Symmetry-specific characterization of bond orientation order in DNA-assembled nanoparticle lattices.

Bond-orientational order in DNA-assembled nanoparticles lattices is explored with the help of recently introduced Symmetry-specific Bond Order Parameters (SymBOPs). This approach provides a more sensitive analysis of local order than traditional scalar BOPs, facilitating the identification of coherent domains at the single bond level. The present study expands the method initially developed for assemblies of anisotropic particles to the isotropic ones or cases where particle orientation information is unavailable. The SymBOP analysis was applied to experiments on DNA-frame-based assembly of nanoparticle lattices. It proved highly sensitive in identifying coherent crystalline domains with different orientations, as well as detecting topological defects, such as dislocations. Furthermore, the analysis distinguishes individual sublattices within a single crystalline domain, such as pair of interpenetrating FCC lattices within a cubic diamond. The results underscore the versatility and robustness of SymBOPs in characterizing ordering phenomena, making them valuable tools for investigating structural properties in various systems.

Lanthanide-Binding Tags for 3D X-ray Imaging of Proteins in Cells at Nanoscale Resolution.

We report the application of lanthanide-binding tags (LBTs) for two- and three-dimensional X-ray imaging of individual proteins in cells with a sub-15 nm beam. The method combines encoded LBTs, which are tags of minimal size (ca. 15-20 amino acids) affording high-affinity lanthanide ion binding, and X-ray fluorescence microscopy (XFM). This approach enables visualization of LBT-tagged proteins while simultaneously measuring the elemental distribution in cells at a spatial resolution necessary for visualizing cell membranes and eukaryotic subcellular organelles.

2D MEMS-based multilayer Laue lens nanofocusing optics for high-resolution hard x-ray microscopy.

We report on the development of 2D integrated multilayer Laue lens (MLL) nanofocusing optics used for high-resolution x-ray microscopy. A Micro-Electro-Mechanical-Systems (MEMS) - based template has been designed and fabricated to accommodate two linear MLL optics in pre-aligned configuration. The orthogonality requirement between two MLLs has been satisfied to a better than 6 millidegrees level, and the separation along the x-ray beam direction was controlled on a micrometer scale. Developed planar 2D MLL structure has demonstrated astigmatism free point focus of ∼14 nm by ∼13 nm in horizontal and vertical directions, respectively, at 13.6 keV photon energy. Approaching 10 nm resolution with integrated 2D MLL optic is a significant step forward in applications of multilayer Laue lenses for high-resolution hard x-ray microscopy and their adoption by the general x-ray microscopy community.

Extending the depth of field for ptychography using complex-valued wavelets.

Ptychography is a scanning variation of the coherent diffractive imaging method for providing high-resolution quantitative images from specimen with extended dimensions. Its capability of achieving diffraction-limited spatial resolution can be compromised by the sample thickness, which is generally required to be thinner than the depth of field of the imaging system. In this Letter, we present a method to extend the depth of field for ptychography by numerically generating the focus stack from reconstructions with propagated illumination wavefronts and combining the in-focus features to a single sharp image using an algorithm based on the complex-valued discrete wavelet transform. This approach does not require repeated measurements by translating the sample along the optical axis as in the conventional focus stacking method, and offers a computation-efficient alternative to obtain high-resolution images with extended depth of fields, complementary to the multi-slice ptychography.

Extending the depth of field for ptychography using complex-valued wavelets: publisher's note.

This publisher's note corrects an error in Eq. (3) of Opt. Lett.44, 503 (2019).OPLEDP0146-959210.1364/OL.44.000503.

Large Aperture and Wedged Multilayer Laue Lens for X-ray Nanofocusing.

Diffraction optics fabricated from multilayers offer an intriguing alternative to lithography-based zone plates due to their advantages of virtually limitless aspect ratio and extremely small feature size. However, other issues, intrinsic to thin-film deposition, such as film stress and deposition rate instability, for example, limit the total achievable aperture. Over the last decade, Multilayer Laue Lens (MLLs) have progressed from a mere curiosity with initial aperture sizes in the 3-10 µm range, to real beamline-deployed optics with apertures in the 40-50 µm range (X. Huang, et al., Scientific Reports 3, 3562 (2013); E. Nazaretski, et al., Rev. Sci. Instrum. 85, 033707 (2014); E. Nazaretski, et al., Journal of Synchrotron Radiation 24, 1113 (2017)). By optimizing deposition conditions and incorporating new materials, MLLs have now broken the 100 µm thickness milestone. A flat WSi2/Al-Si MLL with a deposition thickness of 102 µm, the largest MLL to date, is reviewed. New large aperture wedged MLLs (wMLL), which were first fabricated by APS in 2006 using the WSi2/Si material system, are presented which demonstrate high focusing efficiency across a broad energy range. These results confirm findings by other groups who have also independently fabricated wMLL (A. J. Morgan, et al., Scientific Reports 5, 9892 (2015); S. Bajt, et al., Nature Light: Science and Applications 7, 17162 (2017)) based on a similar material system.

Measuring Three-Dimensional Strain and Structural Defects in a Single InGaAs Nanowire Using Coherent X-ray Multiangle Bragg Projection Ptychography.

III-As nanowires are candidates for near-infrared light emitters and detectors that can be directly integrated onto silicon. However, nanoscale to microscale variations in structure, composition, and strain within a given nanowire, as well as variations between nanowires, pose challenges to correlating microstructure with device performance. In this work, we utilize coherent nanofocused X-rays to characterize stacking defects and strain in a single InGaAs nanowire supported on Si. By reconstructing diffraction patterns from the 21̅1̅0 Bragg peak, we show that the lattice orientation varies along the length of the wire, while the strain field along the cross-section is largely unaffected, leaving the band structure unperturbed. Diffraction patterns from the 011̅0 Bragg peak are reproducibly reconstructed to create three-dimensional images of stacking defects and associated lattice strains, revealing sharp planar boundaries between different crystal phases of wurtzite (WZ) structure that contribute to charge carrier scattering. Phase retrieval is made possible by developing multiangle Bragg projection ptychography (maBPP) to accommodate coherent nanodiffraction patterns measured at arbitrary overlapping positions at multiple angles about a Bragg peak, eliminating the need for scan registration at different angles. The penetrating nature of X-ray radiation, together with the relaxed constraints of maBPP, will enable the in operando imaging of nanowire devices.

Achieving diffraction-limited nanometer-scale X-ray point focus with two crossed multilayer Laue lenses: alignment challenges.

We discuss misalignment-induced aberrations in a pair of crossed multilayer Laue lenses used for achieving a nanometer-scale x-ray point focus. We thoroughly investigate the impacts of two most important contributions, the orthogonality and the separation distance between two lenses. We find that misalignment in the orthogonality results in astigmatism at 45° and other inclination angles when coupled with a separation distance error. Theoretical explanation and experimental verification are provided. We show that to achieve a diffraction-limited point focus, accurate alignment of the azimuthal angle is required to ensure orthogonality between two lenses, and the required accuracy is scaled with the ratio of the focus size to the aperture size.

Hard x-ray scanning imaging achieved with bonded multilayer Laue lenses.

We report scanning hard x-ray imaging with a monolithic focusing optic consisting of two multilayer Laue lenses (MLLs) bonded together. With optics pre-characterization and accurate control of the bonding process, we show that a common focal plane for both MLLs can be realized at 9.317 keV. Using bonded MLLs, we obtained a scanning transmission image of a star test pattern with a resolution of 50 × 50 nm2. By applying a ptychography algorithm, we obtained a probe size of 17 × 38 nm2 and an object image with a resolution of 13 × 13 nm2. The significant reduction in alignment complexity for bonded MLLs will greatly extend the application range in both scanning and full-field x-ray microscopies.

Electrochemical (de)lithiation of silver ferrite and composites: mechanistic insights from ex situ, in situ, and operando X-ray techniques.

The structure of pristine AgFeO2 and phase makeup of Ag0.2FeO1.6 (a one-pot composite comprised of nanocrystalline stoichiometric AgFeO2 and amorphous γ-Fe2O3 phases) was investigated using synchrotron X-ray diffraction. A new stacking-fault model was proposed for AgFeO2 powder synthesized using the co-precipitation method. The lithiation/de-lithiation mechanisms of silver ferrite, AgFeO2 and Ag0.2FeO1.6 were investigated using ex situ, in situ, and operando characterization techniques. An amorphous γ-Fe2O3 component in the Ag0.2FeO1.6 sample is quantified. Operando XRD of electrochemically reduced AgFeO2 and Ag0.2FeO1.6 composites demonstrated differences in the structural evolution of the nanocrystalline AgFeO2 component. As complimentary techniques to XRD, ex situ X-ray Absorption Spectroscopy (XAS) provided insight into the short-range structure of the (de)lithiated nanocrystalline electrodes, and a novel in situ high energy X-ray fluorescence nanoprobe (HXN) mapping measurement was applied to spatially resolve the progression of discharge. Based on the results, a redox mechanism is proposed where the full reduction of Ag+ to Ag0 and partial reduction of Fe3+ to Fe2+ occur on reduction to 1.0 V, resulting in a Li1+yFeIIIFeIIyO2 phase. The Li1+yFeIIIFeIIyO2 phase can then reversibly cycle between Fe3+ and Fe2+ oxidation states, permitting good capacity retention over 50 cycles. In the Ag0.2FeO1.6 composite, a substantial amorphous γ-Fe2O3 component is observed which discharges to rock salt LiFe2O3 and Fe0 metal phase in the 3.5-1.0 V voltage range (in parallel with the AgFeO2 mechanism), and reversibly reoxidizes to a nanocrystalline iron oxide phase.

Achieving hard X-ray nanofocusing using a wedged multilayer Laue lens.

We report on the fabrication and the characterization of a wedged multilayer Laue lens for x-ray nanofocusing. The lens was fabricated using a sputtering deposition technique, in which a specially designed mask was employed to introduce a thickness gradient in the lateral direction of the multilayer. X-ray characterization shows an efficiency of 27% and a focus size of 26 nm at 14.6 keV, in a good agreement with theoretical calculations. These results indicate that the desired wedging is achieved in the fabricated structure. We anticipate that continuous development on wedged MLLs will advance x-ray nanofocusing optics to new frontiers and enrich capabilities and opportunities for hard X-ray microscopy.

Optimization of overlap uniformness for ptychography.

We demonstrate the advantages of imaging with ptychography scans that follow a Fermat spiral trajectory. This scan pattern provides a more uniform coverage and a higher overlap ratio with the same number of scan points over the same area than the presently used mesh and concentric [13] patterns. Under realistically imperfect measurement conditions, numerical simulations show that the quality of the reconstructed image is improved significantly with a Fermat spiral compared with a concentric scan pattern. The result is confirmed by the performance enhancement with experimental data, especially under low-overlap conditions. These results suggest that the Fermat spiral pattern increases the quality of the reconstructed image and tolerance to data with imperfections.

Genome-wide association analysis reveals potential genetic correlation and causality between circulating inflammatory proteins and amyotrophic lateral sclerosis.

BACKGROUND: Amyotrophic Lateral Sclerosis (ALS), a fatal neurodegenerative disease, continues to elude complete comprehension of its pathological underpinnings. Recent focus on inflammation in ALS pathogenesis prompts this investigation into the genetic correlation and potential causal relationships between circulating inflammatory proteins and ALS. METHODS: Genome-wide association study (GWAS) data encompassing 91 circulating inflammatory protein measures from 14,824 individuals of European ancestry, alongside records from 27,205 ALS cases and 110,881 controls, were employed. Assessment of genetic correlation and overlap utilized LD score regression (LDSC), high-definition likelihood (HDL), and genetic analysis integrating pleiotropy and annotation (GPA) methodologies. Identification of shared genetic loci involved pleiotropy analysis, functional mapping and annotation (FUMA), and co-localization analysis. Finally, Mendelian randomization was applied to probe causal relationships between inflammatory proteins and ALS. RESULTS: Our investigation revealed significant genetic correlation and overlap between ALS and various inflammatory proteins, including C-C motif chemokine 28, Interleukin-18, C-X-C motif chemokine 1, and Leukemia inhibitory factor receptor (LIFR). Pleiotropy analysis uncovered shared variations at specific genetic loci, some of which bore potential harm. Mendelian randomization analysis suggested that alterations in specific inflammatory protein levels, notably LIFR, could impact ALS risk. CONCLUSIONS: Our findings uncover a genetic correlation between certain circulating inflammatory proteins and ALS, suggesting their possible causal involvement in ALS pathogenesis. Moreover, the identification of LIFR as a crucial protein may yield new insights into ALS pathomechanisms and offer a promising avenue for therapeutic interventions. These discoveries provide novel perspectives for advancing the comprehension of ALS pathophysiology and exploring potential therapeutic avenues.

A diagnostic model based on bioinformatics and machine learning to differentiate bipolar disorder from schizophrenia and major depressive disorder.

Bipolar disorder (BD) showed the highest suicide rate of all psychiatric disorders, and its underlying causative genes and effective treatments remain unclear. During diagnosis, BD is often confused with schizophrenia (SC) and major depressive disorder (MDD), due to which patients may receive inadequate or inappropriate treatment, which is detrimental to their prognosis. This study aims to establish a diagnostic model to distinguish BD from SC and MDD in multiple public datasets through bioinformatics and machine learning and to provide new ideas for diagnosing BD in the future. Three brain tissue datasets containing BD, SC, and MDD were chosen from the Gene Expression Omnibus database (GEO), and two peripheral blood datasets were selected for validation. Linear Models for Microarray Data (Limma) analysis was carried out to identify differentially expressed genes (DEGs). Functional enrichment analysis and machine learning were utilized to identify. Least absolute shrinkage and selection operator (LASSO) regression was employed for identifying candidate immune-associated central genes, constructing protein-protein interaction networks (PPI), building artificial neural networks (ANN) for validation, and plotting receiver operating characteristic curve (ROC curve) for differentiating BD from SC and MDD and creating immune cell infiltration to study immune cell dysregulation in the three diseases. RBM10 was obtained as a candidate gene to distinguish BD from SC. Five candidate genes (LYPD1, HMBS, HEBP2, SETD3, and ECM2) were obtained to distinguish BD from MDD. The validation was performed by ANN, and ROC curves were plotted for diagnostic value assessment. The outcomes exhibited the prediction model to have a promising diagnostic value. In the immune infiltration analysis, Naive B, Resting NK, and Activated Mast Cells were found to be substantially different between BD and SC. Naive B and Memory B cells were prominently variant between BD and MDD. In this study, RBM10 was found as a candidate gene to distinguish BD from SC; LYPD1, HMBS, HEBP2, SETD3, and ECM2 serve as five candidate genes to distinguish BD from MDD. The results obtained from the ANN network showed that these candidate genes could perfectly distinguish BD from SC and MDD (76.923% and 81.538%, respectively).

Three-dimensional nanoscale metal, metal oxide, and semiconductor frameworks through DNA-programmable assembly and templating.

Controlling the three-dimensional (3D) nanoarchitecture of inorganic materials is imperative for enabling their novel mechanical, optical, and electronic properties. Here, by exploiting DNA-programmable assembly, we establish a general approach for realizing designed 3D ordered inorganic frameworks. Through inorganic templating of DNA frameworks by liquid- and vapor-phase infiltrations, we demonstrate successful nanofabrication of diverse classes of inorganic frameworks from metal, metal oxide and semiconductor materials, as well as their combinations, including zinc, aluminum, copper, molybdenum, tungsten, indium, tin, and platinum, and composites such as aluminum-doped zinc oxide, indium tin oxide, and platinum/aluminum-doped zinc oxide. The open 3D frameworks have features on the order of nanometers with architecture prescribed by the DNA frames and self-assembled lattice. Structural and spectroscopic studies reveal the composition and organization of diverse inorganic frameworks, as well as the optoelectronic properties of selected materials. The work paves the road toward establishing a 3D nanoscale lithography.

Optimization of multilayer Laue lenses for a scanning X-ray microscope.

Multilayer Laue lenses (MLLs) have demonstrated great capabilities for efficiently focusing hard X-rays down to the nanometer scale. Optimized use of MLLs in a scanning X-ray microscope requires careful consideration of a number of practical parameters other than resolution and efficiency in order to optimize the microscope's performance and scientific throughput. Here, relationships among the apodization effect owing to the presence of a beamstop, the monochromaticity requirement and the allowable working distance are discussed, as well as their impacts on the performance of the optics. Based on these discussions, optimal MLL schemes aiming at 10 nm resolution for a scanning X-ray microscope for the Hard X-ray Nanoprobe (HXN) beamline at National Synchrotron Light Source II are presented.

Ion beam lithography for Fresnel zone plates in X-ray microscopy.

Fresnel Zone Plates (FZP) are to date very successful focusing optics for X-rays. Established methods of fabrication are rather complex and based on electron beam lithography (EBL). Here, we show that ion beam lithography (IBL) may advantageously simplify their preparation. A FZP operable from the extreme UV to the limit of the hard X-ray was prepared and tested from 450 eV to 1500 eV. The trapezoidal profile of the FZP favorably activates its 2nd order focus. The FZP with an outermost zone width of 100 nm allows the visualization of features down to 61, 31 and 21 nm in the 1st, 2nd and 3rd order focus respectively. Measured efficiencies in the 1st and 2nd order of diffraction reach the theoretical predictions.

Deep learning enables nanoscale X-ray 3D imaging with limited data.

Deep neural network can greatly improve tomography reconstruction with limited data. A recent effort of combining ptycho-tomography model with the 3D U-net demonstrated a significant reduction in both the number of projections and computation time, and showed its potential for integrated circuit imaging that requires high-resolution and fast measurement speed.

Self-absorption correction on 2D X-ray fluorescence maps.

X-ray fluorescence mapping (XRF) is a highly efficient and non-invasive technique for quantifying material composition with micro and nanoscale spatial resolutions. Quantitative XRF analysis, however, confronts challenges from the long-lasting problem called self-absorption. Moreover, correcting two-dimensional XRF mapping datasets is particularly difficult because it is an ill-posed inverse problem. Here we report a semi-empirical method that can effectively correct 2D XRF mapping data. The correction error is generally less than 10% from a comprehensive evaluation of the accuracy in various configurations. The proposed method was applied to quantify the composition distribution around the grain boundaries in an electrochemically corroded stainless steel sample. Highly localized Cr enrichment was found around the crack sites, which was invisible before the absorption correction.

RadVolViz: An Information Display-Inspired Transfer Function Editor for Multivariate Volume Visualization.

In volume visualization transfer functions are widely used for mapping voxel properties to color and opacity. Typically, volume density data are scalars which require simple 1D transfer functions to achieve this mapping. If the volume densities are vectors of three channels, one can straightforwardly map each channel to either red, green or blue, which requires a trivial extension of the 1D transfer function editor. We devise a new method that applies to volume data with more than three channels. These types of data often arise in scientific scanning applications, where the data are separated into spectral bands or chemical elements. Our method expands on prior work in which a multivariate information display, RadViz, was fused with a radial color map, in order to visualize multi-band 2D images. In this work, we extend this joint interface to blended volume rendering. The information display allows users to recognize the presence and value distribution of the multivariate voxels and the joint volume rendering display visualizes their spatial distribution. We design a set of operators and lenses that allow users to interactively control the mapping of the multivariate voxels to opacity and color. This enables users to isolate or emphasize volumetric structures with desired multivariate properties. Furthermore, it turns out that our method also enables more insightful displays even for RGB data. We demonstrate our method with three datasets obtained from spectral electron microscopy, high energy X-ray scanning, and atmospheric science.