bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Glomerulus-Revisited
Authors: Siew S 
Published: July 2020

Abstract
In the embryologic development of the nephron, the glomerular tuft (renal corpuscle) and the excretory tubules develop from two distinct embryologic origins or anlagen. Nephrotomes constitute the earliest formation of the excretory tubules and appear first as segmentally arranged cell clusters, which grow and become canalized, forming nephric tubules. Formation of the glomerulus begins when the dorsal aorta gives rise to small branches, consisting of tufts of capillaries. Bowman’s capsule forms as a blind terminal expansion at the proximal end of the nephron. in the final stage of development, Bowman’s capsule becomes deeply indented by the glomerular tuft. Which leads to a differentiation of it into 2 layers: 1) an inner, visceral layer and 2) an outer, or external, parietal layer. The two layers are separated by a crescent shaped space, known as Bowman’s or the urinary space.
The inner, visceral layer encloses, and, comes into close apposition with the glomerular capillaries. At the vascular pole of the glomerulus, the visceral layer is reflected off these vessels and becomes continuous with the external, or parietal layer of Bowman’s capsule, which is lined by a very flat polygonal epithelium. Traditionally, it has been depicted that there is a direct opening of the urinary space into the tubule and that the flat cells of the parietal layer of Bowman’s capsule become continuous with the cuboidal epithelium in the neck of the proximal convoluted tubule.
This investigation shows that the junction of the renal corpuscle and the proximal convoluted tubule is a more complicated one. Scanning electron microscopic studies of microdissected nephrons enabled the visualization of the glomerulus, with the two vessels at the vascular pole and the proximal convoluted tubule at the urinary pole. An unexpected finding, was the presence of a gourd-like out-pouching at the urinary pole. (Fig. 1, “A”) Higher magnification showed a saucer shaped depression (50 μm × 25 μm) on its free border. (Fig. 2). This was a consistent finding in the material that was studied.
Structure and Function of the Primary Zygote Wall of Chlamydomonas Monoica
Authors: Salanga M , Van Winkle-Swift K 
Published: July 2020

Abstract
The Chlamydomonas zygospore is formed after gametic cell fusion by a progression of ultrastructural and physiological changes, including the synthesis of a protective and elaborately sculptured secondary wall (Figure 1). Assembly of the secondary wall occurs within the confines of a transient primary zygote wall, synthesized immediately after gamete fusion, and assembled beneath the residual gamete walls. Upon completion of secondary wall assembly, the primary zygote wall is shed from the maturing zygospore (Figure 2). This primary zygote wall, composed primarily of a β-1,3 glucan (callose), may be important in the regulation of secondary zygospore wall formation.
A temperature-sensitive mutant strain of C. monoica, zym30, has been isolated that shows marked abnormalities in both primary and secondary wall ultrastructure. The degree of wall formation in the mutant strain is inversely proportional to temperature. At 25° C most zygotes fail to synthesize either the primary or the secondary wall. At 15° C both primary and secondary wall assembly occurs to some extent and as many as 50% of the zygotes develop a “pseudo-wildtype” phenotype (Figure 3). Although release of the primary wall rarely occurs in the zym30 strain (even at permissive temperatures), those walls that are released appear thinner than the walls shed from wildtype zygospores, as viewed by phase contrast microscopy. Fluorescence images incorporating aniline blue, a fluorochrome specific for β-1,3 glucans, show decreased fluorescence suggesting reduced callose synthesis (Figure 4).
Several permanent, ultrastructurally distinct layers comprise the secondary wall, the assembly of which may be controlled, in part, by the primary wall. One or more of these secondary wall layers contain the highly durable, autofluorescent biopolymer, sporopollenin. Autofluorescence of zym30 zygospores produced at the permissive temperature is enhanced relative to wildtype zygospores. This correlates with ultrastructural changes in the primary wall and overproduction and/or misassembly of the surface secondary wall layer (Figure 5). Work is in progress to determine whether the environmental resistance, and/or viability of the zym30 “pseudowildtype” zygospores are reduced relative to wildtype zygospores.
Increasing Access to Tomographic Resources: Web-based Telemicroscopy and Database
Authors: Martone M E , Peltier S , Lamont S , Gupta A , Ludaescher B , Khetani S , Molina T , Ellisman M H 
Published: July 2020

Abstract
The application of electron tomography to cell biology has led to important insights into the 3D fine structure of subcellular processes and organelles. Tomography has been particularly useful for studying relatively large, multi-component structures such as the Golgi apparatus, mitochondria and synaptic complexes. When combined with very powerful high voltage electron microscopes, tomography has also provided high resolution quantitative views of extended structures such as neuronal dendrites in very thick sections (4 μm) at electron microscopic resolution. The utility of tomography is twofold: first, it provides 3D examination of subcellular structure without the need for serial section analysis; second, because the computed slices through the tomographic volumes can be much thinner than is possible to produce by physical sectioning, it reveals structural detail in the range of 5-30 nm that tends to be obscured in conventional thin sections. Tomographic analysis has forced re-assessment of long-standing views of organelles such as mitochondria and the Golgi apparatus and as the technique advances, additional insights are likely forthcoming.
Electron tomography is an expensive technique, both in terms of the instruments used and the computational resources required. The three major high voltage electron microscope resources in the United States, San Diego, Boulder and Albany, all are actively engaged in tomographic research and offer this important technology to the scientific community at large.
Cryo-Electron Tomography of Isolated Triad Junctions from Skeletal Muscle
Authors: Hsieh C-E , Marko M , Rath BK , Fleischer S , Wagenknecht T 
Published: July 2020

Abstract
In skeletal muscle, depolarization of the plasma membrane, which is initiated at the neuromuscular junction, is transduced to a rise in cytoplasmic calcium at specialized structures known as triad junctions (TJs). TJs occur in the myofiber’s interior at regions near the z-lines, where transversely oriented tubular invaginations of the plasma membrane (T-tubules) form junctions with two elements of the sarcoplasmic reticulum (SR). Isolation of membrane fractions that are enriched in junctional complexes and which retain function has been reported.
Figure 1 shows a region of an electron micrograph containing an isolated TJ in the frozen-hydrated state. in the orientation shown, two SR-derived vesicles sandwich a flattened vesicle derived from the T-tubule. The junctional regions contain a complex distribution of density, presumably due to proteins that are known to be present in TJs. Electron tomography offers the means to determine the three-dimensional mass density from such micrographs, which would greatly aid in their interpretation. Only recently has the automated data collection technology for determining tomograms of non-stained, frozen-hydrated specimens become available. Here we describe the first tomographic reconstruction of a frozen-hydrated triad junction by automated electron tomography.
Detection and Identification of Macromolecular Complexes in Electron Tomograms of ‘Phantom Cells’
Authors: Böhm Jochen , Frangakis Achilleas S , Nicastro Daniela , Nickell Stephan , Hegerl Reiner , Baumeister Wolfgang 
Published: July 2020

Abstract
One of the most promising and exciting developments in electron tomography is its application to ice-embedded cells and cellular organelles. The primary goal of cellular electron tomography is not to obtain a high-resolution structure of a particular protein complex, but to identify a macromolecule by virtue of its structural signature and to locate it in the context of the native cellular environment. We present a computationally feasible approach, which demonstrates that an objective identification of large macromolecular complexes in cells is possible, given that a highresolution reconstruction and the structure of the molecular assembly under scrutiny are available. Our aim is to quantify the identification results using a realistic test specimen, open for the modification of experimental parameters like thickness, protein density or protein composition. in this study, the reliability of the algorithm applied to electron tomograms of ‘phantom cells’ - mimicking a real cell - is shown.
We prepared phospholipid vesicles that were filled with different macromolecular complexes. First, a phospholipid solution (SOPC) was sonicated and mixed with His-tagged macromolecular complexes, such as thermosomes, 20S proteasomes or a mixture of both. The lipid-protein mixture was subjected to several freeze-thaw cycles and extruded to produce uni-laminar ‘phantom cells’ of various sizes.
Environmental SEM (ESEM) in the Study of Biomedical Materials, Cells & Interfaces
Authors: Stokes DJ , Rea SM , Porter AE , Best SM , Bonfield W 
Published: July 2020

Abstract
The ability of ESEM to image insulating and/or moist specimens without the need for the removal of volatile components or the application of a conductive coating has significantly increased the potential range of experiments and observations that can be performed at the high resolution of electron microscopy. Such a technological advance has particularly important implications for the study of soft matter, complex fluids and biological specimens.
An important area of study to which ESEM can be readily applied is that of materials for biomedical applications. Hydroxyapatite (HA) ceramics and HA/polymer composites (e.g. HAPEX™) are being developed for use as synthetic scaffolds in bone tissue engineering. The bioactivity of these materials is dependent upon such factors as phase composition, chemical composition, surface activity, crystallinity and microstructure. Using ESEM it is possible to obtain surface-sensitive, specimen-dependent secondary electron images (in the absence of specimen coating), yielding potentially new perspectives on microstructure to complement information derived from other techniques.
Advanced Raman Spectroscopy for Pharmaceutical and Biological Applications
Authors: Whitley Andrew , Adar Fran , Geiger Ruth 
Published: July 2020

Abstract
With the advent of easy to use analytical and research instrumentation the Raman technique has finally become accepted and is now widely used by pharmaceutical and biomedical companies. Applications range from simple polymorphic crystal form and protein studies to Raman mapping studies of active/excipient distribution and association that give a better understanding of drug dissolution and effectiveness. Examples of such work will be discussed.
More recently with the growing confidence in the power of Raman spectroscopy pharmaceutical and biomedical companies have teamed with instrument companies to develop specific Raman tools. One example of this is the development of a Raman mutiwell/microarray analyzer. High Throughput screening (HTS) is the latest approach in analytical technology. Used particularly in the pharmaceutical industry and in the life science laboratories, this method enables systematic screening of drug design and high throughput analysis of batch production. Combinatorial chemistry is a statistical approach in synthetic chemistry.
Chromium-Doped Luminescent Glasses for Raman Intensity Calibration with 785 nm Laser Excitation
Authors: Etz Edgar S , Hurst Wilbur S , Choquette Steven J , Blackburn Douglas H 
Published: July 2020

Abstract
In work reported previously we, and the McCreery Group at Ohio State University, have proposed the use of glass luminescence standards for the calibration of the Raman spectral intensity. We now have a program underway that is directed at the development of such secondary standards for the calibration of the Raman instrument response function. The first Raman intensity standard to be certified and issued by NIST this year will be for the relative intensity calibration of Raman spectra excited at 785 nm. in general, for any laser excitation wavelength, the calibration procedure is based on the use of luminescent glasses, doped with either transition metal or rare earth ions, that will furnish structureless, broad-band emission spectra upon laser excitation, over any chosen Raman range. For any selected glass standard, the intensity of the luminescence spectrum is calibrated versus the radiant output of a NIST-calibrated white light source, thereby transferring the white light calibration onto the output emission of the luminescent glass.
Emerging Pathogens: Something Old, Something New
Authors: E. Miller Sara , N. Howell David 
Published: July 2020

Abstract
Infectious diseases are the leading cause of death worldwide and the third leading cause in the US. Among these maladies are many that can be classified as emerging diseases. Some of these disorders may be caused by truly novel pathogens. in others, the causative organisms have been present for many years (for some, probably millennia), but have escaped detection until recently. Still others represent the re-emergence of known pathogenic organisms after a long period of quiescence. The mention of emerging pathogens brings to mind sensational exotic and feared microorganisms such as Ebola virus, human immunodeficiency virus (HIV), hantavirus, West Nile virus, Yersinia pestis (plague), and prion diseases such as bovine spongiform encephalitis (BSE, “mad cow” disease) which have been associated with variant Creutzfeldt- Jakob disease (CJD) in humans. However, other organisms that have been known for some time can be classified as emerging pathogens as they continually mutate, recombine, and adapt, causing misery and death.
Past, Present and Future of Analytical Stems
Authors: Colliex C 
Published: July 2020

Abstract
Twenty five years ago, in august 1976, a specialist workshop gathered in Cornell University, at John Silcox's invitation, scientists covering a broad spectrum of interests to assess the potential of analytical electron microscopy, as to instrumentation, fundamental limits, general level of data processing and current theoretical understanding. If the STEM instrument had already been existing for a few years in Crewe's laboratory, its major emphasis, in spite of the existence of an EELS spectrometer, had focused on new modes of high resolution imaging. At the first Cornell workshop, the STEM instrument was for the first time recognized as a potentially formidable analytical instrument because of the possibility of extracting all available signals simultaneously. Furthermore it was directly suitable for digital computer processing and therefore for providing quantitative information. It was also pointed out that a major advantage of the STEM would be its potential to record EELS spectra from every point in the field of view as one scans an area to form an image, thus offering the capability of "chemical" mapping beyond "elemental" mapping.
Contrast Effect of Strain Fields in ADF-STEM Imaging
Authors: Yu Z , Muller DA , Baumann F , Silcox J 
Published: July 2020

Abstract
STEM is an important tool for the study of material by forming Z-contrast ADF images. Studies of strain fields suggest that strain can cause extra contrast in ADF images. Since strain fields exist in many TEM samples, especially interfaces of two different materials, it is necessary to study the contrast effect of strain fields in more detail. in this paper, we study the contrast effect of strain fields by STEM experiments and multislice simulations.
Sample thickness and the dimensions of ADF detector can both affect strain contrast. We first study the influence of sample thickness. A cross-section TEM sample of an interface of crystal silicon and amorphous silicon was prepared by typical tripod polishing and was studied with the 100 kV Cornell VG 5.0 UHV STEM. The sample was tilted so that the crystal was on the (110) zone axis and ADF images of the interface were recorded.
Quantitative Low Loss and Ultra Low Loss Spectroscopy in the STEM
Authors: Howie A , Garcia de Abajo FJ , Yamamoto N 
Published: July 2020

Abstract
Many of the topics in valence spectroscopy originally pioneered with TEM equipment have now been taken over by STEM. Notable exceptions are the studies by J. Silcox and his colleagues of plasmon dispersion and of the guided modes in thin slabs where retardation and other relativistic effects arise. The growing use of STEM valence EELS on increasingly complex nanostructures and the development of dielectric excitation theory for quantitative interpretation of the results were recently reviewed. The spatial resolution approaches the atomic scale, exceeding by orders of magnitude the capability of near field spectroscopy. By using the cathodoluminescence (CDL) signal, optical precision in STEM energy loss measurement can also be achieved, particularly in the difficult region below 5 eV or even 1 eV. High spatial resolution can be preserved provided that an intermediate stage of carrier diffusion is not involved in the radiative decay of excitations.
Figure 1 shows STEM CDL images of an Ag particle obtained from the dipole l=1 and quadrupole l=2 surface plasmon excitations
EELS as a Probe of Local Electronic Structure and Cohesion
Authors: Muller David A 
Published: July 2020

Abstract
There is an intimate connection between the electronic structure of a material and its physical properties. to change one, is to change the other. Some of the most striking illustrations of this relationship can be found at grain boundaries in metals and their alloys. Here, the most important changes in cohesion can be described by changes in the local density of states (LDOS), which in turn can be measured using EELS [1]. The first demonstration that EELS could be used to connect the electronic and mechanical properties of a material was in revealing the role that boron has in restoring a bulk-like bonding to grain boundaries in Ni3Al [2,3]. Boron was known to change the fracture mode in Ni3Al from intergranular to transgranular, possibly by enhancing grain boundary cohesion.
What interested me in this project, when John Silcox first suggested it as a thesis topic, was the potential of using the EELS fine structure to measure materials properties directly.
Automated Analysis of X-Ray Spectrum Images from the STEM
Authors: Kotula PG , Michael JR , Keenan MR 
Published: July 2020

Abstract
For failure analysis and process control it is critical to perform comprehensive microanalysis. The desire to perform this analysis thoroughly but quickly is the ultimate goal. Typical analyses of this sort have been performed by collecting x-ray spectra at points, along lines, by mapping, and more recently by spectrum imaging where a complete x-ray spectrum is collected over a 2D array of points. Spectrum imaging is perhaps of greatest interest for its potential to thoroughly and comprehensively sample a given area of a microstructure. The problem is that the techniques available for analyzing large (&gt; 1000 spectra) spectrum image (SI) data sets have been limited to mapping after the fact and perhaps thresholding the maps and summing the resultant spectra from those pixels. As a result, there is a need for more sophisticated SI analysis tools, capable of reducing the SI to its essence-the chemical components. Software is currently commercially available for the automated analysis of x-ray spectrum images (SIs) from the SEM
Energy Dispersive Spectrometry Calibration of Fe and Co
Authors: Vartuli CB , Stevie FA , Purcell BM , Scwhitter A , Rossie B , Brown S , Shofner TL , Anderson SD , McKinley JM , Irwin RB 
Published: July 2020

Abstract
Energy Dispersive Spectrometry (EDS) is an ubiquitous method of elemental analysis for SEM, TEM, and STEM applications. The elements of interest are generally quantified without standards using theoretical calculations or by using standards that are high purity specimens of the elements measured. However, EDS is often used to determine a small percentage of an element in a matrix. The accuracy and limit of detection of these low concentration measurements has not been established. An earlier report proved the concept that a cross section high dose BF2 implanted specimen could provide a standard for EDS measurement of F. This study extends this quantification approach to transition elements of importance to the semiconductor industry.
The Fe and Co standards were created by high dose ion implantation. For ions implanted into silicon, a dose of lxl016 atoms/cm2 results in a peak concentration of approximately lxl021 atoms/cm3 or 2% atomic. The exact concentration can be determined using methods such as Rutherford Backscattering Spectrometry (RBS) and Secondary Ion Mass Spectrometry (SIMS).
Quantification of Compositional Modulations in Self-Assembled Multisheet (Cd, Zn, Mn)Se Quantum Dot Structures
Authors: Topuria T , Möck P , Browning ND , Titova LV , Dobrowolska M , Lee S , Furdyna JK 
Published: July 2020

Abstract
CdSe/ZnSe based semiconductor quantum dot (Q D) structures are a promising candidate for optoelectronic device applications. However, key to the luminescence properties is the cation distribution and ordering on the atomic level within the CdSe QDs/agglomerates. Here the Z contrast imaging technique in the scanning transmission electron microscope (STEM) is employed to study multisheet (Cd,Zn,Mn)Se QD structures. Since Z-contrast is an incoherent imaging technique, problems associated with strain contrast in conventional TEM are avoided an accurate size and composition determinations can be made.
For this work we used a JEOL JEM 201 OF field emission STEM/TEM. The sample was grown by molecular beam epitaxy in order to achieve vertical self-ordering of Cd rich quasi-2D platelet This sample comprises 8 sequences of 10 ML (2.83 nm)Zn0.9Mn0.1Se cladding layer and 0.3 ML (0.09 nm) CdSe sheet, a further 10 ML of Zn0.9Mn0.1Se, and a 50 nm ZnSe capping layer.
Extension of HRTEM Resolution: Solving Structures of Grain Boundary and Interface Using Gerchberg-Saxton Algorithm and Blind Deconvolution
Authors: Chen F-R , Ichinose H , Kai J J , Chang L 
Published: July 2020

Abstract
Oxides, nitrides, carbides and silicides contain more than one type of atoms that gives one extra degree of freedom in the grain boundary and interfacial structure. This degree of freedom is the choice of the boundary plane containing different type of atoms which results of several structural multiplicities in the boundary. Coexistence of the structural multiplicities (or boundary domains) in the interface and grain boundary were reported [1, 2]. The structural information in high frequency domain is usually blurred and lost in the lens system of a high resolution transmission electron microscopes (HRTEM) such that the HRTEM image may not truly represent the real structure. Conventionally, the structures of grain boundary and interface were solved using forward method. The forward method involves matching the simulated images from guessed possible models with the through focal series experimental images. Recently, rereconstruction methods such as focal variation holography [3, 4], tiltbeam holography [5] and Gerchberg-Saxton algorithm [6] provide a backward (direct) way to recover the structural information lost in a modern microscope.