bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fluorescent Molecules as Direct and Indirect Labels for in situ Hybridization
Authors: Durrant Ian 
Published: June 2020

In situ hybridization has traditionally been performed with radioactive probes. Over recent years effort has been spent in elucidating non-radioactive alternatives for a variety of molecular biology systems. Non-radioactive in situ hybridization is possible, but to date the systems available have, in general, delivered lower sensitivity and higher backgrounds than traditional methods. We have studied a variety of alternative labelling and detection processes; different systems may be required for different applications.Fluorescein has been developed as a new label for all aspects of non-radioactive in situ hybridization. Separate systems have been investigated for DNA, RNA and oligonucleotide probes (see Figure 1). These probes can be applied to frozen sections, paraffin sections, whole mounts, cells and chromosomes. The standard non-radioactive detection system utilizes alkaline phosphatase as an end point to produce a coloured reaction product precipitated at the point of hybridization. This gives both good resolution and sensitivity. Other options becoming available, based on different enzymes and other formats of detection, include peroxidase and gold in conjunction with colour, chemiluminescence and direct and indirect fluorescence. These alternatives have been investigated using the fluorescein based probe labelling systems.
Monte-Carlo Estimations for the Precision of Iterative Structure Refinement in QHREM
Authors: Möbus G. 
Published: June 2020

1.Introduction:Quantitative high-resolution TEM (QHREM) serves for the determination of structures of crystal defects. The structure retrieval problem is usually considered to be solved when a simulated image calculated from a model structure matches with high quality to the experimental image. Often, however, surprisingly large (and continuous) shifts of individual atomic columns are possible before the simulation looses its similarity to the experiment. Therefore, we propose printing structure retrieval results as “atomic ball pictures” with the radius of the ball as a circle of confidence (replacing the chemical atomic radius otherwise used for these pictures). Statistical methods are necessary to derive the proper radius of the circles which are element and site specific : Monte-Carlo based strategies are highly suitable for this purpose. As a model system we use two bulk sections from a micrograph of a Cu/Sapphire interface (Fig. 1). For interface properties see.
Techniques for quantitative HREM analysis of structure and displacements at interfacial steps, facets and facet junctions
Authors: Dahmen U. , Paciomik S. , Michel D. , Hÿtch M. 
Published: June 2020

Quantitative High Resolution Electron Microscopy (QHREM) has made considerable recent advances in the analysis of localized atomic structure, especially in flat, periodic interfaces. This is largely due to the increased speed and sophistication of computer algorithms that compare experimental and simulated images, and to strategies for refining this comparison. However, defects such as dislocations, disclinations or steps often lead to elastic distortion fields in the experimental image that are not included in the simulations of an idealized interface. In the presence of such defects, it is difficult to separate the short-range atomic structure immediately at the core of the interface from the Ionger-range displacement fields due to steps and dislocations.In this work we describe quantitative techniques to measure atomic structure and displacement fields in these two different regimes, and to refine the structure of the core when defects lead to deviations from ideal periodic conditions. For the regime of the localized structure, we have introduced a template matching technique which measures the precise location and similarity of structural units characteristic for an interface structure. In the regime of longer-range displacement fields, the moiré technique and the closely related geometrical phase technique have been shown to be useful quantitative tools.
Quantitative structure determination of interfaces through Z-contrast imaging and electron energy loss spectroscopy
Authors: Pennycook S. J. , Nellist P. D. , Browning N. D. , Langjahr P. A. , Rühle M. 
Published: June 2020

The simultaneous use of Z-contrast imaging with parallel detection EELS in the STEM provides a powerful means for determining the atomic structure of grain boundaries. The incoherent Z-contrast image of the high atomic number columns can be directly inverted to their real space arrangement, without the use of preconceived structure models. Positions and intensities may be accurately quantified through a maximum entropy analysis. Light elements that are not visible in the Z-contrast image can be studied through EELS; their coordination polyhedra determined from the spectral fine structure. It even appears feasible to contemplate 3D structure refinement through multiple scattering calculations.The power of this approach is illustrated by the recent study of a series of SrTiC>3 bicrystals, which has provided significant insight into some of the basic issues of grain boundaries in ceramics. Figure 1 shows the structural units deduced from a set of 24°, 36° and 65° symmetric boundaries, and 24° and 45° asymmetric boundaries. It can be seen that apart from unit cells and fragments from the perfect crystal, only three units are needed to construct any arbitrary tilt boundary. For symmetric boundaries, only two units are required, each having the same Burgers, vector of a<100>. Both units are pentagons, on either the Sr or Ti sublattice, and both contain two columns of the other sublattice, imaging in positions too close for the atoms in each column to be coplanar. Each column was therefore assumed to be half full, with the pair forming a single zig-zag column. For asymmetric boundaries, crystal geometry requires two types of dislocations; the additional unit was found to have a Burgers’ vector of a<110>. Such a unit is a larger source of strain, and is especially important to the transport characteristics of cuprate superconductors. These zig-zag columns avoid the problem of like-ion repulsion; they have also been seen in TiO2 and YBa2Cu3O7-x and may be a general feature of ionic materials.
Simulated Chemical Imaging of InGaAs/InAlAs Interfaces
Authors: Mountjoy G. , Crozier P.A. , Fejes P.L. , Tsui R.K. , Kramer G.D. 
Published: June 2020

For many semiconductor devices, a detailed knowledge of interface composition on an atomic scale is important for understanding the device performance. One technique for obtaining such knowledge is “chemical imaging”. This technique has previously been applied to Si/Ge and GaAs/AlAs interfaces. Recently, there has been interest in constructing quantum wells using the (In0.532Ga0.468)As/(In0.522Al0.478)As system (hereafter InGaAs/InAlAs), which is lattice-matched to InP (lattice constant of 5:869Å).The chemical imaging technique uses high resolution electron microscopy (HREM) images taken under special conditions of microscope defocus df, and specimen thickness t. Under the correct conditions, the images contain features which are linearly dependent on composition x. For heterogeneous structures (e.g. InGaAs/InAlAs), a change in x affects <200> beams preferentially. In this case, imaging in the <100> orientation is favorable, because four <200> beams occur. It is necessary to define a function of the image intensity h(I) which is proportional to x for some values of t and df. Here we follow the approach of Thoma and Cerva and use h(I) equal to the <200> frequency component of the image intensity (I200) normalized relative to I200 for x=0 and x=1. The resolution of h(I) is limited to one <200> period, or 1/2 unit cell (2.93Å).
Gapless Single-Pole Magnetic Lens for Low-Voltage SEM
Authors: Tsai F.C. , Crewe A.V. 
Published: June 2020

An unconventional single pole lens design has attracted attention because it promises a highly confined strong field distribution which in turns results in smaller third aberrations than that of the conventional lenses. However in this type of lens heat dissipation becomes crucial. In the low electron energy range (less than 5 KV), however, we can keep all the benefits from the single pole piece without being concerned about the cooling requirement.The key to the design is to avoid the unnecessary strong fields in any region away from the axis, which can absorb a lot of applied magnetomotive force (MMF) if this off-axis region happens to be in the air. This implies that a reasonable design is a gapless geometry. In our design (Fig. 1), a hemisphere tip sits on the top of a central pole. At the rim between the boundary of the central tapered pole and the tip is a 45° semi-angle funnel-shaped exterior pole. These three parts physically contact each other and form a gapless geometry. The central and exterior poles also contact each other at the bottom of the lens to form the high permeability magnetic circuit loop. The cross section of each part of the lens has been chosen in such a way that the region close to the tip will saturate first.
Characterization of Mo/SiO2 interfacial reactions in metal halide arc tube by analytical TEM
Authors: Jeon S.J. , Sung C. , Chao Chung 
Published: June 2020

The purpose of this study is to investigate the interfacial reactions between Mo foil and quartz in metal halide arc tubes. After welding to a tungsten cathode, the Mo foil was specially treated before Mo/SiO2 pinch seal operation. Mo foils in arc tubes show different performance in lamp depending on the type of the treatment. Mo/SiO2 interfacial reactions and amounts of Mo diffusion into the SiO2 were analyzed using TEM, SEM and EDS in order to understand the different properties of arc tubes.Arc tubes were treated with one of the following conditions : (A)untreated, (B)dry hydrogen fired, (C)process “B” plus humidity exposure. Cross-sectional TEM and SEM samples in the longitudinal direction of the arc tube through the center of Mo foil were prepared. Two Mo/SiO2 interfacial areas, one near the end of the W cathode and the other the longitudinal center of the foil were compared each other.
A computer-generated three-dimensional view of the developing human biliary system
Authors: Vijayan V. , Tan CEL 
Published: June 2020

With the advent of computers, microscopy has entered an exciting new era of computerised three dimensional (3D) reconstruction. Using serial sections, it is now possible to generate complex 3D images, that can be rotated at various angles to study the organ systems of interest. In this project, the first of its kind, we have used computer generated 3D reconstruction to study the developing human biliary system.The human biliary system consists of the extra and intrahepatic components. The extrahepatic system develops from the embryonic hepatic diverticulum and is tubular from the start. The intrahepatic bile ducts arise from the Ductal Plate. The Ductal Plate comprises of sheets of biliary epithelium, with discontinuous luminal spaces, that appear within the mesenchyme along the portal vein branches. The Ductal Plate is remodelled into tubular definitive bile ducts by an orderly process of epithelial deletion and selection which occurs between 11-13 weeks of gestation
Morphological evolution of nanometer-sized BaTiO3particles
Authors: Chun C. M. , Navrotsky A. , Aksay I. A. 
Published: June 2020

Highly pure, stoichiometric, nanometer-sized, and fairly monodispersed anhydrous crystalline BaTiO3particles are synthesized under hydrothermal conditions in a single process step without further heat treatment by reacting titanium isopropoxide [Ti(OC3H7)4] precursor in aqueous solutions of Ba(OH)2at 80°C. Traditional considerations of solution hydrolysis, solute condensation, and nucleation only partly explain the generation of the “raspberry-like” BaTiO3particles composed of 5∼10 nm primary crystalline particles. Consequently, the colloidal interaction of the precipitating particles and, therefore, controlled aggregation of freshly nucleated particles must be taken into account. Our TEM studies show aggregation growth of small subunits to form uniform, rounded polyhedral particles, suggesting colloidal stability may play a key role in controlling precipitate size and shape.In order to investigate the evidence supporting the aggregation growth, Ti(OC3H7)4precursor (Aldrich) has been added to l.OM Ba(OH)2solution and hydrothermally reacted at 80°C in polyethylene bottles. Four molecules of water and two hydroxyl ions attach through their oxygen atoms to the titanium of Ti(OC3H7)4in a nucleophilic process.
Quantitative elemental analysis of bacterial polyphosphate bodies using scanning transmission electron microscopy and energy-dispersive x-ray spectroscopy
Authors: Goldberg J. , Gonzalez H. , Jensen T.E. , Corpe W.A. 
Published: June 2020

The elemental composition of polyphosphate bodies (PPB's) has been determined qualitatively previously using energy dispersive x-ray spectrometers (EDX) and in bodies isolated from cells. In this present study we determine in several bacteria their quantitative elemental composition using EDX in conjunction with a STEM.Bacteria were grown as previously described or were collected from natural sources. Portions of each sample were air dried on formvar coated grids. Separate samples were fixed and embedded in Epon. For x-ray analysis cells of interest were first located using the TEM mode. The microscope was then switched to the STEM mode. Analysis of cell components was carried out in the spot mode (75 kV) of the STEM. The spot diameter at 100,000x is approximately 20nm. The objective lens current was adjusted so a total x-ray count of 600 to 1,000 cps was attained for the 100 sec. count time. Spectra were collected on a PGT IMIX (EDX). The data was analyzed using a bulk sample analysis program (ZAF method) in standardless mode (w/w). Latex spheres of known density (1.05 g per cu cent) and volume were analyzed to obtain a standard (mass/weight).
Multiple-fracturing and viewing of the same frozen sample at different depths using a low temperature FESEM
Authors: Parthasarathy M.V. , Daugherty C. 
Published: June 2020

The versatility of Low Temperature Field Emission SEM (LTFESEM) for viewing frozen-hydrated biological specimens, and the high resolutions that can be obtained with such instruments have been well documented. Studies done with LTFESEM have been usually limited to the viewing of small organisms, organs, cells, and organelles, or viewing such specimens after fracturing them.We use a Hitachi 4500 FESEM equipped with a recently developed BAL-TEC SCE 020 cryopreparation/transfer device for our LTFESEM studies. The SCE 020 is similar in design to the older SCU 020 except that instead of having a dedicated stage, the SCE 020 has a detachable cold stage that mounts on to the FESEM stage when needed. Since the SCE 020 has a precisely controlled lock manipulator for transferring the specimen table from the cryopreparation chamber to the cold stage in the FESEM, and also has a motor driven microtome for precise control of specimen fracture, we have explored the feasibility of using the LTFESEM for multiple-fracture studies of the same sample.
“Leaky vacuum” SEM for materials scientists
Authors: Horsewell A. , Appel C.C. , Bilde-Sørensen J.B. 
Published: June 2020

‘Leaky vacuum’ SEM is carried out at Risø using the Electroscan™ E-3 Environmental SEM and the low vacuum JEOL 5310 LVSEM. In our laboratory, a wide variety of materials problems has led us to develop several novel ‘leaky vacuum’ SEM methods which will be described here; a) in-situ fracture mechanics experiments, b) utilization of charge contrast to characterize local conductivity of insulators, c) removal of beam skirting error in energy dispersive X-ray analysis.In-situ fracture-mechanics experimentsCrack tip processes in non-conducting materials such as ceramics and polymer composites cannot be observed in the conventional SEM because the vacuum deposited conductive coatings peel away around the edges of the growing cracks. Charge prevention is readily achieved in die ESEM through ionization of the 5-10 torr atmosphere around the specimen surface. Not only is the large specimen chamber convenient for special rigs, but the poor vacuum means low demands on the rig construction with respect to out-gassing of lubricants, strain gauges and electrical monitors.
An overview of functional magnetic-resonance imaging
Authors: Hu Xiaoping , Le Tuong , Kim Seong-Gi , Ugurbil Kamil 
Published: June 2020

In the past few years, one of the most significant developments in magnetic resonance imaging (MRI) is the use of MR imaging to non-invasively map human cortical function without the use of exogenous contrast agents . Since its introduction in 1992, functional magnetic resonance imaging (fMRI) has emerged as a powerful tool for studying neuronal function and generated an enormous amount of interest among neuroscientists, NMR scientists, and clinicians. The purpose of this paper is to outline the principle of fMRI and the associated technical issues and illustrate the utility of fMRI with representative applications.The basis of fMRI is the blood oxygenation level dependent (BOLD) contrast which is derived from the fact that deoxyhemoglobin is paramagnetic and changes in the local concentration of deoxyhemoglobin within the brain lead to alterations in the magnetic resonance signal. Neuronal activation within the cerebral cortex causes an increase in blood flow without a commensurate increase in oxygen extraction.
Structural Investigation of B+ Ion Implantation Induced Amorphization in Polycrystalline Ni Thin Films
Authors: Liu P.C. , Zaluzec N.J. , Okamoto P.R. , Meshii M. 
Published: June 2020

High fluence metalloid ion implantation have been shown to induce amorphous phase formation in transition metals systems1,2 In this study Electron Energy Loss Spectroscopy (EELS) and Energy Filtered Selective Area Electron Diffraction (EFSAED) techniques have been employed along with conventional TEM to characterize the structural and electronic changes resulting from B+ ion implantation into polycrystalline Ni thin films.Polycrystalline Ni thin films of thickness ~500Å have been prepared by evaporating pure Ni (99.99%) onto commercial Bioden R.F.A. acetyl cellulose films in a vacuum of 5 × 106 Torr at room temperature. The TEM samples are obtained by dissolving the underlying acetyl cellulose layer using acetone wetting from below the TEM grids. The resulting films exhibit a continuous, non-textured fee polycrystalline rings pattern with an average grain size of 17 ± 4 nm.Ion implantation was performed in an implantation chamber using 50 keV B+ ions directed at normal incidence to the Ni TEM samples. The sample configuration consists of a -500 Å Ni energy degrader films on the 100 mesh Cu grids situated in front of the polycrystalline Ni thin films on the 300 mesh Cu grids. Such configuration maintains optimum efficiency of B+ ion implantation while producing a more homogeneous profile. After a total incident dose of 4.22x1017 ions/cm2, the implanted polycrystalline Ni thin films was transferred to the Philips EM420 electron microscope equipped with a Gatan (M-607) serial EELS detector for structural characterization.
TEM microscopical examination of the magnetic domain boundaries in a super Duplex austenitic-ferritic stainless steel
Authors: Fourlaris G. , Gladman T. , Maylin M. , Lane R. , Papadimitriou G. D. 
Published: June 2020

It is well known that, due to the good corrosion resistance certain grades of stainless steels have significant applications in marine environments. For the development of certain large naval structures, in addition to the good corrosion resistance, other requirements are imposed such as high strength and toughness coupled with suitable magnetic characteristics.It has been demonstrated in an earlier publication that significant improvements in the coercivity, maximum induction and remanence values can be achieved, by using a 2205 type Duplex austenitic -ferritic stainless steel (DSS) instead of the low alloy medium carbon steels currently being used. These improvements are achieved in the as received 2205 material, and after small amounts of cold rolling have been applied, to increase the strength. In addition, the modification of the duplex austenitic-ferritic microstructure, via a heat treatment route, results in a finer austenite ‘island’ dispersion in a ferritic matrix and provides an attractive option for further modification of the magnetic characteristics of the material.
Merging of electron-diffraction intensities acquired with a slow-scan CCD camera of crotoxin complex crystals to 3.5Å resolution
Authors: Brink Jaap , Chiu Wah 
Published: June 2020

Crotoxin complex is the principal neurotoxin of the South American rattlesnake, Crotalus durissus terrificus and has a molecular weight of 24 kDa. The protein is a heterodimer with subunit A assigneda chaperone function. Subunit B carries the lethal activity, which is exerted on both sides ofthe neuro-muscular junction, and which is thought to involve binding to the acetylcholine receptor. Insight in crotoxin complex’ mode of action can be gained from a 3 Å resolution structure obtained by electron crystallography. This abstract communicates our progress in merging the electron diffraction amplitudes into a 3-dimensional (3D) intensity data set close to completion. Since the thickness of crotoxin complex crystals varies from one crystal to the other, we chose to collect tilt series of electron diffraction patterns after determining their thickness. Furthermore, by making use of the symmetry present in these tilt data, intensities collected only from similar crystals will be merged.Suitable crystals of glucose-embedded crotoxin complex were searched for in the defocussed diffraction mode with the goniometer tilted to 55° of higher in a JEOL4000 electron cryo-microscopc operated at 400 kV with the crystals kept at -120°C in a Gatan 626 cryo-holder. The crystal thickness was measured using the local contrast of the crystal relative to the supporting film from search-mode images acquired using a 1024 x 1024 slow-scan CCD camera (model 679, Gatan Inc.).
400-kV electron imaging of ice-embedded fascin-actin bundle
Authors: Jakana Joanita , Edwards Robert , Bryan Joseph , Schmid Michael F. , Chiu Wah 
Published: June 2020

Fascin is a 55 kDa actin filament bundling protein first isolated from sea urchin egg actin gels by Kane. These gels consist of actin-fascin bundles cross linked by spectrin. Purified actin and fascin produce bundles when mixed in vitro, with an actin-fascin stoichiometry of 4.6 to 1 at saturation. Cloning of sea urchin fascin cDNA revealed homology to an uncharacterized Drosophila protein called singed. The singed phenotype, misshapen bristles and female sterility, canbe explained by a lack of actin bundles and Cant el al has shown recently that the singed gene product can bundle actin. Mammalian fascins have now been cloned from humans and mice. Murinefascin is highly expressed in brain; immunofluorescence reveals fascin localized to filopodia extending from the leading edge of hippocampal neuron growth cones.A soluble, active recombinant mouse fascin has been produced as a fusion protein with E. coli thioredoxin. When mixed with F-actin this fusion protein produces bundles with an actin-fascin ratio of approximately 4.1:1. The bundle was frozen in a thin layer of vitreous ice and examined at 400 kV in the JEOL 4000 electron microscope under low dose condition with a procedure previously described.