4D label-free proteomics analysis of oxygen-induced retinopathy with or without anti-VEGF treatment.

Oxygen-induced retinopathy (OIR) animal model is widely used for retinopathy of prematurity (ROP) researches. The purpose of this study was to identify proteins and related pathways of OIR with or without anti-vascular endothelial growth factor (VEGF) treatment, for use as biomarkers in diagnosing and treating ROP. Nine samples were subjected to proteomic analysis. Retina specimens were collected from 3 OIR mice, 3 OIR mice with anti-VEGF treatment and 3 normal mice (control group). Liquid chromatography-tandem mass spectrometry analysis was performed using the 4D label-free technique. Statistically significant differentially expressed proteins, gene ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway representations, InterPro (IPR) and protein interactions were analyzed. In total, 4585 unique proteins were identified as differentially expressed proteins (DEPs). Enrichment analysis of the GO and KEGG indicated functional clusters related to peptide biosynthetic and metabolic process, cellular macromolecule biosynthetic process and nucleic acid binding in OIR group. For anti-VEGF treatment group, DEPs were clustered in DNA replication, PI3K/Akt signaling pathway and Jak/STAT signaling pathway. Proteomic profiling is useful for the exploration of molecular mechanisms of OIR and mechanisms of anti-VEGF treatment. These findings may be useful for identification of novel biomarkers for ROP pathogenesis and treatment.

Neural network enabled fringe projection through scattering media.

The projection of fringes plays an essential role in many applications, such as fringe projection profilometry and structured illumination microscopy. However, these capabilities are significantly constrained in environments affected by optical scattering. Although recent developments in wavefront shaping have effectively generated high-fidelity focal points and relatively simple structured images amidst scattering, the ability to project fringes that cover half of the projection area has not yet been achieved. To address this limitation, this study presents a fringe projector enabled by a neural network, capable of projecting fringes with variable periodicities and orientation angles through scattering media. We tested this projector on two types of scattering media: ground glass diffusers and multimode fibers. For these scattering media, the average Pearson's correlation coefficients between the projected fringes and their designed configurations are 86.9% and 79.7%, respectively. These results demonstrate the effectiveness of the proposed neural network enabled fringe projector. This advancement is expected to broaden the scope of fringe-based imaging techniques, making it feasible to employ them in conditions previously hindered by scattering effects.

Single-Shot Intensity- and Phase-Sensitive Compressive Sensing-Based Coherent Modulation Ultrafast Imaging.

Ultrafast imaging can capture the dynamic scenes with a nanosecond and even femtosecond temporal resolution. Complementarily, phase imaging can provide the morphology, refractive index, or thickness information that intensity imaging cannot represent. Therefore, it is important to realize the simultaneous ultrafast intensity and phase imaging for achieving as much information as possible in the detection of ultrafast dynamic scenes. Here, we report a single-shot intensity- and phase-sensitive compressive sensing-based coherent modulation ultrafast imaging technique, shortened as CS-CMUI, which integrates coherent modulation imaging, compressive imaging, and streak imaging. We theoretically demonstrate through numerical simulations that CS-CMUI can obtain both the intensity and phase information of the dynamic scenes with ultrahigh fidelity. Furthermore, we experimentally build a CS-CMUI system and successfully measure the intensity and phase evolution of a multimode Q-switched laser pulse and the dynamical behavior of laser ablation on an indium tin oxide thin film. It is anticipated that CS-CMUI enables a profound comprehension of ultrafast phenomena and promotes the advancement of various practical applications, which will have substantial impact on fundamental and applied sciences.

High-performance reconstruction method combining total variation with a video denoiser for compressed ultrafast imaging.

Compressed ultrafast photography (CUP) is a novel two-dimensional (2D) imaging technique to capture ultrafast dynamic scenes. Effective image reconstruction is essential in CUP systems. However, existing reconstruction algorithms mostly rely on image priors and complex parameter spaces. Therefore, in general, they are time-consuming and result in poor imaging quality, which limits their practical applications. In this paper, we propose a novel reconstruction algorithm, to the best of our knowledge, named plug-in-plug-fast deep video denoising net-total variation (PnP-TV-FastDVDnet), which exploits an image's spatial features and correlation features in the temporal dimension. Therefore, it offers higher-quality images than those in previously reported methods. First, we built a forward mathematical model of the CUP, and the closed-form solution of the three suboptimization problems was derived according to plug-in and plug-out frames. Secondly, we used an advanced video denoising algorithm based on a neural network named FastDVDnet to solve the denoising problem. The peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) are improved on actual CUP data compared with traditional algorithms. On benchmark and real CUP datasets, the proposed method shows the comparable visual results while reducing the running time by 96% over state-of-the-art algorithms.

Flexible and accurate total variation and cascaded denoisers-based image reconstruction algorithm for hyperspectrally compressed ultrafast photography.

Hyperspectrally compressed ultrafast photography (HCUP) based on compressed sensing and time- and spectrum-to-space mappings can simultaneously realize the temporal and spectral imaging of non-repeatable or difficult-to-repeat transient events with a passive manner in single exposure. HCUP possesses an incredibly high frame rate of tens of trillions of frames per second and a sequence depth of several hundred, and therefore plays a revolutionary role in single-shot ultrafast optical imaging. However, due to ultra-high data compression ratios induced by the extremely large sequence depth, as well as limited fidelities of traditional algorithms over the image reconstruction process, HCUP suffers from a poor image reconstruction quality and fails to capture fine structures in complex transient scenes. To overcome these restrictions, we report a flexible image reconstruction algorithm based on a total variation (TV) and cascaded denoisers (CD) for HCUP, named the TV-CD algorithm. The TV-CD algorithm applies the TV denoising model cascaded with several advanced deep learning-based denoising models in the iterative plug-and-play alternating direction method of multipliers framework, which not only preserves the image smoothness with TV, but also obtains more priori with CD. Therefore, it solves the common sparsity representation problem in local similarity and motion compensation. Both the simulation and experimental results show that the proposed TV-CD algorithm can effectively improve the image reconstruction accuracy and quality of HCUP, and may further promote the practical applications of HCUP in capturing high-dimensional complex physical, chemical and biological ultrafast dynamic scenes.

Human Leukocyte Antigen Polymorphism HLA-A*24:02 is Associated with Acute Liver Disease in HBV-Infected Han Chinese Adults.

BACKGROUND: Whether polymorphic Human Leukocyte Antigen (HLA)-A, HLA-B and HLA-DRB1 alleles were associated with acute liver disease after hepatitis B virus (HBV) infections was investigated. METHODS: In this study, from initially 100 participants in each group, HLA-A, HLA-B and HLA-DRB1 sequences were available from 86 acute hepatitis B (AHB) patients and from 84 HBV-resistant individuals (controls), using sequencing-based typing allele groups and alleles that exhibited differences in distribution between the case and control groups were subjected to chi-squared and logistic regression analyses to identify those associated with AHB. A dose response analysis was also performed on the effect of HLA-A*24:02 allele number on acute liver disease following HBV infection. RESULTS: The frequency distribution of HLA-B and HLA-DRB1 alleles in the control group were in Hardy-Weinberg Equilibrium (P > .05). HLA-A*24:02 (χ2 = 6.949, P = .008) occurred most frequently in the AHB and HLA-DRB1*12:02 (χ2 = 7.768, P = .005) in the control group. With adjustment for sex, the logistic regression model showed that the HLA-A*24:02 allele was significantly associated with AHB liver injury (P = .0326, OR = 2.270, 95% CI: 1.070-4.816), whereas the other HLA-A, HLA-B, and HLA-DRB1 alleles were not (P > .05). A linear response was observed for the association between HLA-A*24:02 allele number and acute liver disease after HBV infections (χ2 = 4.428, P = .025). CONCLUSION: The HLA-A*24:02 allele may influence the severity of the cellular response to HBV infection, increasing the elimination of HBV-infected hepatocytes. The HLA-A*24:02 allele may be a potential screening marker for identifying people or regional populations in China at higher risk of acute liver disease following HBV infection.

Laser polarization-controlled photoreduction of samarium ions in sodium aluminoborate glass.

The valence state conversion of lanthanide ions induced by femtosecond laser fields has attracted considerable attention due to their potential applications in areas like high-density optical storage. However, the physical mechanisms involved in valence state conversions still remain unclear. Here, we report the first experimental study of controlling the reduction of trivalent samarium ions to divalent ones in sodium aluminoborate glass by varying the polarization status of the 800 nm femtosecond laser field. As the laser field is varied from linear to circular polarization, the reduction efficiency can be greatly decreased by about fifty percent. This polarization-dependent reduction behavior is found to directly correlate with the nonresonant two-photon 4f-4f absorption probability of the trivalent samarium ions in both experiment and theory. Multiphoton excited charge transfer between oxygen and samarium is considered to be responsible for the photoreduction. Our work demonstrates a controllable and effective way in tuning the valence state conversion efficiency and sheds light on the underlying mechanisms.

Overexpression of SSR2 promotes proliferation of liver cancer cells and predicts prognosis of patients with hepatocellular carcinoma.

Signal Sequence Receptor Subunit 2 (SSR2) is a key endoplasmic reticulum gene involved in protein folding and processing. Previous studies found that it was upregulated in several cancers, but its precise role in hepatocellular carcinoma (HCC) remains unclear. To have a better understanding of this gene in HCC, we examined the expression of SSR2 in HCC tissues by analysing The Cancer Genome Atlas (TCGA) data and immunohistochemistry. We also assessed the association between SSR2 expression and clinicopathological characteristics of HCC patients and patient survival. Potential function of SSR2 was predicted through GSEA and protein-protein interaction analysis. MTT, flowcytometry, transwell and a nude mice xenograft model were employed to investigate the biological functions in vivo and in vitro. The results showed that the expression of SSR2 was significantly increased in HCC tissues, and SSR2 expression was associated with several clinical characteristics. In addition, patients with higher SSR2 expression had poorer survival. Enrichment analysis suggested that SSR2 was probably involved in biological process or signalling pathways related to G2/M checkpoint, passive transmembrane transporter activity, ATF2_S_UP. V1_UP and ncRNA metabolic process. Further experimental study showed that SSR2 knockdown inhibited cell proliferation, migration and invasion ability and promoted apoptosis and cell cycle arrest in vitro. Moreover, downregulation of SSR2 also repressed the growth of HepG2 cells in vivo. In conclusion, our study suggests that SSR2 may act as an oncogene in HCC.

High-speed super-resolution imaging with compressive imaging-based structured illumination microscopy.

Structured illumination microscopy (SIM) has been widely applied to investigating fine structures of biological samples by breaking the optical diffraction limitation. So far, video-rate imaging has been obtained in SIM, but the imaging speed was still limited due to the reconstruction of a super-solution image through multi-sampling, which hindered the applications in high-speed biomedical imaging. To overcome this limitation, here we develop compressive imaging-based structured illumination microscopy (CISIM) by synergizing SIM and compressive sensing (CS). Compared with conventional SIM, CISIM can greatly improve the super-resolution imaging speed by extracting multiple super-resolution images from one compressed image. Based on CISIM, we successfully reconstruct the super-resolution images in biological dynamics, and analyze the effect factors of image reconstruction quality, which verify the feasibility of CISIM. CISIM paves a way for high-speed super-resolution imaging, which may bring technological breakthroughs and significant applications in biomedical imaging.

Weighted multi-scale denoising via adaptive multi-channel fusion for compressed ultrafast photography.

Being capable of passively capturing transient scenes occurring in picoseconds and even shorter time with an extremely large sequence depth in a snapshot, compressed ultrafast photography (CUP) has aroused tremendous attention in ultrafast optical imaging. However, the high compression ratio induced by large sequence depth brings the problem of low image quality in image reconstruction, preventing CUP from observing transient scenes with fine spatial information. To overcome these restrictions, we propose an efficient image reconstruction algorithm with multi-scale (MS) weighted denoising based on the plug-and-play (PnP) based alternating direction method of multipliers (ADMM) framework for multi-channel coupled CUP (MC-CUP), named the MCMS-PnP algorithm. By removing non-Gaussian distributed noise using weighted MS denoising during each iteration of the ADMM, and adaptively adjusting the weights via sufficiently exploiting the coupling information among different acquisition channels collected by MC-CUP, a synergistic combination of hardware and algorithm can be realized to significantly improve the quality of image reconstruction. Both simulation and experimental results demonstrate that the proposed adaptive MCMS-PnP algorithm can effectively improve the accuracy and quality of reconstructed images in MC-CUP, and extend the detectable range of CUP to transient scenes with fine structures.

Surface birefringence of regular periodic surface structures produced on glass coated with an indium tin oxide film using a low-fluence femtosecond laser through a cylindrical lens.

Large-area regular laser-induced periodic surface structures (LIPSSs) with a birefringence effect were efficiently produced on a glass surface coated with an indium tin oxide (ITO) film, through irradiation by a femtosecond laser (800 nm, 50 fs, 3 mJ, 1 kHz) focused with a cylindrical lens. The laser fluence of 0.44 J/cm2 on the coated glass was only one-tenth of that on bare glass, which significantly reduced the thermal effect. Moreover, regular LIPSSs with a period as short as 100 nm could be produced efficiently. The retardance of the fabricated LIPSSs was measured to be up to 44 nm, which is eight times that of LIPSSs fabricated on bare glass. The mechanisms of such a large difference of retardance were studied by measuring the nanostructures and the concentration of In3+ ions on the cross section of nano-corrugated surface layer on bare glass and ITO-coated glass.

Single-shot compressed ultrafast photography based on U-net network.

The compressive ultrafast photography (CUP) has achieved real-time femtosecond imaging based on the compressive-sensing methods. However, the reconstruction performance usually suffers from artifacts brought by strong noise, aberration, and distortion, which prevents its applications. We propose a deep compressive ultrafast photography (DeepCUP) method. Various numerical simulations have been demonstrated on both the MNIST and UCF-101 datasets and compared with other state-of-the-art algorithms. The result shows that our DeepCUP has a superior performance in both PSNR and SSIM compared to previous compressed-sensing methods. We also illustrate the outstanding performance of the proposed method under system errors and noise in comparison to other methods.

Hyperspectrally Compressed Ultrafast Photography.

The spatial, temporal, and spectral information in optical imaging play a crucial role in exploring the unknown world and unencrypting natural mysteries. However, the existing optical imaging techniques can only acquire the spatiotemporal or spatiospectral information of the object with the single-shot method. Here, we develop a hyperspectrally compressed ultrafast photography (HCUP) that can simultaneously record the spatial, temporal, and spectral information of the object. In our HCUP, the spatial resolution is 1.26 lp/mm in the horizontal direction and 1.41 lp/mm in the vertical direction, the temporal frame interval is 2 ps, and the spectral frame interval is 1.72 nm. Moreover, HCUP operates with receive-only and single-shot modes, and therefore it overcomes the technical limitation of active illumination and can measure the nonrepetitive or irreversible transient events. Using our HCUP, we successfully measure the spatiotemporal-spatiospectral intensity evolution of the chirped picosecond laser pulse and the photoluminescence dynamics. This Letter extends the optical imaging from three- to four-dimensional information, which has an important scientific significance in both fundamental research and applied science.

Ultrafast dynamics of the thin surface plasma layer and the periodic ripples formation on GaP crystal irradiated by a single femtosecond laser pulse.

Ultrafast dynamic of thin surface plasma layer plays a crucial role in the formation of periodic surface ripples after laser pulse irradiation. Using the pump-probe imaging technique, a complete scenario of the periodic ripples formation on a GaP surface is demonstrated after being irradiated by single femtosecond laser pulse. The ripples firstly emerge at delay time of several tens of picoseconds, and disappear completely at several hundreds of picoseconds, resulting in a transient overheating solid state ablation crater. It's interesting that new ripples appear and gradually become deep and clear after hundreds of picoseconds. A part of these ripples remain after the ablation crater is solidified. The period of the remained ripples is measured and approximately equal to the periods of the two transient ripples. The thin surface plasma model with multi-layer is introduced to study the formation of periodic ripples. The dynamics of the carrier excitation, carrier and lattice temperature, transient dielectric constant, and other factors are obtained by the two-temperature model and the Drude model. The results show that the periods of electric field distributions at different depths of the plasma layer are the same. The formation of the two transient ripples and the remained ripples are all related to the periodic energy deposition due to the SPP excitation at the air-plasma interface.

Ultrafast imaging on the formation of periodic ripples on a Si surface with a prefabricated nanogroove induced by a single femtosecond laser pulse.

This paper reports the ultrafast imaging on the formation of periodic surface ripples induced by a single 800 nm, 50 fs laser pulse. The evolution process is observed on a Si surface with a prefabricated nanogroove. The ripples emerge very quickly, only 3 ps after the laser pulse with a fluence of 0.18 J/cm2 irradiating on the surface, and last for several hundreds of picoseconds. The ultrafast dynamics of laser-matter interaction, such as free carrier excitation, carrier and lattice heating, surface plasmon polariton (SPP) excitation, etc, are studied theoretically. The theoretical and experimental results support that the periodic ripples are caused by the periodic energy deposition due to SPP excitation. The emerge time could identify the surface melting causing the formation of periodic ripples, and exclude the other thermal effects, for example, hydrodynamics.

Depleted upconversion luminescence in NaYF4:Yb3+,Tm3+ nanoparticles via simultaneous two-wavelength excitation.

We report optical depletion of upconversion luminescence (UCL) in NaYF4:Yb3+,Tm3+ nanoparticles excited simultaneously by 980 nm and 1550 nm lasers. The UCL intensity is greatly depleted, while the downshifted emission at 1210 nm is obviously enhanced. The disturbances of 1550 nm photons on energy transfer between Yb3+ and Tm3+, cross relaxation (CR), the thermal effect and the stimulated emission depletion (STED) process are qualitatively evaluated. Our investigations verify that the unexpected depletion phenomena are governed by the STED process. The power densities of the 980 nm and 1550 nm lasers are both less than 100 W cm-2, which will greatly reduce the thermal effect and damage and extend the applications of such nanomaterials. These results provide keen insights into controlling emission colors in optical processes, and offer potential applications in multicolor displays and STED nanoscopy.

Theoretical study of excited states of DNA base dimers and tetramers using optimally tuned range-separated density functional theory.

Excited states of various DNA base dimers and tetramers including Watson-Crick H-bonding and stacking interactions have been investigated by time-dependent density functional theory using nonempirically tuned range-separated exchange (RSE) functionals. Significant improvements are found in the prediction of excitation energies and oscillator strengths, with results comparable to those of high-level coupled-cluster (CC) models (RI-CC2 and EOM-CCSD(T)). The optimally-tuned RSE functional significantly outperforms its non-tuned (default) version and widely-used B3LYP functional. Compared to those high-level CC benchmarks, the large mean absolute deviations of conventional functionals can be attributed to their inappropriate amount of exact exchange and large delocalization errors which can be greatly eliminated by tuning approach. Furthermore, the impacts of H-bonding and π-stacking interactions in various DNA dimers and tetramers are analyzed through peak shift of simulated absorption spectra as well as corresponding change of absorption intensity. The result indicates the stacking interaction in DNA tetramers mainly contributes to the hypochromicity effect. The present work provides an efficient theoretical tool for accurate prediction of optical properties and excited states of nucleobase and other biological systems. © 2015 Wiley Periodicals, Inc.

Mechanisms of the blue emission of NaYF4:Tm(3+) nanoparticles excited by an 800 nm continuous wave laser.

A thorough understanding of energy transfer and upconversion (UC) processes between trivalent lanthanide (Ln(3+)) ions is essential and important for improving UC performance. However, because of the abundant energy states of Ln(3+) ions, UC mechanisms are very complicated, which makes it a challenge to exclusively verify and quantitatively evaluate the dominant process. In this study, the fundamental excitation processes of Tm(3+)-doped NaYF4 nanocrystals under 800 nm continuous wave (CW) laser excitation were experimentally investigated on the basis of the quantum transition principle. An 800 nm CW laser combined with other wavelength CW lasers, including 471 nm, 657 nm, 980 nm, and 1550 nm lasers, were designed to study in-depth the excitation processes of UC luminescence via simultaneous two-wavelength laser excitation. The results indicate that the excited state absorption of (3)H6→(3)H4∼∼(3)H5→(1)G4 is the dominant pathway of the 481 nm and 651 nm emission bands, and two kinds of energy transfer UC pathways, uniformly expressed as (1)G4 + (3)H4→(1)D2 + (3)F4, play the primary roles in the 456 nm emission band.

Femtosecond Laser-Induced Upconversion Luminescence in Rare-Earth Ions by Nonresonant Multiphoton Absorption.

The upconversion luminescence of rare-earth ions has attracted considerable interest because of its important applications in photoelectric conversion, color display, laser device, multiplexed biolabeling, and security printing. Previous studies mainly explored the upconversion luminescence generation through excited state absorption, energy transfer upconversion, and photon avalanche under the continuous wave laser excitation. Here, we focus on the upconversion luminescence generation through a nonresonant multiphoton absorption by using the intense femtosecond pulsed laser excitation and study the upconversion luminescence intensity control by varying the femtosecond laser phase and polarization. We show that the upconversion luminescence of rare-earth ions under the intense femtosecond laser field excitation is easy to be obtained due to the nonresonant multiphoton absorption through the nonlinear interaction between light and matter, which is not available by the continuous wave laser excitation in previous works. We also show that the upconversion luminescence intensity can be effectively controlled by varying the femtosecond pulsed laser phase and polarization, which can open a new technological opportunity to generate and control the upconversion luminescence of rare-earth ions and also can be further extended to the relevant application areas.

Applicability of optimal functional tuning in density functional calculations of ionization potentials and electron affinities of adenine-thymine nucleobase pairs and clusters.

The intrinsic properties of DNA and RNA nucleic acid bases (NABs) such as ionization potentials (IPs) and electron affinities (EAs) are crucial to reveal various biochemical mechanisms. Successful application of density functional theory (DFT) using nonempirically tuned long-range corrected (LC) functionals for calculation of vertical ionization potentials (VIPs) and electron affinities (VEAs) of various adenine-thymine (AT) nucleobase pairs and clusters is demonstrated. We employ a tuning method by applying an asymptotically correct exchange-correlation potential adjusted to give frontier orbital energies (-εHOMO and -εLUMO) representing IPs and EAs and assess the quality of prediction which is comparable to high-level EOM-IP-CCSD/CCSD methods. The delocalization error calculated using different DFT functionals is quantified by calculations using fractional electron numbers. The cooperative effect of H-bonding and π-stacking on the IPs of AT clusters, as well as the reactivity parameters (global hardness and electrophilicity), is quantitatively characterized using the tuned LC functionals. The present work aims at providing a reliable and efficient theoretical tool for the prediction of the related electron donor and acceptor abilities of the NAB systems.