Using convolutional neural network denoising to reduce ambiguity in X-ray coherent diffraction imaging.

The inherent ambiguity in reconstructed images from coherent diffraction imaging (CDI) poses an intrinsic challenge, as images derived from the same dataset under varying initial conditions often display inconsistencies. This study introduces a method that employs the Noise2Noise approach combined with neural networks to effectively mitigate these ambiguities. We applied this methodology to hundreds of ambiguous reconstructed images retrieved from a single diffraction pattern using a conventional retrieval algorithm. Our results demonstrate that ambiguous features in these reconstructions are effectively treated as inter-reconstruction noise and are significantly reduced. The post-Noise2Noise treated images closely approximate the average and singular value decomposition analysis of various reconstructions, providing consistent and reliable reconstructions.

The novel role of ER protein TXNDC5 in the pathogenesis of organ fibrosis: mechanistic insights and therapeutic implications.

Fibrosis-related disorders account for an enormous burden of disease-associated morbidity and mortality worldwide. Fibrosis is defined by excessive extracellular matrix deposition at fibrotic foci in the organ tissue following injury, resulting in abnormal architecture, impaired function and ultimately, organ failure. To date, there lacks effective pharmacological therapy to target fibrosis per se, highlighting the urgent need to identify novel drug targets against organ fibrosis. Recently, we have discovered the critical role of a fibroblasts-enriched endoplasmic reticulum protein disulfide isomerase (PDI), thioredoxin domain containing 5 (TXNDC5), in cardiac, pulmonary, renal and liver fibrosis, showing TXNDC5 is required for the activation of fibrogenic transforming growth factor-ß signaling cascades depending on its catalytic activity as a PDI. Moreover, deletion of TXNDC5 in fibroblasts ameliorates organ fibrosis and preserves organ function by inhibiting myofibroblasts activation, proliferation and extracellular matrix production. In this review, we detailed the molecular and cellular mechanisms by which TXNDC5 promotes fibrogenesis in various tissue types and summarized potential therapeutic strategies targeting TXNDC5 to treat organ fibrosis.

Glial response to hypoxia in mutants of NPAS1/3 homolog Trachealess through Wg signaling to modulate synaptic bouton organization.

Synaptic structure and activity are sensitive to environmental alterations. Modulation of synaptic morphology and function is often induced by signals from glia. However, the process by which glia mediate synaptic responses to environmental perturbations such as hypoxia remains unknown. Here, we report that, in the mutant for Trachealess (Trh), the Drosophila homolog for NPAS1 and NPAS3, smaller synaptic boutons form clusters named satellite boutons appear at larval neuromuscular junctions (NMJs), which is induced by the reduction of internal oxygen levels due to defective tracheal branches. Thus, the satellite bouton phenotype in the trh mutant is suppressed by hyperoxia, and recapitulated in wild-type larvae raised under hypoxia. We further show that hypoxia-inducible factor (HIF)-1α/Similar (Sima) is critical in mediating hypoxia-induced satellite bouton formation. Sima upregulates the level of the Wnt/Wingless (Wg) signal in glia, leading to reorganized microtubule structures within presynaptic sites. Finally, hypoxia-induced satellite boutons maintain normal synaptic transmission at the NMJs, which is crucial for coordinated larval locomotion.

Glia-derived exosomal miR-274 targets Sprouty in trachea and synaptic boutons to modulate growth and responses to hypoxia.

Secreted exosomal microRNAs (miRNAs) mediate interorgan/tissue communications by modulating target gene expression, thereby regulating developmental and physiological functions. However, the source, route, and function in target cells have not been formally established for specific miRNAs. Here, we show that glial miR-274 non-cell-autonomously modulates the growth of synaptic boutons and tracheal branches. Whereas the precursor form of miR-274 is expressed in glia, the mature form of miR-274 distributes broadly, including in synaptic boutons, muscle cells, and tracheal cells. Mature miR-274 is secreted from glia to the circulating hemolymph as an exosomal cargo, a process requiring ESCRT components in exosome biogenesis and Rab11 and Syx1A in exosome release. We further show that miR-274 can function in the neurons or tracheal cells to modulate the growth of synaptic boutons and tracheal branches, respectively. Also, miR-274 uptake into the target cells by AP-2-dependent mechanisms modulates target cell growth. In the target cells, miR-274 down-regulates Sprouty (Sty) through a targeting sequence at the sty 3' untranslated region, thereby enhancing MAPK signaling and promoting cell growth. miR-274 expressed in glia of an mir-274 null mutant is released as an exosomal cargo in the circulating hemolymph, and such glial-specific expression resets normal levels of Sty and MAPK signaling and modulates target cell growth. mir-274 mutant larvae are hypersensitive to hypoxia, which is suppressed by miR-274 expression in glia or by increasing tracheal branches. Thus, glia-derived miR-274 coordinates growth of synaptic boutons and tracheal branches to modulate larval hypoxia responses.

Hard X-ray ptychography at Taiwan Photon Source at 11-20†nm spatial resolution.

X-ray ptychography, a technique based on scanning and processing of coherent diffraction patterns, is a non-destructive imaging technique with a high spatial resolution far beyond the focused beam size. Earlier demonstrations of hard X-ray ptychography at Taiwan Photon Source (TPS) using an in-house program successfully recorded the ptychographic diffraction patterns from a gold-made Siemens star as a test sample and retrieved the finest inner features of 25 nm. Ptychography was performed at two beamlines with different focusing optics: a pair of Kirkpatrick-Baez mirrors and a pair of nested Montel mirrors, for which the beam sizes on the focal planes were 3 µm and 200 nm and the photon energies were from 5.1 keV to 9 keV. The retrieved spatial resolutions are 20 nm to 11 nm determined by the 10-90% line-cut method and half-bit threshold of Fourier shell correlation. This article describes the experimental conditions and compensation methods, including position correction, mixture state-of-probe, and probe extension methods, of the aforementioned experiments. The discussions will highlight the criteria of ptychographic experiments at TPS as well as the opportunity to characterize beamlines by measuring factors such as the drift or instability of beams or stages and the coherence of beams. Besides, probe functions, the full complex fields illuminated on samples, can be recovered simultaneously using ptychography. Theoretically, the wavefield at any arbitrary position can be estimated from one recovered probe function undergoing wave-propagating. The verification of probe-propagating has been carried out by comparing the probe functions obtained by ptychography and undergoing wave-propagating located at 0, 500 and 1000 µm relative to the focal plane.

Integrated optical chip for a high-resolution, single-resonance-mode x-ray monochromator system.

An integrated optical chip that minimizes the size of the energy-tuning single-resonance-mode x-ray monochromator system into a 3cm×5cm silicon wafer is proposed. A Fabry-Perot x-ray resonator and two back-reflecting Si mirrors are employed on the wafer as the optical components, where Si(12 4 0) back reflection is used for both Fabry-Perot resonance and re-diffraction of the x-ray beams from the resonator in the incident direction. We can achieve an energy bandwidth of 3.4 meV in single-mode x rays and tune the energy by temperature variation. Such Si chips can be readily employed at the synchrotron beamlines and conventional x-ray laboratories for high-resolution investigations.

Synchrotron X-Ray Analysis and Morphology Evidence for Stereo-Assemblies of Periodic Aggregates in Poly(3-hydroxybutyrate) with Unusual Photonic Iridescence.

3D morphology of poly(3-hydroxybutyrate) (PHB), crystallized in the presence of diluents of poly(1,3-trimethylene adipate) and poly(ethylene oxide), is probed using a novel approach coupled with selective etching. For interpreting the mechanisms of crystal periodic aggregation, various microscopic techniques and synchrotron microbeam X-ray analysis are used to observe the top surface in connection with the 3D crystal assemblies. Periodic grating architectures, with the cross-bar pitch exactly matching with the optical band spacing, are proved in banded PHB. The crystals under the ridge branch out to spawn finer crystals orienting/bending horizontally underneath the valley band, repeating till species drainage or impingement. The grating structure in the banded PHB resembles many nature's iridescence crystals and is further proved by photonic reflection results as a critical breakthrough novel finding.

Time-resolved X-ray reflection phases of the nearly forbidden Si(222) reflection under laser excitation.

The covalent electron density, which makes Si(222) measurable, is subject to laser excitation. The three-wave Si(222)/(13 {\overline 1}) diffraction at 7.82 keV is used for phase measurements. It is found that laser excitation causes a relative phase change of around 4° in Si(222) in the first 100 ps of excitation and this is gradually recovered over several nanoseconds. This phase change is due to laser excitation of covalent electrons around the silicon atoms in the unit cell and makes the electron density deviate further from the centrosymmetric distribution.

Design, fabrication, and characterization of a multidimensional prism.

In this research, a novel multidimensional prism with three distinct 45°, 135°, and 225° inclined optical surfaces were realized by using inclined exposure technology and SU-8 polymer. To obtain a smooth surface, the solvent loss percentage and temperature of post-exposure bake (PEB) are two key factors that need to be well controlled during fabrication. The experimental results showed that surface roughness can achieve 42.9±7.6 nm, which is one-tenth of high-precision machining or molding processes, under the processes parameter combinations of PEB temperature, and solvent loss percentage is 95°C and 82.86%, respectively. The surface reflectivity of the prism was measured by using a He-Ne laser, and reflectivity of the prism surface without and with aluminum metal film was 90.8% and 91.8%, respectively. The slight difference of reflectivity means that a prism with a high-quality inclined surface can be realized. The functionality of the prism for three lasers was also verified with RGB lasers, and it successfully demonstrated the feasibility of application of a multidimensional prism on the optical system. Finally, the utilization of inclined exposure technology not only monolithically integrates three 45° inclined surfaces into one prism without precision assembly but also greatly simplifies the fabrication processes to further reduce the cost. This component and technology can also be applied to medical endoscope systems if the SU-8 is replaced by PDMS or other biocompatible materials using a molding process. These results provide the potential for mass manufacturing, which is of considerable value to the optical markets.

High-resolution monochromator using a high-efficiency single-mode x-ray resonator at Laue incidence.

We report a high-resolution and high-efficiency monochromator with energy resolution, ΔE/E∼2.08*10-7, utilizing a hard x-ray single-mode Fabry-Perot (FP) resonator at Laue incidence at 14.4388 keV. Instead of using multiple-crystal diffraction via several asymmetric-cut crystals, a 3 meV single-peak is generated from the interference of a Si-made two-plate cavity with a thickness of 70 µm and a gap of 45 µm, where a (0-40) Laue reflection is used to excite the backreflection (12 4 0) for the enhancement of the FP efficiency. Due to the large angular acceptance of (12 4 0) and (0-40), the energy tunability can be achieved by changing the incident angle into the resonator. The application of x-ray resonators at Laue incidence as a monochromator can be further implemented to x-ray optics.