bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microscopic Evidence Of Biofilm Formation In The Gut Of Two Pest Tephritidae
Authors: Potter SE , Lauzon CR , Smith NR 
Published: July 2020

Abstract
Tephritidae are the true fruit flies, which include the Mediterranean fruit fly, Ceratitis capitata (Wiedemann), the walnut husk fly, Rhagoletis completa Cresson, the Mexican fruit fly, Anastrepha ludens (Loew), and the apple maggot fly, Rhagoletis pomonella (Walsh). Fruit fly infestation causes major damage to many economically-important food crops and is of major concern in agriculture worldwide.
Tephritidae are controlled primarily by repeated applications of organophosphate pesticides. Health concerns, environmental pollution, and costs associated with pesticide use press researchers to find new methods for control. One approach to finding new control methods involves investigating the associations that exist between tephritids and microorganisms. Currently, bacterial odors are being used to lure these pest tephritids into traps. These flies are specifically attracted to odors from certain bacteria found to inhabit their gut. Data suggest that these bacteria are likely involved in important aspects of fruit fly nutrition and reproduction.
Effectiveness Of Immunolabeling Gfap For Estimating Astrocytic Shape And Volume
Authors: Bushong E , Martone M E , Foster C , Ellisman M H 
Published: July 2020

Abstract
Each astrocyte forms an extensive network of fine processes within the surrounding neural tissue, interacting extensively with neighboring neurons and blood vessels. Fine glial processes surround synapses and probably modulate synaptic transmission. Glial endfeet on capillaries are responsible for transport of ions and metabolites and possibly control blood flow. Alterations in these fine structures may be of significance in brain function and disease. Glial fibrillary acidic protein (GFAP) is an intermediate filament found in astrocytes of the central nervous system. GFAP is commonly found in the perikarya and processes of protoplasmic and fibrous type astrocytes. Immunohistochemical labeling of GFAP is extensively used as a means of determining the location and shape of astrocytes. However, its labeling pattern varies with brain region (e.g. cortex vs. hippocampus), with cell state (natural vs. reactive astrocytes), and with the specific α- GFAP antibody used. Furthermore, Golgi-stained or dye-filled astrocytes show numerous small appendages or vellate structures that conform to the surrounding tissue and do not stain for GFAP.
Wax Particle Morphology And Ultrastructure Of Two Species Of Adult Insects: Prey And Predator
Authors: Freeman T , Nelson D , Buckner J , Jackson G 
Published: July 2020

Abstract
Some insects cover themselves with waxy particles including all parts of their body except the eyes. Two examples of insects that produce waxy particles from specialized glands on their abdominal surfaces are the adult stages of the silverleaf whitefly (Bemisia argentifolii) and one of its predators, the dusty wing (Semidalis flinti). In both species, the production of the waxy particles begins at adult eclosion. The silverleaf whitefly, a major plant pest, produces ribbons of waxy material that extrude from the numerous microtrichia that cover the surface of abdominal wax plates. Silverleaf whitefly males have 4 pair of wax plates and females have 2 pair. The adults use their tibia to break off the extruding ribbons, forming semicircular waxy particles about 1 micrometer in diameter. The semicircular waxy particles are composed of a mixture of long-chain aldehydes and alcohols, 34 carbons in length.
For the dustywing predator, the particles are formed by wax producing pores that cover most abdominal surfaces of the adults.
Uses Of Microscopy In The Crime Lab
Authors: Mc Adam T 
Published: July 2020

Abstract
Recent celebrated criminal cases have raised the public's awareness of forensic science. The advent of DNA technology, in particular, has led to a perception of instrumental techniques that lead to a mathematical probability of guilt that approaches certainty. Mostly passed over in press accounts of forensic operations is the use of the microscope in the examination of physical evidence. By the use of an example from an adjudicated criminal case it is hoped that a greater appreciation is gained of the microscope, that in its various forms, is by far the most widely used instrument in a crime laboratory today.
A middle-aged woman was reported missing by her son after the Memorial Day weekend in 1997. An examination of her apartment by members of the Washington State Patrol Crime Scene Response Team revealed a small amount of blood on her bedding. This bedding, together with other items, was taken into evidence.
Detecting And Optimizing Fluorescence Signals
Authors: Metcalfe Walter K 
Published: July 2020

Abstract
Classical fluorphores have been widely utilized in biological research, and have been extensively modified to promote particular qualities. Here we review practical methods of optimizing fluorescence signals for microscopy, discuss experimental solutions to common laboratory applications of fluorescent probes, and describe advantages of the sulfonated rhodamines.
Fluorescence output of dyes The usefulness of a fluorescent probe depends critically on how bright it is and on its ability to resist photobleaching.
The brightness of a dye depends on two factors: first, its efficiency in capturing excitation photons, called the molar extinction coefficient, and second, on the number of photons emitted for each photon absorbed, called the quantum yield. The product of these two factors describes the brightness of a dye. Both the molar extinction coefficient and the quantum yield are constants under specific environmental conditions. Consequently, this is a measure that is useful to compare the brightness of dyes.
Factors Which Influence The Development And Success Of An Academic Electron Microscope Facility: A Case Study
Authors: Wheatley J C 
Published: July 2020

Abstract
There are many electron microscope centers around the world and it is well recognized that there is no single “right” way to develop successful research and teaching electron microscope organizations.
The model for this discussion is that of the Center for High Resolution Electron Microscopy (CHREM) at Arizona State University. Several factors, including but not limited to those discussed below, have contributed to the continuing growth and development of this Center.
The Center serves students and faculty from eight separate academic units. It is also accessible to a significant number of microscope users from outside the university. These include researchers from industry as well as other academic institutions. The number of active instrument users typically averages eighty per year. There are ten instruments available to those who successfully complete the requirements for microscope use. It is not necessary to discuss the physical plant which houses the Center's instruments. Although very important, this topic has been adequately discussed elsewhere by experienced researchers.
Atomic Resolution Electronic Structure in Device Development
Authors: Batson PE , Domenicucci AG , Lemoine E 
Published: July 2020

Abstract
Recently, we have seen that the STEM can produce 0.12-0.26nm atomic resolution image detail in Annular Dark Field (ADF) mode even at modest acceleration voltages and in partnership with EELS for bonding studies. In the semi-conductor field, we are in a good position to take advantage of this imaging capability, because several atomic plane spacings range from 0.14 - 0.26 nm in the [100], [011] and [111] projections of Si and Ge. Figure 1. shows a result for the Si [111] projection obtained in the IBM VG Microscopes HB501UX, modified to produce a 0.19nm probe at 120KeV. The image has been filtered to remove spatial distances shorter than 0.15 nm, yielding the inset power spectrum. Each bright spot in the image corresponds to a single atomic column, separated from its neighbors by 0.19 nm. At 20Mx, the atom columns show enough contrast on the screen to allow astigmatism correction. These are similar to those discussed previously.
Digitally Enhanced, Polarization-Based Microscopy: Reality and Dreams
Authors: Inoué Shinya 
Published: July 2020

Abstract
Polarized light microscopy is used to identify and image optically anisotropic regions of the specimen; to determine their optical character; and to explore the arrangement of the molecules, fine structure, or atomic lattices that are responsible for the anisotropy. These studies can be carried out non-destructively in real time, and reveal events or structures that lie far below the resolution limit of the light microscope, or indeed at times even the electron microscope.
In biology, to study the dynamically changing, minute and weakly anisotropic domains within living cells, the polarizing microscope must be able to detect and measure birefringence retardances to a fraction of a nm, record the image with high microscopic resolution at nearvideo rate, and do so while the cell remains active.
Over the years, the extinction property and imaging capability of the basic polarizing microscope have been substantially improved by advances in optical design. More recently, video and CCD imaging and digital electronic processing have further enhanced the quality of the polarizing microscope image and our ability to rapidly detect and measure weak anisotropy.
Spectral Imaging for Separation of Fluorescent Signals from Autofluorescence
Authors: Levenson Richard M 
Published: July 2020

Abstract
Autofluorescence, also known as adventitious fluorescence or background fluorescence, often poses a significant problem in many applications of fluorescence microscopy. It contributes to unwanted noise and can overwhelm the desired signal. Particularly difficult samples to image include many pathology specimens that have been processed using crosslinking fixatives (typically formaldehyde). This procedure dramatically increase the autofluorescence level, leading to bright, broad spectrum emissions, particularly from connective tissue components. Unprocessed plant tissue and neuronal tissue also have extremely high levels of endogenous autofluorescence that can make many convenient labeling strategies, including most green fluorescent protein (GFP) labels, extremely problematic. Various solutions have been proposed for the reduction or elimination of autofluorescence. These include using narrow bandpass emission filters to try to isolate the desired fluorescence signal, the use of labels that can be excited at wavelengths that are much less likely to induce autofluorescence (moving the excitation towards the NIR is effective), and post-processing aldehyde-fixed samples with such reagents as sodium borohydride or toluidine blue to chemically suppress the autofluorescence signal. However, in many cases, these approaches are either infeasible or ineffective. Spectral imaging, that is, the acquisition of a high-resolution optical spectrum at every pixel of an image, offers another approach to elimination of the contribution of autofluorescence. This has recently become possible due to the development of a number of technologies that allow the collection of spectral datasets from fluorescently labeled samples using fluorescence microscopy. Such technologies include liquid crystal tunable filters (LCTFs) and Fourier transform imaging spectrometers, both of which are now commercially available.
High Performance Hyperspectral Imager for Microimaging
Authors: Malak Henryk , Herman Petr , Moore Wayne , Vecer Jaroslav 
Published: July 2020

Abstract
A high performance hyperspectral imager with high light throughput suitable for microscopy and analytical imaging was built and tested. The imager utilizes phenomenon of optical activity. The new technique provides a continuous spectral range of several hundreds of nanometers starting in deep UV. Similar spectral range starting in the near IR is also achievable.
A performance of a low cost implementation of the new technology is presented. The imager has a form of a microscope adaptor, which is inserted between the microscope and a low-cost 8-bit CCD camera. The resulting instrument is simple, robust, and highly compact. The imager module is placed in-line to the microscope imaging system and does not introduce observable image aberrations. Advantageously, the imager is transparent to conventional imaging operations, thus with the imager in-place there is no need for reconfiguration of the microscope to switch between conventional and hyperspectral video/digital imaging modes.
The presented spectral imager answers the need for a practical, sensitive, compact, and affordable imaging spectrometer. The instrument is well suited for a broad range of applications requiring rapid parallel acquisition of highly resolved concurrent spatial and spectral information such as high throughput screening, biochip analysis, remote sensing or nondestructive semiconductor testing.
Mammalian Apoptosis in Whole Neonatal Ovaries using Confocal Laser Scanning Microscopy
Authors: Zucker Robert M , Jeffery Susan C , Perreault Sally D 
Published: July 2020

Abstract
Confocal Laser Scanning Microscopy (CLSM) is being used to visualize folliculogenesis and presumed apoptotic events in whole neonatal mouse/rat ovaries. Our laboratory has previously demonstrated that apoptosis can be visualized in 8-9 day whole mouse embryos, 12 day fetal mouse eyes or 12-15 fetal rat limbs stained with the fluorescent lysosomal stain, LysoTracker Red (LT). The observed LT staining has been correlated with Nile blue staining (lysosomes and phagocytosis), TUNEL staining (DNA breaks) and apoptotic tissue morphology in rat and mouse developmental systems. This increased LT staining intensity appeared to be associated with acidic tissue, lysosomes, phagocytosis and dying cells. Here we describe recent progress using LT to evaluate the apoptotic process in whole ovaries. We are currently optimizing sample preparation and confocal machine operation to improve the image quality. to increase depth of visualization, ovaries derived from 10-45 day old mice/rats are fixed with an aldehyde and then made transparent by MEOH dehydration followed by benzyl alcohol/benzyl aldehyde (BABB) clearing. Such whole ovaries or tissue sections are viewed by CLSM using 568-wavelength laser light to obtain images of oocytes and follicles. Follicles showing gross morphologic changes typical of atresia were also characterized by intense LT staining of granulosa cells. This increased LT staining intensity appeared to be associated with acidic tissue and dying cells contained within the follicle.
Spectral Imaging: Fluorescence and Brightfield
Authors: Levenson Richard 
Published: July 2020

Abstract
Spectral imaging is a relatively new technique that provides images of a scene at multiple wavelengths and can generate precise optical spectra at every pixel. Mathematical approaches may then be used to extract the maximum information from the spectral image. Spectral imaging is routinely used in “remote sensing”, that is, the analysis of distant landscapes and structures from airplanes or satellites. Minor differences in spectra can be used to detect different crops, or mineral deposits, for example. Closer in, spectral imaging has uses in industrial process control, detection of otherwise invisible bruising in fruit, vascular integrity in transplanted organs, and so on. Finally, spectral imaging has newly been adapted for easy use in microscopy, with applications in surgical pathology, multicolor fluorescence and immunohistochemistry, and in DNA expression arrays, among others. A variety of technologies can be used to perform imaging spectroscopy, including Fourier transform interferometry, tunable filters, line-scanning prism or gratings-based devices, and others based on polarization effects. Recently, CRI has developed a novel approach for brightfield microscopy which uses a spectrally agile light source. The latter has a number of advantages over previous techniques.
A Close-To-Native System to Study Membrane Protein Dynamics by Single-Molecule Optical Microscopy: an Application to Bacteriorhodopsin
Authors: Kahya Nicoletta , Pécheur Eve I , Wiersma Douwe A , Hoekstra Dick 
Published: July 2020

Abstract
Biological membranes are not just a passive component of the cells, they actively support their functioning as the imbedded protein machineries carry out a wide range of crucial biochemical processes. Although studies in vivo are becoming more and more accessible to single-molecule optical microscopy, in vitro studies are still very much informative for the understanding of individual biological machineries. One of the major goals is to define the minimum number of components of a machinery that is necessary for a particular step, thereby allowing detailed studies of the mechanism of action. Reconstitution of a transmembrane protein system in artificial membranes (liposomes) is the main method for such a strategy, which thus may provide the option to investigate the functioning of transport proteins, ion channels, fusion machineries, and signal transducers in relation to their environment.
We present a novel procedure in order to reconstitute transmembrane proteins in chemically well-defined and close-to-native lipid bilayers, providing an in vitro system for single-molecule optical microscopy. Furthermore, an application of this technique is shown in the case of a single-molecule study of protein-protein and protein-lipid interactions for the light-induced proton pump bacteriorhodopsin.
In this study, Giant Unilamellar Vesicles (GUV), 10-100 μm sized, are used as lipid bilayer models for several reasons.
Application of Novel Laser Capture Microdissection and RT-PCR to a Functional Analysis of Osteopontin in Mouse Growth Plate Cartilage
Authors: Jacquet R , Hillyer J , Zhang J , Landis W J 
Published: July 2020

Abstract
The long bones of vertebrates, such as the tibiae and femurs of humans, extend in length by means of genotypic and phenotypic changes orchestrated by the chondrocytes comprising growth plate cartilage. Among the constituents synthesized by these cartilage cells, osteopontin (OPN), a phosphorylated glycoprotein, is thought to play a critical role in events leading to normal growth plate function and ultimate mineralization of the deeper zones of this cartilage region. The precise role of OPN, however, is uncertain with regard to mineralization, and present evidence supports the alternative possibilities that the protein may be either facilitative or inhibitory to mineral deposition. in order to investigate OPN function in a model growth plate, cartilage from normal 1-11 day old postnatal mice was examined by the novel techique of laser capture microdissection (LCM) followed by RT-PCR to obtain a measure of OPN gene expression by chondrocytes of known age and specific location in the plate. LCM permits identification of individual or clusters of cells within a tissue section and subsequent unique isolation (“capture”) of such cells for a variety of molecular analyses.
In this study, mouse tibiae were dissected, placed in RNAlater (Ambion, Austin, TX) to preserve message, and stored at −20°C. Sections (5 μm thick) of fresh frozen developing epiphyseal growth plates were obtained in a cryostat maintained at −20°C, fixed briefly in 70% ethanol, and stained with eosin. Sections were examined in a Pixcell LCM system (Arcturus Engineering, Mountain View, CA) where chondrocytes were attached to the surface of polymer film substrates and lifted free of sections. in separate experiments, ∼200-1200 cells were captured and analyzed. Substrates were transferred to Eppendorf tubes containing RNA extraction buffer. RNA was extracted from cells by microisolation (Stratagene, La Jolla, CA), DNAse-treated, reverse-transcribed, and then subjected to PCR (40 cycles) with AmpliTaq DNA polymerase (PE Applied Biosystems, Foster City, CA). Ethidium bromide agarose gels revealed OPN mRNA from groups of chondrocytes isolated from whole cartilage and from resting, proliferating, and hypertrophic growth plate zones from the mouse tibiae. Brain cells captured by LCM from the same mouse sections served as positive controls and reactions containing no reverse transcriptase were negative controls. 18S rRNA was used as a marker for semiquantitation and standardization of expressed message from captured cells.
[URE3] Prion forms Filamentous Networks in Yeast Cytoplasm
Authors: Speransky Vladislav V , Taylor Kimberly L , Edskes Herman K , Wickner Reed B , Steven Alasdair C 
Published: July 2020

Abstract
The concept of prion (infectious protein) originated in studies of transmissible spongioform encephalopathies (TSE) in mammals, but more recently, two nonchromosomal genes of yeast- [PSI] and [URE3] - were identified as prions. While the agents of TSEs kill infected cells and [URE3] or [PSI+] only slow growth at most, these infections are believed to have similar mechanisms, i.e. self-propagating amyloids. TSEs are often associated with amyloid deposition in infected tissues, and both Sup35p and Ure2p have been shown to form amyloid in vitro.
[URE3] is a prion of the Ure2 protein, that normally regulates nitrogen catabolism. Its ‘prion’ domain (residues 1-65) is necessary and sufficient for propagation of the prion, whereas the C-terminal portion (residues 81-354) is sufficient to carry out the nitrogen regulation function. The prion domain peptide spontaneously forms amyloid filaments in vitro. Full-length native Ure2p is a stable soluble dimer, but forms co-filaments when the prion domain peptide is added. This in vitro amyloid formation is highly specific and self-propagating, thus providing a possible explanation for the [URE3] prion. We have sought to clarify this hypothesis by examining the state of Ure2p in [URE3] cells by thin-section electron microscopy.
Yeast cells with the [URE3] prion and control [ure-o] cells were thin-sectioned after fixation and embedding in an epoxy resin. We found distinctive filamentous aggregates in the cytoplasm of [URE3] cells of a strain that overexpresses Ure2p (Fig. 1). These aggregates were seen in some cell profiles represented in 50-70 nm sections, and were never seen in control sections of [ure-o] cells. in cell sections showing these structures, there was typically one such aggregate, which could be quite large - up to several μm across - and approximately globular in outline. They contain irregularly associated filaments about 25 nm in diameter.