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Interactions between the microbiota and their colonized environments mediate critical pathways from biogeochemical cycles to homeostasis in human health. Here we report a soil-inspired chemical system that consists of nanostructured minerals, starch granules and liquid metals. Fabricated via a bottom-up synthesis, the soil-inspired chemical system can enable chemical redistribution and modulation of microbial communities. We characterize the composite, confirming its structural similarity to the soil, with three-dimensional X-ray fluorescence and ptychographic tomography and electron microscopy imaging. We also demonstrate that post-synthetic modifications formed by laser irradiation led to chemical heterogeneities from the atomic to the macroscopic level. The soil-inspired material possesses chemical, optical and mechanical responsiveness to yield write-erase functions in electrical performance. The composite can also enhance microbial culture/biofilm growth and biofuel production in vitro. Finally, we show that the soil-inspired system enriches gut bacteria diversity, rectifies tetracycline-induced gut microbiome dysbiosis and ameliorates dextran sulfate sodium-induced rodent colitis symptoms within in vivo rodent models.

Here we demonstrate a theory-driven, novel dual-shell coating system of Li2SrSiO4 and Al2O3, achieved via a facile and scalable sol-gel technique on LiCoO2 electrode particles. The optimal thickness of each coating can lead to increased specific capacity (∼185 mAh/g at 0.5 C-rate) at a cut-off potential of 4.5 V, and greater cycling stability at very high C rates (up to 10 C) in half-cells with lithium metal. The mechanism of this superior performance was investigated using a combination of X-ray and electron characterization methods. It shows that the results of this investigation can inform future studies to identify still better dual-shell coating schemes, achieved by such industrially feasible techniques, for application on similar, nickel-rich cathode materials.

We study the assembly of DNA-functionalized nanocubes under lateral confinement in microscale square trenches on a DNA-functionalized substrate. Microfocus small-angle X-ray scattering (SAXS) and scanning electron microscopy (SEM) are used to characterize the superlattices (SLs). The results indicate that nanocubes form simple-cubic SLs with square-prism morphology and a (100) out-of-plane orientation to maximize DNA bonding. In-plane, SLs align with the template, exposing their {100} side facets, and the degree of alignment depends on trench size. Interestingly, the distribution of in-plane orientations determined from SAXS and SEM do not agree, indicating that the internal and external structures of the SLs differ. To understand this discrepancy, X-ray ptychography is employed to image the internal structures of the SLs, revealing that SLs which appear to be single-crystalline in SEM may have subsurface grain boundaries, depending on trench size. SEM reveals that the SLs grow via nucleation and growth of randomly oriented domains, which then coalesce; this mechanism explains the observed dependence of alignment and defect structure on size. Interestingly, crystallization occurs via an unusual growth mode, whereby continuous SL layers grow on top of several misoriented islands. Overall, this work elucidates the effect of lateral confinement on the crystallization of DNA-functionalized nanoparticles and shows how X-ray ptychography can be used to gain insight into nanoparticle crystallization.

X-ray ptychographic tomography is a nondestructive method for three dimensional (3D) imaging with nanometer-sized resolvable features. The size of the volume that can be imaged is almost arbitrary, limited only by the penetration depth and the available scanning time. Here we present a method that rapidly accelerates the imaging operation over a given volume through acquiring a limited set of data via large angular reduction and compensating for the resulting ill-posedness through deeply learned priors. The proposed 3D reconstruction method “RAPID” relies initially on a subset of the object measured with the nominal number of required illumination angles and treats the reconstructions from the conventional two-step approach as ground truth. It is then trained to reproduce equal fidelity from much fewer angles. After training, it performs with similar fidelity on the hitherto unexamined portions of the object, previously not shown during training, with a limited set of acquisitions. In our experimental demonstration, the nominal number of angles was 349 and the reduced number of angles was 21, resulting in a $$\times 140$$ × 140 aggregate speedup over a volume of $$4.48\times 93.18\times 3.92\, \upmu \text {m}^3$$ 4.48 × 93.18 × 3.92 μ m 3 and with $$(14\,\text {nm})^3$$ ( 14 nm ) 3 feature size, i.e. $$\sim 10^8$$ ∼ 10 8 voxels. RAPID’s key distinguishing feature over earlier attempts is the incorporation of atrous spatial pyramid pooling modules into the deep neural network framework in an anisotropic way. We found that adjusting the atrous rate improves reconstruction fidelity because it expands the convolutional kernels’ range to match the physics of multi-slice ptychography without significantly increasing the number of parameters.

Single-crystal Ni-rich Li[Ni

Doping have been considered as a prominent strategy to stabilize crystal structure of battery materials during the insertion and removal of alkali ions. The instructive knowledge and experience acquired from doping strategies predominate in cathode materials, but doping principle in anodes remains unclear. Here, we demonstrate that trace element doping enables stable conversion-reaction and ensures structural integrity for potassium ion battery (PIB) anodes. With a synergistic combination of X-ray tomography, structural probes, and charge reconfiguration, we encode the physical origins and structural evolution of electro-chemo-mechanical degradation in PIB anodes. By the multiple ion transport pathways created by the orderly hierarchical pores from “surface to bulk” and the homogeneous charge distribution governed in doped nanodomains, the anisotropic expansion can be significantly relieved with trace isoelectronic element doping into the host lattice, maintaining particle mechanical integrity. Our work presents a close relationship between doping chemistry and mechanical reliability, projecting a new pathway to reengineering electrode materials for next-generation energy storage.

Broadband X-ray ptychography is developed based on the multi-wavelength reconstruction method and is systematically demonstrated in both simulation and experiment. In addition, a combined reconstruction approach is proposed to further increase the ptychographic imaging rate., Ptychography is a rapidly developing scanning microscopy which is able to view the internal structures of samples at a high resolution beyond the illumination size. The achieved spatial resolution is theoretically dose-limited. A broadband source can provide much higher flux compared with a monochromatic source; however, it conflicts with the necessary coherence requirements of this coherent diffraction imaging technique. In this paper, a multi-wavelength reconstruction algorithm has been developed to deal with the broad bandwidth in ptychography. Compared with the latest development of mixed-state reconstruction approach, this multi-wavelength approach is more accurate in the physical model, and also considers the spot size variation as a function of energy due to the chromatic focusing optics. Therefore, this method has been proved in both simulation and experiment to significantly improve the reconstruction when the source bandwidth, illumination size and scan step size increase. It is worth mentioning that the accurate and detailed information of the energy spectrum for the incident beam is not required in advance for the proposed method. Further, we combine multi-wavelength and mixed-state approaches to jointly solve temporal and spatial partial coherence in ptychography so that it can handle various disadvantageous experimental effects. The significant relaxation in coherence requirements by our approaches allows the use of high-flux broadband X-ray sources for high-efficient and high-resolution ptychographic imaging.

In this article, a systematic framework for designing the control for fine positioning (scanning) stages of X-ray microscopes is presented. This framework facilitates designs that simultaneously achieve specifications on positioning resolution and tracking bandwidth while guaranteeing robustness of the closed loop device to unmodeled uncertainties. We use robust optimal control techniques for modeling, quantifying design objectives and system-specific challenges, and designing the control laws. The control designs were implemented on a three degree of freedom piezoactuated flexure stages dedicated for fine positioning of X-ray optics. Experimental results demonstrate significant improvements in positioning performance of 134%, 150%, and 132% in tracking bandwidths along the lateral ( X ), vertical ( Y ), and beam ( Z ) directions, respectively, when compared to proportional–integral–derivative controller designs. This was achieved while keeping similar or better positioning resolution and robustness measures. Fast scanning for X-ray imaging was demonstrated in both the step scan and flyscan modes, where bandwidth was improved by over 450 times with flyscan compared to the step scan.

Summary Halide perovskites have emerged as a new class of inorganic-based soft semiconductors that are revolutionizing the field of (opto)electronics. However, the fundamental structures and properties or functions of halide perovskites are still far from being fully understood, calling for the need of precise, quantitative, and high-spatiotemporal-resolution characterizations. As one of the most powerful multimodal characterization techniques, synchrotron radiation offers high-brilliance X-ray beams for high-resolution observations across multiple length scales obtained within extremely short time spans. Performing a brief review of synchrotron-based perovskite studies in the literature, here we provide perspectives on the use of synchrotron characterizations not only for studying multiple-length-scale structures and dynamic variations of perovskite materials, but also for in situ monitoring of device functions and dynamics. The goal of this perspective is to present many capabilities and evoke emerging opportunities of synchrotron characterizations for providing decisive answers to the outstanding science problems in the perovskite field, pushing forward the technological development.

X-ray ptychography imaging at synchrotron facilities like the Advanced Photon Source (APS) involves controlling instrument hardwares to collect a set of diffraction patterns from overlapping coherent illumination spots on extended samples, managing data storage, reconstructing ptychographic images from acquired diffraction patterns, and providing the visualization of results and feedback. In addition to the complicated workflow, ptychography instrument could produce up to several TB's of data per second that is needed to be processed in real time. This brings up the need to develop a high performance, robust and user friendly processing software package for ptychographic data analysis. In this paper we present a software framework which provides functionality of visualization, work flow control, and data reconstruction. To accelerate the computation and large datasets process, the data reconstruction part is implemented with three algorithms, ePIE, DM and LSQML using CUDA-C on GPU., Comment: X-Ray Nanoimaging: Instruments and Methods V

Simple Summary Metal-oxide nanomaterials enter cancer and normal cells even when not specifically targeted, and often interact with specific cellular structures and biological molecules solely due to their innate physical-chemical properties. This raises concerns for the use of nanoparticles, which can be alleviated only with rigorous studies of nanoparticle–cell interactions, studies independent of post-interaction labeling of nanomaterials. X-ray fluorescence microscopy is an imaging technique that quantifies and maps all chemical elements from the periodic table solely based on their native fluorescence excited by the incoming X-ray. We used two different instruments to interrogate the same sample in 3D at two different resolutions and determine heterogeneity of cell-to-cell interactions with nanomaterials, as well as subcellular nanoparticle distribution. This is the first example of multi-scale 3D X-ray fluorescence imaging. This work begins a new era of study on how nanoparticle-based therapies can be developed to be more predictable and safer for use. Abstract Research in cancer nanotechnology is entering its third decade, and the need to study interactions between nanomaterials and cells remains urgent. Heterogeneity of nanoparticle uptake by different cells and subcellular compartments represent the greatest obstacles to a full understanding of the entire spectrum of nanomaterials’ effects. In this work, we used flow cytometry to evaluate changes in cell cycle associated with non-targeted nanocomposite uptake by individual cells and cell populations. Analogous single cell and cell population changes in nanocomposite uptake were explored by X-ray fluorescence microscopy (XFM). Very few nanoparticles are visible by optical imaging without labeling, but labeling increases nanoparticle complexity and the risk of modified cellular uptake. XFM can be used to evaluate heterogeneity of nanocomposite uptake by directly imaging the metal atoms present in the metal-oxide nanocomposites under investigation. While XFM mapping has been performed iteratively in 2D with the same sample at different resolutions, this study is the first example of serial tomographic imaging at two different resolutions. A cluster of cells exposed to non-targeted nanocomposites was imaged with a micron-sized beam in 3D. Next, the sample was sectioned for immunohistochemistry as well as a high resolution “zoomed in” X-ray fluorescence (XRF) tomography with 80 nm beam spot size. Multiscale XRF tomography will revolutionize our ability to explore cell-to-cell differences in nanomaterial uptake.

Ptychography has become a popular technique for high-throughput and high-resolution characterization of 2D/3D materials. When objects introduce significantly large phase shifts, a multi-slice model needs to be considered to account for long-distance wave propagation within the sample. Although many groups have demonstrated multi-slice ptychography using specimens that are several times larger than the depth of field (DOF), the benefits of applying the multi-slice ptychography algorithm on small objects within the DOF is rarely discussed. Here we address this question and demonstrate that multi-slice ptychography can play an important role in improving reconstruction quality for continuous objects that are smaller than the DOF.

Examining chemical and structural characteristics of micro-features in complex tissue matrices is essential for understanding biological systems. Advances in multimodal chemical and structural imaging using synchrotron radiation have overcome many issues in correlative imaging, enabling the characterization of distinct microfeatures at nanoscale resolution in ex vivo tissues. We present a nanoscale imaging method that pairs X-ray ptychography and X-ray fluorescence microscopy (XFM) to simultaneously examine structural features and quantify elemental content of microfeatures in complex ex vivo tissues. We examined the neuropathological microfeatures Lewy bodies, aggregations of superoxide dismutase 1 (SOD1) and neuromelanin in human post-mortem Parkinson's disease tissue. Although biometals play essential roles in normal neuronal biochemistry, their dyshomeostasis is implicated in Parkinson's disease aetiology. Here we show that Lewy bodies and SOD1 aggregates have distinct elemental fingerprints yet are similar in structure, whilst neuromelanin exhibits different elemental composition and a distinct, disordered structure. The unique approach we describe is applicable to the structural and chemical characterization of a wide range of complex biological tissues at previously unprecedented levels of detail., Structural and chemical characterisation of microfeatures in unadulterated Parkinson's disease brain tissue using synchrotron nanoscale XFM and ptychography.

Scanning of lightweight circular diffractive optics, separate from central stops and apertures, is emerging as an approach to exploit advances in synchrotron x-ray sources. We consider the effects in a scanning microscope of offsets between the optic and its central stop and find that scan ranges of up to about half the diameter of the optic are possible with only about a 10% increase in the focal spot width. For large scanning ranges, we present criteria for the working distance between the last aperture and the specimen to be imaged.

The lack of precision therapies combined with limited therapeutic access to intracranial tumor sites due to the presence of the blood-brain/blood-tumor barriers have contributed to glioblastoma (GBM) being one of the most difficult cancers to effectively treat. We have developed a novel precision medicine approach for GBM treatment that involves the use of brain-penetrant RNA interference (RNAi)-based spherical nucleic acids (SNAs). In this study, we used SNAs consisting of gold nanoparticle cores covalently conjugated with radially oriented and densely packed siRNA oligonucleotides. Based upon previous preclinical evaluation, we conducted toxicology and toxicokinetic studies in non-human primates, and a single-arm, open-label phase 0 first-in-human trial (NCT03020017) to determine safety, pharmacokinetics, intratumoral accumulation and gene-suppressive activity of systemically administered SNAs carrying siRNA specific for the GBM oncogene Bcl2Like12 (Bcl2L12). Patients with recurrent GBM were treated with intravenous administration of siBcl2L12-SNAs (drug moniker: NU-0129), at a dose corresponding to 1/50th of the no-observed-adverse-event-level (NOAEL), followed by tumor resection. Safety assessment revealed no significant treatment-related toxicities. Inductively coupled plasma mass spectrometry, X-ray fluorescence microscopy, and silver staining of resected GBM tissue demonstrated that intravenously administered SNAs reached patient tumors, with gold (Au) enrichment observed in the tumor-associated endothelium, macrophages and tumor cells. NU-0129 uptake into glioma cells correlated with significant reduction in tumor-associated Bcl2L12 protein expression, as indicated by comparison of NU-0129-treated recurrent vs. matched primary (i.e., untreated) tumor. Our results establish SNA nanoconjugates as a brain-penetrant precision medicine approach for the systemic treatment of GBM.

As a coherent diffraction imaging technique, ptychography provides high-spatial resolution beyond Rayleigh’s criterion of the focusing optics, but it is also sensitively affected by the decoherence coming from the spatial and temporal variations in the experiment. Here we show that high-speed ptychographic data acquisition with short exposure can effectively reduce the impact from experimental variations. To reach a cumulative dose required for a given resolution, we further demonstrate that a continuous multi-pass scan via high-speed ptychography can achieve high-resolution imaging. This low-dose scan strategy is shown to be more dose-efficient, and has potential for radiation-sensitive sample studies and time-resolved imaging.

X-ray ptychography has gained tremendous success in providing quantitative high-resolution imaging for extended samples. Here we report on recent developments in ptychography imaging techniques and the improvement of reconstruction methods to increase ptychographic imaging throughput at the Advanced Photon Source.

Additional file 1. Additional tables and figures.

The large volume of ptychographic dataset presents a challenge on computa- tional resources. We propose an unsupervised method that automatically identifies probes with diminished quality, and allows optimal distribution of resources on the most “informa- tive” dataset.

Supplemental Document

We describe and demonstrate an optimization-based X-ray image reconstruction framework called Adorym. Our framework provides a generic forward model, allowing one code framework to be used for a wide range of imaging methods ranging from near-field holography to fly-scan ptychographic tomography. By using automatic differentiation for optimization, Adorym has the flexibility to refine experimental parameters including probe positions, multiple hologram alignment, and object tilts. It is written with strong support for parallel processing, allowing large datasets to be processed on high-performance computing systems. We demonstrate its use on several experimental datasets to show improved image quality through parameter refinement. (C) 2021 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

Background Neuroblastoma is the most common extracranial solid malignancy in childhood which, despite the current progress in radiotherapy and chemotherapy protocols, still has a high mortality rate in high risk tumors. Nanomedicine offers exciting and unexploited opportunities to overcome the shortcomings of conventional medicine. The photocatalytic properties of Fe3O4 core-TiO2 shell nanocomposites and their potential for cell specific targeting suggest that nanoconstructs produced using Fe3O4 core-TiO2 shell nanocomposites could be used to enhance radiation effects in neuroblastoma. In this study, we evaluated bare, metaiodobenzylguanidine (MIBG) and 3,4-Dihydroxyphenylacetic acid (DOPAC) coated Fe3O4@TiO2 as potential radiosensitizers for neuroblastoma in vitro. Results The uptake of bare and MIBG coated nanocomposites modestly sensitized neuroblastoma cells to ionizing radiation. Conversely, cells exposed to DOPAC coated nanocomposites exhibited a five-fold enhanced sensitivity to radiation, increased numbers of radiation induced DNA double-strand breaks, and apoptotic cell death. The addition of a peptide mimic of the epidermal growth factor (EGF) to nanoconjugates coated with MIBG altered their intracellular distribution. Cryo X-ray fluorescence microscopy tomography of frozen hydrated cells treated with these nanoconjugates revealed cytoplasmic as well as nuclear distribution of the nanoconstructs. Conclusions The intracellular distribution pattern of different nanoconjugates used in this study was different for different nanoconjugate surface molecules. Cells exposed to DOPAC covered nanoconjugates showed the smallest nanoconjugate uptake, with the most prominent pattern of large intracellular aggregates. Interestingly, cells treated with this nanoconjugate also showed the most pronounced radiosensitization effect in combination with the external beam x-ray irradiation. Further studies are necessary to evaluate mechanistic basis for this increased radiosensitization effect. Preliminary studies with the nanoparticles carrying an EGF mimicking peptide showed that this approach to targeting could perhaps be combined with a different approach to radiosensitization – use of nanoconjugates in combination with the radioactive iodine. Much additional work will be necessary in order to evaluate possible benefits of targeted nanoconjugates carrying radionuclides. Graphic abstract Supplementary Information The online version contains supplementary material available at 10.1186/s12645-021-00081-z.

X-ray ptychography is a rapidly developing coherent diffraction imaging technique that provides nanoscale resolution on extended field-of-view. However, the requirement of coherence and the scanning mechanism limit the throughput of ptychographic imaging. In this paper, we propose X-ray ptychography using multiple illuminations instead of single illumination in conventional ptychography. Multiple locations of the sample are simultaneously imaged by spatially separated X-ray beams, therefore, the obtained field-of-view in one scan can be enlarged by a factor equal to the number of illuminations. We have demonstrated this technique experimentally using two X-ray beams focused by a house-made Fresnel zone plate array. Two areas of the object and corresponding double illuminations were successfully reconstructed from diffraction patterns acquired in one scan, with image quality similar with those obtained by conventional single-beam ptychography in sequence. Multi-beam ptychography approach increases the imaging speed, providing an efficient way for high-resolution imaging of large extended specimens.

The development of commercially friendly and stable catalysts for oxygen reduction reaction (ORR) is critical for many energy conversion systems such as fuel cells and metal-air batteries. Many Co-based perovskite oxides such as LaCoO3 have been discovered as the stable and active ORR catalysts, which can be good candidates to replace platinum (Pt). Although researchers have tried substituting various transition metals into the Co-based perovskite catalysts to improve the ORR performance, the influence of substitution on the ORR mechanism is rarely studied. In this paper, we explore the evolution of ORR mechanism after substituting Fe into LaCoO3, using the combination of X-ray photoelectron spectroscopy, high-resolution X-ray microscopy, X-ray diffraction, surface-sensitive soft X-ray absorption spectroscopy characterization, and electrochemical tests. We observed enhanced catalytic activities and increased electron transfer numbers during the ORR in Co-rich perovskite, which are attributed to the optimized eg filling numbers and the stronger hybridization of transition metal 3d and oxygen 2p bands. The discoveries in this paper provide deep insights into the ORR catalysis mechanism on metal oxides and new guidelines for the design of Pt-free ORR catalysts.

X-ray ptychography, a powerful scanning lensless imaging technique, has become attractive for nondestructively imaging internal structures at nanoscale. Stage positioning overhead in conventional step-scan ptychography is one of the limiting factors on the imaging throughput. In this work, we demonstrate the use of advanced fly scan ptychography to achieve high-resolution ptychograms of modern integrated circuits on a large field-of-view at millimeter scale. By completely removing stage overheads between scan points, the imaging time for millimeter-size sample can be significantly reduced. Furthermore, we implement the orthogonal probe relaxation technique to overcome the variation of illumination across the large scan area as well as local vibrations. The capability of x-ray ptychography shown here is broadly applicable for various studies, which requires both high spatial resolution and large scan area.

X-ray ptychography is being utilized for a wide range of imaging experiments with a resolution beyond the limit of the X-ray optics used. Here, strategies for data sampling and for increasing imaging throughput when the specimen is at the focus of an X-ray beam are discussed, and the tradeoffs between large and small illumination spots are examined., X-ray ptychography is being utilized for a wide range of imaging experiments with a resolution beyond the limit of the X-ray optics used. Introducing a parameter for the ptychographic resolution gain G p (the ratio of the beam size over the achieved pixel size in the reconstructed image), strategies for data sampling and for increasing imaging throughput when the specimen is at the focus of an X-ray beam are considered. The tradeoffs between large and small illumination spots are examined.