LORF9 of Marek's disease virus is involved in the early cytolytic replication of B lymphocytes and can act as a target for gene deletion vaccine development.

IMPORTANCE: Marek's disease virus (MDV) is a highly infectious and oncogenic virus that can induce severe T cell lymphomas in chickens. MDV encodes more than 100 genes, most of which have unknown functions. This work indicated that the LORF9 gene is necessary for MDV early cytolytic replication in B lymphocytes. In addition, we have found that the LORF9 deletion mutant has a comparative immunological protective effect with CVI988/Rispens vaccine strain against very virulent MDV challenge. This is a significant discovery that LORF9 can be exploited as a possible target for the development of an MDV gene deletion vaccine.

Honeycomb effect elimination in differential phase fiber-bundle-based endoscopy.

Fiber-bundle-based endoscopy, with its ultrathin probe and micrometer-level resolution, has become a widely adopted imaging modality for in vivo imaging. However, the fiber bundles introduce a significant honeycomb effect, primarily due to the multi-core structure and crosstalk of adjacent fiber cores, which superposes the honeycomb pattern image on the original image. To tackle this issue, we propose an iterative-free spatial pixel shifting (SPS) algorithm, designed to suppress the honeycomb effect and enhance real-time imaging performance. The process involves the creation of three additional sub-images by shifting the original image by one pixel at 0, 45, and 90 degree angles. These four sub-images are then used to compute differential maps in the x and y directions. By performing spiral integration on these differential maps, we reconstruct a honeycomb-free image with improved details. Our simulations and experimental results, conducted on a self-built fiber bundle-based endoscopy system, demonstrate the effectiveness of the SPS algorithm. SPS significantly improves the image quality of reflective objects and unlabeled transparent scattered objects, laying a solid foundation for biomedical endoscopic applications.

Transgenic expression of artificial microRNA targeting soybean mosaic virus P1 gene confers virus resistance in plant.

RNA silencing is an innate immune mechanism of plants against invasion by viral pathogens. Artificial microRNA (amiRNA) can be engineered to specifically induce RNA silencing against viruses in transgenic plants and has great potential for disease control. Here, we describe the development and application of amiRNA-based technology to induce resistance to soybean mosaic virus (SMV), a plant virus with a positive-sense single-stranded RNA genome. We have shown that the amiRNA targeting the SMV P1 coding region has the highest antiviral activity than those targeting other SMV genes in a transient amiRNA expression assay. We transformed the gene encoding the P1-targeting amiRNA and obtained stable transgenic Nicotiana benthamiana lines (amiR-P1-3-1-2-1 and amiR-P1-4-1-2-1). Our results have demonstrated the efficient suppression of SMV infection in the P1-targeting amiRNA transgenic plants in an expression level-dependent manner. In particular, the amiR-P1-3-1-2-1 transgenic plant showed high expression of amiR-P1 and low SMV accumulation after being challenged with SMV. Thus, a transgenic approach utilizing the amiRNA technology appears to be effective in generating resistance to SMV.

CIRP attenuates acute kidney injury after hypothermic cardiovascular surgery by inhibiting PHD3/HIF-1α-mediated ROS-TGF-ß1/p38 MAPK activation and mitochondrial apoptotic pathways.

BACKGROUND: The ischemia-reperfusion (IR) environment during deep hypothermic circulatory arrest (DHCA) cardiovascular surgery is a major cause of acute kidney injury (AKI), which lacks preventive measure and treatment. It was reported that cold inducible RNA-binding protein (CIRP) can be induced under hypoxic and hypothermic stress and may have a protective effect on multiple organs. The purpose of this study was to investigate whether CIRP could exert renoprotective effect during hypothermic IR and the potential mechanisms. METHODS: Utilizing RNA-sequencing, we compared the differences in gene expression between Cirp knockout rats and wild-type rats after DHCA and screened the possible mechanisms. Then, we established the hypothermic oxygen-glucose deprivation (OGD) model using HK-2 cells transfected with siRNA to verify the downstream pathways and explore potential pharmacological approach. The effects of CIRP and enarodustat (JTZ-951) on renal IR injury (IRI) were investigated in vivo and in vitro using multiple levels of pathological and molecular biological experiments. RESULTS: We discovered that Cirp knockout significantly upregulated rat Phd3 expression, which is the key regulator of HIF-1α, thereby inhibiting HIF-1α after DHCA. In addition, deletion of Cirp in rat model promoted apoptosis and aggravated renal injury by reactive oxygen species (ROS) accumulation and significant activation of the TGF-ß1/p38 MAPK inflammatory pathway. Then, based on the HK-2 cell model of hypothermic OGD, we found that CIRP silencing significantly stimulated the expression of the TGF-ß1/p38 MAPK inflammatory pathway by activating the PHD3/HIF-1α axis, and induced more severe apoptosis through the mitochondrial cytochrome c-Apaf-1-caspase 9 and FADD-caspase 8 death receptor pathways compared with untransfected cells. However, silencing PHD3 remarkably activated the expression of HIF-1α and alleviated the apoptosis of HK-2 cells in hypothermic OGD. On this basis, by pretreating HK-2 and rats with enarodustat, a novel HIF-1α stabilizer, we found that enarodustat significantly mitigated renal cellular apoptosis under hypothermic IR and reversed the aggravated IRI induced by CIRP defect, both in vitro and in vivo. CONCLUSION: Our findings indicated that CIRP may confer renoprotection against hypothermic IRI by suppressing PHD3/HIF-1α-mediated apoptosis. PHD3 inhibitors and HIF-1α stabilizers may have clinical value in renal IRI.

Infection phase-dependent dynamics of the viral and host N6-methyladenosine epitranscriptome in the lifecycle of an oncogenic virus in vivo.

Dynamic alteration of the epitranscriptome exerts regulatory effects on the lifecycle of oncogenic viruses in vitro. However, little is known about these effects in vivo because of the general lack of suitable animal infection models of these viruses. Using a model of rapid-onset Marek's disease lymphoma in chickens, we investigated changes in viral and host messenger RNA (mRNA) N6-methyladenosine (m6 A) modification during Marek's disease virus (MDV) infection in vivo. We found that the expression of major epitranscriptomic proteins varies among viral infection phases, reprogramming both the viral and the host epitranscriptomes. Specifically, the methyltransferase-like 3 (METTL3)/14 complex was suppressed during the lytic and reactivation phases of the MDV lifecycle, whereas its expression was increased during the latent phase and in MDV-induced tumors. METTL3/14 overexpression inhibits, whereas METTL3/14 knockdown enhances, MDV gene expression and replication. These findings reveal the dynamic features of the mRNA m6 A modification program during viral replication in vivo, especially in relation to key pathways involved in tumorigenesis.

Quantitative evaluation on thermal seeing induced 2m ring solar telescope.

Thermal seeing is one of the factors that affect solar telescope observations. A comprehensive analysis method is developed to quantify the thermal seeing effects. A three-dimensional Large Eddy Simulation (LES) turbulence model is used to obtain the transient flow fields around the primary mirror, the secondary mirror and the heat-stop. The thermal seeing is calculated based on the stochastic dynamic influence of turbulence on the light rays. The key parameters of the simulation were calibrated by experiments, and the simulation results were validated by empirical formulas. This method has been applied to evaluate the thermal seeing of the 2m Ring Solar Telescope (2m-RST). Error allocation is performed based on the research results to ensure the Observation effect of 2m-RST.

Prevalence and associated factors of smoking among chinese adolescents: a school-based cross-sectional study.

BACKGROUND: Shenzhen has made great efforts to address the tobacco epidemic in the past decade. This study aims to evaluate the current status of the tobacco epidemic among adolescent in Shenzhen, China. METHODS: The multi-stage random cluster sampling method was used in the school-based cross-sectional study in 2019 and a total of 7,423 junior and high school (both senior and vocational) students were recruited. Information on cigarette use was collected by the electronic questionnaire. Logistic regression analysis was used to examine the associations between current cigarette use and associated factors. ORs with their 95% CIs were reported. RESULTS: The prevalence of current cigarette use among adolescents was 2.3%, with boys (3.4%) significantly higher than girls (1.0%). Smoking rates in junior high schools, senior high schools, and vocational senior high schools were 1.0%, 2.7%, and 4.1%, respectively. The results of multivariate logistic regression analysis indicated that gender, age, parental smoking, teachers smoking in schools, friends smoking, exposure to tobacco marketing, and misconceptions about cigarette use were associated factors for adolescent smoking behaviour. CONCLUSIONS: The prevalence of current smoking was relatively low among adolescent in Shenzhen, China. Personal characteristics, family, and school were associated with current adolescent smokers.

Probing the Effect of Ubiquitinated Histone on Mononucleosomes by Translocation Dynamics Study through Solid-State Nanopores.

Post-translational modifications (PTMs), such as ubiquitination, are critically important in regulating genetic expressions by adjusting the nucleosome stability. A fast and label-free technology inspecting dynamic nucleosome structures can facilitate the interrogation of PTMs effects. Here we leverage the advantages of mechanically stable solid-state nanopores and detect the effect of a ubiquitinated histone on mononucleosomes at the single-molecule level. By comparing the translocation dynamics of natural and cross-linked mononucleosomes, we verified that the nucleosomal DNA unravelled from histones in natural mononucleosomes. Furthermore, we found that a turning point of voltage corresponds to the onset of nucleosome rupture. More importantly, we reveal that ubH2A stabilizes the nucleosome by shifting the turning point to a larger value and investigated the effect of ubiquitination on different histones (ubH2A and ubH2B). These findings open promising possibilities for developing a miniaturized and portable device for the fast screening of PTMs on nucleosomes.

Asymmetry robust centroid localization in confocal microscopy.

We present a centroid algorithm with asymmetry-robust error compensation for the peak position localization of asymmetrical axial response signals in confocal microscopy. Compared with the state-of-the-art algorithms, which are usually developed for symmetrical signals, our asymmetry robust centroid algorithm is found to have much smaller localization bias and higher precision for an asymmetrical confocal signal in numerical simulations and experiments.

Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores.

Discrimination of nucleotides serves as the basis for DNA sequencing using solid-state nanopores. However, the translocation of DNA is usually too fast to be detected, not to mention nucleotide discrimination. Here, we utilized polyphenolic TA and Fe3+, an attractive metal-organic thin film, and achieved a fast and robust surface coating for silicon nitride nanopores. The hydrophilic coating layer can greatly reduce the low-frequency noise of an original unstable nanopore, and the nanopore size can be finely tuned in situ at the nanoscale by simply adjusting the relative ratio of Fe3+ and TA monomers. Moreover, the hydrogen bonding interaction formed between the hydroxyl groups provided by TA and the phosphate groups of DNAs significantly increases the residence time of a short double-strand (100 bp) DNA. More importantly, we take advantage of the different strengths of hydrogen bonding interactions between the hydroxyl groups provided by TA and the analytes to discriminate between two oligonucleotide samples (oligodeoxycytidine and oligodeoxyadenosine) with similar sizes and lengths, of which the current signal patterns are significantly different using the coated nanopore. The results shed light on expanding the biochemical functionality of surface coatings on solid-state nanopores for future biomedical applications.

Crosstalk decoupling measurement method to determine the six degrees of freedom of motion error of linear stages.

The simultaneous measurement of all six degrees of freedom of motion error for a linear stage is significantly faster than methods that measure each degree of freedom separately. However, in current simultaneous measurement methods, error crosstalk issues significantly affect measurement accuracy. In this paper, a direct and simple crosstalk decoupling simultaneous measurement method to determine the six degrees of freedom of motion error of a linear stage is proposed. Based on the combination of single-frequency laser interferometry and laser self-collimation, a novel, to the best of our knowledge, optical configuration with a complete error decoupling relationship is designed, and a mathematical model is derived for error decoupling to address the crosstalk issue. A prototype system based on the new method is developed, and experiments are conducted to verify its effectiveness. Analysis shows that, compared with a commercial laser interferometer for linear stage measurement, the deviations of the positioning, horizontal straightness, vertical straightness, roll, pitch, and yaw errors are±0.50µm, ±0.58µm, ±0.50µm, ±1.02in., ±0.72in., and ±0.87in. respectively, over a 200 mm measurement range.

Improved calibration method of a four-quadrant detector based on Bayesian theory in a laser auto-collimation measurement system.

Reliable and accurate calibration for a four-quadrant detector (QD) is a prerequisite for high-accuracy laser auto-collimation measurements. However, the calibration accuracy is limited largely by the non-linearity of QD, especially for large-range detection. To address this issue, an improved calibration method of QD based on Bayesian theory in laser auto-collimation measurement is proposed in this paper. First, the non-linearity problem of QD is analyzed, and for accurate calibration of QD, a high-precision identification model based on Bayesian theory is presented. An analytical expression between the output signal of QD and the position of the laser spot is established, and then a calibration system with laser drift compensation to avoid influences from the laser source as a datum is constructed. A series of experiments is conducted to verify the performance of the improved calibration method. The results reveal that the improved method can effectively enhance the calibration accuracy of QD and reduce the residuals in root mean square error by 86% compared to the 15-order polynomial fitting over a detection range of ±1mm. The comparison experiments also demonstrate that the proposed calibration method has advantages over the conventional method in terms of accuracy and robustness.

Two-dimensional spectral signal model for chromatic confocal microscopy.

In chromatic confocal microscopy, the signal characteristics influence the accuracy of the signal processing, which in turn determines measurement performance. Thus, a full understanding of the spectral characteristics is critical to enhance the measurement performance. Existing spectral models only describe the signal intensity-wavelength characteristics, without taking the displacement-wavelength relation into consideration. These models require prior knowledge of the optical design, which reduces the effectiveness in the optical design process. In this paper, we develop a two-dimensional spectral signal model to describe the signal intensity-wavelength-displacement characteristics in chromatic confocal microscopy without prior knowledge of the optical design layout. With this model, the influence of the dimensional characteristics of the confocal setup and the displacement-wavelength characteristics and monochromatic aberrations of the hyperchromatic objective are investigated. Experimental results are presented to illustrate the effectiveness of our signal model. Using our model, further evaluation of the spectral signal can be used to enhance the measurement performance of chromatic confocal microscopy.

Locally adaptive thresholding centroid localization in confocal microscopy.

We introduce an iteration-free approach, based on a centroid algorithm with a locally adaptive threshold, for nanometer-level peak position localization of the axial response signal in confocal microscopy. This approach has localization accuracies that are near theoretical limits, especially when there is a small number of sampling points within the discrete signal. The algorithm is also orders of magnitude faster compared to fitting schemes based on maximum likelihood estimation. Simulations and experiments demonstrate the localization performance of the approach.

Single-shot wavelength-selective quantitative phase microscopy by partial aperture imaging and polarization-phase-division multiplexing.

We propose a single-shot wavelength-selective quantitative phase microscopy by annular white-light illumination, polarization-phase-division, and parallel phase-shifting. Compared to conventional multi-wavelength incoherence digital holography, the proposed microscopy presents the following merits: no switching of illumination or mechanical scanning, high spatiotemporal phase sensitivity, and single-shot reconstruction at each wavelength. Experiments validate these characteristics by quantitative phase imaging of gratings, cells, and tissues.

Real-time Jones phase microscopy for studying transparent and birefringent specimens.

Tissue birefringence is an intrinsic marker of potential value for cancer diagnosis. Traditionally, birefringence properties have been studied by using intensity-based formalisms, through the Mueller matrix algebra. On the other hand, the Jones matrix description allows for a direct assessment of the sample's anisotropic response. However, because Jones algebra is based on complex fields, requiring measurements of both phase and amplitude, it is less commonly used. Here we propose a real-time imaging method for measuring Jones matrices by quantitative phase imaging. We combine a broadband phase imaging system with a polarization-sensitive detector to obtain Jones matrices at each point in a megapixel scale image, with near video rate capture speeds. To validate the utility of our approach, we measured standard targets, partially birefringent samples, dynamic specimens, and thinly sliced histopathological tissue.

Lead Tolerance and Enrichment Characteristics of Several Ornamentals Under Hydroponic Culture.

The growth response, tolerance, and enrichment characteristics of six ornamental species, Chlorophytum comosum, Calendula officinalis, Iris lacteal, Belamcanda chinensis, Saponaria officinalis, and Polygonum lapathifolium were studied under hydroponic culture with lead (Pb) concentrations ranging from 0 to 1000 mg/L. The results showed that the growth of the tested ornamental species under Pb stress was inhibited. Belamcanda chinensis presented the largest tolerance index (0.75), and Calendula officinalis had the highest toxicity threshold (500 mg/L) under Pb stress. The highest Pb contents in the shoots were detected in Iris lacteal and Belamcanda chinensis. The enrichment coefficients in the shoots of Iris lacteal and Belamcanda chinensis were significantly higher than those in the other ornamental species. In conclusion, Iris lacteal and Belamcanda chinensis are the most tolerant and have the greatest Pb enrichment and translocation abilities under Pb stress, and thus, they have a strong potential to restore Pb-contaminated water bodies and soils.

Corrected parabolic fitting for height extraction in confocal microscopy.

Accurate and reliable peak extraction of axial response signals plays a critical role in confocal microscopy. For axial response signal processing, nonlinear fitting algorithms, such as parabolic, Gaussian or sinc2 fitting may cause significant systematic peak extraction errors. Also, existing error compensation methods require a priori knowledge of the full-width-at-half-maximum of the axial response signal, which can be difficult to obtain in practice. In this paper, we propose a generalised error compensation method for peak extraction from axial response signals. This full-width-at-half-maximum-independent method is based on a corrected parabolic fitting algorithm. With the corrected parabolic fitting algorithm, the systematic error of a parabolic fitting is characterised using a differential equation, following which, the error is estimated and compensated by solving this equation with a first-order approximation. We demonstrate, by Monte Carlo simulations and experiments with various axial response signals with symmetrical and asymmetrical forms, that the corrected parabolic fitting algorithm has significant improvements over existing algorithms in terms of peak extraction accuracy and precision.

Characterization of the displacement response in chromatic confocal microscopy with a hybrid radial basis function network.

Characterization of the displacement response is critical for accurate chromatic confocal measurement. Current characterization methods usually provide a linear or polynomial relationship between the extracted peak wavelengths of the spectral signal and displacement. However, these methods are susceptible to errors in the peak extraction algorithms and errors in the selected model. In this paper, we propose a hybrid radial basis function network method to characterise the displacement response. With this method, the peak wavelength of the spectral signal is firstly extracted with a state-of-art peak extraction algorithm, following which, a higher-accuracy chromatic dispersion model is applied to determine the displacement-wavelength relationship. Lastly, a radial basis function network is optimized to provide a mapping between the spectral signals and the residual fitting errors of the chromatic dispersion model. Using experimental tests, we show that the hybrid radial basis function network method significantly improves the measurement accuracy, when compared to the existing characterizing methods.

Correction of errors due to uneven intensity distribution and inaccurate phase shifts in prism-based simultaneous phase-shifting interferometry.

Simultaneous phase-shifting interferometry (SPSI) is a suitable technique for dynamic surface measurement due to its rapid measurement capability. Based on whether there are obvious multiple phase-shifting channels in the setup, it can be divided into the multi-channel type and the pixelated phase-mask type. For the former type, two important error sources are the uneven intensity distribution among different phase-shifting channels and inaccurate phase shifts in each phase-shifting channel. In order to diminish the influence of these two error sources, several methods have been proposed. However, in some of these methods, only one error source of the two was considered and corrected. In the methods where the two error sources were both considered, some assumptions such as the uniform background intensity and fringe contrast are needed, so a complete and universal suppression method for both error sources is still needed in actual applications. In this paper, for a prism-based SPSI, we proposed such an error-correction method that mainly contains the following contributions. First, the intrinsic parameters of the system, including intensity distribution coefficients and relative phase shifts among phase-shifting channels, are calibrated in advance. We also checked the uniformity of phase shifts in each phase-shifting channel. Second, based on the obtained parameters, a corrected four-step phase-shifting algorithm is deduced to recover the more accurate measured phase. Results of both simulation and experiment verify the effectiveness of the proposed method.