Where is the orbital angular momentum in vortex superposition states?

In this paper, we explore the distribution of the orbital angular momentum (OAM) in the coaxial vortex superposition states based on the independent propagation principle of light in this interference process. We find that in this case, some specific singular points exist in the spatial intensity distribution. The first type of singular point is located at the center point of the spatial intensity distribution. The second type of specific singular point is at the critical location of the overlapping area in angular direction. By analogy with the angular momentum superposition of two axially rotating homogeneous disks with different radius in rigid body, We present a suggestion: the center point is located at the overlapping area of all the superposed components. Therefore, the topological charge value in the center point should be doubled by the actual number of superposition field components. The singular point at the critical location of the overlapping area in angular direction should also be co-owned by the superposition components outside the position of the ring (including the corresponding component of the ring). The total OAM is exactly equal to the sum of those two types contained in the superposition states, which is equal to the input OAM of the superposition state components. The conservation of the OAM in the coaxial interference process is demonstrated.

Generation of arbitrarily structured optical vortex arrays based on the epicycle model.

Optical vortex arrays (OVAs) are complex light fields with versatile structures that have been widely studied in large-capacity optical communications, optical tweezers, and optical measurements. However, generating OVAs with arbitrary structures without explicit analytical expressions remains a challenge. To address this issue, we propose an alternative scheme for customizing OVAs with arbitrary structures using an epicycle model and vortex localization techniques. This method can accurately generate an OVA with an arbitrary structure by pre-designing the positions of each vortex. The influence of the number and coordinates of the locating points on customized OVAs is discussed. Finally, the structures of the OVA and each vortex are individually shaped into specifically formed fractal shapes by combining cross-phase techniques. This unique OVA will open up novel potential applications, such as the complex manipulation of multiparticle systems and optical communication based on optical angular momentum.

Generation for high-dimensional caustics and artificially tailored structured caustic beams.

We theoretically propose and demonstrate topological parabolic umbilic beams (PUBs) with high-dimensional caustic by mapping catastrophe theory into optics. The PUBs are first experimentally observed via dimensionality reduction. Due to the high-dimensionality, such light beams exhibit rich caustic structures characterized by optical singularities where the high-intensity gradient appears. Further, we propose an improved caustic approach to artificially tailored structured beams which exhibit significant intensity gradient and phase gradient. The properties can trap and drive particles to move along the predesigned trajectory, respectively. The advantages for structured caustic beams likely enable new applications in flexible particle manipulation, light-sheet microscopy, and micromachining.

Switchable hybrid-order optical vortex lattice.

Optical vortex (OV) modulation is a powerful technique for enhancing the intrinsic degrees-of-freedom in structured light applications. Particularly, the lattices involving multiple OVs have garnered significant academic interest owing to their wide applicability in optical tweezers and condensed matter physics. However, all OVs in a lattice possess the same order, which cannot be modulated individually, limiting its versatile application. Herein, we propose, to our knowledge, a novel concept, called the hot-swap method, to design a switchable hybrid-order OV lattice, in which each OV is easily replaced by arbitrary orders. We experimentally generated the switchable hybrid-order OV lattice and studied its characteristics, including interferograms, retrieved phase, energy flow, and orbital angular momentum. Furthermore, the significant advantages of the switchable hybrid-order OV lattice are demonstrated through the independent manipulation of multiple yeast cells. This study provides a novel scheme for accurate control and modulation of OV lattices, which greatly facilitates the diverse applications of optical manipulation and particle trapping and control.

Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation.

The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.

Reactive oxygen species-induced long intergenic noncoding RNA p21 accelerates abdominal aortic aneurysm formation by promoting secretary smooth muscle cell phenotypes.

Whether long noncoding RNAs participate in the formation of abdominal aortic aneurysms (AAAs) through the regulation of SMC phenotypic switching is unknown. lincRNA-p21 induced by reactive oxygen species (ROS) is likely functionally associated with SMC phenotypic switching. We thus investigated the role of lincRNA-p21 in SMC phenotypic switching-associated AAA formation and its underlying mechanisms. An analysis of human and mouse abdominal aortic samples revealed that the lincRNA-p21 levels were significantly higher in AAA tissue. Stimulation with hydrogen peroxide upregulated the expression of lincRNA-p21 in a dose-dependent manner and converted SMCs from a contractile phenotype to a synthetic, proteolytic, and proinflammatory phenotype in vitro. Moreover, lincRNA-p21 promoted fracture of elastic fibres, reconstruction of the vascular wall, and AAA formation in vivo by modulating SMC phenotypic switching in two mouse models of AAA induced by angiotensin II or porcine pancreatic elastase (PPE) perfusion. Using a bioinformatics prediction method and luciferase reporter gene assays, we further proved that lincRNA-p21 sponged miR-204-5p to release the transcriptional activity of Mekk3 and promoted the NF-κB pathway and thereby played a role in the SMC phenotypic switch and AAA formation. The ROS levels were positively correlated with the lincRNA-p21 levels in human and mouse AAA tissues. The knockdown of lincRNA-p21 in a PPE-induced mouse AAA model increased the miR-204-5p levels and reduced the expression of Mekk3, whereas lincRNA-p21 overexpression had the opposite effect. Collectively, the results indicated that ROS-induced lincRNA-p21 sponges miR-204-5p to accelerate synthetic and proinflammatory SMC phenotypes through the Mekk3/NF-κB pathway in AAA formation. Thus, lincRNA-p21 may have therapeutic potential for AAA formation.

Comparative analysis of the organelle genomes of three Rhodiola species provide insights into their structural dynamics and sequence divergences.

BACKGROUND: Plant organelle genomes are a valuable resource for evolutionary biology research, yet their genome architectures, evolutionary patterns and environmental adaptations are poorly understood in many lineages. Rhodiola species is a type of flora mainly distributed in highland habitats, with high medicinal value. Here, we assembled the organelle genomes of three Rhodiola species (R. wallichiana, R. crenulata and R. sacra) collected from the Qinghai-Tibet plateau (QTP), and compared their genome structure, gene content, structural rearrangements, sequence transfer and sequence evolution rates. RESULTS: The results demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes in three Rhodiola species, with the former possessing more conserved genome structure but faster evolutionary rates of sequence, while the latter exhibiting structural diversity but slower rates of sequence evolution. Some lineage-specific features were observed in Rhodiola mitogenomes, including chromosome fission, gene loss and structural rearrangement. Repeat element analysis shows that the repeats occurring between the two chromosomes may mediate the formation of multichromosomal structure in the mitogenomes of Rhodiola, and this multichromosomal structure may have recently formed. The identification of homologous sequences between plastomes and mitogenomes reveals several unidirectional protein-coding gene transfer events from chloroplasts to mitochondria. Moreover, we found that their organelle genomes contained multiple fragments of nuclear transposable elements (TEs) and exhibited different preferences for TEs insertion type. Genome-wide scans of positive selection identified one gene matR from the mitogenome. Since the matR is crucial for plant growth and development, as well as for respiration and stress responses, our findings suggest that matR may participate in the adaptive response of Rhodiola species to environmental stress of QTP. CONCLUSION: The study analyzed the organelle genomes of three Rhodiola species and demonstrated the contrasting evolutionary pattern between plastomes and mitogenomes. Signals of positive selection were detected in the matR gene of Rhodiola mitogenomes, suggesting the potential role of this gene in Rhodiola adaptation to QTP. Together, the study is expected to enrich the genomic resources and provide valuable insights into the structural dynamics and sequence divergences of Rhodiola species.

When optical vortex array meets cycloid.

Optical vortex arrays (OVAs) have drawn widespread attention owing to their multiple optical vortices and higher dimensions. However, existing OVAs have not yet been utilized to exploit the synergy effect as an entire system, particularly for manipulating multiple particles. Thus, the functionality of OVA should be explored to respond to application requirements. Hence, this study proposes a functional OVA, called cycloid OVA (COVA), based on a combination of cycloid and phase-shift techniques. By modifying the cycloid equation, multiple structural parameters are designed to modulate the structure of the COVAs. Subsequently, versatile and functional COVAs are experimentally generated and modulated. In particular, COVA executes local dynamic modulation, whereas the entire structure remains unchanged. Further, the optical gears are first designed using two COVAs, which exhibit potential for transferring multiple particles. Essentially, OVA is endowed the characteristics and capacity of the cycloid when they meet. This work provides an alternative scheme to generate OVAs, which will open up advanced applications for the complex manipulation, arrangement and transfer of multiple particles.

Polarization helicity and the optical spin-orbit Hall effect.

The optical spin-orbit Hall effect manifests the separation of the spin angular momentum (SAM) and the orbital angular momentum (OAM), yet it can be obtained for the radially polarized light and well controlled by the initial phase of the polarization state which leads to the twist of its distribution. In this paper, we introduce the polarization helicity to characterize the effect of the initial phase of the polarization states in the optical spin-orbit Hall effect. We find the polarization helicity of the radial polarization state can be modulated by changing its initial phase, and the polarization helicity of the high-order polarization state always is zero. We show that the separation magnitude of the SAM and the OAM reach the maximum value when the initial phase of the radial polarization state equals π/4 (or -π/4). The sign of the SAM and the OAM are determined by the polarization helicity of incident light and the anisotropy of uniaxial crystal, and its evolution follows a sinusoidal function. Furthermore, the polarization state of the incident radially polarized light will evolve into the left-handed (or right-handed) elliptical polarization state as the change of the polarization helicity of incident light. Our studies further deepen the understanding of the spin-orbit coupling of the vector beams, and provide a potential technique for modulating the polarization state of the light in uniaxial crystal.

Twisted sinc-correlation Schell-model array beams.

We introduce a class of twisted sinc-correlation partially coherent array sources, by applying the construction theory of correlation function. Spectral density of such novel focused beam propagating in free space is analyzed. It is shown that the intensity distribution presents a good twisted effect and splitting phenomenon upon propagation. The array dimension, the intensity distribution and spatial distribution of the lobes can be flexibly regulated by altering the source parameters. We also explore the spatial evolution of multiple correlation singularities of this light field, where the phase distribution appears as a rotational spiral windmill profile during propagation. Furthermore, the coherence orbital angular momentum of the twisted source beam is investigated. These findings could be useful in the particle manipulation and free-space optical communication.

Generation of high-dimensional caustic beams via phase holograms using angular spectral representation.

Using angular spectral representation, we demonstrate a generalized approach for generating high-dimensional elliptic umbilic and hyperbolic umbilic caustics by phase holograms. The wavefronts of such umbilic beams are investigated via the diffraction catastrophe theory determined by the potential function, which depends on the state and control parameters. We find that the hyperbolic umbilic beams degenerate into classical Airy beams when the two control parameters are simultaneously equal to zero, and elliptic umbilic beams possess an intriguing autofocusing property. Numerical results demonstrate that such beams exhibit clear umbilics in 3D caustic, which link the two separated parts. The dynamical evolutions verify that they both possess prominent self-healing properties. Moreover, we demonstrate that hyperbolic umbilic beams follow along a curve trajectory during propagation. As the numerical calculation of diffraction integral is relatively complex, we have developed an effective approach for successfully generating such beams by using phase hologram represented by angular spectrum. Our experimental results are in good agreement with the simulations. Such beams with intriguing properties are likely to be applied in emerging fields such as particle manipulation and optical micromachining.

Shaping focal field by grafted polarization.

In this paper, we propose a novel (to our knowledge) vector beam by combining the radially polarized beams with the different polarization orders, which is called the grafted polarization vector beam (GPVB). Compared with the tight focusing of traditional cylindrical vector beams, GPVB can present more flexible focal field patterns by adjusting the polarization order of two (or more) grafted parts. Moreover, because the GPVB possesses the non-axisymmetrical polarization state distribution, which will lead to the spin-orbit coupling in its tight focusing, it can obtain the spatial separation of spin angular momentum (SAM) and orbital angular momentum (OAM) in the focal plane. The SAM and the OAM are well modulated by adjusting the polarization order of two (or more) grafted parts. Furthermore, we also find the on-axis energy flow in the tight focusing of the GPVB can be changed from positive to negative by adjusting its polarization order. Our results provide more modulation freedom and potential applications in optical tweezers and particles trapping.

Cycloid-structured optical tweezers.

We designed novel cycloid-structured optical tweezers based on a modified cycloid and holographic shaping techniques. The optical tweezers realize all the dynamic characteristics of the trapped particles, including start, stop, and variable-velocity motions along versatile trajectories. The superiority of the tweezers is experimentally verified using polystyrene micro-sphere manipulation. This work provides a novel platform for more complex manipulations of particles.

Generation of discrete higher-order optical vortex lattice at focus.

Higher-order vortices (HOVs) extend the dimensions of optical vortex regulation, which is of great significance in optical communication and optical tweezers. Herein, we demonstrate an alternative scheme to produce a HOV in the focus plane using multiple Laguerre-Gaussian (LG) beam interference, termed a discrete higher-order optical vortex lattice (DHOVL). The modulation depth of the DHOVL exceeds 2π. In this case, the topological charge (TC) of the DHOVL is determined by the difference of the phase period between the innermost and the outermost interference beams. Compared with a conventional HOV (CHOV), the vortex exists in a form of multiple unit singularities sharing a dark core. In addition, the average orbital angular momentum per photon of the DHOVL increases with increasing TC, surpassing that of the CHOV. This work provides a novel, to the best of our knowledge, scheme to produce a HOV, which will facilitate several advanced applications, including optical micromanipulation, optical sensing and imaging, and optical fabrication.

CircRNA Samd4 induces cardiac repair after myocardial infarction by blocking mitochondria-derived ROS output.

Reactive oxygen species (ROS) derived from oxygen-dependent mitochondrial metabolism are the essential drivers of cardiomyocyte (CM) cell-cycle arrest in adulthood. Mitochondria-localized circular RNAs (circRNAs) play important roles in regulating mitochondria-derived ROS production, but their functions in cardiac regeneration are still unknown. Herein, we investigated the functions and underlying mechanism of mitochondria-localized circSamd4 in cardiac regeneration. We found that circSamd4 was selectively expressed in fetal and neonatal CMs. The transcription factor Nrf2 controlled circSamd4 expression by binding to the promoter of circSamd4 host gene. CircSamd4 overexpression reduced while circSamd4 silenced increased mitochondrial oxidative stress and subsequent oxidative DNA damage. Moreover, circSamd4 overexpression induced CM proliferation and prevented CM apoptosis, which reduced the size of the fibrotic area and improved cardiac function after myocardial infarction (MI). Mechanistically, circSamd4 reduced oxidative stress generation and maintained mitochondrial dynamics by inducing the mitochondrial translocation of the Vcp protein, which downregulated Vdac1 expression and prevented the mitochondrial permeability transition pore (mPTP) from opening. Our findings suggest that circSamd4 is a novel therapeutic target for heart failure after MI.

Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau.

KEY MESSAGE: Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.

Improved GNSS Ambiguity Fast Estimation Reduction Algorithm.

The fast and accurate solution of integer ambiguity is the key to achieve GNSS high-precision positioning. Based on the lattice theory of high-dimensional ambiguity solving, the reduction time consumption is much larger than the search time consumption, and it is especially important to improve the efficiency of the lattice basis reduction algorithm. The Householder QR decomposition with minimal column pivoting is utilized to pre-sort the basis vectors and reduce the number of basis vector exchanges during the reduction process by partial size reduction and relaxing the basis vector exchange condition to improve the reduction efficiency of the LLL algorithm. The improved algorithm is validated using simulated and measured data, respectively, and the performance advantages and disadvantages of the improved algorithm are evaluated from the perspectives of the extent of reduction basis orthogonality and the quality of reduction basis size reduction. The results show that the improved LLL algorithm can significantly reduce the number of basis vector exchanges and the reduction time consumption. The HSLLL and PSLLL algorithms with the Siegel condition as the basis vector exchange condition have a better reduction effect, but are slightly less stable. The PLLLR algorithm significantly improves the search ambiguity resolution efficiency, which is conducive to the rapid realization of ambiguity resolution.

Fused inverse-normal method for integrated differential expression analysis of RNA-seq data.

BACKGROUND: Use of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose a p-value combination method for meta-analysis of multiple independent but related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies. RESULTS: The proposed method generalizes the inverse-normal method without an increase in statistical or computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expressed tumour suppressor gene RAD51 in GBM compared to healthy controls, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such as TCF7L2 and MAPT as important upstream regulators in GBM. CONCLUSIONS: The proposed meta-analysis method generalizes the existing inverse-normal method by providing a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease.

Spin-orbit Hall effect in the tight focusing of a radially polarized vortex beam.

When the first-order radially polarized vortex beam propagates in an uniaxial crystal, the spin and the orbital angular momentum parts can be separated. It is called the optical spin-orbit Hall effect. In this study, we investigate the tight focusing of the radially polarized vortex beam theoretically and find the spatial separation of the spin and the orbital angular momentum parts occurs in the focal plane when the polarization order equals 1 and the vortex charge equals 1 (or -1). Moreover, when the initial phase of the polarization state takes π/2, the spatial separation of intensity in the focal plane corresponds to the spatial separation of the spin and the orbital angular momentum parts. This phenomenon can be considered as a manifestation of the optical spin-orbit Hall effect in the tight focusing of radially polarized vortex beam. Also, we show that, when the polarization order is greater than 1, the initial phase change of polarization state just leads to the rotation of the focal field and the spin and the orbital angular momentum density in the focal plane. Our results provide the potential application in the field of optical micro-manipulation.

Loss of Super-Enhancer-Regulated circRNA Nfix Induces Cardiac Regeneration After Myocardial Infarction in Adult Mice.

BACKGROUND: circRNAs (circular RNAs) are emerging as powerful regulators of cardiac development and disease, but their roles in cardiac regeneration are still unknown. This study used superenhancers to distinguish key circRNAs in the regulation of cardiac regeneration and explored the mechanisms underlying circRNA functions. METHODS: We used integrated bioinformatics analysis of RNA sequencing data and superenhancer catalogs to identify superenhancer-associated circRNAs. Quantitative polymerase chain reactions and in situ hybridization were performed to determine the circRNA expression patterns in hearts. Gain- and loss-of-function assays were conducted to detect the role of circRNAs in cardiomyocyte proliferation and cardiac repair after myocardial infarction. Chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays were used to determine the binding of Meis1 (Meis homeobox 1) on circNfix-associated superenhancers. RNA pulldown and luciferase reporter assays were used to study circRNA interactions with proteins and miRNAs (micro RNAs). RESULTS: We identified a circRNA, Nfix circRNA (circNfix), that was regulated by a superenhancer and overexpressed in the adult heart in humans, rats, and mice. The transcription factor Meis1 bound to the superenhancer at the circNfix locus, and increased its expression. In vitro and in vivo, cardiomyocyte proliferation was increased by knockdown of circNfix, whereas it was inhibited by circNfix overexpression. Moreover, circNfix downregulation promoted cardiomyocyte proliferation and angiogenesis and inhibited cardiomyocyte apoptosis after myocardial infarction, attenuating cardiac dysfunction and improving the prognosis. Mechanistically, circNfix reinforced the interaction of Ybx1 (Y-box binding protein 1) with Nedd4l (an E3 ubiquitin ligase), and induced Ybx1 degradation through ubiquitination, repressing cyclin A2 and cyclin B1 expression. In addition, circNfix acted as a sponge for miR-214 to promote Gsk3ß (glycogen synthase kinase 3 ß) expression and repress ß-catenin activity. CONCLUSIONS: Loss of superenhancer-regulated circNfix promotes cardiac regenerative repair and functional recovery after myocardial infarction by suppressing Ybx1 ubiquitin-dependent degradation and increasing miR-214 activity and thus may be a promising strategy for improving the prognosis after MI.