bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Non-Interferometric X-Ray Phase Imaging
Authors: Nugent KA , Paganin D , Tiller J , Allman B 
Published: July 2020

Abstract
The phase of a coherent wave is an intuitively well understood concept and efforts to measure the phase of a wave are a staple of visible, x-ray, electron and atom optics. However, in a subtle way, phase is often measured where it is not even defined. An example of this is adaptive optics where the atmospheric phase distortion of light from astronomical objects is measured using polychromatic light. The assumption buried under this work is that it is possible to sensibly talk about phase even though the context of the discussion does not permit phase to be defined according to elementary concepts.
We have been undertaking an ongoing program investigating the nature of wavefields and exploring their characterisation using more robust approaches than standard techniques such as interferometry In a very recent paper we have developed a new viewpoint on phase defined via the Poynting vector of the radiation and where the phase acts as a set of potentials leading to the Poynting vector field.
A State-of-the-art X-Ray Microprobe and its Applications at the Advanced Photon Source
Authors: Yun W , Cai Z , Lai B , Maser J , Legnini D 
Published: July 2020

Abstract
We have developed a state-of-the-art x-ray microprobe with many unprecedented capabilities for a broad range of scientific applications. The combination of the high brilliance third-generation synchrotron radiation sources and the development of high performance x-ray focusing optics have led to the construction of a x-ray microprobe at Argonne National Laboratory with a FWHM focal size less than 0.25 μm and photon flux exceeding 5×l010 photons/cm2/sec/0.01% BW. The microprobe is very flexible and versatile and can be used simultaneously to perform x-ray diffraction microscopy, fluorescence microscopy, spectromicroscopy, and 3D tomography with submicron spatial resolution. It has been used for a broad range of applications since its commissioning in December of 1996. For example, it was used in the study of the symbiotic relation between plant root and fungi, platinum-based anticancer agents, integrated laser/modulator microdevices, electromigration in Al wires in semiconductor devices, and submicron spatial resolution threedimensional tomography of a single cell. The capabilities of the microprobe are described below, and applications using these capabilities will be presented.
Precise X-Ray Microfluorescence Measurements of Sr/Ca Ratios In Corals For Paleotemperature Analysis
Authors: Pingitore Nicholas E , Pogue Ted 
Published: July 2020

Abstract
Coral aragonite encodes a rich, complex record of ambient environmental conditions (including temperature, salinity, pollutants) during skeletogenesis. Annual growth banding in appropriate species provides an internal calendar, and the rapidity of skeletal growth permits temporal sampling to at least a sub-monthly basis. The longevity of reef coral colonies can provide continuous centuries-long environmental records. The presence of well-dated Pleistocene coral reefs at sites across the world ocean extends this record into the more distant past. Thus corals are a remarkable resource for the investigation of environmental conditions over perhaps 7 orders of magnitude of time.
The past few years have seen considerable use of Sr/Ca ratios in scleractinian corals to reconstruct sea surface temperatures (SSTs) to document global change. The detailed correlation between Sr/Ca ratios in living corals and measured ambient water temperature is often remarkable, as is the match in older corals between Sr/Ca ratios and such other SST temperature proxies as 18O /16O ratios.
Bragg and Fresnel Diffraction Imaging Using Highly Coherent X-Rays
Authors: Cloetens P , Baruchel J , Guigay JP , Ludwig W , Mancini L , Pemot P , Schlenker M 
Published: July 2020

Abstract
X-ray imaging started over a century ago. For several decades its only form was absorption radiography, in which contrast is due to local variations in beam attenuation. About forty years ago, a new form of X-ray imagery, Bragg-diffraction imaging or X-ray topography, developed into practical use. It directly reveals crystal defects in the bulk of large single crystals, and paved the way to microelectronics by leading to the growth of large, practically perfect, crystals. The advent of third-generation synchrotron radiation sources of X-rays such as ESRF and APS is now making possible, through the coherence of the X-ray beams, a novel form of radiography, in which contrast arises from phase variations across the transmitted beam, associated with optical path length differences, through Fresnel diffraction. Phase radiography and its three-dimensional companion, X-ray phase tomography, are providing new information on the mechanics of composites as well as on biological materials.
Recent Developments In Monochromatic Microprobe X-Ray Fluorescence (MMXRF)
Authors: Chen Z W , Wittry D B 
Published: July 2020

Abstract
A monochromatic x-ray microprobe based on a laboratory source has recently been developed in our laboratory and used for fluorescence excitation. This technique provides high sensitivity (ppm to ppb), nondestructive, quantitative microanalysis with minimum sample preparation and does not require a high vacuum specimen chamber. It is expected that this technique (MMXRF) will have important applications in materials science, geological sciences and biological science.
Three-dimensional focusing of x-rays can be obtained by using diffraction from doubly curved crystals. In our MMXRF setup, a small x-ray source was produced by the bombardment of a selected target with a focused electron beam and a toroidal mica diffractor with Johann pointfocusing geometry was used to focus characteristic x-rays from the source. In the previous work ∼ 108 photons/s were obtained in a Cu Kα probe of 75 μm × 43 μm in the specimen plane using the fifth order reflection of the (002) planes of mica.
Experimental Gun Brightness Measurements on a 300 kV CFEG
Authors: Zaluzec Nestor J , Nicholls Alan 
Published: July 2020

Abstract
Effective use of the ANL 300kV CFEG/A AEM requires a knowledge of the probe current and size distribution during operation. In most cases this can be calculated once basic parameters of the system are experimentally determined. Central to this is a determination of the source brightness of the Cold Field Emission Gun (CFEG) under standard operating conditions of the instrument. For the last ten years most probe calculations of CFEG's have been done assuming a brightness parameter of β∼×109 A/cm2/sterad2 at 100 kV, while few if any experimental values have been reported at 300 kV. Using β and the relationship that the operating probe diameter is obtained by adding in quadrature the Gaussian probe size (dg, the CFEG source contribution), and the diameters of least confusion due to spherical abberation (ds) and diffraction limits (dd) one obtains the total probe size dt as :
Measuring and Tuning TEM Energy Filter Performance
Authors: Brink H , Kothleitner G , Kundmann MK 
Published: July 2020

Abstract
Although, critical performance criteria of TEM objective lenses, such as spherical and chromatic aberration and, more recently, 3-fold astigmatism, are of common concern, the important properties of TEM energy filters are less well-known and not often measured or quoted. In an effort to bring these to light, we have developed methods for automatically measuring and tuning three optical properties important to practical filter performance: non-isochromaticity, geometric distortion, and non-achromaticity.
A filter is perfectly isochromatic if the range of electron energies that contribute to an energy-filtered image is the same across all image pixels. In practice, energy filters display some degree of nonisochromaticity, i.e. the energy-loss range forming the periphery of the image differs by anywhere from a fraction of an eV to as much as few eV from that forming the center of the field of view.
Energy Filtering Imaging Of Thick Biological Specimens With In-Column "Omega"-Filter Microscopes.
Authors: Ellisman Mark H , Fan GY , Honda T , Kanayama T , Kersker M 
Published: July 2020

Abstract
Preliminary results were obtained from thick sections of biological specimens using 200 keV electron microscopes with an in-column “Omega” energy filter. Images of selectively stained specimens prepared by osmium impregnation of frog spinal ganglia, with thickness ranging from 0.5 μm to 2.5 μm, show drastic improvement in image quality with the use of the energy filter.
Two instruments with Omega filters were used. One was a non-commercial research prototype at JEOL Ltd. equipped with a LaB6 gun and the other was a commercial instrument (JEM-2010FEF) with a field-emission gun, installed at Kyushu University. We found that, although the field-emission gun offered a brightness 2 to 3 orders of magnitude higher, the LaB6 gun was more suitable for studying thick specimens, primarily due to the higher beam current of the LaB6 gun.
Magnetic Deflecting Microscopy: A Novel Visualizing Method of Magnetic Stray Fields for Thick or Non-Transparent Magnetic TEM Samples
Authors: Volkov VV , Zhu Y 
Published: July 2020

Abstract
For microstructure analysis of magnetic materials, in particular, for a new class of Nd-Fe-B hard magnets, a number of magnetic imaging techniques can be applied to gain different microstructure information. For instance, SEM magnetic imaging can be successfully used for very thick samples from a bulk ones down to a sample thickness of 10-20 μ. Below this limit the resolution of SEM magnetic images generally is too low to visualize fine details of magnetic structure. For very thin samples (less then 0.5 μm) magnetic Lorentz microscopy methods in conventional TEM are very useful tools to reveal magnetic domains and their structure. Therefore, it seems that relatively thick films of 0.5-20 μm in thickness are left out of the experimental limits of the methods discussed.
We report on a novel, indirect TEM method that allows us to extend the limits of magnetic imaging for TEM non-transparent magnetic samples by viewing the surface stray fields and fringing fields generated by magnetic domains at specimen edge.
An Infinity Corrected All-Reflecting Microscope for Infrared Microspectrometry
Authors: Reffher John A , Vogel Steven H 
Published: July 2020

Abstract
A confocal, all-reflecting, infinity corrected microscope was developed to improve infrared microspectrometer (IMS) systems. This system consists of a Fourier transform spectrometer, an infinity corrected all-reflecting microscope, a viewing system for visible light microscopy, a single remote confocal mask for aperturing in either a transmission or reflection mode and an infrared detector. The radiant energy passes through a confocal aperture mask as it travels from the source to the sample and through the same confocal aperture mask as it travels from the sample to the radiant energy detector. A single confocal mask insures that the sample defining mask's size, geometrical shape and orientation are always matched. Mask alignment is assured and simplified since only one adjustment is needed. An aperture beam-splitter is used for reflection measurements. This system simplifies the operation of the microspectrometer, permits the use of standard commercial infinity corrected microscope optical components and reduces the cost of IMS accessory microscopes.
High-Qe Photodetector for Laser Confocal
Authors: Pawley J , Blouke M , Janesick J 
Published: July 2020

Abstract
The laser confocal microscope (LCM) is now an established research tool in biology and materials science. In biological applications, it is usually employed to detect the location of fluorescent marker molecules and, under these conditions, detected signal levels from bright areas often represent &lt;20 photons/pixel (assuming a standard 1.6 μs pixel time) while those from dark areas are likely to average &lt;1 photon/pixel. Although this data rate limits the speed at which information can be derived from the specimen, saturation of the fluorophor, photobleaching of the dye, and phototoxicity often prevent it being increased by simply using more laser power. Over the past 10 years, the optical photon efficiency of commercial confocal instruments has improved significantly and it is now reaching the point where further improvement is becoming very expensive. The only component is which a significant improvement is still possible is the photodetector.
Video-Rate Scanning Two-Photon Excitation Fluorescence Microscopy
Authors: Fan GY , Fujisaki H , Tsay R-K , Tsien RY , Ellisman Mark H 
Published: July 2020

Abstract
A video-rate scanning two-photon excitation microscope (TPEM) has been successfully constructed and tested. The TPEM, based on a Nikon RCM-8000, incorporates a femtosecond pulsed laser, a pre-chirper, and a non-confocal detection box for ratio imaging. Fig. 1 shows the schematic layout of the main components of the instrument, each of which is briefly discussed below.
Laser System: A Tsunami Ti: Sapphire laser (from Spectra-Physics) is optically pumped by a 5 W green laser (Millennia from Spectra-Physics) and is capable of generating 100 fs pulses at a repetition rate of 82 MHz and an average power of 0.8 W. The output wavelength is tunable from 690 to 1050 nm with three optical sets, each covering part of the spectrum with some overlapping.
Pre-chirper: After leaving the Tsunami, the laser beam enters an optic unit known as a pre-chirper which pre-chirps laser pulses to compensate for the group velocity dispersion which will result when the laser beam goes through the microscope optics.
Electron Tomographic Studies of a Large Macromolecular Assembly Preserved In Vitreous Ice: The Yeast Spindle Pole Body Core
Authors: Bullitt E 
Published: July 2020

Abstract
Advances in both electron cryomicroscopy and tomographic reconstruction methods have made it possible to collect and analyze data from large macromolecular assemblies frozen without fixation, sectioning, or staining. The Spindle Pole Body (SPB) is the microtubule organizing center in the yeast Saccharomyces, and is involved in mitosis, nuclear movement, budding, and mating. We have used electron cryomicroscopy and tomographic reconstruction to investigate the 1500Å diameter, 600Å high cylindrical core structure produced by limited heparin treatment of isolated SPBs.
Tilt series' of SPB cores preserved in vitreous ice were taken under low electron dose conditions. These images have been analyzed using iterative correlation alignment and computed back projections for tilt data without fiducial markers. In these studies, electron micrographs were digitized, and translationally aligned using correlation methods.
The Three Dimensional Organization of Smooth Muscle: Information from Serial Section Reconstructions
Authors: Horowitz RA , Powers CM , Valero P , Craig R 
Published: July 2020

Abstract
Smooth muscle is a machine consisting of working and supporting elements whose structure and 3D organization must be elucidated for the mechanics of shortening and tension generation to be understood. Based on longitudinal and serial transverse sections of rabbit portal vein it was suggested that the contractile elements of smooth muscle formed “mini-sarcomeres”, analogous to skeletal muscle, containing parallel arrays of 3-5 myosin filaments 1.6-2.2 um long. Observations at the light microscopic level were consistent with this idea. The past decade has seen little further investigation into the in situ ultrastructure of this or other smooth muscles, and the general applicability of these findings remains unknown. We have taken advantage of recent methodological advances, which can provide full 3D computer representations of cellular organization based on EM data, using guinea pig taenia coli muscle as a model system.
Serial transverse sections (Fig 1) were used to generate 3D reconstructions of the organization of the myosin filaments and their relation to dense bodies, actin bundles, mitochondria and other organelles.
Quantitative Image Processing in 3D
Authors: Skoglund Ulf 
Published: July 2020

Abstract
Three-dimensional reconstructions from projections are usually ridden by noise from different sources. A common problem among many three-dimensional reconstruction techniques is the systematic absence of certain projections, but also the accidental absence of spurious projections. In these three-dimensional reconstructions such absences are visible as directional smearing due to convolution. Other convolution effects such as those due to the optics of the instrument used to record the data usually cause severe damping of high frequencies and even contrast reversal (common in images from electron microscopes).
Several approaches to overcome these ‘noise’ effects in three-dimensional reconstructions have been developed, but they usually suffer from the very small radius of convergence. Very easily and commonly, the refinement iterations end up stuck in a premature choice of a minimum. We have developed another algorithm, constrained maximum entropy tomography (COMET), that in practice has been shown to overcome these problems.
Fluorescent Indicators for Calcium Based on Green Fluorescent Proteins (GFPs) and Calmodulin
Authors: Miyawaki A , Llopis J , Heim R , McCafFery JM , Adams JA , Ikura M , Fujisaki H , Fan GY , Ellisman MH , Tsien RY 
Published: July 2020

Abstract
Cytosolic and organellar free Ca2+ concentrations are very dynamic; they are often extremely localized and hard to measure. To overcome this problem we have constructed new fluorescent indicators for Ca2+ that are genetically encoded without cofactors and are targetable to specific intracellular locations.
Green fluorescent protein (GFP) is a spontaneously fluorescent protein from the jelly fish Aequorea victoria. Its cDNA can be concatenated with those encoding many other proteins, and the resulting fusion proteins are usually fluorescent and often preserve the biochemical functions and cellular localizations of the partner proteins. Mutagenesis has produced GFP mutants with shifted wavelengths of excitation or emission that can serve as donors and acceptors for fluorescence resonance energy transfer (FRET).
Our new indicators consist of tandem fusions of a blue- or cyan-emitting mutant of GFP, calmodulin (CaM), the calmodulin-binding peptide Ml3, and an enhanced green- or yellow-emitting GFP. Binding of Ca2+ makes calmodulin wrap around the Ml3 domain, increasing the FRET between the flanking GFPs (Fig. 1).
Correlative Confocal and Electron Microscopy of the Connexin43 Gap Junction Protein in NRK Cells: Balancing Fixation Conditions, Cell Permeabilization, Antigen-Antibody Interaction and Cell Ultrastructure.
Authors: Sosinsky Gina , Martone Maryann , Handel Galen , Musil Linda , Ellisman Mark 
Published: July 2020

Abstract
Synthesis and assembly of gap junction proteins into intercellular channels is an important biological problem with direct bearing on embryonic development. In particular, transgenic mice Cx43 gap junction protein knock-outs 1 and mutations in Cx43 sequence in human Viscera Hyper Taxia patients result in severely deformed hearts.
NRK cells are one of the best studied systems for gap junction synthesis, transport and assembly. Gap junctions contain numerous cell-cell channels which are composed of two paired oligomers (called a connexon or hemichannel) each contributed from the plasma membrane of apposing cells. Although biochemical studies have shown indirectly that unpaired Cx43 connexons are in the plasma membrane, direct hemichannel visualization has not been demonstrated. Musil and Goodenough have shown that oligomerization occurs in the trans-Golgi network and the connexon is transported to the plasma membrane.
Structure of the Calcium Pump from Sarcoplasmic Reticulum at 8 Å Resolution: Architecture of the Transmembrane Helices and Localization of the Binding Site for Thapsigargin
Authors: Zhang P , Toyoshima C , Yonekura K , Inesi G , Green M , Stokes DL 
Published: July 2020

Abstract
The calcium pump (Ca2+-ATPase) from sarcoplasmic reticulum (SR) is a prominent member of the large family of ATP-dependent cation pumps, which include Na+ /K+-ATPase, H+/K+-ATPase from the stomach, H+-ATPase from yeast and Neurospora, and various detoxifying pumps for Cd+, Cu+ and other metals. In muscle, calcium is stored inside the SR and contraction is initiated by regulated release through specific calcium channels; Ca2+ -ATPase is responsible for relaxation by pumping calcium back into the SR lumen. Many techniques (chemical modification, site mutagenesis, reaction kinetics) have been used to correlate Ca2+-ATPase sequence with function, but no high resolution three-dimensional structure of Ca2+-ATPase, or any P-type pump, has yet been determined. In the current work, we have determined the structure from helical crystals at 8 A resolution and thus revealed the alpha-helical architecture of the transmembrane domain. In addition, a specific inhibitor of Ca2+-ATPase, thapsigargin, was used to promote crystallization and we have characterized the structural consequences of its inhibition.
Shared Research Equipment at OAK Ridge National Laboratory
Authors: Evans N D , Kenik E A , Miller M K 
Published: July 2020

Abstract
The Shared Research Equipment (SHaRE) User Facility and Program at Oak Ridge National Laboratory (ORNL) provides microanalytical facilities for studies within the materials sciences. Available instrumentation includes advanced analytical electron microscopes, atom probe field ion microscopes, and nanoindentation facilities. Through SHaRE, researchers from U.S. universities, industries, and government laboratories may collaborate with Facility scientists to perform research not possible at their home institutions. International collaborations are also possible. Most SHaRE projects seek correlations at the microscopic or atomic scale between structure and properties in a wide range of metallic, ceramic, and other structural materials. Typical research projects include studies of magnetic materials, advanced alloys, catalysts, semiconductor device materials, high Tc superconductors, and surface-modified polymers. Projects usually involve one or more external researchers visiting the SHaRE Facility for up to three weeks during the fiscal year (October 1 - September 30). Project approval is based upon the scientific excellence and relevance of proposed collaborative research.
Microscopical Examination of Indoor Dusts
Authors: Millette J R , Few P , Hopen T J 
Published: July 2020

Abstract
Several case studies are shown as examples of the results of analyses using various microscopical instruments to characterize the particles in building dusts. Characterizing the particles and identifying possible sources of particles in dusts are often important parts of solving indoor indoor air quality (IAQ) and environmental problems. Samples of the dust particles can be collected by filtering the air with cassette air filters or by gathering the dust that has accumulated on surfaces. Depending on the size and types of particles in the dust either polarized light microscopy (PLM), scanning electron microscopy with x-ray analysis (SEM/EDS), analytical transmission electron microscopy (ATEM) or Fourier transform infrared microspectroscopy (FTIR) may be used solely or in combination. PLM can characterize most of the common dust particle in residential and commercial buildings. SEM/EDS is helpful in identifying metal particles and when used in the backscatter electron mode, a large number of particles can be surveyed and those containing heavy metals such as lead and cadmium can be identified quickly.