bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Procedure For Detecting Scrapie-Associated Fibrils In Chronic Wasting Disease Of Elk And Mule Deer
Authors: Hearne CE , Clapper JL , DeVries KL , Williams ES 
Published: July 2020

Abstract
Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy (TSE) of mule deer and elk. Affected animals are characterized clinically by a combination of abnormal behavior and gradual loss of body condition. The disease is invariably fatal. Diagnosis of CWD is made by histologic examination of the central nervous system and microscopic lesions of CWD are typical of the TSEs. Brains from CWD-suspect elk and mule deer can be examined by transmission electron microscopy (TEM) for the presence of scrapie-associated fibrils (SAF). Western blot methods identify abnormal prion protein (PrPres) which accumulates in the brains of animals with TSE, including CWD.
Conventional SAF purification procedures for TEM examination of CWD-suspect brain tissue require both high speed and ultracentrifugation steps followed by Proteinase K enzyme treatment. Modifications used in this experiment include early Proteinase K, or Proteinase K and Collagenase treatment prior to high speed centrifugation and the elimination of the ultracentrifugation step.
Glucose-6-Sulfate Is A Negative Stain/Sustain
Authors: Massover W H 
Published: July 2020

Abstract
It is increasingly suspected that negative staining should be capable of imaging protein structure at much higher resolution levels than are usually achieved. The heavy metal salts traditionally used as negative stains give structural information only to 20-25Å (2.0-2.5nm); this limit probably is caused by several defective properties of these compounds. If new reagents without these defects can be identified, then higher resolution details should be imaged. The finding that some light atom salts can be used successfully for negative staining greatly increases the range of candidate compounds available for evaluation.
A covalently modified monosaccharide, glucose-6-phosphate, recently was shown to function as an unconventional negative stain. This natural organic reagent directly combines the desirable structurepreserving actions of glucose with added scattering from phosphorus and potassium atoms. It is not known if sugar derivatives containing other light atoms in place of phosphorus can serve as a negative stain.
Age-Related Changes In Acetylcholinesterase Activity In The Efferent System Of The Cochlea Of C57bl/6 Mice
Authors: Cohen Glenn M , Shah Bela A 
Published: July 2020

Abstract
C57BL/6 mice, along with other mouse genotypes, have served as models of human presbycusis. C57BL/6 mice suffer from progressively severe hearing impairments, attributable primarily to losses of both hair cells (sensory receptors) and spiral ganglion cells (afferent neurons). Their age-related hair cell degeneration in the cochlea begins in the basal turn and progresses to the apex.
Auditory nerves also undergo age-related changes. The mammalian cochlear nerve is mixed, being composed largely of afferent (sensory) fibers and a small population of efferent fibers. Because efferent nerves are primarily cholinergic, we used acetylcholinesterase (AChE) as a marker enzyme for determining both age-related changes in AChE activity of the efferent fibers and also for tracing degenerative patterns in efferent pathways within the organ of Corti.
Twelve C57BL/6 mice of the following ages were used: four young (23 days), four middle-aged (13 months), and four old (22.5 months) mice.
Utility Of Secondary Guard Hairs In Animal Hair Identification
Authors: Yates B C 
Published: July 2020

Abstract
Variability among hairs of humans is dependent on body source and ethnicity. Variability in the hairs of non-human mammals is also dependent on somatic source, but may exhibit a wide range of characteristics among hairs from any given site. Humans do not have secondary guard hairs as defined below, but forensic scientists involved in trace analysis must recognize a different suite of variability that exists when examining animal hairs. Hairs other than primary guard hairs from the dorsum, which are often the only representative hairs illustrated in animal hair atlases, may be present as trace evidence in a forensic case in which the origin of the hair is unknown. An overview of the different grades of animal hair that could be present in a forensic case or natural history inquiry places the secondary, tertiary, etc. guard hairs in a continuum that is based on relative diameters.
Typical Application In A Metallurgical Failure Analysis Laboratory
Authors: P.E. Bruce LWong 
Published: July 2020

Abstract
Metallurgical failure analysis is generally straight forward in many cases. However, there are times when it is difficult to really discern the fracture characteristics due to surface degradation, improper handling, or subsequent mechanical damage from improper planning.
Dr. Alan Tettleman, a founder of Failure Analysis and Associates, in San Jose, CA, once told me you can not properly conduct any product failure analysis without metallography, and especially without scanning electron microscopy. In many ways, I agree with him. There are obvious times, however, when various physical properties and deformations are apparent. Those are generally when a consultant is not required. As in your field, there are many references that assist the usage and implementation of the scanning electron microscope and energy dispersive x-ray analysis system. Many of the references introduce the procedure and some of the cautionary steps that should be taken in preparation of samples and in the interpretation of the fracture.
Insights Into The Past: The Use Of Microscopy In The Conservation Of Cultural Materials.
Authors: Claire Dean J 
Published: July 2020

Abstract
Probably an example of every type of material ever manipulated and utilized by man through out history will eventually find its way to a conservator for treatment and preservation. The term “art conservator”, commonly used to describe those that work to protect and preserve the physical remains of mankind's invention and creativity, is a misnomer. We are better described as conservators of cultural materials, as our work involves the preservation of a huge range of materials and artifacts, many of which would not qualify as “art” under its most accepted definition. From the sublime (a Leonardo da Vinci cartoon) to the ridiculous (a 19th century saloon singer's dress made entirely from rattlesnake skins), from the ancient (paleolithic cave paintings) to the new (a pair of Nike® Air Jordans), if they are in a collection somewhere, they are candidates for examination by a conservator.
Despite the variety of materials and artifacts facing us, professional conservators use common approaches to the care of collections and we share the same arsenal of tools.
Mapping Organism Expression Levels at Cellular Resolution in Developing Drosophila
Authors: Knowles David W , Biggin Mark D , Richards Stephen , Sudar Damir 
Published: July 2020

Abstract
Sequence specific transcription factors are the predominant regulators of animal gene expression controlling nearly all biological processes. We are developing novel quantitative optical imaging techniques to map gene expression levels at cellular and sub-cellular resolution within an entire organism. Pregastrula Drosophila embryos have been chosen because these embryos allow high resolution 3D optical imaging since they comprise a single layer of dividing cells surrounding a yolk sac. in addition, the transcription network controlling gene expression is well characterized in early Drosophila embryos[1], and is being further dissected by a multi-laboratory collaboration, the Berkeley Collaboration in Drosophila Genomics, which encompasses this work.
Embryos at different stages of development are labeled for total DNA and specific gene products using different fluorophors and imaged in 3D with confocal microscopy (Figure 1). Intensity-based segmentation of the total DNA image[2] produces a nuclear mask which defines the nuclear boundaries, their location and the number of cells within the embryo (Figure 2). Presently, dilation of the nuclear volumes into their nearest-neighbours[3] is used to estimate the boundary of the cell (Figure 3) and superposition of these images produces a morphological mask defining each cell and its nucleus.
Enzyme-Dependant Fluorescence Recovery After Photobleaching (ED-FRAP): Application to Imaging Dehydrogenase Activity in Living Single Cells
Authors: Combs Christian A , Balaban Robert S 
Published: July 2020

Abstract
Fluorescent recovery from photobleaching coupled with confocal microscopy was explored as a potential high-resolution method of imaging the distribution of enzyme activity in single living cardiac myocytes without relying on steady state measurements of fluorescence. On a fundamental level, much remains to be determined regarding how local conditions within a cell affect metabolism. Many studies have suggested that energy metabolism in muscle cells cannot be accurately described assuming a homogenous system of enzymatic reactions [1,2]. The autofluorescence of NADH has been used in many studies as a quantitative assay of mitochondrial energy metabolism [3,4], but studies of steady state fluorescence cannot distinguish between changes in energy production or utilization.
In this study conditions were created where the fluorescent recovery of a probe would be solely dependent on cellular enzymatic activity (Enzyme Dependent Fluorescence Recovery after Photobleaching (ED-FRAP)). Experiments examining the inherent fluorescence of NADH (351nm excitation, 450 nm emission) were conducted on small droplets (less than 325 μm diameter) containing NADH alone, in droplets containing an enzyme system capable of synthesis of NADH (Figure 1A) and on isolated rabbit cardiac myocytes (Figure 1D). Photobleaching of the entire cell or droplet eliminated diffusion or bulk transport of NADH from non-bleached regions. Droplets containing NADH alone did not recover, while droplets containing enzyme were shown to recover exponentially (Figure 1B) with a rate constant of fluorescent recovery (kf) that was proportional to enzyme concentration (Figure 1C).
Unfolding Single RNA Molecules with Optical Tweezers
Authors: Bustamante Carlos , Liphardt Jan , Onoa Bibiana , Smith Steven B , Collin Delphine , Tinoco Ignacio 
Published: July 2020

Abstract
RNA molecules must fold into specific three-dimensional shapes to perform their structural and catalytic functions. Unlike proteins, RNAs secondary structural features are usually stable enough to form by themselves in solution. The reason is that in RNA, the stabilization energy gained from the formation of secondary structure is substantially larger than the energies involved in tertiary interactions. As a result, the formation of tertiary interactions is expected to alter only slightly the pre-existing secondary structural contacts. Moreover, secondary structure prediction is robust and can be made without taking into consideration tertiary folding. However, bulk studies of the energetics and kinetics of their secondary and tertiary folding are often frustrated by the presence of multiple species and multiple folding pathways in solution. These problems are circumvented in single-molecule studies in which the folding/unfolding trajectories of the individual molecules can be followed. The T. thermophila group I intron ribozyme is organized into several domains whose mechanical unfolding can be investigated independently, and whose tertiary contacts are stabilized by numerous Mg++ ions.
We have begun characterization of the ribozyme by analysis of the P5abc domain because:
Probing Single Molecules in Single Living Cells
Authors: Byassee Tyler A , Chan Warren C W , Nie Shuming 
Published: July 2020

Abstract
Direct observation of single molecules and single molecular events inside living cells could dramatically improve our understanding of basic cellular processes (e.g., signal transduction and gene transcription) as well as improving our knowledge on the intracellular transport and fate of therapeutic agents (e.g., antisense RNA and gene therapy vectors). However, a key remaining question is whether single-molecule methodologies could be developed to study complex molecular processes in living cells. in contrast to clean and well-controlled conditions in-vitro, the intracellular environment contains a broad collection of biological macromolecules and fluorescent materials such as porphyrins and flavins. This complex environment is known to produce intense background fluorescence, commonly known as autofluorescence. Thus, a major concern is that this intracellular background could overwhelm the relatively weak signals arising from single molecules.
We demonstrate that fluorescence detection of single molecules can be achieved by tightly focusing a laser beam into a living cell (see Figure 1). The observed background fluorescence is indeed higher than that in-vitro (e.g., pure biological buffer), but this background is continuous and stable, and does not significantly interfere with the measurement of single-molecule photon bursts. Specifically, we report single-molecule results on three types of extrinsic fluorescent molecules in cultured human HeLa cells (a cervical cancer cell line).
Study of Ultrastructure and Permeability of Brain Cortex Vascular Endothelium in Rats under Rhythmic Cooling
Authors: A.S. Kaprelyants , L.M. Marchenko , R.K. Migunova 
Published: July 2020

Abstract
Cooling significantly affects cellular ultrastructure [1], as well as structural and functional state of histohematic barrier [2]. The aim of the given work was to study ultrastructural mechanisms of the permeability of brain cortex vascular endothelium under the effect of rhythmic hypothermia. Experiments were conducted on 180-220 g white males rats. Cooling of caudal part of animals was conducted in an automatic regimen by an ice water with 0.1 Hz frequency during 40 and 80 min. Experimental animals were narcotized by intraperitoneal injection of thiopenthal sodium and sodium hydroxybutyrate mixture in respect of 30mg/kg, 100 mg/kg of mass, correspondingly. Material from parietal lobe of brain cortex for electron-microscopic investigations was taken immediately after the effect finishing. Rectal temperature, which made 36-35C, was measured during the experiment. For electron microscopic investigations the samples were fixed by immerging into 4% glutar aldehyde on a phosphate buffer and were additionally fixed by 1% osmium fixative on a phosphate buffer. After dehydration in ethanol, samples were placed into the mixture of epoxy resins Epon-Araldit (Fluka, Sweden). Colloid carbon was used as a tracer for the estimation of permeability of brain capillary endothelium. with this aim 3-5 ml of 10% colloid carbon solution, prepared on 0,85% NaCl solution, were injected into a tail vein of the animals immediately after their decapitation. Preliminary estimation of the material quality was done on semi-fine tissue sections after the staining by toluidine blue.
Increased DNA Damage and Decreased H-MYH Protein Expression in Human Myocardium with End-Stage Congestive Heart Failure
Authors: Lin R , Dong Y , Conte JV , Lu-Chang A-L , Wei C 
Published: July 2020

Abstract
The reactive oxygen species (ROS) such as superoxide radical (O2), hydrogen peroxide (H2O2), and hydroxyl radical (OH), plays a critical role in the pathogenesis of hypertension, atherosclerosis, ischemia-reperfusion injury, stroke, myocardial infarction, and congestive heart failure. A recent study demonstrated that the frequency of mutation in a reporter gene increased in cortical DNA after forebrain ischemia-reperfusion. Eight DNA lesions that are characteristic of DNA damage mediated by free radicals were detected. Among the different oxidative-damage DNA products, 8-oXo-7,8-dihydrodeoxyguanine (8-oxoG) is the most stable and deleterious adduct. Recent studies demonstrated that human MutY homologue (hMYH) protein plays important role in repairing oxidative damage. to date, there is no information regarding the role of hMYH expression in human myocardium with congestive heart failure (CHF). Therefore, the current study designed to investigate the levels of hMYH expression and 8-oxoG in myocardium in the absence or presence of end-stage congestive heart failure. The hypothesis of this study is that increasing DNA damage such as 8-oxoG generation is associated with a reduction of hMYH expression in human myocardium with congestive heart failure.
Observation of the Internal Structure of a Biological Sample using a Fluoresence Type 3-Dimensional Internal Structure Microscope
Authors: YOKOTA Hideo , NAKAMURA Sakiko , MAKTNOUCHI Akitake , HIGUCHI Toshiro 
Published: July 2020

Abstract
We developed a new type 3-Dimensional Internal Structure Microscope (3D-ISM) for the observation of internal structures of samples. The internal structure of a sample is obtained by cutting it into thin slices and observing the cutting side continuously while cutting. The position of the camera, as well as the sample position are fixed. Therefore there is no shift between the sections, and this system can obtain a true color image of the sample, which is a high resolution and a high-quality three-dimensional image compared with X-ray CT and MRI. After repeatedly slicing a sample, the digital image data from the sectional views is transferred to a computer, where 3-dimensional images of the internal structure of the sample are reconstructed. Using this system we analyzed many biological organisms. Just now, we are developing the system which builds in a fluorescent microscope. in this paper, We therefore observed fluorescent-stained samples by a fluorescence microscope installed in the 3D-ISM instrument are shown.
This article presents the outline of the device and the principle of the observation. This system, consisting of a slicing device, reflecting optical microscope, a CCD camera, a laser video recorder, a PC-based control system and an image processing workstation. FIG. 1 shows a schematic view of the cross secsional machine. Before slicing, the sample is embedded into either paraffin or OCT compound. Subsequently, the sample is positioned into a cross-sectioning machine for the slicing operation, which is performed using a cutting blade. The maximum size of the sample which can be observed with this device is ϕ 8x10mm. The thickness of the slices can be adjusted mechanically between 0.5-10 μ m. The cutting speed can range from 0.5 to 4 slices/ s. Each cross-section is viewed by employing a epi-fluoresence microscope and a CCD camera. The object lens used for the observation can use the x2-80. The resulting image is recorded on a laser video disc. After the slicing operation, the 3D sample image is reconstructed on the basis of volume rendering by using a Workstation. These observations can be completely done by full automation.
3D Visualization of Maize Stem by MRI Technology
Authors: Cheng P C , Chen J H , Hwang S C , Sun C K , Walden D B , Cheng W Y 
Published: July 2020

Abstract
Recent development in confocal and multi-photon microscopy allows 3D imaging of plant tissue in high resolution. However, other than physical sectioning, macroscopical study of plant organs in 3D remains a difficult task. Among various available technologies for macroscopical imaging (e.g., Xray macro-tomography, optical coherent tomography and MRI), MRI is an ideal choice for its contrasting modality in volumetric imaging of soft tissues. A 3T Biospect MRI system (Brucker, Germany)(FIG 1) equipped with a 6cm inner diameter micro-quadrature coil (FIG 2) for RF transmission and reception of MRI signals was used in this study. Spin echo based RARE sequence was used to obtain T2 weighted images with TR/TE = 3160.5/58.5ms and field-of-view of 1.67cm × 1.67cm (256 × 256 pixels) at a slice thickness of 0.8mm. This corresponds to a voxel size of 65 × 65 × 800μm. Data was obtained within 1/2 hour with number-of-excitations (nex) set at 16. Figure 4 (a-x) shows a series of MRI sections through a stem node (the node below the main ear insertion) from field-grown maize (Zea mays, van Odyssey sweet corn). The stem was fixed in 1:3 EtOH/acetic acid, washed thoroughly in water prior to imaging. Air bubbles trapped in the tissue were removed by vacuuming, to avoid imaging artifact due to low magnetic susceptibility of air. Figure 5 (a-g) shows reconstructed longitudinal sections. Three-dimensional reconstruction (FIG. 3) was performed by using Vaytek VoxBlast™ and AutoQuant’s AutoVisulize 3D™ software. in combination with image segmentation and tracing tools, the MRI technology will greatly enhance our capability in the understanding of vascular architecture and its development in plants.
Electron Tomography of Corneal Collagen Fibrils
Authors: Gilpin C J , Holmes DF , Ziese U , Koster AJ , Kadler KE 
Published: July 2020

Abstract
The ability of cornea to transmit light whilst being mechanically resilient is directly attributable to the formation of an extracellular matrix containing orthogonally arranged sheets of densely packed uniformly-narrow collagen fibrils, in which each sheet contains parallel arrays of fibrils. An understanding of the molecular basis of tissue organisation requires knowledge of the detailed 3-dimensional structure of individual collagen fibrils and how they interact to generate higher order structures. in this study adult bovine corneal collagen fibrils were examined using transmission electron microscopy and automated electron tomography to generate three-dimensional volumes of individual fibrils which had been negatively stained. Tilt series images were collected with an angular increment of 2° over a range of ± 70° using a Philips CM200FEG coupled to a TVIPS automated electron tomography system. A microfibrillar substructure was observed throughout the thickness of the fibril (Figure 1). The microfibrils were ∼4 nm in diameter and were oriented in a right-handed helical twist along the length of fibrils. The microfibrils were observed at an angle of 15° to the long axis of the fibril. As the technique of electron tomography generates a threedimensional volume from the data it was possible, for the first time, to visualise the lateral arrangement of molecules within individual fibrils. There were regions where there was a distinct lateral order and other regions which showed a more fluid-like arrangement. The axial positions of most crystallinity corresponded with the location of the C-telopeptides and N-telopeptides as well as a region close to the d-band in the gap structure of the fibrils. The study also demonstrated that the microfibrils are organised in a quasi-hexagonal packing arrangement
Multiscale Microscopies in the Design and Fabrication of Novel Nanocomposites
Authors: Eppell SJ , Tong W 
Published: July 2020

Abstract
The smallest apatite mineralites found in nature reside in vertebrate bone tissue. These nanoapatites participate in the formation of a protein/mineral composite with unique physical and biological properties. The composite has distinct structural features at the 10 nm, 100 nm, 1 um, 100 um, and 1 cm length scales. We analyzed the natural material on the 1-1000 nm length scale with the purpose of setting the design criteria for synthetically duplicating the material. Using a biomimetic motif, we synthesized nanomineralites with size and shape approximately equal to the natural material.
We show that our synthetic mineralites compare with the natural apatites. Recently the average size of naturally occurring mineralites in mature bovine bone was shown to be 12 nm X 10 nm X 0.61 nm. Similar experiments on 1-3 week old bovine bone mineralites showed an average size of9nm X 6nm X 2.0 nm. Within a standard deviation, the length and width of the two populations are equal.