the mixed system. The refresh rate is presently limited more by the readout time of the slow-scan digital camera than by the computational time of the computer.
Structure-Property Correlation in Genetically-Engineered Mouse Enamel
Authors: Fong Hanson , Heidel Daniel , Sarikaya Mehmet , Paine Michael , Lou Wen , White Shane N , Snead Malcolm L 
Published: July 2020

Abstract
Dental enamel is the most durable bioceramics produced by a vertebrate as it is designed to perform masticatory functions throughout its lifetime. The understanding of the mechanism of enamel formation and effects of proteins during the biomineralization process are fundamental issues, essential for both potential enamel regeneration and as a base for synthesis, via self-assembly, of biomimetic composites.
The biomineralization process of enamel is carried out by ameloblast cells that line the inner enamel epithelium and secrete an extracellular protein matrix onto a mineralized dentin surface at the dentin-enamel junction (DEJ). A major matrix protein, amelogenin, is believed to regulate the mineralization of hydroxyapatite (HAP) in the enamel tissue. It has been shown to undergo self-assembly in vitro and in vivo to form nanospheres of ∼20nm in diameter. Previous TEM studies have shown that the nanospheres align along the length (c-axis) of hydroxyapatite (HA) crystals. There are two domains, namely A (residues 1-42) and B (residues 157-173), that control the self-assembly behavior of the nanospheres.
Trace Metal Detection by X-ray Microanalysis in Vascular Cells of Roots and Leaves from Field-Grown Sugar Maple Seedlings
Authors: McQuattie CJ , Long RP 
Published: July 2020

Abstract
The low survival of sugar maple (Acer saccharum) seedlings growing in unglaciated acidic forest soils (pH&lt;4.0) in north-central Pennsylvania may be due in part to aluminum (Al) or manganese (Mn) phytotoxicity. Although foliar analysis has shown high concentrations (&gt;2,000 ppm) of Mn, the location of potentially toxic elements in leaves or absorptive fine roots has not been studied in field-grown seedlings. This study of vascular (xylem and phloem) cells was conducted to determine by energy-dispersive X-ray microanalysis (EDX) whether Mn and/or Al could be detected in fine root or leaf midvein vascular cells. A secondary objective was to determine if vascular cells prepared by chemical fixation (CF) for conventional TEM or by freeze-substitution (FS) for EDX showed similar ultrastructural characteristics.
Four sugar maple seedlings from an unglaciated field site (Potter County PA) were excavated, and roots were washed carefully. Two mm-long segments of fine roots and leaf midveins from each seedling were immersed in 3% glutaraldehyde for 6 hours, transferred to 0.1 M phosphate buffer, and transported to the Delaware Research Lab where tissues were post-fixed in OsO4 (in buffer), dehydrated in ethanol, and embedded in PolyBed-Araldite epoxy resin (CF method).
A Comparison of the Elemental Concentrations Obtained using X-ray Microanalysis of Bulk Cryofractured and Ultrathin Cryosectioned Mucus Layer of the Airway Surface Liquid in Mouse Trachea
Authors: Ackerley CA , Kent G , Heng YM , Tilups A , Becker LE 
Published: July 2020

Abstract
The airways are lined with a thin film consisting of two layers. A watery layer, the airway surface liquid (ASL) surrounds the cilia and its major function is to serve as a medium for ciliary boating of mucus out of the respiratory system. The other layer is a viscous mucus layer consisting mainly of airway cellular secretions and cellular debris.
The composition and effects of altered concentrations of the constitutive elements in the ASL and mucus layer remain a mystery. in human patients, attempts have been made to determine the composition of these layers by sampling with a filter paper by touching it to the mucosa and wetting it by capillary action. This material was then removed from the filter paper and quantitative analyses using energy dispersive x-ray spectrometry (EDS) and a Hall’s thin film correction routine performed on the residue. Although differences were detected between normal and pathological material, these results did not reflect the composition of the individual layers but an average of both.
Attempts have been made to determine the elemental composition of these layers in intact and in cultured rabbit trachea, bovine trachea and hamster trachea.
Defining the Tools: an Analysis of Laser Scanning Confocal and Wide-Field/Restoration Fluorescence Microscope Imaging
Authors: Swedlow Jason R , Andrews Paul D , Hu Ke , RoosT David S , Murray John M 
Published: July 2020

Abstract
Digital fluorescence microscopy is now a standard tool for determining the localization of cellular components in fixed and living cells. Two fundamentally different imaging technologies are available for imaging fluorescently labelled cells and tissues, in either the fixed or living state. The laser scanning microscope uses a diffraction-limited focused beam to scan the sample and develop an image point by point. in addition, a pinhole placed in a plane confocal to the specimen prevents emitted out-of focus fluorescence from reaching the photomultiplier tube (PMT) detector. By combining spot illumination and selection of infocus fluorescence signal, the laser scanning confocal microscope (LSCM) creates an image of the specimen largely free of out-of-focus blur. By contrast, a wide-field microscope (WFM) illuminates the whole specimen simultaneously and detects the signal with a spatial array of point detectors, usually a charge-coupled device camera (CCD). This approach collects an image of all points of the specimen simultaneously and includes all the out-of-focus blurred light. Subsequent restoration by iterative deconvolution generates an estimate of the specimen, largely free of out-of-focus blur. While many other fluorescence imaging modalities exist, these two methods represent the majority of the fluorescence imaging systems currently in use in biomedical research.
Live Confocal Analysis of Fertilization and Early Development
Authors: Tram Uyen , Sullivan William 
Published: July 2020

Abstract
Embryonic development is a dynamic event and is best studied in live animals in real time. Much of our knowledge of the early events of embryogenesis, however, comes from immunofluourescent analysis of fixed embryos. While these studies provide an enormous amount of information about the organization of different structures during development, they can give only a static glimpse of a very dynamic event. More recently real-time fluorescent studies of living embryos have become much more routine and have given new insights to how different structures and organelles (chromosomes, centrosomes, cytoskeleton, etc.) are coordinately regulated. This is in large part due to the development of commercially available fluorescent probes, GFP technology, and newly developed sensitive fluorescent microscopes. For example, live confocal fluorescent analysis proved essential in determining the primary defect in mutations that disrupt early nuclear divisions in Drosophila melanogaster. For organisms in which GPF transgenics is not available, fluorescent probes that label DNA, microtubules, and actin are available for microinjection.
Artifacts in Biological Confocal and Non-linear Microscopy
Authors: Cheng Ping-chin , Cheng Wayne Y 
Published: July 2020

Abstract
Conventional histological sectioning and staining techniques produce tissue sections, by large, independent from each other (e.g. the staining intensity depends on the total stainable substance within the section, but not influence by the section above or below it). Although the hardness of the structure in a given section may influence the quality of the following sections, never the less, each physical section can be generally regarded as an independent sampling event. However, the image intensity and relative contrast in an optical section obtained from confocal or non-linear optical microscopy varies depending on the position of the section where it was obtained. Therefore, in sampling terms, optical sections are dependent sampling events. Artifacts caused by the geometry and optical properties (e.g. absorption, scattering, refractive index) of objects within a specimen can interfere the interpretation of the result and hinder the usefulness of three-dimension reconstruction. Figure 1 demonstrates intensity variation in confocal and multi-photon micrographs due to the geometry of the specimen. Depends on the absorption coefficient and path length of the illumination and the fluorescecent light, a solid spherical object produced a 3D data set, when reconstructed, resemble an inverted Chinese rice bowl. Figure 2 shows a 3D reconstruction of an Arabidopsis thaliana mesophyll protoplast; note only half of the spherical cell facing the illumination is imaged as shown in the cut-off view in FIG 3.
Multicolor Labeling for Multidimensional Microscopy: Labels to Dye for
Authors: Rosa-Molinar Eduardo , Quiron Mitch , Smith Jeffery 
Published: July 2020

Abstract
We previously described two techniques to selectively label and/or stain myelinated and unmyelinated nerve fibers and simultaneously stain bone and cartilage. We used antiacetylated α-tubulin immunohistochemistry and anterograde and retrograde transport of selectively applied 3000 molecular weight (MW) biotin dextran amines (Molecular Probes, Inc. Eugene OR) to follow the course, peripheral branching, and origin of the ventral spinal nerve innervating the axial musculature. Those procedures were combined with an enzyme clearing and staining procedure for the simultaneous visualization of bone (alizarin red S) and cartilage (alcian blue) in whole-mount preparations. Use of the techniques enabled us to describe spatial and temporal changes of nerve fibers and the corresponding changes of the osseous elements during the transposition of the anal fin appendicular support of the Western Mosquitofish, Gambusia affinis affinis.
We have extended these techniques by selective multicolor anterograde and retrograde labeling of spinal motor neuron cell bodies, their dendritic arbors, and their ventral motor nerves. We used low (3000) molecular weight (MW) fluorescent lysine-fixable dextrans (Texas Red® and fluorescein) and biotinylated lysine-fixable dextrans (biotin and fluorescein conjugated to biotin), Nissl stains, and fluorescent conjugates of cholera toxin subunit B (Molecular Probes, Inc, Eugene OR).
DNA Nanowires
Authors: Hainfeld JF , Furuya FR , Powell RD , Liu W 
Published: July 2020

Abstract
Current computer chip technology is based on lithographic methods that limit components to ∼0.3 microns in size, due to the wavelength of light, and the photoresist/coating/etching processes. The size directly determines computer speed, complexity and cost, and advances in computers over the years have mostly been due to reduction in component size. It is here proposed to construct nanowires that are approximately 2 nm in diameter, or 150 times smaller than currently available. For 2 dimensions, this translates into a 1502 = 22,500-fold computational advantage. Additionally, 3 dimensional construction is proposed, bringing the potential improvement factor to 3,375,000. While it is probably unrealistic that this factor of packing density can be fully achieved, even several orders of magnitude improvement over current technology would be significant.
A wire width 2 nm may be achieved by placing gold quantum dots along a DNA template. Ends of the DNA-nanowire may be designed with sequences to attach by hybridization to complementary sequences on target connection pads, so that the two ends will seek and automatically wire correctly in solution. This strategy is easily adaptable to 3-dimensional wiring. Conduction between gold quantum dots may be studied as a function of spacing, size and coatings.
Development of New Marker Compounds for the Detection of Chemical Element Labels by Electron Spectroscopic Imaging (ESI)
Authors: Raddatz S , Mark E P , Haking A , Probst W , Wiessler M , Trendelenburg M F , Troester H 
Published: July 2020

Abstract
A promising aspect of ESI is its application in the detection of elemental labels introduced into biomolecules for cell and molecular biological techniques. Even though colloidal gold labeling for electron microscopy (EM) is highly developed, availability of alternative labels, especially for double or triple labeling applications would be helpful because of difficulties with gold concerning i) detection (gold diameters ≤1nm), ii) discrimination due to gold particle size variations in one size class, and iii) different labeling efficiencies depending on gold granule size. An alternative labeling molecule should contain a high concentration of a specific chemical element which is not or in minor concentrations present in the system under surveillance, and has to have the potential to be discriminated from “biological” elements by ESI.
With respect to ESI, one candidate for elemental labeling is boron. It meets the criteria described above and substantial experience in the synthesis of labeling compounds exists. From the chemical point of view, the preferred labeling structure is a so called dendrimer, a highly branched regular three-dimensional monodisperse macromolecule. Dendritic structures offer a large variety of functionalities to incorporate an element detectable by energy filtering transmission electron microscopy (EFTEM).
The Complex Oxidation Behavior of Pd Combustion Catalysts
Authors: Lester K , Datye AK 
Published: July 2020

Abstract
Combustion of natural gas for power generation leads to NOx formation due to the high temperatures encountered. Catalytic combustion allows the entire combustion process to be completed at temperatures where NOx formation can be avoided. The catalyst of choice is supported PdO. As temperature is increased, PdO decomposes to Pd metal with profound effects on catalyst reactivity. Persistent hysteresis in reaction rates have been related to the decomposition of PdO into Pd and its reformation.
Understanding and controlling the phase transformations, and the resulting activity variations, is of enormous importance for high temperature combustion catalysts where predictable catalyst activity is necessary for stable operation. Farrauto et al. studied the phase transformations of PdO to Pd using thermogravimetric analysis (TGA). They concluded that while PdO decomposes to Pd at high temperatures during the heating cycle, upon cooling the Pd does not transform to PdO till the temperature drops by several hundred degrees.