bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome sequencing analysis of human bocavirus detected in South Korea
Authors: Kang L. H. , Won Y. J. , Lee A. R. , Lee S. G. , Cho H. G. , Park Y. J. , Han J. I. , Paik S. Y. 
Published: March 2018

AbstractHuman bocaviruses (HBoVs) have been detected in human gastrointestinal infections worldwide. In 2005, HBoV was also discovered in infants and children with infections of the lower respiratory tract. Recently, several genotypes of this parvovirus, including HBoV genotype 2 (HBoV2), genotype 3 (HBoV3) and genotype 4 (HBoV4), were discovered and found to be closely related to HBoV. HBoV2 was first detected in stool samples from children in Pakistan, followed by detection in other countries. HBoV3 was detected in Australia and HBoV4 was identified in stool samples from Nigeria, Tunisia and the USA. Recently, HBoV infection has been on the rise throughout the world, particularly in countries neighbouring South Korea; however, there have been very few studies on Korean strains. In this study, we characterised the whole genome and determined the phylogenetic position of CUK-BC20, a new clinical HBoV strain isolated in South Korea. The CUK-BC20 genome of 5184 nucleotides (nt) contains three open-reading frames (ORFs). The genotype of CUK-BC20 is HBoV2, and 98.77% of its nt sequence is identical with those of other HBoVs, namely Rus-Nsc10-N386. Especially, the ORF3 amino acid sequences from positions 212–213 and 454 corresponding to a variable region (VR)1 and VR5, respectively, showed genotype-specific substitutions that distinguished the four HBoV genotypes. As the first whole-genome sequence analysis of HBoV in South Korea, this information will provide a valuable reference for the detection of recombination, tracking of epidemics and development of diagnosis methods for HBoV.
The Identification of Particles in a Polymer Film Using Nano-Thermal Analysis
Authors: Grandy David , Kjoller Kevin 
Published: March 2018

Abstract
Nano-TA is a local thermal analysis technique that combines the high spatial resolution imaging capabilities of atomic force microscopy (AFM) with the ability to obtain understanding of the thermal behaviour of materials with a spatial resolution of sub-100nm. This breakthrough in spatial resolution of thermal analysis, which is ~50× better than previously reported, has profound implications for the fields of polymers and pharmaceuticals where local thermal understanding is key.
The conventional AFM tip is replaced by a special nano-TA probe that has an embedded miniature heater and is controlled by the specially designed nano-TA hardware and software. The nano-TA probe enables a surface to be visualised at nanoscale resolution using the routine imaging modes of AFM. The user is able to select the spatial locations for the investigation of the thermal properties of the surface. Heat is supplied locally via the probe tip and the thermomechanical response is measured.
Using the PMT in a Laser Scanning Confocal Microscope as a Digital Light Meter to Measure Detection Photon Efficiency
Authors: Pawley Jim 
Published: March 2018

Abstract
If we accept that the optical layouts of single-beam laser scanning confocals are generally quite similar, the most important variable is “Photon Efficiency” (PE): the fraction of photons leaving the focal plane that actually contribute to the number stored in the image memory. Unfortunately, this parameter is a function of a very large number of operator settings, design decisions and optical performance specifications (BioTechniques The 39 Steps; A Cautionary Tale about “quantitative” 3D fluorescence microscopy, April 2000 28:884-7). As a result, although all manufactures claim excellent “Photon Efficiency” none actually provide any specifications. We have to determine the PE ourselves.
Visualisation of Native Surfaces by Two-Step Molding
Authors: Gorb Stanislav N 
Published: March 2018

Abstract
One of the most important tasks of microscopy is to provide information about structures in their natural state. Since most life science microscopy procedures require fixation, dehydration, drying, and sectioning, diverse artefacts are unavoidable. It is also possible to dehydrate the water content of a specimen by freeze-drying. However, even relatively stable surface structures are changed during such treatments. Methods of liquid substitution and freezing-substitution show good results for biological specimens with a waxy solid coverage (Ensikat and Barthlott, 1993) and soft specimens in a mechanically deformed state (Gorb et al., 2000).
However, all these methods have certain restrictions for some types of specimens. For example, there are numerous biological surfaces covered with secretory fluids. Some specimens bear solid waxy coverings, which can be partly dissolved and washed out in organic solvents, such as ethanol, acetone, or propylenoxide. Often one would like to visualise dynamic processes (growth, deformation, or crystallisation) under environmental conditions, but at the high resolution in the SEM.
New Developments in Gemini® Fesem Technology
Authors: Jaksch H , Vermeulen J-P 
Published: March 2018

Abstract
The Field Emission SEM was introduced to improve imaging resolution available with conventional SEMs with a tungsten source. Thermal assisted or Schottky Field Emission SEMs were introduced in s the nineties by a number of companies as a stable source to overcome the beam instability of the cold FESEMs introduced earlier. The Gemini® based Field Emission SEM launched by Zeiss 12 years ago has been designed from the beginning as a high stability FESEM with a relatively large multi-ported chamber. The drive to develop Gemini® technology was the need for a FESEM capable of ultra-high resolution performance over the entire accelerating voltage range that also possessed the flexibility needed for a wide range of analytical applications.
Nondestructive, High-Resolution Materials Characterization with the Confocal Raman-AFM
Authors: Schmidt U , Jauss A , Ibach W , Weishaupt K , Hollricher O 
Published: March 2018

Abstract
Materials research, biomedical research, and semiconductor manufacturing can all benefit from nondestructive, high-resolution methods of analysis. As most materials are heterogeneous, it is important to not only acquire high resolution topographic information, but also to identify the chemical composition of samples. A combination of high resolution microscopy with chemically sensitive spectroscopy combined in one instrument allows the detailed characterization of samples with different analytical techniques. When individual instruments are used, returning to a previously surveyed sample area can be very time consuming if not impossible without surface markers.
How to Promote a Facility in Order to Increase Use, Acquire New Equipment and, as a Result, Increase Revenue
Authors: Humphrey Elaine , Sherman Debby 
Published: March 2018

Abstract
Promoting and maintaining a facility is a major concern to many of us. I had the pleasure last spring of participating in the 2nd International Cryo-workshop held in the Bio-Imaging Facility at the University of British Columbia. I talked to the facility director, Elaine Humphrey, and saw what she has done in a relatively short number of years in building that facility. I was incredibly impressed so I asked Elaine if she would address mis topic.
Elaine started out as a marine biologist in England and came across a problem that required electron microscopy. The first facility she went to was very discouraging saying that it was an extremely difficult technique. She managed to find another facility that made it easy.
Laboratory Design for High-Performance Electron Microscopy
Authors: O'Keefe Michael A , Turner John H , Musante John A , Hetherington Crispin JD , Cullis AG , Carragher Bridget , Jenkins Ron , Milgrim Julie , Milligan Ronald A , Potter Clinton S , Allard Lawrence F , Blom Douglas A , Degenhardt Lynn , Sides William H 
Published: March 2018

Abstract
Since publication of the classic text on the electron microscope laboratory by Anderson, the proliferation of microscopes with field emission guns, imaging filters and hardware spherical aberration correctors (giving higher spatial and energy resolution) has resulted in the need to construct special laboratories. As resolutions iinprovel transmission electron microscopes (TEMs) and scanning transmission electron microscopes (STEMs) become more sensitive to ambient conditions. State-of-the-art electron microscopes require state-of-the-art environments, and this means careful design and implementation of microscope sites, from the microscope room to the building that surrounds it. Laboratories have been constructed to house high-sensitive instruments with resolutions ranging down to sub-Angstrom levels; we present the various design philosophies used for some of these laboratories and our experiences with them. Four facilities are described: the National Center for Electron Microscopy OAM Laboratory at LBNL; the FEGTEM Facility at the University of Sheffield; the Center for Integrative Molecular Biosciences at TSRI; and the Advanced Microscopy Laboratory at ORNL.
TEM Sample Preparation Using Focused Ion Beam - Capabilities And Limits
Authors: Engelmann HJ , Volkmann B , Ritz Y , Saage H , Stegmann H , de Robiliard Q , Zschech E 
Published: March 2018

Abstract
TEM sample preparation using Focused Ion Beam (FIB) methods becomes more and more interesting for microscopists because the technique allows for reliable and very efficient sample preparation. The first application of TEM sample preparation by FIB-cutting was reported more than 10 years ago. Meanwhile, a lot of experience has been gathered that allows one to discuss the capabilities and limits of the FIB technique in detail.
Several TEM sample preparation techniques are known that all include FIB-cutting but differ in sample pre-preparation, sample handling, etc. This paper focuses on the actual FIB process, FIB tools are closely related to Scanning Electron Microscopes, but instead of an electron beam an ion beam (mostly Ga+ ions) is used to remove and deposit material.
How to Recognize and Avoid AFM Image Artifacts
Authors: West Paul , Starostina Natalia 
Published: March 2018

Abstract
Images produced by an atomic forces microscope (AFM) often contain spurious features and image distortion that can render accurate imaging and metrology suspect. These “artifacts” are caused by the manner in which the image is produced. Artifacts can originate from the probe tip geometry, scanner non-linearity, image processing software, vibration, sample contamination, electronic noise, and poor sample stability. This article describes and illustrates common AFM image artifacts and suggests means to eliminate or minimize them.
Microscopy of Silicified Wood
Authors: Mustoe George 
Published: March 2018

Abstract
Ancient forests comprised an enormous biomass and typically flourished in lowland habitats that offered favorable conditions for fossllization, so it is not surprising that petrified wood is the most abundant terrestrial fossil. Petrifaction of wood by carbonates, sulfides, oxides, and phosphates is evidence that fossilization can occur under diverse geochemical conditions, but silicification is by far the most common process.
Microwave Processing in Diagnostic Electron Microscopy
Authors: Gerrity Ross G , Forbes George W 
Published: March 2018

Abstract
Transmission electron microscopy (TEM) continues to play an important role in diagnostic surgical pathology, particularly in such areas as kidney pathology and tumor diagnosis, among others. Diagnostic TEM is subject to unique time constraints, quality control regulations, and other problems not seen in other TEM applications. The diagnostic TEM laboratory must produce high-quality electron microscopy on small samples which frequently are suboptirnal in fixation and tissue quality due to the pathology involved and time factors associated with biopsy and surgery.
Colocalization of Fluorescent Probes Using Image-Pro® Plus v. 5.0
Authors: Casavan Will , Gaidoukevitch Yuri 
Published: March 2018

Abstract
Fluorescence labeling techniques are quite useful to microscopists. Not only can fluorescent probes label sub-cellular structures with a high degree of specificity, they can also do so with a very high degree of sensitivity. This combination of specificity and sensitivity permits observations of cellular events that are not always visible using traditional methodologies, such as brightfield microscopy.
Practical Issues for Quantitative X-ray Microanalysis in SEM at Low kV
Authors: Statham Peter 
Published: March 2018

Abstract
In the three decades following Castaing's seminal thesis [1] x-ray analysis received widespread attention from research groups. By 1980, the methods and correction procedures for quantitative analysis of elements with atomic number 11 and above, using accelerating voltages between 15kV and 25kV, were well established and available in commercial instrumentation. At the time, scanning electron microscopes (SEMs) could rarely deliver high and stable beam current at much lower kV, and x-ray spectrometers had poor efficiency below lkeV so that low kV analysis received comparatively little attention.
Ethics and Digital Imaging
Authors: Mackenzie J M , Burke M G , Carvalho T , Eades A 
Published: March 2018

Abstract
The amazing growth of digital imaging in the past several years has blurred the line between "real" images and those that are digitally enhanced. In most of our movies and print advertisements, we see amazing effects that create images that look real but are not.
For the last several decades film has been the predominant method that scientists employ to record the images viewed through their microscopes. Film has been readily accepted as a valid, archival recording medium because it was difficult to alter once the exposure was made and the film or print developed. The improvements in computer power and image resolution, coupled with environmental considerations, have spurred the scientific community to replace photographic processes with digital images. Processes that took hours and days are now performed in minutes. Imaging programs like Adobe Photoshop can perform all of the same photographic steps that required a darkroom, and then can do much more. The image can be “burned” onto a CD or DVD disk which is difficult to alter. Printer technology has advanced so rapidly that inkjet prints rival photographic prints. Images are often distributed digitally and viewed on displays that continue to improve. As the hardware for digital imaging improves, the quality of digital images is approaching photographic quality for a fraction of the cost, and publication quality images are produced in a fraction of the time required for film-based photography.
Some Considerations for EM Cooling Systems
Authors: Mitchell Allan 
Published: March 2018

Abstract
For numerous reasons a closed-circuit water cooling system is the preferred option for providing cooling water to the electron microscope. Cooling water is required by the electron microscope to cool the diffusion pumps and to keep the electronics' and coiumn temperature stable.
A closed-circuit water cooling system is essential if the local water supply has a high chloride concentration, has floating particles, is acidic, has a water temperature that fluctuates and is uncontrollable. This potentially leads to specimen drift problems in the TEW, and/or has a water temperature that is very cold. This potentially leads to condensation problems or diffusion pumps not functioning properly in the TEM.
X-Ray Analysis in a Vacuum?
Authors: Chernoff Don 
Published: March 2018

Abstract
Performing X-ray analysis on a sample in an SEM used to be relatively straightforward. Straightforward and not always very exciting. Things have gotten a lot more interesting, In jus! the past few years, the amazing development oi variable pressure SEMs has revolutionized the way we can look at samples. At the same time these new machines have changed the way we can image samples, they have also affected how we perform X-ray analysis on those samples.
I apologize in advance for the following gross simplification. For quite a lot of samples, the point and click method of X-ray analysis was and is sufficient to get meaningful data from a sample. Put the beam on a feature, collect a spectrum, and move onto the next sample.
Preparation of Geological and Biological TEM Specimens by Embedding in Sulfur
Authors: Hugo Richard C , Cady Sherry L 
Published: March 2018

Abstract
The technique of embedding TEM specimens in polymer resins for subsequent ultra-thin sectioning is well established. For geological materials, this protocol prevents specimen damage introduced by ion beam thinning, and is often used for preparing friable or porous materials. However, traditional polymer-based embedding resins may introduce organic carbon contaminants, producing artifacts in carbon analyses. Thus, a carbon-free substitute for traditional embedding media is required to ensure accurate carbon analyses of embedded and ultramicrotomed TEM specimens.
A suitable technique that was first reported by Bradley is to embed specimens in pure sultur. In this technique, the specimen is immersed in liquid sulfur, the liquid is solidified, and the resulting block is ultramicrotomed as with traditional resins. Since sulfur has a high vapor pressure at room temperature, the ultra-thin sections are then placed in a separate vacuum chamber to sublimate the sulfur, yielding TEM specimens free of any embedding medium.
Glutaraldehyde Autofluorescence Useful in Confocal Studies of Fungi
Authors: Singh Adya , Xiao Ying , Wakeling Robin 
Published: March 2018

Abstract
In this note we show the potential usefulness of glutaraldehyde (GA) in confocai microscopic studies of wood-fungal interaction. We are presently developing methods to examine by the confocai laser scanning microscope (CLSM), the pattern of distribution of fungal hyphae within wood in relation to fungal degradation and sapstaining of wood. CLSM has the potential to be a very useful tool in such studies for a variety of reasons, including its use for optical sectioning to produce computer assisted 3-D images.
Formaldehyde, Formalin, Paraformaldehyde And Glutaraldehyde: What They Are And What They Do
Authors: Kiernan John A 
Published: March 2018

Abstract
Aldehydes are the most commonly used fixatives. They serve to stabilize the fine structural details of cells and tissues prior to examination by light or electron microscopy. Research workers, technicians, pathologists and others who regularly use aldehyde fixatives frequently do not appreciate the nature and properties of these compounds or the reasons for choosing to fix a specimen in formaldehyde, glutaraldehyde or a mixture of the two. Misconceptions are widespread also about formalin and paraformaldehyde, the commercial products from which formaldehyde-containing solutions are made.
Watching Neurons Hand Off Molecules
Authors: Carmichael Stephen W 
Published: March 2018

Abstract
Since the discovery of nerve growth factor, it has been thought that neurotrophic factors are released or secreted from target cells. However, more recently it has been suggested that a specific neurotrophic factor known as brain-derived neurotrophic factor (BDNF) may reach target cells directly from presynaptic axons. It has not been known how these molecules get from the neuron in which they are produced to the target cells. Keigo Kohara, Akihiko Kitamura, Mieko Morishima, and Tadaharu Tsumoto have demonstrated that BDNF is transported anterogradely from presynaptic neurons to target neurons.
Novel Use of Fluorescence Illumination with an Infrared Microscope
Authors: Tague Thomas J , Miller Lisa M 
Published: March 2018

Abstract
It has become increasingly obvious that infrared microspectroscopy can be the analysis tool of choice when determining the chemical composition of biological and biomedical samples. Frequently, fluorescence illumination is required for sample characterization, which previously required the use of a separate optical microscope. There has also been a need in the semiconductor manufacturing industry for a single tool for visualizing particle contaminants on integrated wafers as well as the ability to chemically determine their nature. There is now a single microscope platform for conducting rapid Nomarski differential interference contrast and fluorescence illumination sample visualization as well as infrared analysis. This novel infrared microscope has applicability to many fields of investigation, including pharmacology, forensics, cell biology, histology, gemology, and geology.
Low Voltage Scanning Electron Microscopy and Jack Ramsey's principle
Authors: Wells Oliver C 
Published: March 2018

Abstract
“Low Voltage Scanning Electron Microscopy (LVSEM), defined as operation in the energy range below 5 keV” was described by David Joy and Dale Newbury (1) in the previous issue of this journal as being “perhaps the most important single operational mode of the SEM.” In their paper they describe both the advantages and disadvantages of this method.
Ramsey's principle, which was established by Jack Ramsey over many years as a microscopist and microanalyst, is to say: “There is no best way of doing ANYTHING.”
Training in Forensic Microscopy
Authors: Chapin William 
Published: March 2018

Abstract
The world of forensic microscopy is complex and challenging. There is a never-ending variety of requested examinations and consequently, the analyst is often asked to work in an area of little familiarity. Adding to the challenge is the inherent problem of having no exact information as to the condition of the sample prior to the crime. The forensic microscopist is expected to have mastered proficiency in polarized light microscopy in order to identify fibers, minerals, insect parts, woods, metals, biological fluids, pollution particles, microchemical techniques, paints, pigments, pollens, drugs, explosives, diatoms, safe insulation, etc. and to compare samples of all the these plus hairs, glass, etc., etc.
Retention of Calcium and Other Ions for Microanalysis by Freeze-Drying
Authors: Ryan Keith P , Berry Lorraine S 
Published: March 2018

Abstract
Calcium (Ca++) and other diffusible ions cannot be preserved for x-ray microanalysis if specimens have been preserved by fixation using formaldehyde, glutaraldehyde or other fixatives. Atoms, such as Ca, are not diffusible when they are bound to something insoluble, such as bone or hard granules in cells which are sometimes mechanisms for detoxifying. Ions, loosely bound elements and other components such as sugars and amino acids are leached out during chemical fixation and dehydration by solvents. This problem was recognized over a hundred years ago by Richard Altmann. An alternative to wet chemical processing is the purely physical method that involves rapidly freezing the specimen and then removing the frozen water by the process of freeze drying, which is the subject of this article.
Optimal Noise Filters in High-Resolution Electron Microscopy
Authors: Ishizuka Kazuo , Eilers Paul H C , Kogure Toshihiro 
Published: March 2018

Abstract
Most of the specimens for high-resolution electron microscopy have amorphous surface layers due to contamination during observation and/or damaged surface layers during specimen preparation. Moreover, many specimens are radiation sensitive, and a part of the specimen easily becomes amorphous during the observation. These amorphous materials make clear observation of crystal structure difficult. A periodic structure may be extracted by simply using a periodic mask in Fourier space. However, this kind of mask often introduces a periodic feature in addition to the crystal structure. To reduce such artifacts a Wiener filter or an average background subtraction filter has been discussed. However, these filters do not work for non-ideal crystals, such as cylindrical crystals and nano-crystals, where a translational periodicity is limited to the order of nano-meter. In this report we improve these filters by introducing new ways to estimate a contribution from the amorphous materials.