bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Technique to Determine Platelet Deposition on an Experimental Nylon Membrane Using Lvsem and Tem
Authors: Murphy MA , DiOrio JP 
Published: July 2020

Abstract
Porous nylon fabric is used as a filter in blood devices. This study was undertaken to evaluate the interaction between an experimental nylon filter and the cellular elements which pass through it. Our investigation was mainly centered on determining the deposition of cellular material on the nylon filter using Low Voltage Scanning Electron Microscopy (LVSEM) and Transmission Electron Microscopy (TEM).
The filter was prepared for LVSEM by cutting a 2.5 cm2 of the nylon filter material with a razor and placing it in a nylon mesh bag which was stapled shut. The bag was rinsed three times for ten minutes each in fresh Sorensen's phosphate buffer. A graded alcohol series of 25%, 35%, 50%, 70%, 80%, and 90% was used to dehydrate the filter for ten minutes each. This was followed by dehydration twice for 20 minutes in fresh 100% ETOH. The filter was then Critical Point Dried (CPD) in the Tousimis AUTOSAMDRI-814.
The Effect of Focused Ion Beam (Fib) Specimen Geometry on X-Ray Fluorescence During Energy Dispersive X-Ray Spectroscopy (EDS) Analysis in the Transmission Electron Microscope (TEM)
Authors: Longo David M , Howe James M , Johnson William C 
Published: July 2020

Abstract
The focused ion beam (FIB) has become an indispensable tool for a variety of applications in materials science, including that of specimen preparation for the transmission electron microscope (TEM). Several FIB specimen preparation techniques have been developed, but some problems result when FIB specimens are analyzed in the TEM. One of these is X-ray fluorescence from bulk material surrounding the thin membrane in FIB-prepared samples. This paper reports on a new FIB specimen preparation method which was devised for the reduction of X-ray fluorescence during energy dispersive X-ray spectroscopy (EDS) in the TEM.
Figure 1 shows three membrane geometries that were investigated in this study on a single-crystal Si substrate with a RF sputter-deposited 50 nm Ni film. Membrane 1 is the most commonly reported geometry in the literature, with an approximately 20 urn wide trench and a membrane having a single wedge with a 1.5° incline.
Material Dependence of Sputtering Behavior During Focused Ion Beam Milling: A Correlation Between Monte Carlo Based Simulation and Empirical Observation
Authors: Prenitzer BI , Giannuzzi LA , Brown SR , Irwin RB , Shofner TL , Stevie F A 
Published: July 2020

Abstract
The focused ion beam (FIB) lift-out method is a high precision technique by which site-specific cross-section transmission electron microscopy (TEM) specimens may be rapidly prepared from virtually any material. The technique is particularly useful when the sample geometry or composition is complex (e.g., fibers, powders, composites and interfaces). In addition to the preparation of TEM specimens, FIB milling has also found widespread utility in micromachining and microfabrication applications as well as specimen preparation for scanning electron microscopy (SEM) and secondary ion mass spectrometry (SIMS).
As the applications of the FEB instrument continue to become more universally recognized, the need to understand the interrelationships between the target material, processing parameters, and process efficiency of the milling phenomena becomes more critical. Incident ion attack angle, target material stopping efficiency and sputtering yield, Y, are important variables governing the milling process. TRIM, a binary collision approximation Monte Carlo simulation code, is used to physically model variables that influence FIB sputtering behavior.
The Small Angle Cleavage Technique for XTEM Sample Preparation
Authors: Walck S D , McCaffrey J P 
Published: July 2020

Abstract
The Small Angle Cleavage Technique (SACT) is a relatively simple and inexpensive method of producing superior cross sectional TEM specimens. For speed of preparation, it is unsurpassed; for example, ten samples can easily be prepared in about an hour from a typical material. It is particularly well suited for rapidly examining coatings and thin films very soon after they have been deposited. A major limitation of the technique is that it does require the substrate material to cleave or fracture. For this reason, it has been applied almost exclusively to semiconductor materials, but the technique has been extended quite successfully to other substrates such as glass, silicon carbide, quartz, sapphire, and other hard materials. Several procedures have been added or modified to the original technique developed by McCaffrey that makes it much easier to get started in using the technique. A detailed pictorial outline of the technique has been described elsewhere by the authors.
The Basics of Microtomy for Materials Science Microscopy
Authors: Malis Tom 
Published: July 2020

Abstract
The common theme of most forms of thin specimen preparation for the physical sciences has been the controlled, gradual removal of material, whether by electrolytic dissolution, ion bombardment, careful mechanical dimpling or step-by-step tripod polishing. It is somewhat ironic that a “brute force” method, wherein the material is forced at a high rate against an atomically sharp diamond wedge so that an ultrathin slice, or section, is sheared, or fractured, from a ‘block’ of the material, should be viewed not only as acceptable, but with growing enthusiasm in the last several years. This process, known as ultramicrotomy, originated in life science TEM, but has been modified by materials scientists and applied to an impressive array of materials as illustrated in Table 1, culminating, perhaps, with the recent successful sectioning of diamond film.
Deconvolution in 3-D Microscopy: Applications and Limitations
Authors: Shaw PJ 
Published: July 2020

Abstract
Many imaging processes, including both conventional wide-field and confocal fluorescence microscopy, can be described to a good approximation as linear and spatially-invariant. Linearity means that the image of an extended specimen is simply the sum of the images of the parts of the specimen - in the limit the specimen can be regarded as a collection of points, and its image is the sum of the images of the points - i.e. weighted instances of the imaging system's point spread function (psf). In the case of spatially invariant imaging the psf is the same over the entire field of imaging. Mathematically, the image is the convolution of the specimen with the system psf. In principle, this convolution can be reversed to remove degradation introduced by the imaging process, a computational procedure often called deconvolution or, more generally, restoration.
Wide-Field Deconvolution for Time-Lapse 3D Microscopy Of Cell Locomotion: The Good, The Bad and the Artifactual
Authors: McNally JG 
Published: July 2020

Abstract
We are using wide-field deconvolution microscopy to study the locomotion of cells within a three-dimensional cell mass. How cells move within such an environment is poorly understood, even though such movement occurs widely, for example, during embryonic development or tumor cell invasion. In these and other cases, cells moving within a cell mass face challenges not encountered by isolated cells crawling on a flat substrate. Cells within a mass must clear a path for themselves, and also gain traction on other cells which themselves may be moving in the same or another direction. To understand the mechanisms of such 3D movement, we observe and analyze it in both normal and mutant cells. The mutant analysis sheds light on which molecules are important for 3D locomotion.
To visualize either normal or mutant cell locomotion within a three-dimensional cell mass, we require time-lapse 3D imaging at light levels low enough to maintain specimen viability.
Optimization of Microfluidics for Genetic Analysis
Authors: St. John Pamela M , Connell Kip , Woudenberg T M , Deshpande M , Gilbert J R 
Published: July 2020

Abstract
Novel microfluidic designs are needed for fluid delivery and transport in an integrated micro-genetic analysis system and these designs often lead to complex relationships between the shape and size of the microchannels and the behavior of multi-component fluids. We are studying both pressure-driven and electrokinetic flow in various microfluidic channel designs fabricated from both glass and silicone substrates to understand chemical containment and transport. In conjunction with the experiments, simulations are being performed to predict behavior in microdevices and models are being used to develop a CAD tool for designers.
Fluorescent flow profiles are generated using a charged caged dye which fluoresces upon irradiation with 355 nm light from a Nd:YAG laser. The starting position of the dye is determined by a tightly focused laser spot &lt;20 μm in diameter.
Scanned Probe Microscopy (AFM, et al.): How to Choose and Use
Authors: Russell Phillip E , Batchelor A D 
Published: July 2020

Abstract
Virtually everyone associated with a science or engineering discipline has some baseline knowledge of optical microscopy; and most attendees at this conference have a reasonable exposure to at least some form of electron microscopy. The many developments in instrumentation and application require the modern microscopist to continuously follow the literature to stay aware of the ongoing improvements and advances in these microscopies. While electron and optical microscopes have been around for many decades, the family of microscopes known as Scanned Probe Microscopy (SPM) are just entering their second decade; and are actually in there first decade of widespread use.
The most commonly used forms of scanned probe microscopy are the force microscopes; commonly referred to as Atomic Force Microscopy (AFM). This includes a wide variety of microscopy modes that are generally made available as modifications of a basic AFM. Before describing the basic versions of AFM, the fundamentals of instrument design must be addressed.
Fixing and Embedding “Difficult” Biological Material
Authors: Mollenhauer Hilton H 
Published: July 2020

Abstract
Introduction: This is a personal account of the author's attempts to solve some of the problems associated with the fixation and embedding of difficult biological materials such as plant tissues, almost all insect tissues, and large pieces of tissues including whole organs.
Historically, the search began in the 1950's with the study of the maize root tip using the relatively new technique of electron microscopy. This system of cells, separated by thick and partially impermeable walls, did not respond well to the procedures most suitable for animal tissues. New approaches were needed and, in time, some were found that were at least useful if not ideal. A brief account of several of these is given in the following paragraphs.
Fixation of plant cells: Potassium permanganate was chosen very early in the study primarily because it worked better for plant cells than did any of the fixation procedures currently available.
The Pulmonary Circulation in Health and Disease
Authors: Aharinejad S , Schraufnagel DE 
Published: July 2020

Abstract
SEM analysis of pulmonary vascular casts shows basket-like alveolar capillaries that are about 6 μm in diameter. Generally pulmonary arteries are adjacent to airways and veins are not. The pleural surface and the airways capillaries have a planar meshwork with few large vessels. Uncommonly are lymphatics cast in normal lungs but they are regularly found in casts of edematous lungs. Casts of pulmonary veins in several species have smooth surfaces with a slight notch occurring at regular intervals; these notches will deepen after physiological interventions and are sharply constricted in spontaneously hypertensive rats (SHR) with pulmonary hypertension and cattle. The circular bands are caused by tufts of smooth muscle cells and have been called pulmonary venous sphincters (Fig. 1). The depth of the constrictions can be measured to show the effect of an experimental intervention on individual small veins, which is important in understanding the pulmonary microcirculation and its control.
Using Correlative Microscopy in the Study of Biological-Biomaterial Interactions
Authors: Albrecht RM 
Published: July 2020

Abstract
The application of two or more imaging-based technologies to portions of a sample prepared in parallel or preferably to the exact same sample in series is the basis for correlative microscopy. Simultaneous visualization of structure in conjunction with other cellular parameters such as cell motility, intracellular ion concentration, receptor expression, and protein distribution/movement can be followed in living cells by various forms of photon, acoustic, and force based microscopy. The same cells can subsequently be prepared by various physical or chemical based procedures and reexamined by other microscopic methodologies to gain additional qualitative and quantitative information often at significantly increased levels of resolution. Recent advances key to correlative microscopy have been the development of high sensitivity, high resolution video cameras, and computer image processing, image enhancement, image analysis, and reconstruction capabilities. New instrumentation such as video enhanced, rectified interference-based light microscopy,LM; confocal LM, and two and three photon LM also have been critical.
A Novel Approach for Characterisation of Adhesive Toothbiomaterial Interfaces by ATM.
Authors: Van Meerbeek B , Yoshida Y , Snauwaert J , Hellemans L , Lambrechts P , Vanherle G , Wakasa K , Pashley DH 
Published: July 2020

Abstract
The ability to adhere biomaterials to tooth tissue has drastically changed today's dental restorative practice. Modern adhesive techniques enable dentists to restrict operative procedures to the sole removal of diseased tooth tissue without further destruction of the remaining sound tissue. However, adhesive restorations have only a short lifetime of ca. 5 years. Extending the restoration lifetime is therefore one of the primary goals of present research in dental materials science. In practical relevance and direct benefit to that objective are studies that contribute to a better understanding of the interfacial phenomena that take place between restorative material and tooth tissue. Therefore, the resolution of instruments available to elucidate this interfacial interaction is essential. Besides the transmission electron microscope (TEM), a more recent powerful tool to study tooth-biomaterial interaction with high resolution is the atomic force microscope (AFM).
Imaging of Explanted Mechanical Heart Valves
Authors: Goodman SL , Harasaki H , Wika KE , Brendzel AM 
Published: July 2020

Abstract
Prosthetic mechanical heart valves (MHVs) made from pyrolytic carbon (PYC) are a highly successful biomaterial application due to their excellent durability and clinically adequate blood compatibility. Their thromboresistance has been attributed to a combination of hemodynamics, material inertness, and surface properties which minimize platelet adhesion and activation. These surface properties include that polished PYC is smooth and that it strongly adsorbs plasma albumin, which is well known to reduce platelet adhesion. However, recent evidence suggests that this explanation is incomplete. Low voltage SEM shows that PYC valve leaflets are actually quite rough at submicron scales and that PYC induces extensive platelet spreading in vitro in the presence of albumin. Surprisingly few studies have examined MHVs explanted from humans or research animals for platelet adhesion and thrombosis using SEM. Moreover, in most studies it appears that even routine sample preparation methods for the preservation of biological samples for SEM,
CTF Corrected Structure of the Closed-State Calcium Release Channel
Authors: Ludtke S , Serysheva I , Hamilton S L , Chiu W 
Published: July 2020

Abstract
Several structures of the Ryanodine receptor in different functional states with various bound ligands have been determined using electron cryo-microscopy in recent years. These structures have varied in resolution from 25-40Å, however, to date, none have been corrected for the CTF (contrast transfer function) of the microscope. The CTF can have a significant effect on the detailed structure of the molecule, causing features in the 40-70Å range to be unnaturally emphasized. This causes small holes to become larger and small protrusions to become elongated. Unfortunately due to zero points in the CTF, correction cannot be properly accomplished with individual images. Several approaches to correcting the CTF have been proposed and/or used by combining information from images taken at different defocus settings. We have taken the approach of performing CTF correction as a preprocessing step. There are both advantages and disadvantages to this method. There are 2 primary advantages: First, by combining data from identical regions of focal pairs,
FEISEM, Form and Function in the Nuclear Pore Complex
Authors: Allen TD , Bcnnion G R , Rutherford S A , Kiscleva E , Goldberg M W 
Published: July 2020

Abstract
Recent initiatives have resulted in a considerable increase in our understanding of the structure of the nuclear pore complex (NPC). The biochemical factors involved in both import and export have been rapidly characterised, with steady progress in the molecular dissection of the structural elements of the NPC, which is a unit of considerable molecular architecture (MW 125 kD), comprising an estimated 50- 100 different proteins. Despite this progress, the crucial molecular interactions involved in the mechanics of transport through the central transporter of the NPC remain unclear. NPC structure in Diptera, fish, (Fig 1) amphibians, birds and mammals shows a high degree of evolutionary conservation. 3D reconstructions of isolated yeast NPCs, show that the core structure is very similar to ‘higher’ organisms, but peripheral structures may be considerably reduced in structural complexity (1).
Individual NPC components have been accessed in FEISEM by a variety of methods, including proteolysis,
Structural Studies of Translocation Channels: The Nuclear Pore Complex and the Translocon
Authors: Yang Q , Ménétret J-F , Akey IV , Plath K , Rapoport T A , Akey C W 
Published: July 2020

Abstract
Protein translocation plays a critical role in the targeting of both soluble and membrane proteins to their correct intra- and inter-cellular compartments. We are studying the 3D architecture of two rather different translocation machines, the Nuclear Pore Complex (NPC) and the ribosome-Sec61p complex (translocon), with the aim of understanding their physical mechanisms of gating and transport. Towards this end, we are using single particle electron cryomicroscopy and 3D reconstruction of frozen hydrated specimens to obtain interpretable maps that are biologically relevant.
Previous work suggested that a central channel complex (termed the transporter) is present in vertebrate NPCs. Based on classification studies of the transporter and STEM images of Chironomus NPCs caught translocating large mRNPs, we have hypothesized that the transport mechanism utilizes a double iris-like gating mechanism, in which oppositely facing gates located at either end of the transporter open asynchronously. Recently, we have extended our studies to yeast NPCs and shown that this organelle is markedly smaller than its vertebrate cousin.
Cytomegalovirus Capsid Structure and Tegument Binding
Authors: Steven A C , Gibson W , Cheng N , Trus B L 
Published: July 2020

Abstract
Herpesviruses form an extensive family of DNA viruses, in which three subfamilies called alpha-, beta- and gammaherpesviruses, respectively, are distinguished on the basis of biological properties. In terms of overall structure, all herpesviruses conform to a common plan: the virion consists of a thick-walled capsid, ∼ 1250 Å in diameter, containing the genome, surrounded by a complex layer of proteins called the tegument (a feature unique to herpesviruses), and a lipoprotein envelope. At a more detailed level, it has not been clear whether the three subfamilies are also differentiated structurally. The molecular architecture of alphaherpesvirus capsids has been studied by cryoelectron microscopy of herpes simplex virus 1, revealing its icosahedral (T=16) surface lattice and the locations of the four abundant shell proteins. To ascertain how closely these features are emulated in a betaherpesvirus, we have studied capsids of simian cytomegalovirus (SCMV) by similar methods. By comparing the structures of nuclear capsids and cytoplasmic capsids (which have bound some tegument proteins),
Cryo-Electron Microscopy and Image Processing Methods for Studying the Ribonucleoprotein Vault
Authors: Kong L B , Rome L H , Stewart P L 
Published: July 2020

Abstract
Vaults are highly conserved ribonucleoprotein complexes found in thousands of copies per cell in various tissues. The major vault protein, pi 04, accounts for over 70% of the particle mass and has been recently found to be involved in cancer cell multidrug resistance. We have utilized cryoelectron microscopy (cryo-EM), and three-dimensional image reconstruction to generate a 3-D structure of the vault particle. Individual particle images were isolated using the QVIEW software package, which simultaneously performs density exclusion, planar background subtraction, and application of an elliptical mask. The IMAGIC-5 software package was used for the subsequent particle orientation and reconstruction steps (Fig. I).
A symmetry self-search test was used to measure the signal strength for a variety of point groups and the highest correlation was found for the cyclic 8-fold point group. We have utilized the sinogram correlation algorithms in IMAGIC-5 to find the Euler angles of both 1 μm and 2 μm defocus particle images.
Protein Unfolding and Degradation by the CLP Family of Proteases
Authors: Kessel Martin , Beuron Fabienne , Booy Frank , Kocsis Eva , Maurizi Michael , Steven Alasdair 
Published: July 2020

Abstract
ATP-dependent proteases play a major role in regulatory protein degradation in both prokaryotic and eukaryotic cells. ATP-dependent proteases in E. coli fall into two classes. The first class requires the interaction of structurally separate proteases with an ATPase, whereas in the second class both the protease and ATPase are formed from regions of the same polypeptide chain. We have studied the structure of several of these protein degrading complexes in E. coli and have found a remarkable similarity in the architecture of these macromolecular assemblies.
The prototypical protease of the first class has as its proteolytic component ClpP, a 14 subunit (MW 21,500) complex arranged as two lOnm-diameter stacked rings of seven subunits each. ClpP can interact with either one of two ATPases, ClpA or ClpX, each with unique substrate specificity. ClpA has two ATP-binding sites per subunit (MW 84,000), and its subunits are arranged as a 13nm (diameter) hexameric ring (MW -500,000).