High-resolution, large field-of-view label-free imaging via aberration-corrected, closed-form complex field reconstruction.

Computational imaging methods empower modern microscopes to produce high-resolution, large field-of-view, aberration-free images. Fourier ptychographic microscopy can increase the space-bandwidth product of conventional microscopy, but its iterative reconstruction methods are prone to parameter selection and tend to fail under excessive aberrations. Spatial Kramers-Kronig methods can analytically reconstruct complex fields, but is limited by aberration or providing extended resolution enhancement. Here, we present APIC, a closed-form method that weds the strengths of both methods while using only NA-matching and darkfield measurements. We establish an analytical phase retrieval framework which demonstrates the feasibility of analytically reconstructing the complex field associated with darkfield measurements. APIC can retrieve complex aberrations of an imaging system with no additional hardware and avoids iterative algorithms, requiring no human-designed convergence metrics while always obtaining a closed-form complex field solution. We experimentally demonstrate that APIC gives correct reconstruction results where Fourier ptychographic microscopy fails when constrained to the same number of measurements. APIC achieves 2.8 times faster computation using image tile size of 256 (length-wise), is robust against aberrations compared to Fourier ptychographic microscopy, and capable of addressing aberrations whose maximal phase difference exceeds 3.8π when using a NA 0.25 objective in experiment.

The SmMYC2-SmMYB36 complex is involved in methyl jasmonate-mediated tanshinones biosynthesis in Salvia miltiorrhiza.

The jasmonic acid (JA) signaling pathway plays an important role in promoting the biosynthesis of tanshinones. While individual transcription factors have been extensively studied in the context of tanshinones biosynthesis regulation, the influence of methyl jasmonate (MeJA)-induced transcriptional complexes remains unexplored. This study elucidates the positive regulatory role of the basic helix-loop-helix protein SmMYC2 in tanshinones biosynthesis in Salvia miltiorrhiza. SmMYC2 not only binds to SmGGPPS1 promoters, activating their transcription, but also interacts with SmMYB36. This interaction enhances the transcriptional activity of SmMYC2 on SmGGPPS1, thereby promoting tanshinones biosynthesis. Furthermore, we identified three JA signaling repressors, SmJAZ3, SmJAZ4, and SmJAZ8, which interact with SmMYC2. These repressors hindered the transcriptional activity of SmMYC2 on SmGGPPS1 and disrupted the interaction between SmMYC2 and SmMYB36. MeJA treatment triggered the degradation of SmJAZ3 and SmJAZ4, allowing the SmMYC2-SmMYB36 complex to subsequently activate the expression of SmGGPPS1, whereas SmJAZ8 inhibited MeJA-mediated degradation due to the absence of the LPIARR motif. These results demonstrate that the SmJAZ-SmMYC2-SmMYB36 module dynamically regulates the JA-mediated accumulation of tanshinones. Our results reveal a new regulatory network for the biosynthesis of tanshinones. This study provides valuable insight for future research on MeJA-mediated modulation of tanshinones biosynthesis.

Smart Task Assistance in Mixed Reality for Astronauts.

Mixed reality (MR) registers virtual information and real objects and is an effective way to supplement astronaut training. Spatial anchors are generally used to perform virtual-real fusion in static scenes but cannot handle movable objects. To address this issue, we propose a smart task assistance method based on object detection and point cloud alignment. Specifically, both fixed and movable objects are detected automatically. In parallel, poses are estimated with no dependence on preset spatial position information. Firstly, YOLOv5s is used to detect the object and segment the point cloud of the corresponding structure, called the partial point cloud. Then, an iterative closest point (ICP) algorithm between the partial point cloud and the template point cloud is used to calculate the object's pose and execute the virtual-real fusion. The results demonstrate that the proposed method achieves automatic pose estimation for both fixed and movable objects without background information and preset spatial anchors. Most volunteers reported that our approach was practical, and it thus expands the application of astronaut training.

Reviving the Dynamics of Attacked Reservoir Computers.

Physically implemented neural networks are subject to external perturbations and internal variations. Existing works focus on the adversarial attacks but seldom consider attack on the network structure and the corresponding recovery method. Inspired by the biological neural compensation mechanism and the neuromodulation technique in clinical practice, we propose a novel framework of reviving attacked reservoir computers, consisting of several strategies direct at different types of attacks on structure by adjusting only a minor fraction of edges in the reservoir. Numerical experiments demonstrate the efficacy and broad applicability of the framework and reveal inspiring insights into the mechanisms. This work provides a vehicle to improve the robustness of reservoir computers and can be generalized to broader types of neural networks.

The SmMYB36-SmERF6/SmERF115 module regulates the biosynthesis of tanshinones and phenolic acids in salvia miltiorrhiza hairy roots.

Tanshinone and phenolic acids are the most important active substances of Salvia miltiorrhiza, and the insight into their transcriptional regulatory mechanisms is an essential process to increase their content in vivo. SmMYB36 has been found to have important regulatory functions in the synthesis of tanshinone and phenolic acid; paradoxically, its mechanism of action in S. miltiorrhiza is not clear. Here, we demonstrated that SmMYB36 functions as a promoter of tanshinones accumulation and a suppressor of phenolic acids through the generation of SmMYB36 overexpressed and chimeric SmMYB36-SRDX (EAR repressive domain) repressor hairy roots in combination with transcriptomic-metabolomic analysis. SmMYB36 directly down-regulate the key enzyme gene of primary metabolism, SmGAPC, up-regulate the tanshinones biosynthesis branch genes SmDXS2, SmGGPPS1, SmCPS1 and down-regulate the phenolic acids biosynthesis branch enzyme gene, SmRAS. Meanwhile, SmERF6, a positive regulator of tanshinone synthesis activating SmCPS1, was up-regulated and SmERF115, a positive regulator of phenolic acid biosynthesis activating SmRAS, was down-regulated. Furthermore, the seven acidic amino acids at the C-terminus of SmMYB36 are required for both self-activating domain and activation of target gene expression. As a consequence, this study contributes to reveal the potential relevance of transcription factors synergistically regulating the biosynthesis of tanshinone and phenolic acid.

Overexpression of SmMYC2 enhances salt resistance in Arabidopsis thaliana and Salvia miltiorrhiza hairy roots.

Soil salinity significantly affects both Salvia miltiorrhiza growth and development as well as seed germination throughout field cultivation and production. The basic helix-loop-helix (bHLH) transcription factor (TF) MYC2 contributes significantly to plant stress resistance as a key regulator of the jasmonic acid signaling pathway. In transgenic S. miltiorrhiza hairy roots, SmMYC2 has been shown to promote the accumulation of tanshinone and salvianolic acid, but its role in S. miltiorrhiza of resistance to abiotic stress is unclear. Herein, we found methyl jasmonate (MeJA), NaCl, and PEG treatment all significantly increased SmMYC2 expression. In response to salt stress, SmMYC2 overexpression in yeast increased its rate of growth. Additionally, overexpression of SmMYC2 transgenic Arabidopsis thaliana and S. miltiorrhiza hairy root showed that it might improve salt resistance in transgenic plant. In particular, compared to WT, overexpression of SmMYC2 transgenic Arabidopsis had higher levels of three antioxidant enzymes (superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT)), proline (Pro) content, and ABA-dependent and ABA-independent genes expression. They also had lower levels of malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation. What's more, overexpression of SmMYC2 increases the expression of flavonoid synthesis genes and the accumulation of related components in Arabidopsis. These findings imply that SmMYC2 functions as a positive regulator that regulates plant tolerance to salt through ABA-dependent and independent signaling pathways.

Plasma Membrane H+-ATPase SmPHA4 Negatively Regulates the Biosynthesis of Tanshinones in Salvia miltiorrhiza.

Salvia miltiorrhiza Bunge has been widely used in the treatment of cardiovascular and cerebrovascular diseases, due to the pharmacological action of its active components such as the tanshinones. Plasma membrane (PM) H+-ATPase plays key roles in numerous physiological processes in plants. However, little is known about the PM H+-ATPase gene family in S. miltiorrhiza (Sm). Here, nine PM H+-ATPase isoforms were identified and named SmPHA1-SmPHA9. Phylogenetic tree analysis showed that the genetic distance of SmPHAs was relatively far in the S. miltiorrhiza PM H+-ATPase family. Moreover, the transmembrane structures were rich in SmPHA protein. In addition, SmPHA4 was found to be highly expressed in roots and flowers. HPLC revealed that accumulation of dihydrotanshinone (DT), cryptotanshinone (CT), and tanshinone I (TI) was significantly reduced in the SmPHA4-OE lines but was increased in the SmPHA4-RNAi lines, ranging from 2.54 to 3.52, 3.77 to 6.33, and 0.35 to 0.74 mg/g, respectively, suggesting that SmPHA4 is a candidate regulator of tanshinone metabolites. Moreover, qRT-PCR confirmed that the expression of tanshinone biosynthetic-related key enzymes was also upregulated in the SmPHA4-RNAi lines. In summary, this study highlighted PM H+-ATPase function and provided new insights into regulatory candidate genes for modulating secondary metabolism biosynthesis in S. miltiorrhiza.

Imaging through highly scattering human skulls with ultrasound-modulated optical tomography.

Advances in human brain imaging technologies are critical to understanding how the brain works and the diagnosis of brain disorders. Existing technologies have different drawbacks, and the human skull poses a great challenge for pure optical and ultrasound imaging technologies. Here we demonstrate the feasibility of using ultrasound-modulated optical tomography, a hybrid technology that combines both light and sound, to image through human skulls. Single-shot off-axis holography was used to measure the field of the ultrasonically tagged light. This Letter paves the way for imaging the brain noninvasively through the skull, with optical contrast and a higher spatial resolution than that of diffuse optical tomography.

Single-shot surface 3D imaging by optical coherence factor.

We report a single-shot three-dimensional (3D) topographical imaging method, optical coherence factor (OCF) imaging, which uses optical coherence as the contrast mechanism to acquire the surface height (${z}$z-direction) information of an object. A 4-f imaging system records the light field reflected from the surface of the object. The illumination of the imaging system comes from a laser source with the optical coherence length comparable to the depth of field (DoF) of the optical system. Off-axis holographic recording is used to retrieve the coherence factor from the interference fringes, which is then converted to ${z}$z-direction information. In this experiment, we validate our 3D imaging results comparing them to axial scanning full-field optical coherence tomography images. We also analyze the contrast mechanism of OCF and show that it is able to provide additional information over conventional coherent and incoherent imaging using the same imaging setup. This single-shot computationally efficient method may have potential applications in industrial quality control inspection.

Molecular Reaction Mechanism for the Formation of 3-Chloropropanediol Esters in Oils and Fats.

3-Chloro-1,2-propanediol fatty acid esters (3-MCPD esters) are a group of process-induced contaminants that form during the refining and heating of fats and oils. In this study, a combined method of simulated deodorization and computational simulation was used to explore the precursor substance and the generation path of 3-MCPD esters. From the results, 3-MCPD esters reached a content level of 2.268 mg/kg when the diacylglyceride (DAG) content was 4% and temperature was 220 °C. A good correlation was observed between DAG and 3-MCPD ester contents ( y = 0.0612 x2 - 1.6376 x + 10.558 [ R2 = 0.958]). There were three pathways for the formation of 3-MCPD esters: (A) a direct nucleophilic substitution reaction, (B) an indirect nucleophilic substitution reaction, and (C) a mechanism of an intermediate (glycidyl ester) from the calculation of Gaussian software at the B3LYP/6-31+g** level. The data showed that the ester-based direct nucleophilic substitution reaction was the most likely reaction pathway. The energy barriers for the formation of the 3-MCPD esters dipalmitin, diolein, and dilinolein were 74.261, 66.017, and 59.856 kJ/mol, respectively, indicating that the formation process of 3-MCPD esters is a high-temperature endothermic process. Therefore, by controlling the introduction of precursor (DAG) and reducing the temperature, 3-MCPD ester formation was prevented.

Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy.

Imaging and tracking of near-surface three-dimensional volumetric nanoscale dynamic processes of live cells remains a challenging problem. In this paper, we propose a multi-color live-cell near-surface-volume super-resolution microscopy method that combines total internal reflection fluorescence structured illumination microscopy with multi-angle evanescent light illumination. We demonstrate that our approach of multi-angle interference microscopy is perfectly adapted to studying subcellular dynamics of mitochondria and microtubule architectures during cell migration.

Inverse matrix based phase estimation algorithm for structured illumination microscopy.

The fast imaging speed and low-intensity requirement of structured illumination microscopy (SIM) have made it one of the most widely used imaging tools in live cell imaging. In order to obtain a high fidelity reconstructed image, a precise estimation of the phase of the illumination pattern is required, especially in those structured illumination based techniques that rely on high-order harmonics to improve the resolution. This can be achieved in one of two fundamental ways. The first is to build a high-end control system capable of shifting a sinusoidal pattern with high precision, while the second is to apply estimation algorithms to determine how patterns shift during post-processing. The latter method is preferred in low-cost super-resolution imaging systems; however, existing algorithms are either time-consuming or fail due to noise and a low modulation depth. In this paper, we introduce additional matrixes into the phase estimation algorithm and propose an inverse matrix based phase estimation method with which analytical solutions of the phases can be determined without iteration. The proposed algorithm was validated via simulation and experiments using a home-made total internal reflection fluorescent SIM system (TIRF-SIM). When tested, the method obtained the true phase even when the modulation depth was low. The source code is now available for download by researchers and others.

Widefield and total internal reflection fluorescent structured illumination microscopy with scanning galvo mirrors.

We present an alternative approach to realize structured illumination microscopy (SIM), which is capable for live cell imaging. The prototype utilizes two sets of scanning galvo mirrors, a polarization converter and a piezo-platform to generate a fast shifted, s-polarization interfered and periodic variable illumination patterns. By changing the angle of the scanning galvanometer, we can change the position of the spots at the pupil plane of the objective lens arbitrarily, making it easy to switch between widefield and total internal reflection fluorescent-SIM mode and adapting the penetration depth in the sample. Also, a twofold resolution improvement is achieved in our experiments. The prototype offers more flexibility of pattern period and illumination orientation changing than previous systems.

Pattern-illuminated Fourier ptychography microscopy with a pattern-estimation algorithm.

In this paper we proposed a new method that combines random pattern illumination, the pattern-estimation algorithm, and the Fourier ptychography (FP) algorithm to recover a super-resolution image. We shifted one multispot pattern to different positions to capture images, and estimated these illumination patterns using a gradient descent algorithm that shares the same root with blind structured illumination microscopy (SIM). Based on the captured images and estimated patterns, the FP algorithm is then applied to recover a super-resolution image. Our method, termed as pattern-estimated Fourier ptychography (PEFP) microscopy, does not need the prior information about the scanning position, and is thus insensitive to rotational errors and shift errors. The performance of PEFP has been demonstrated both in simulations and experiments, and PEFP achieves better resolution than the pattern-illuminated FP method when shift errors appear in our simulations. Moreover, PEFP shows strong resistance towards aberrations and works fine when there is noise in the captured image. Compared with a newly proposed blind-SIM method, PEFP also shows better resolution enhancement both in our simulations and experiments. Our method also provides the possibility to extend the application of pattern-illuminated FP to any illumination pattern because we estimated every illumination pattern separately, as blind-SIM does.

Repair of the peripheral nerve defect with the combination of allogeneic nerve and autologous neuroma.

AIM: To explore the effect of nerve regeneration through repairing the defect of sciatic nerve in rats with the combination of optimized acellular allogeneic nerve and autologous neuroma. MATERIAL AND METHODS: 30 SD rats were randomly divided into two groups A and B, with 15 in each, which were used in preparing the models of the autologous neuroma and the defect of sciatic nerve. In the group A, the combination of allogeneic nerve and autologous neuroma was transplanted; in the group B, the autogenous nerve was transplanted. 15 Wistar rats were used to provide acellular allogeneic nerve, which came from the sciatic nerve in one side of the leg. The electrophysiology examination, the evaluation of sciatic nerve function index and the histological examination were done at the 8th weeks and the 16th weeks after the operation. RESULTS: At the 8th week, the limb escape response appeared in all rats; at the 16th week, there were many nerve fibers passing through the transplant in group A and group B. There was no significant difference in the number of the regenerated nerve fiber, diameter and the thickness of medullary sheath. At the 8th week, the conduction velocity of the regenerative nerve in group A were lower than that in group B (p < 0.05), and there was no statistical difference in two groups at the 16th week; there was no significant deviation in the function index of sciatic nerve in group A and group B(P > 0.05). CONCLUSION: The combination of allogeneic nerve and autologous neuroma, which repairs the defect of peripheral nerve, can promote the regeneration of nerve, and the function of nerve conduction can be recovered, which is a good substitute of nerve grafts.