A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families.

BACKGROUND: The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck's adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). RESULTS: We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIß, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. CONCLUSIONS: These observations supported the hypothesis that duck's adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control.

Design of an image-based BRDF measurement method using a catadioptric multispectral capture and a real-time Lambert calibration.

By utilizing a catadioptric system and a calibration Lambertian sample, a compact measurement method of bidirectional reflectance distribution function (BRDF) has been proposed for rapid and accurate measurement. With the help of an ellipsoidal dome mirror, a hyperboloid mirror, and a high-resolution camera, spatial reflectance distributions from reflected directions with a large field of view (FOV) can be obtained. The built-in Lambertian standard allows for real-time calibration to account for fluctuations in the illumination spectrum, effectively reducing the measurement drift and achieving a high accuracy. Moreover, a multispectral camera captures images at 8 spectral bands for accurate spectral color reconstruction from different directions. To verify the method, a prototype capable of fast, high-resolution measurements with a large FOV has been developed for characterizing the scattering properties of objects. It achieves a measured angular range up to 160°. Multispectral BRDF data for each sample can be obtained within 5 minutes with an angular resolution of less than 0.6°. Eight ceramic samples with different colors were selected for the verification of measurement accuracy, and their mean relative bias of BRDF measurement was found to be as low as 2.5%.

Identification of alternative splicing events related to fatty liver formation in duck using full-length transcripts.

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is one of most common diseases in the world. Recently, alternative splicing (AS) has been reported to play a key role in NAFLD processes in mammals. Ducks can quickly form fatty liver similar to human NAFLD after overfeeding and restore to normal liver in a short time, suggesting that ducks are an excellent model to unravel molecular mechanisms of lipid metabolism for NAFLD. However, how alternative splicing events (ASEs) affect the fatty liver process in ducks is still unclear. RESULTS: Here we identify 126,277 unique transcripts in liver tissue from an overfed duck (77,237 total transcripts) and its sibling control (69,618 total transcripts). We combined these full-length transcripts with Illumina RNA-seq data from five pairs of overfed ducks and control individuals. Full-length transcript sequencing provided us with structural information of transcripts and Illumina RNA-seq data reveals the expressional profile of each transcript. We found, among these unique transcripts, 30,618 were lncRNAs and 1,744 transcripts including 155 lncRNAs and 1,589 coding transcripts showed significantly differential expression in liver tissues between overfed ducks and control individuals. We also detected 27,317 ASEs and 142 of them showed significant relative abundance changes in ducks under different feeding conditions. Full-length transcript profiles together with Illumina RNA-seq data demonstrated that 10 genes involving in lipid metabolism had ASEs with significantly differential abundance in normally fed (control) and overfed ducks. Among these genes, protein products of five genes (CYP4F22, BTN, GSTA2, ADH5, and DHRS2 genes) were changed by ASEs. CONCLUSIONS: This study presents an example of how to identify ASEs related to important biological processes, such as fatty liver formation, using full-length transcripts alongside Illumina RNA-seq data. Based on these data, we screened out ASEs of lipid-metabolism related genes which might respond to overfeeding. Our future ability to explore the function of genes showing AS differences between overfed ducks and their sibling controls, using genetic manipulations and co-evolutionary studies, will certainly extend our knowledge of genes related to the non-pathogenic fatty liver process.

Effect of surrounding objects in the adapting scene on chromatic adaptation.

Most of the existing chromatic adaptation transforms (CATs) were developed for flat uniform stimuli presented in a uniform background, which substantially simplifies the complexity of the real scene by excluding surrounding objects from the viewing field. The impact of the background complexity, in terms of the spatial properties of the objects surrounding the stimulus, on chromatic adaptation is ignored in most CATs. This study systematically investigated how the background complexity and color distribution affect the adaptation state. Achromatic matching experiments were conducted in an immersive lighting booth, with the illumination varying in chromaticity and the adapting scene varying in surrounding objects. Results show that compared to the uniform adapting field, increasing the scene complexity can significantly improve the degree of adaptation for the Planckian illuminations with low CCT levels. In addition, the achromatic matching points are substantially biased by the color of the surrounding object, implying the interactive effect of the illumination color and the dominant scene color on the adapting white point.

PTB: Not just a polypyrimidine tract-binding protein.

Polypyrimidine tract-binding protein (PTB), as a member of the heterogeneous nuclear ribonucleoprotein family, functions by rapidly shuttling between the nucleus and the cytoplasm. PTB is involved in the alternative splicing of pre-messenger RNA (mRNA) and almost all steps of mRNA metabolism. PTB regulation is organ-specific; brain- or muscle-specific microRNAs and long noncoding RNAs partially contribute to regulating PTB, thereby modulating many physiological and pathological processes, such as embryonic development, cell development, spermatogenesis, and neuron growth and differentiation. Previous studies have shown that PTB knockout can inhibit tumorigenesis and development. The knockout of PTB in glial cells can be reprogrammed into functional neurons, which shows great promise in the field of nerve regeneration but is controversial.

Transition type influences the adaptation state under dichromatic illuminations.

The CATs models proposed over these years (such as CMCCAT97, CAT02 and CAT16) were derived from simple stimuli surrounded by a uniform background with a single illuminant. However, the real scene always consists of more than one illumination, especially in many artificially lit environments. Some previous studies indicate an influence of the transition type between two illuminations on the adaptation state, but the visual data is insufficient to conclude a general trend applicable for any color pair. To systematically investigate how the transition type and illumination color pair interactively influence the adapted white point and degree of adaptation, a series of achromatic matching experiments were conducted under (simultaneously) spatially dichromatic illuminations. Transition type was found to have an impact on the adaptation state, but it is significant only for an illumination pair with a large color difference. In addition, for those sharp-transitioned dichromatic illuminations, the illumination that more easily gets adapted tends to have a higher contribution to the adapted white point than the other one. A more comprehensive CAT model for dichromatic illuminations was derived from the collected visual data.

Imaging stretching and displacement using gradient-index elements during the lens design process.

In this study, we propose an approach to stretch or translate images using gradient-index (GRIN) elements with a rotationally symmetric shape in lens systems. In this method, the GRIN material, instead of optical surfaces, are utilized to enable a breaking of rotational symmetry for the two image translations. GRIN expression with anamorphic and tilting terms is introduced. A pair of GRIN elements in front of the given system alters the magnification in two orthogonal directions using the anamorphic terms in the expression, which realizes image stretching. A pair of GRIN elements with tilting terms is used after the given system tilts the optical path to achieve a transverse displacement of the image. The structure of the given system remains unchanged when these translations are performed. A design method for the GRIN elements is presented. Additionally, a design example is presented whose image is stretched by 1.33 times in one direction and displaced to one side of its axis to demonstrate the feasibility of the proposed approach. The approach in this study may enable novel imaging GRIN lens system designs with flexible image positions or special optical functions.

Design, analysis and optimization of a waveguide-type near-eye display using a pin-mirror array and a concaved reflector.

Waveguides have become one of the most promising optical combiners for see-through near-eye displays due to the thickness, weight, and transmittance. In this study, we propose a waveguide-type near-eye display using a pin-mirror array and a concaved reflector with a compact outlook, optimized image uniformity and stray light. Issues have been discussed in detail, which include field of view (FOV), eye-box, resolution, depth of field (DOF), display uniformity and stray light artifacts. It can be shown that the DOF can be extended (when compared with traditional waveguide-type near-eye displays) to alleviate the vergence-accommodation conflict (VAC) problem, and the uniformity & stray light can be improved with an optimal structure. Moreover, reflective surfaces have been introduced as the input and output coupling with a compact outlook, an easy-processing structure and the achromatic performance. A prototype based on the proposed method have been successfully developed, and virtual images with an extended DOF can be shown along with the real-world.

Design of a linear field-of-view oblique imaging system with a low distortion.

For conventional ultra-wide-angle or oblique cameras, it is difficult to fully correct the f-tanθ distortion without the scarification of the edge image performance. In this paper, we propose a linear field-of-view (FOV) oblique imaging system by varying the entrance pupil size over the FOV with freeform mirrors, and thus the diffraction limit around the edge field can be improved. An off-axis reflective system with conic surfaces has been selected as the initial system, and a point-by-point surface design method is then applied on the primary mirror to increase the entrance pupil size for edge fields in the FOV direction. All surfaces for the system converted to freeform during the optimization process, and the FOV of the final design can achieve +35∘ to +65∘, with a distortion less than 1.1%. It is possible to achieve a wide-linear FOV over 130° with a low distortion by the integration of two oblique systems and a central imaging channel.

Three-dimensional image authentication with double random phase encryption in one capture.

We propose a new, to the best of our knowledge, three-dimensional (3D) authentication method based on double random phase integral imaging, and only one image at one viewpoint is used during the authentication process. Two neural networks are applied to estimate depth information and the inpainted synthesized viewpoint image. The usage of deep learning and geometric refocusing techniques greatly simplifies the whole authentication process including capture, transmission, and storage. Experimental results verify the presented method and successfully prove the developed 3D authentication process using a nonlinear correlation method.

Design of a dual focal-plane near-eye display using diffractive waveguides and multiple lenses.

We propose a method to construct a compact dual focal-plane optical see-through near-eye display using diffractive waveguides and multiple lenses. A virtual image from a display device is projected into a three-grating waveguide using an objective lens, and a virtual image can be shown at a far distance with an extended eye box. One negative lens is employed to reduce the focus distance of the virtual image, and a corresponding positive lens is used to compensate for the distortion and accommodation errors. Thus, not only can a virtual image with a near distance be achieved, but also a virtual plane with a further distance can be generated by introducing another projection module and waveguide. Only two waveguides and two pieces of lenses are used in front of one eye to obtain a lightweight outlook. To verify the proposed method, a proof-of-concept prototype was developed to provide vivid virtual images at different depths in front of the human eye.

Transplantation of reprogrammed peripheral blood cells differentiates into retinal ganglion cells in the mouse eye with NMDA-induced injury.

The generation of patient-specific induced pluripotent stem cells (iPSCs) holds significant implications for replacement therapy in treating optic neuropathies such as glaucoma. Stem-cell-based therapy targeted at replacing and replenishing retinal ganglion cells is progressing at a fast pace. However, clinical application necessitates an efficient and robust approach for cell manufacturing. Here, we examine whether the embryo body derived from human peripheral blood-derived iPSC can localize into the host retina and differentiate into retinal ganglion cells after transplantation into a glaucoma injury model. Human peripheral blood T cells were isolated and reprogrammed into an induced pluripotent stem cell (TiPSC) line using Sendai virus transduction carrying transcription factors Sox2, Klf4, c-Myc, and Oct4. TiPSCs were differentiated into RGC using neural basal culture. For in vivo studies, embryo bodies derived from TiPSCs (TiPSC-EB) were injected into the vitreous cavity of N-Methyl-d-aspartic acid (NMDA)-treated mice 2 weeks before sacrifice and retinal dissection. Induced pluripotent stem cells generated from human peripheral blood T cells display stem cell morphology and pluripotency markers. Furthermore, RGC-like cells differentiated from TiPSC exhibit extending axons and RGC marker TUJ1. When transplanted intravitreally into NMDA-treated mice, embryo bodies derived from TiPSC survived, migrated, and incorporated into the retina's GCL layer. In addition, TiPSC-EB transplants were able to differentiate into TUJ1 positive RGC-like cells. Retinal ganglion cells can be differentiated using human peripheral blood cells derived iPSC. Transplantation of embryo body derived from TiPSCs into a glaucoma mouse model could incorporate into host GCL and differentiate into RGC-like cells.

VEGF-mediated angiogenesis in retinopathy of prematurity is co-regulated by miR-17-5p and miR-20a-5p.

The microRNAs miR-17-5p and miR-20a-5p play important roles on angiogenesis; however, it is arguable whether they regulate the formation of retinal blood vessels in retinopathy of prematurity (ROP). We used a mouse model of oxygen-induced retinopathy (OIR) to simulate the development of retinas in mice suffering from ROP, and the expression levels of miR-20a-5p, miR-17-5p, hypoxia-inducible factor 1-alpha (HIF-1α), and vascular endothelial growth factor (VEGF) were measured by RT-qPCR and Western blotting. Cell proliferation, apoptosis, and angiogenesis in the OIR model mice were measured using MTT assays, flow cytometry, and Matrigel assays, respectively. The interaction between HIF-1α/VEGF and miR-20a-5p/miR-17-5p were further validated using dual-luciferase reporter assays, biotin-labeled RNA-pulldown, and RNA immunoprecipitation (RIP) assays. In our OIR model, retinal angiogenesis in the mice was associated with down-regulation of miR-20a-5p and miR-17-5p, as well as up-regulation of HIF-1α and VEGF. In addition, the miR-20a-5p and miR-17-5p inhibited cell proliferation and angiogenesis through regulating HIF-1α and VEGF in the retinal cells of the OIR model mice. Moreover, it was found that miR-20a-5p and miR-17-5p bind to HIF-1α and VEGF at the 3'UTR, and there was a combined effect between miR-20a-5p and miR-17-5p on the regulation of HIF-1α and VEGF. It is worth noting that miR-17-5p and miR-20a-5p can preferentially regulate HIF-1α, then act on VEGF, thereby affecting the angiogenesis associated with ROP.

Full-color retinal-projection near-eye display using a multiplexing-encoding holographic method.

We propose a novel method to construct an optical see-through retinal-projection near-eye display using the Maxwellian view and a holographic method. To provide a dynamic full-color virtual image, a single phase-only spatial light modulator (SLM) was employed in conjunction with a multiplexing-encoding holographic method. Holographic virtual images can be directly projected onto the retina using an optical see-through eyepiece. The virtual image is sufficiently clear when the crystal lens can focus at different depths; the presented method can resolve convergence and accommodation conflict during the use of near-eye displays. To verify the proposed method, a proof-of-concept prototype was developed to provide vivid virtual images alongside real-world ones.

Design of a near-eye display measurement system using an anthropomorphic vision imaging method.

We developed a new near-eye display measurement system using anthropomorphic vision imaging to measure the key parameters of near-eye displays, including field-of-view (FOV), angular resolution, eye box, and virtual image depth. The characteristics of the human eye, such as pupil position, pupil size variation, accommodation function, and the high resolution of the fovea, are imitated by the proposed measurement system. A FOV scanning structure, together with a non-vignetting image-telecentric lens system, captures the virtual image from the near-eye display by imitating human eye function. As a proof-of-concept, a prototype device was used to obtain large-range, high-resolution measurements for key parameters of near-eye displays.

Differential Gene Expression in Post-Finasteride Syndrome Patients.

BACKGROUND: An organic etiology underpinning post-finasteride syndrome, a constellation of persistent sexual, neuropsychiatric, and somatic symptoms reported by men exposed to 5-alpha-reductase inhibitors (5ARIs), is debated. Persistent changes in neurosteroid levels or androgen receptor expression have been implicated. AIM: To determine whether differences in gene expression, especially in relevant biologic pathways, exist between patients reporting post-finasteride syndrome symptoms and healthy controls. METHODS: This was a single center, prospective case-control study taking place between March 2013 and September 2018. Men 18 years and older being evaluated for sexual dysfunction (study) or circumcision (control) were eligible for inclusion. Twenty-six men with a history of 5ARI use reporting symptoms consistent with post-finasteride syndrome were included in the patient group. Twenty-six men consented to inclusion in the control group. OUTCOMES: The primary outcome measure is gene expression data for genes affecting neurosteroid levels and androgen receptor activity from penile skin cells. RESULTS: Gene expression of cells from penile skin samples from twenty-six men of median age 38 years (IQR, 33-42) in the study group was compared with that from twenty-six men of median age 41 years (IQR, 35-62) in the control group (P = .13), with 1,446 genes significantly over-expressed and 2,318 genes significantly under-expressed in study patients. Androgen receptor expression was significantly higher in study patients compared to controls (9.961 vs 9.494, adjusted P value = .01). Serum levels of androgen receptor activity markers 5α-androstanediol (0.950 ng/mL [0.749-1.587] vs 0.949 [0.817-1.337], P = .34) or 3α-androstanedione (3.1 ng/mL [1.925-5.475] vs 6.7 [3.375-11.4], P = .31) revealed no significant differences. No significant differences were found between the number of trinucleotide repeats (21.5 [20-23.75], 22 [19-25], P = .94). CLINICAL IMPLICATIONS: In this study we present evidence of gene expression correlating with observed biologic differences in patients with post-finasteride syndrome; providers who prescribe 5ARIs should be aware and advise their patients accordingly. STRENGTHS & LIMITATIONS: Strengths of this study include the evaluation of multiple proposed etiologies for post-finasteride syndrome. The study is also strengthened by the fact that not all data matched the initial hypotheses, qualifying the argument for the existence of PFS. Limitations include potential selection bias arising from more severe phenotypes seeking care; lack of gene expression data prior to 5ARI exposure; lack of non-penile tissue samples supposedly involved; and a lack of mechanistic data to imply causality. CONCLUSION: This study is the first to consider and demonstrate gene expression differences in patients with PFS as a potential etiology of sexual dysfunction. Howell S, Song W, Pastuszak A, et al. Differential Gene Expression in Post-Finasteride Syndrome Patients. J Sex Med 2021;18:1479-1490.

Latent fingerprint residue detection method using Sagnac Fourier transform imaging spectroscopy.

We propose a new method to detect latent fingerprints and their residues based on Sagnac ultraviolet Fourier transform imaging spectroscopy. The three-dimensional data cube including two-dimensional images and spectrum dimensions can be obtained by the new hyperspectral imaging technique. The method to inhibit the redundancy from the spectra-image data is also presented, which includes the self-adaptive differential filtering, the apodization algorithm, and a fast Fourier transform method. The whole process is also discussed in detail. Not only the latent fingerprint but also its residues' distribution are provided in experimental results, and the proposed method is demonstrated.

Two-step induction of trabecular meshwork cells from induced pluripotent stem cells for glaucoma.

Glaucoma is a leading cause of irreversible blindness worldwide. Reducing intraocular pressure is currently the only effective treatment. Elevated intraocular pressure is associated with increased resistance of the outflow pathway, mainly the trabecular meshwork (TM). Despite great progress in the field, the development of novel and effective treatment for glaucoma is still challenging. In this study, we reported that human induced pluripotent stem cells (iPSCs) can be cultured as colonies and monolayer cells expressing OCT4, alkaline phosphatase, SSEA4 and SSEA1. After induction to neural crest cells (NCCs) positive to NGFR and HNK1, the iPSCs can differentiate into TM cells. The induced iPSC-TM cells expressed TM cell marker CHI3L1, were responsive to dexamethasone treatment with increased expression of myocilin, ANGPTL7, and formed CLANs, comparable to primary TM cells. To the best of our knowledge, this is the first study that induces iPSCs to TM cells through a middle neural crest stage, which ensures a stable NCC pool and ensures the high output of the same TM cells. This system can be used to develop personalized treatments using patient-derived iPSCs, explore high throughput screening of new drugs focusing on TM response for controlling intraocular pressure, and investigate stem cell-based therapy for TM regeneration.

Involvement of regulated necrosis in blinding diseases: Focus on necroptosis and ferroptosis.

Besides apoptosis, necrosis can also occur in a highly regulated and genetically controlled manner, defined as regulated necrosis, which is characterized by a loss of cell membrane integrity and release of cytoplasmic content. Depending on the involvement of its signal pathway, regulated necrosis can be further classified as necroptosis, ferroptosis, pyroptosis and parthanatos. Numerous studies have demonstrated that regulated necrosis is involved in the pathogenesis of many diseases covering almost all organs including the brain, heart, liver, kidney, intestine, blood vessel, eye and skin, particularly myocardial infarction and stroke. Most recently, growing evidence suggests that multiple types of regulated necrosis contribute to the degeneration of retinal ganglion cells, retinal pigment epithelial cells or photoreceptor cells, which are the main pathologic features for glaucoma, age-related macular degeneration or retinitis pigmentosa, respectively. This review focuses on the involvement of necroptosis and ferroptosis in these blinding diseases.

Riemerella anatipestifer infection affects intestinal barrier structure and immune reactions in the duck caecum.

Riemerella anatipestifer (RA) infection causes high mortality and poor feed conversion, leading to great economic losses to the duck industry. This study investigated the effects of RA on the intestinal morphology and immune response of ducks. Histological examination showed that RA infection caused intestinal injury, including significantly reduced mucosal thickness on days 2, 3 and 5, significantly reduced villus height on days 1, 2, 3 and 5 (P < 0.05) and significantly reduced villus height to crypt depth ratios on days 2, 3, 5 and 9 of RA infection (P < 0.05). The expression of intestinal mucosal layer construction-associated genes and tight junction genes was significantly altered on at least one time point (day 1, 2, 3, 5, 9 or 14) after RA infection. Quantitative real-time polymerase chain reaction revealed that RA infection affected intestinal mucosal immune function. The genes encoding TLR4 (toll like receptor-4), TRAF6 (TNF receptor-associated factor 6), MYD88 (myeloid differentiation factor 88), IFN-γ (interferon-γ), IL (interleukin)-4 and IL-8 were significantly upregulated on day 2 of RA infection. Taken together, these results indicate that RA infection negatively affects intestinal barrier function in ducks due to impaired mucosal and villus-crypt structure and alters the mRNA expression of mucous layer construction-, intestinal tight junction-, and intestinal mucosal immunity-related genes.