A new Kirkpatrick-Baez-based scanning microscope for the Submicron Resolution X-ray Spectroscopy (SRX) beamline at NSLS-II

The development, construction, and first commissioning results of a new scanning microscope installed at the 5-ID Submicron Resolution X-ray Spectroscopy (SRX) beamline at NSLS-II are reported. The developed system utilizes Kirkpatrick-Baez mirrors for X-ray focusing. The instrument is designed to enable spectromicroscopy measurements in 2D and 3D with sub-200 nm spatial resolution. The present paper focuses on the design aspects, optical considerations, and specifics of the sample scanning stage, summarizing some of the initial commissioning results.

High-sensitivity nanoscale chemical imaging with hard x-ray nano-XANES

Resolving chemical species at the nanoscale is of paramount importance to many scientific and technological developments across a broad spectrum of disciplines. Hard x-rays with excellent penetration power and high chemical sensitivity are suitable for speciation of heterogeneous (thick) materials. Here, we report nanoscale chemical speciation by combining scanning nanoprobe and fluorescence-yield x-ray absorption near-edge structure (nano-XANES). First, the resolving power of nano-XANES was demonstrated by mapping Fe(0) and Fe(III) states of a reference sample composed of stainless steel and hematite nanoparticles with 50-nm scanning steps. Nano-XANES was then used to study the trace secondary phases in lithium iron phosphate (LFP) particles. We observed individual Fe-phosphide nanoparticles in pristine LFP, whereas partially (de)lithiated particles showed Fe-phosphide nanonetworks. These findings shed light on the contradictory reports on Fe-phosphide morphology in the literature. Nano-XANES bridges the capability gap of spectromicroscopy methods and provides exciting research opportunities across multiple disciplines.

Augmented decision-making for acral lentiginous melanoma detection using deep convolutional neural networks

BACKGROUND

Several studies have achieved high-level performance of melanoma detection using convolutional neural networks (CNNs). However, few have described the extent to which the implementation of CNNs improves the diagnostic performance of the physicians.

OBJECTIVE

This study is aimed at developing a CNN for detecting acral lentiginous melanoma (ALM) and investigating whether its implementation can improve the initial decision for ALM detection made by the physicians.

METHODS

A CNN was trained using 1072 dermoscopic images of acral benign nevi, ALM and intermediate tumours. To investigate whether the implementation of CNN can improve the initial decision for ALM detection, 60 physicians completed a three-stage survey. In Stage I, they were asked for their decisions solely on the basis of dermoscopic images provided to them. In Stage II, they were also provided with clinical information. In Stage III, they were provided with the additional diagnosis and probability predicted by the CNN.

RESULTS

The accuracy of ALM detection in the participants was 74.7% (95% confidence interval [CI], 72.6-76.8%) in Stage I and 79.0% (95% CI, 76.7-81.2%) in Stage II. In Stage III, it was 86.9% (95% CI, 85.3-88.4%), which exceeds the accuracy delivered in Stage I by 12.2%p (95% CI, 10.1-14.3%p) and Stage II by 7.9%p (95% CI, 6.0-9.9%p). Moreover, the concordance between the participants considerably increased (Fleiss-κ of 0.436 [95% CI, 0.437-0.573] in Stage I, 0.506 [95% CI, 0.621-0.749] in Stage II and 0.684 [95% CI, 0.621-0.749] in Stage III).

CONCLUSIONS

Augmented decision-making improved the performance of and concordance between the clinical decisions of a diverse group of experts. This study demonstrates the potential use of CNNs as an adjoining, decision-supporting system for physicians' decisions.

Multimodal X-ray imaging of grain-level properties and performance in a polycrystalline solar cell

The factors limiting the performance of alternative polycrystalline solar cells as compared with their single-crystal counterparts are not fully understood, but are thought to originate from structural and chemical heterogeneities at various length scales. Here, it is demonstrated that multimodal focused nanobeam X-ray microscopy can be used to reveal multiple aspects of the problem in a single measurement by mapping chemical makeup, lattice structure and charge collection efficiency simultaneously in a working solar cell. This approach was applied to micrometre-sized individual grains in a Cu(In,Ga)Se₂ polycrystalline film packaged in a working device. It was found that, near grain boundaries, collection efficiency is increased, and that in these regions the lattice parameter of the material is expanded. These observations are discussed in terms of possible physical models and future experiments.

Design and performance of an X-ray scanning microscope at the Hard X-ray Nanoprobe beamline of NSLS-II

A hard X-ray scanning microscope installed at the Hard X-ray Nanoprobe beamline of the National Synchrotron Light Source II has been designed, constructed and commissioned. The microscope relies on a compact, high stiffness, low heat dissipation approach and utilizes two types of nanofocusing optics. It is capable of imaging with ∼15 nm × 15 nm spatial resolution using multilayer Laue lenses and 25 nm × 26 nm resolution using zone plates. Fluorescence, diffraction, absorption, differential phase contrast, ptychography and tomography are available as experimental techniques. The microscope is also equipped with a temperature regulation system which allows the temperature of a sample to be varied in the range between 90 K and 1000 K. The constructed instrument is open for general users and offers its capabilities to the material science, battery research and bioscience communities.

Pushing the limits: an instrument for hard X-ray imaging below 20 nm

Hard X-ray microscopy is a prominent tool suitable for nanoscale-resolution non-destructive imaging of various materials used in different areas of science and technology. With an ongoing effort to push the 2D/3D imaging resolution down to 10 nm in the hard X-ray regime, both the fabrication of nano-focusing optics and the stability of the microscope using those optics become extremely challenging. In this work a microscopy system designed and constructed to accommodate multilayer Laue lenses as nanofocusing optics is presented. The developed apparatus has been thoroughly characterized in terms of resolution and stability followed by imaging experiments at a synchrotron facility. Drift rates of ∼2 nm h(-1) accompanied by 13 nm × 33 nm imaging resolution at 11.8 keV are reported.

Design and performance of a scanning ptychography microscope

We have designed and constructed a dedicated instrument to perform ptychography measurements and characterization of multilayer Laue lenses nanofocusing optics. The design of the scanning microscope provides stability of components and minimal thermal drifts, requirements for nanometer scale spatial resolution measurements. We performed thorough laboratory characterization of the instrument in terms of resolution and thermal drifts with subsequent measurements at a synchrotron. We have successfully acquired and reconstructed ptychography data yielding 11 nm line focus.

Performance and characterization of the prototype nm-scale spatial resolution scanning multilayer Laue lenses microscope

Synchrotron based x-ray microscopy established itself as a prominent tool for noninvasive investigations in many areas of science and technology. Many facilities around the world routinely achieve sub-micrometer resolution with a few instruments capable of imaging with the spatial resolution better than 100 nm. With an ongoing effort to push the 2D/3D resolution down to 10 nm in the hard x-ray regime both fabrication of the nano-focusing optics and stability of a microscope become extremely challenging. In this work we present our approach to overcome technical challenges on the path towards high spatial resolution hard x-ray microscopy and demonstrate the performance of a scanning fluorescence microscope equipped with the multilayer Laue lenses focusing optics.

Compact prototype apparatus for reducing the circle of confusion down to 40 nm for x-ray nanotomography

We have constructed a compact prototype apparatus for active correction of circle of confusion during rotational motion. Our system combines fiber optic interferometry as a sensing element, the reference cylinder along with the nanopositioning system, and a robust correction algorithm. We demonstrate dynamic correction of run-out errors down to 40 nm; the resolution is limited by ambient environment and accuracy of correcting nanopositioners. Our approach provides a compact solution for in-vacuum scanning nanotomography x-ray experiments with a potential to reach sub-nm level of correction.

Study of magnetic anisotropy and magnetization reversal using the quadratic magnetooptical effect in epitaxial Co(x)Mn(y)Ge(z)(111) films

Magnetic anisotropy, magnetization reversal and the magnetooptic Kerr effect in Co(x)Mn(y)Ge(z) have been studied over a range of compositions between 0 and 50 at.% of Ge and between 1 and 3 in the Co to Mn atomic ratio, including the Heusler alloy Co(2)MnGe. A strong quadratic magnetooptic Kerr effect has been observed within a narrow region of composition centered around the Co to Mn atomic ratio of 2, which has been used to probe and quantify the magnetic anisotropy and magnetization reversal of the system. The anisotropy is sixfold with a weak uniaxial component, and it exhibits sensitive dependence on composition, especially on the atomic ratio between Co and Mn. The magnetization reversal process is consistent with the single-domain Stoner-Wohlfarth model.

X-ray diffractometry and topography of lattice plane curvature in thermally deformed Si wafer

The correlation between the microscopic lattice plane curvature and the dislocation structure in thermal warpage of 200 mm-diameter Czochralski Si (001) wafers has been investigated using high-resolution X-ray diffractometry and topography. It is found that the (004) lattice plane curvature is locally confined between two neighboring slip bands, with the rotation axis parallel to the slip bands. High-resolution topography reveals that the curvature resulted from a fragmented dislocation structure. The local confinement is attributed to the multiplication of the dislocations that are generated between the two slip bands.

X-ray bright-field imaging analyzes crystalline quality and defects of SiC wafers

A new variety of the recently developed technique `X-ray bright-field imaging' is presented. In its basic version, this approach simultaneously yields diffraction-based information on lattice distortions and radiographic information on structural inhomogeneities, and is based on the detection of reversed diffraction contrast in transmission images. The new version extends the scope of the technique to the quantitative analysis of crystalline quality parameters such as the lattice plane curvature and mosaic distribution in SiC wafers, and makes it possible to correlate such parameters directly with defect (distortions/inhomogeneities) structures.

Analytic determination of the three-dimensional distribution of dislocations using synchrotron X-ray topography

A technique, using a symmetric reflectionviaazimuthal rotation of a sample, is presented for characterization of the three-dimensional distribution of dislocations in single crystals. An analytic formula is derived to transform the three-dimensional geometry of a straight dislocation into its two-dimensional projection onto the detector plane. By fitting topographs to the formula, the orientations and locations of dislocations are quantitatively determined. The dislocations in a thermally stressed Si wafer are examined as an example.

An X-ray nanodiffraction technique for structural characterization of individual nanomaterials

An X-ray micro/nanodiffraction technique that allows structural characterization of individual nanomaterials has been developed at an insertion-device beamline of the Advanced Photon Source. Using the extremely high brightness of the third-generation synchrotron radiation source and advanced high-resolution high-energy zone-plate focusing optics, X-rays of energies from 6 to 12 keV have been focused into a spot smaller than 200 nm with a photon density gain of more than 50,000 so that significant photon flux can be intercepted by a nanoscale material to generate a measurable diffraction signal for structural characterization. This paper describes the instrumentation of the technique and discusses the application of the technique to studies of tin oxide nanobelts.

Diffraction and imaging study of imperfections of crystallized lysozyme with coherent X-rays

Phase-contrast X-ray diffraction imaging and high-angular-resolution diffraction combined with phase-contrast radiographic imaging were employed to characterize defects and perfection of a uniformly grown tetragonal lysozyme crystal in the symmetric Laue case. The full-width at half-maximum (FWHM) of a 4 4 0 rocking curve measured from the original crystal was approximately 16.7 arcsec and imperfections including line defects, inclusions and other microdefects were observed in the diffraction images of the crystal. The observed line defects carry distinct dislocation features running approximately along the <1 1 0> growth front and have been found to originate mostly in a central growth area and occasionally in outer growth regions. Inclusions of impurities or formations of foreign particles in the central growth region are resolved in the images with high sensitivity to defects. Slow dehydration led to the broadening of a fairly symmetric 4 4 0 rocking curve by a factor of approximately 2.6, which was primarily attributed to the dehydration-induced microscopic effects that are clearly shown in X-ray diffraction images. The details of the observed defects and the significant change in the revealed microstructures with drying provide insight into the nature of imperfections, nucleation and growth, and the properties of protein crystals.

Novel germanium-based magnetic semiconductors

Epitaxial synthesis and properties of novel Co and Mn-doped Ge magnetic semiconductors were studied. Epitaxial growth of high quality films with high doping concentrations has been stabilized by the use of two dopants. The magnetic and transport properties of the system exhibit high T(C) and large magnetoresistance effects that can be controlled systematically by the doping concentration. The maximum T(C) achieved in the semiconducting materials is approximately 270 K at a composition of Co0.12Mn0.03Ge0.85.

Phase sensitive x-ray diffraction imaging of defects in biological macromolecular crystals

Conventional x-ray diffraction topography is currently used to map defects in the bulk of protein crystals, but the lack of sufficient contrast is frequently a limiting factor. We experimentally demonstrate that this barrier can be circumvented using a method that combines phase sensitive and diffraction imaging principles. Details of defects revealed in tetragonal lysozyme and cubic ferritin crystals are presented and discussed. The approach enabling the detection of the phase changes of diffracted x rays should prove to be useful in the study of defect structures in a broad range of biological macromolecular crystals.

Commensurate water monolayer at the RuO2(110)/water interface

We demonstrate the presence of two types of commensurate, registered water monolayers with different densities at the RuO2(110)/bulk-water (0.1 M NaOH solution) interface with off-specular, oxygen crystal truncation rods. At anodic potentials (close to oxygen evolution), the extraneous water layer and the surface hydroxide layer form a bilayer with O-H-O bond distances similar to that of ice X. At cathodic potentials, the water molecules converted from the bridging OH molecules form a low-density water layer.

Stimulatory and entraining effect of melatonin on tuberoinfundibular dopaminergic neuron activity and inhibition on prolactin secretion

The aims of the present study were to determine if melatonin exerts an effect on prolactin (PRL) secretion via the tuberoinfundibular dopaminergic (TIDA) neurons and if endogenous or exogenous melatonin has an entraining effect on the rhythmic changes of TIDA neuronal activity and PRL secretion. Melatonin given in the morning (10:00 h), dose- (0.01-1 mg/kg, ip) and time- (at 15 and 60 min, but not at 30 min) dependently stimulated TIDA neuronal activity in ovariectomized (OVX), estrogen-treated rats as determined by 3,4-dihydroxyphenylacetic acid (DOPAC) levels in the median eminence (ME). Serum PRL was concurrently inhibited by the injection. Melatonin administered in the afternoon (15:00 h) was even more effective in stimulating the lowered TIDA neuronal activity and inhibiting the increased PRL level than that given in the morning (10:00 h). S-20098, a melatonin agonist was also effective in stimulating the TIDA neurons. In contrast, S-20928, a putative melatonin antagonist, while it had no effect by itself, blocked the effect of S-20098. Although S-20928 failed to prevent melatonin's effect on ME DOPAC levels, six interspaced injections of S-20928, from 18:00 to 01:30 h, significantly blocked the increase of ME DOPAC levels at 03:00 h, indicating that the endogenous melatonin may play a role. We further used rats that received daily injection of melatonin (1 mg/kg, ip) at 18:00 h for 10 days and found that the injection augmented basal TIDA neuronal activity at 11:00 h and blunted the afternoon PRL surge. In all, melatonin can have an inhibitory effect on PRL secretion by stimulating the TIDA neurons, and it may help to entrain the circadian rhythms of both TIDA neuronal activity and PRL secretion.

Molecular study of the Na+/Ca2+ exchanger in bovine adrenal chromaffin cells

To identify the Na+/Ca2+ exchanger expressed in bovine chromaffin cells, the ncx gene was cloned from a bovine chromaffin cell cDNA library. Five partial clones were obtained and their nucleotide sequences showed that there were at least three isoforms containing different intracellular loops. The 3'-untranslated region was the same in all the clones. To examine the Na+/Ca2+ exchange activity of the clones, full-length ncx1 genes were constructed by replacing the corresponding region of bovine cardiac ncx1 clone p17 with the different regions from two bovine chromaffin cell clones; these were designated p17c and p17h. p17h, but not p17c, showed Na+/Ca2+ exchange activity when expressed in Chinese hamster ovary cells and Xenopus oocytes. The expressed exchange activity of p17 was inhibited by 8-bromoadenosine 3':5'-cyclic monophosphate (8-Br-cAMP) but was not affected by PMA. However, the activity of p17h was inhibited by PMA but enhanced by 8-Br-cAMP. The agents that changed the activity of protein kinase C and cAMP-dependent protein kinase modulated the endogenous Na+/Ca2+ exchange current of chromaffin cells in a manner similar to that of p17h. Our results suggest that the p17h clone is the major isoform of the exchanger in chromaffin cells and is similar to the major ncx1 isoform in kidney. The exchange activity could be regulated by phosphorylation, and the variable region in the intracellular loop is important for the different effects of phosphorylation on the different isoforms.

Circadian change of dopaminergic neuron activity: effects of constant light and melatonin

Twenty-four hour profiles of tuberoinfundibular (TI), nigrostriatal and mesolimbic dopaminergic (DA) neuronal activities were assessed in estrogen-primed ovariectomized rats using DOPAC and DOPA levels in terminal regions of DA neurons. Significant decreases in DOPAC and DOPA levels in the median eminence were observed at 17.00 and 21.00 h, which corresponded with higher serum prolactin levels. DOPAC or DOPA levels in the striatum and nucleus accumbens were, however, significantly higher during the dark (21.00-05.00 h) phase. In rats kept under conditions of continuous light, no late afternoon decline in median eminence DOPA was observed; this decline could be reinstated by repeated injections of melatonin between 18.00 and 01.30 h for 3 days. In summary, circadian rhythms of central DA neurons were shown and melatonin may play an entraining role.

A 3 kb sequence from the mouse cellular retinoic-acid-binding protein gene upstream region mediates spatial and temporal LacZ expression in transgenic mouse embryos

A 3233 base pair (bp) sequence of the 5′-flanking region of the mouse cellular retinoic-acid-binding protein (CRABP) gene is determined. From this region, a 3 kb fragment located 150 bp upstream from the transcriptional initiation site is isolated and fused to a LacZ reporter sequence. Transgenic mouse embryos of this fusion gene show spatially and temporally specific expression of LacZ protein and the expression of this fusion gene at the RNA level is confirmed by RNAase protection assays, which detect specific fusion transcripts in RNA samples from tissues of transgenic mouse embryos. In contrast, transgenic mouse embryos of a shorter fusion gene containing only 583 bp from the same upstream region of the mouse CRABP gene fused to the same reporter sequence show no LacZ activities. Thus, it is concluded that the 3 kb sequence, but not the 583 bp sequence, of the mouse CRABP gene contains information for its temporally and spatially specific expression in mouse embryos.

Molecular cloning and transcriptional mapping of the mouse cellular retinoic acid-binding protein gene

The gene encoding the mouse cellular retinoic acid-binding protein (CRABP) has been isolated from a mouse genomic library and its structure has been determined. This gene spans approximately 10.5 kb and consists of four exons encoding 24, 59, 38, and 16 amino acid residues, respectively. This gene structure is very similar to the structures of other related genes belonging to the same protein family such as the human cellular retinol-binding protein, the rat cellular retinol-binding protein II, the rat fatty acid-binding protein, and the mouse adipocyte P2 protein. The site for transcription initiation has been mapped to the 93rd nucleotide upstream from the translation initiation codon ATG using both primer extension and RNase protection assays. From the DNA sequence, the promoter of the CRABP gene resembles those found in the "housekeeping" genes in that it is very G/C rich, lacks a TATA box, and contains multiple copies of the sequence GGGCGG. The deduced amino acid sequence of the translated region is identical to the amino acid sequence of the known bovine CRABP, and the DNA sequence of the transcribed region from the mouse gene shows approximately 78% homology to that of the bovine cDNA.