bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Construction of an EBSD Stage for the Electroscan E3 SEM
Authors: Yurek Peter , McKernan Stuart , Lee Kyung-Ho 
Published: July 2020

Abstract
With recent advances in computing power and application specific software it has become practical for smaller microcopy labs to either purchase or build a electron backscatter diffraction (EBSD) systems. This system can be used to probe the crystallography and microstructure of many different materials. One set of such materials is geological samples from deep within the earth's crust. In collaboration with the Geology and Geophysics department an EBSD system has been built to function with the Philips Electroscan E3 Environmental Scanning Electron Microscope (ESEM). Using an existing low light level SIT camera, the system was completed with the addition of a phosphor screen and appropriate software and acquisition cards.
One main advantage of the ESEM for EBSD is that since it is an environmental SEM samples can be imaged without coating. For insulating materials this is means that the sample can be imaged without coating.
Improved Signal Processing in Multi-Photon Imaging
Authors: Fisher Wait G , Wachter Eric A 
Published: July 2020

Abstract
Multi-photon excitation has been used in microscopy for nearly a decade, providing a number of demonstrated advantages over other methods for fluorescence imaging. Because excitation is achieved using longer, less energetic light, photodamage and photobleaching of the sample are reduced. Furthermore, since excitation occurs only at the focal point, this approach allows the practical collection of three-dimensionally resolved fluorescence images of live cells. However, due to the small two-photon cross-section of most fluorophores, pulsed lasers are required to generate detectable signal levels. This is due to the quadratic dependence of twophoton absorption on the instantaneous power of the laser. Typically, these lasers are pulsed at very high repetition frequencies, on the order of 106 pulses per second with pulse durations of a few hundreds of femtoseconds. For example, a titanium:sapphire (Ti:S) laser mode-locked at 76 Mhz can provide up to 100,000 watts of instantaneous power and is ideal for exciting two-photon events.
Two-Photon Microscopy of Single Molecules
Authors: Fourkas J T , Previte M J R , Farrer R A , Olson C , Peyser L A 
Published: July 2020

Abstract
The ability to observe the fluorescence arising from single molecules has revolutionized our ability to study the structure and dynamics of materials on a microscopic level and to probe the properties of individual members of a heterogeneous ensemble. A variety of near-field and far-field excitation techniques have been employed to study single molecules. Multiphoton excitation (MPE) techniques have a number of advantages that make them particularly attractive for singlemolecule detection. First, because the excitation and fluorescence wavelengths are significantly different from one another, Rayleigh and Raman scattering can easily be filtered out, leading to a low number of background counts. Second, because the probability for MPE depends on the excitation intensity to the second or higher power, the excitation is localized to the point in space where the excitation beam is most tightly focussed, thus providing three-dimensional resolution.
Second Harmonic Imaging Microscopy: A New Non-Linear Optical Modality for Cell Membrane Physiology
Authors: Campagnola Paul , Lewis Aaron , Loew Leslie M 
Published: July 2020

Abstract
Confocal microscopy is an excellent high resolution method to image fluorescently labeled cells. However, the use of confocal microscopy to monitor physiological events, such as membrane potential changes, in living cells is hampered by photobleaching and phototoxicity. To reduce the collateral damage from excitation of fluorescent probes outside the optical slice, Webb and co-workers introduced the use of two-photon excited (TPE) fluorescence in laser scanning microscopy.1 Two-photon absorption depends on the square of the incident light intensity; this has the effect of confining excitation to the plane of focus where the photon flux density is greatest. The wavelength of the exciting light is in the near infrared facilitating penetration of thick tissues. Due to these significant advantages this methodology is rapidly gaining popularity as a tool for live cell and tissue imaging.
To further exploit non-linear optical processes in laser scanning microscopy, we have developed surface second harmonic generation (SHG) as a powerful new imaging modality.
Third Harmonic Microscopy: Imaging Applications in the Biological and Material Sciences
Authors: Squier Jeff , Müller Michiel 
Published: July 2020

Abstract
Tightly focused beams of ultrashort optical pulses such as produced with a high numerical aperture optic as found in a microscope exhibit an interesting property: a strong third harmonic signal is produced when the axial focal symmetry is broken through a change in material properties. This change can be manifested as either a change in refractive index and/or a change in the nonlinear susceptibility of the specimen. Conversely, third harmonic production is inhibited in those cases when the axial focal symmetry is unbroken. This property can be effectively exploited to produce volumetric images of biological and non-biological specimens. The third harmonic is localized to interfaces within the specimen making it possible to produce optical sections in much the same manner as in confocal, and two-photon fluorescence microscopy. Unlike these techniques however, no exogenous fluorophore is necessary for labeling - the signal is produced by endogenous interfaces.
Confocal Fluorescence Microscopy with CCD Sensors Speed by Parallelization, Low Cost by Using More Electronics
Authors: Großkopf Rudolf E 
Published: July 2020

Abstract
CCD sensors are able to image a few megapixels within one frame. The image is scanned electronically within the semiconductor chip (instead of mechanical-optical scanning with moving mirrors, Nipkow discs or acousto-optical devices). Through parallelization. the novel concept yields speed at an unprecedented degree for confocal imaging Routine applications requiring high speed and low costs will profit from this principle. Thus, confocal imaging technology will take the same path television technology has taken—from mechanical scanning to the broadest possible application of electronics
In order to go this way, a pinhole matrix is used on the illumination side. It has as many pinholes and the same pitch as the pitch and number of pixels of the CCD (Figure 1). In front of the receiver, a second pinhole matrix with the same pitch and number of pinholes is used All pinholes of both matrices and the pixels of the CCD are in confocal position.
A Robust Two-View Method for Increasing the Imaging Depth and Correcting for Signal Attenuation in Confocal Microscope Images
Authors: Can Ali , Lasek Shade , Szarowski Donald H , Turner James N , Roysam Badrinath 
Published: July 2020

Abstract
Confocal Microscopy is now an essential, and widely used tool for biological research. Particularly valuable is its ability to image thick sections of intact tissue. A compelling need in this field is to improve the imaging depth, as well as quantitative accuracy, and minimize the possibility of missing important structures/phenomena due to attenuation of the imaging signal. Previous methods work by amplifying the signal from deeper parts of the specimen. In these methods, amplification of noise is an unavoidable artifact. We describe a novel method that not only corrects confocal stacks for attenuation without noise amplification, but also enhances the achievable imaging depth. Interestingly, it does not require explicit estimation of the extinction factor, It relies on a synergistic combination of specimen preparation and image reconstruction algorithms.
The key idea is to image the specimen from two angles (Fig. 1), separated by 180° and then to reconstruct the complete thick image using computational methods.
Multi-Photon Fluorescence Spectroum of Common Nucleic Acid Probes
Authors: Bailey GW , McKernan S , Price RL , Walck SD , Charest P-M , Gauvin R , Cheng P C , Lin B L , Kao F J , Sun C K , Johnson I 
Published: July 2020

Abstract
Fluorescent probes are commonly used in biological fluorescence microscopy for tracking specific structures and sub-cellular compartments, and for indicating cellular ionic conditions. Recent development in multi-photon fluorescence microscopy has greatly expanded the usage of fluorescent probes in biomedical research. Considering its non-linear nature, two-photon excitation may generate very different fluorescence spectral response in the sample when compared with single photon excitation. It is thus necessary to measure the two-photon spectra of various fluorescent probes, so that two-photon fluorescence microscopy may be operated effectively and the images properly interpreted. This report represents the first installment of a continued effort in characterizing the multi-photon fluorescence spectra of commonly used bio-probes.
Two-photon fluorescence spectra excited with near infrared at 780nm were obtained with a SpectraPro-500 spectrophotometer (Acton Research) equipped with a TE-cooled PMT and coupled to a Spectra-Physics Tsunami Ti-sapphire laser pumped by a Coherent Verdi solid-state laser operated at 85MHz, l00fs pulse.
FRET: A Spectral Ruler for Interacting Molecules Involved in Apoptosis
Authors: Centonze Victoria E , Liang Xiao H , Casanova Elizabeth A , Levine Beth , Herman Brian 
Published: July 2020

Abstract
Fluorescence Resonance Energy Transfer (FRET) is a process by which a fluorophore (the donor) in the excited state transfers its energy to a neighboring fluorophore (the acceptor) non-radiatively through dipole-dipole interactions. Since the efficiency of energy transfer varies as the inverse of the sixth power of the distance separating the donor and acceptor chromophores, for FRET to occur the distance between the two molecules cannot exceed 10 to 100 angstroms (1 to l0nm). The combination of FRET and optical microscopy allows examination and quantitation of dynamic molecular interactions between cellular constituents at resolutions beyond the Abbe diffraction limit of light microscopy. Through the microscope one may detect FRET by an overall decrease in fluorescence emission of the donor with a concomitant increase in fluorescence emission of the acceptor.
Studying Subnuclear Dynamics in Living Cells
Authors: Spector David L 
Published: July 2020

Abstract
Green fluorescent protein (GFP) and its variants have become powerful tools with which to study the dynamics of many fundamental processes in living cells. I will first discuss the advantages of GFP and important parameters that one must consider in performing live-cell microscopy experiments including how to keep cells happy on the microscope stage. I will then go on to discuss work from our laboratory using multiple microscopic approaches to address questions related to gene expression.
Many of the basic processes that are essential for normal cell growth and division are regulated in the nucleus, ie. DNA replication, transcription, RNA processing and transport. The organization of these functions in the nucleus must be highly controlled in order to enable cells and/or the entire organism to function properly. However, relatively little has been known about the relationship of nuclear organization to gene expression.
Field Emission Scanning Electron Microscopy Of Mouse Cerebellar Synaptic Contacts
Authors: Castejón OJ , Apkarian R P , Castejón H V 
Published: July 2020

Abstract
Samples of albino mice cerebellar cortex were processed by the cryofracture method for scanning electron microscopy and examined with the field emission scanning electron microscope (FESEM). Albino mouse cerebellar cortex was excised, cut into 1-2 mm slices and inmersed in 4% glutaraldehyde in O. l M phosphate buffer solution, pH 7.4, for 24h at 4°C; and postfixed for 1 h in a similarly buffered 1% osmium tetroxide solution. Specimens were dehydrated in a graded serie of ethanol (30, 50, 70, 80, 90 2x100%) prior to wrapping individual tissue pieces in preformed absolute ethanol filled parafilm cryofracture packets. Rapid freezing of packets was performed by plunging into LN2. First, the packet was transferred from the LN2 storage vessel with LNT chilled forceps in order to avoid themial damage. Secondly, the cooled fracture blade was removed from the LN2, the packet was orientated under the blade, and immediately struck with a heavy tool.
Ordered Intracellular Reca-Dna Assemblies
Authors: Wolf S G , Levin-Zaidman S , Frenkiel-Krispin D , Shimoni E , Sabanay I , Minsky A 
Published: July 2020

Abstract
The inducible SOS response increases the ability of bacteria to cope with DNA damage through various DNA repair processes in which the RecA protein plays a central role. We find that induction of the SOS system in wild-type E. coli bacteria results in fast and massive intracellular coaggregation of RecA and DNA into lateral assemblies, which comprise substantial portions of both the cellular RecA and the DNA complement. The structural features of the coaggregates and their relation to in-vitro RecA-DNA are consistent with the possibility that the intracellular assemblies represent a functional entity in which RecA-mediated DNA repair and protection activities occur.
Bacterial chromatin is demarcated in electron micrographs of metabolically active cells as amorphous ribosome-free spaces that are irregularly spread over the cytoplasm (Fig. A). Wild-type E. coli cells exposed to DNA-damaging agents that induce the SOS response reveal a strikingly different morphology (Fig. B).
Three-Dimensional Reconstruction of a Node of Ranvier Obtained by Serial Section Electron Tomography
Authors: Sosinsky G , Deerinck T , Greco R , Ellisman M 
Published: July 2020

Abstract
Nodes of Ranvier are sites on myelinated axons where the insulating layers of myelin are interrupted. They represent an excellent example of a complex cellular structure that contains highly differentiated sub-regions. At these sites of cell-cell specialization, ion fluxes occur which are required for propagation of action potentials. Myelinated axons and their nodes of Ranvier represent an important evolutionary advance for vertebrates that permit very rapid propagation of action potentials without large increases in axonal diameter. This physiological achievement is based on adaptations at a molecular level resulting in an elegant cooperation between glial cells and the axons of neurons.
The organization and sub-specialization of the molecular components of the node of Ranvier are complex but often inter-related. The nodal region of axons are enriched in several channel and pump proteins including the voltage-gated Na+ channel, Na+-K+ ATPase and a number of different K+ channel isotypes.
Localization of Misprocessed Pulmonary Surfactant Protein C in Tubular Myelin Enriched Fractions By Cryo Immunogold Labeling
Authors: Na C-L , Evans E A , Akinbi H T , Weaver T E 
Published: July 2020

Abstract
Pulmonary surfactant is secreted by alveolar type II cells and reduces the surface tension at the air-liquid interface of alveoli. After pulmonary surfactant is secreted into the alveolar space, it transforms into tubular myelin, a highly ordered 3-dimensional lattice-like structure. Pulmonary surfactant protein C (SP-C), one of four pulmonary surfactant associated proteins, is synthesized as a proprotein which is processed to biologically active 35 amino acid mature peptide by proteolytic cleavage of N- and C-terminal peptides from the SP-C propeptide (Weaver, 1998). Processing of SP-C is linked to the expression of pulmonary surfactant protein B (SP-B): In SP-B deficient mice, SP-C is misprocessed and present in the bronchoalveolar lavage (BAL; Vorbroker et. al., 1995a). Although the intracellular localization of SP-C is well established (Vorbroker et. al., 1995b), there is no ultrastructure study available regarding the localization of misprocessed SP-C in the airway. In this study, we used transgenic mice expressing a truncated human SP-B propeptide (hSP-BΔC+/+) bred into the murine granulocyte macrophage colony stimulating factor (GMCSF) and SP-B double knockout background (hSP-BΔC+/+: GMCSF-/-: mSP-B-/-) as a model to localize the misprocessed SP-C by cryoimmunogold labeling.
Imaging Phospholipid Arrangement in Pultonary Surfactant Using Atomic Force Microscopy
Authors: Nag K , Possmayer F , Petersen N O , Hearn S A 
Published: July 2020

Abstract
Lung surfactant stabilizes the pulmonary air-water interface, by enriching this interface with films of amphipathic phospholipids. These films reduce the surface tension of the air-water interface to very low values (∼ 1 mN/m) at end expiration and prevents alveolar collapse. Surfactant contains mainly phospholipids (90%), and small amounts of associated proteins. Among the phospholipids, saturated dipalmitoylphosphatidylcholine (DPPC) and monounsaturated phosphatidylcholine are the main surfactant components, although significant amounts of other lipids are also present (1). DPPC is the only component of surfactant which exists in gel phase at physiological temperature, films of which can reduce the air-water surface tension to low values. DPPC films can undergo a fluid to gel transition with increase in the molecular packing leading to superstructures or domains (2). However it is not clear how the molecules of surfactant pack at the air-water interface to form highly compact films, and if DPPC phase segregate in such films.
Examination of Frozen, Hydrated Mites Using Low Temperature Field Emission Scanning Electron Microscopy
Authors: Ochoa Ronald , Erbe Eric F , Pettis Jeffery S , Wergin William P 
Published: July 2020

Abstract
Mites, the second largest arthropod group after insects, occupy every conceivable terrestrial and aquatic habitat in our environment. They feed on plants, infest food products such as meat, cheese and grains, parasitize invertebrates and vertebrates, and transmit fungal, bacterial, rickettsial and viral diseases. Estimates indicate that as many as 1,000,000 species of mites may exist; however, partly because of their microscopic size, only about 40,000 species have been described and classified. During the last 30 years, researchers have increasingly utilized the greater magnification and depth of field available in a conventional scanning electron microscope (SEM) to supplement descriptions of mites that were historically based on light microscopic observations. In addition, this technique provided a better understanding of the relative positions and functionality of organs and improved attempts to elucidate their biology. However, before mites can be imaged with a conventional SEM, they are typically chemically fixed, dehydrated and/or thoroughly dried.
Light and Electron Microscopic Examination of the Parasitic Dinoflagellate Haplozoon
Authors: Landers Stephen C 
Published: July 2020

Abstract
The parasitic dinoflagellate Haplozoon is found in the intestine of marine polychaetes. It is composed of a chain of cells that hang from the intestinal wall into the lumen, and releases daughter cells from the posterior end of the chain which leave the host and reinfect other polychaetes. Few studies exist in the recent literature regarding Haplozoon and it has not been reported from the Gulf Coast of the United States. This study reports the genus Haplozoon from the maldanid polychaete Axiothella mucosa in St. Andrew Bay, Florida, and examines the structure of the organism by light and electron microscopy.
Axiothella mucosa was collected in St. Andrew Bay, Florida and maintained in seawater at the Troy State University campus. Haplozoon spp. was prepared for whole mounts by smearing minced setigers of the worms onto a slide with a drop of seawater.
The Technical Aspects for Studying Morphology of Purified Lacrimal Gland Acinar Cells Cultured on Matrigel Rafts: A New Model System for Studying Lacrimal Physiology
Authors: Pidgeon Mike , Schechter, Ph.D Joel , Chang, M.S. Natalie , Chang Donald , Trousdale, Ph.D. Melvin , Stevenson Doug 
Published: July 2020

Abstract
Objective: To demonstrate the quality of a new model which gives a close representation of the in situ gland for studying functional characteristics of lacrimal acinar cells. A method has been long sought which would serve as a good in-situ model for studying functional attributes of lacrimal acinar cells. Previous methods used cell plates coated with Matrigel as a growth interface for lacrimal acinar cells.
Two problems associated with this method are: cell cultures seeded this way provided a restrictive, planar growth interface, and the inability to maintain cultures beyond seven days, due in part to a lack of proliferation. A modification of recent methods (Guo et al., 1998) was implemented. The cell preparations were coated with a Hepato Stim® Medium (supplemented with EGF, DHT) and Matrigel. The medium is an extracellular matrix enriched solubilized preparation developed from the basement membranes of the Englebreth-Holm-Swarm mouse sarcoma line.
Localization of Z-RNA in Normal Lens Epithelium: Middle Fibers
Authors: Gagna CE , Kuo HR , Schulz R , Cordova R , Crippen G , Lambert WC 
Published: July 2020

Abstract
The goal of this project was to analyze the cellular localization of Z-RNA, within middle fibers (MF) of the adult dog ocular lens (1.5 yr) (Fig. 1), using anti-Z-RNA IgG polyclonal antibodies. B-DNA can adopt the left-handed Z-DNA conformation in vitro (1). Right-handed A-RNA can be transformed into left-handed Z-RNA (2). Z-RNA has been studied in cultured cells (3). Evidence supports the presence of Z-DNA in vivo (1). Removal of DNA binding proteins by fixatives can initiate supercoiling which stabilizes Z-DNA sequences (1).
Anti-Z-RNA polyclonal antibody probes were developed in rabbits immunized with multiple injections of Z-RNA: Br-poly[ribosomal(G-C)]. Regarding immunohistochemistry, lens tissues were fixed in Carnoy's, embedded in paraffin and sectioned (2.5 μm) (Fig. 2). Computerized image analysis was performed using a Leitz DM-RB microscope and Leica Quantiment 500 + image analyzer.
Detection of Iodine by Scanning Electron Microscopy(SEM) and Energy Dispersive Spectroscopy(EDS) Following Contact with an Iodine Releasing Coating
Authors: Lyden LM , Zaruba KS , Gysbers JE , Kato KH 
Published: July 2020

Abstract
The detection and localization of iodine in biological tissues have traditionally presented problems associated with sample preparation of soluble elements. Standard sample preparation for biological tissue involves methods which solubilize or extract iodine.Furthermore, analytical methods for detection of elements typically have been studied in smooth flat materials. We describe two methods using frozen pig skin for detecting iodine in tissue, creating digital color maps of iodine concentrations in cross sections of pig skin, and visualizing flow properties of an iodine-releasing coating at skin surfaces.
Biological samples were analyzed with the Philips XL30 SEM integrated EDAX systems using peak identification and digital color mapping software packages. Iodine-releasing coatings were applied to pig skin explants and processed by freeze-drying. The stratum corneum and hair follicle regions of pig skin remained undistorted and identifiable after dissection and processing. Iodine was detected in the coating, in the stratum corneum, and in the tissue surrounding hair follicles (Fig. 1).