Precise mode control of laser-written waveguides for broadband, low-dispersion 3D integrated optics.

Three-dimensional (3D) glass chips are promising waveguide platforms for building hybrid 3D photonic circuits due to their 3D topological capabilities, large transparent windows, and low coupling dispersion. At present, the key challenge in scaling down a benchtop optical system to a glass chip is the lack of precise methods for controlling the mode field and optical coupling of 3D waveguide circuits. Here, we propose an overlap-controlled multi-scan (OCMS) method based on laser-direct lithography that allows customizing the refractive index profile of 3D waveguides with high spatial precision in a variety of glasses. On the basis of this method, we achieve variable mode-field distribution, robust and broadband coupling, and thereby demonstrate dispersionless LP21-mode conversion of supercontinuum pulses with the largest deviation of <0.1 dB in coupling ratios on 210 nm broadband. This approach provides a route to achieve ultra-broadband and low-dispersion coupling in 3D photonic circuits, with overwhelming advantages over conventional planar waveguide-optic platforms for on-chip transmission and manipulation of ultrashort laser pulses and broadband supercontinuum.

3D Laser Writing of Low-Loss Cross-Section-Variable Type-I Optical Waveguide Passive/Active Integrated Devices in Single Crystals.

Optical waveguides fabricated in single crystals offer crucial passive/active optical components for photonic integrated circuits. Single crystals possess inherent advantages over their amorphous counterpart, such as lower optical losses in visible-to-mid-infrared band, larger peak emission cross-section, higher doping concentration. However, the writing of Type-I positive refractive index modified waveguides in single crystals using femtosecond laser technology presents significant challenges. Herein, this work introduces a novel femtosecond laser direct writing technique that combines slit-shaping with an immersion oil objective to fabricate low-loss Type-I waveguides in single crystals. This approach allows for precise control of waveguide shape, size, mode-field, and refractive index distribution, with a spatial resolution as high as 700 nm and a high positive refractive index variation on the order of 10-2, introducing new degrees of freedom to design and fabricate passive/active optical waveguide devices. As a proof-of-concept, this work successfully produces a 7 mm-long circular-shaped gain waveguide (≈10 µm in diameter) in an Er3+-doped YAG single crystal, exhibiting a propagation loss as low as 0.23 dB cm-1, a net gain of ≈3 dB and a polarization-insensitive character. The newly-developed technique is theoretically applicable to arbitrary single crystals, holding promising potential for various applications in integrated optics, optical communication, and photonic quantum circuits.

Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs.

Teat number (TNUM) is an important reproductive trait of sows, which affects the weaning survival rate of piglets. In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and total teat number (TTN) were 0.21, 0.19 and 0.3, respectively. Based on chip data, significant SNPs for RTN on SSC2, SSC5, SSC9 and SSC13 were identified using genome-wide association analysis (GWAS). Significant SNPs for TTN were identified on SSC2, SSC5 and SSC7. Based on imputed data, the GWAS identified a significant SNP (rs329158522) for LTN on SSC17, two significant SNPs (rs342855242 and rs80813115) for RTN on SSC2 and SSC9, and two significant SNPs (rs327003548 and rs326943811) for TTN on SSC5 and SSC6. Among them, four novel QTL were discovered. The Bayesian fine-mapping method was used to fine map the QTL identified in the GWAS of the imputed data, and the confidence intervals of QTL affecting LTN (SSC17: 45.22-46.20 Mb), RTN (SSC9: 122.18-122.80 Mb) and TTN (SSC5: 14.01-15.91 Mb, SSC6: 120.06-121.25 Mb) were detected. A total of 52 candidate genes were obtained. Furthermore, we identified five candidate genes, WNT10B, AQP5, FMNL3, NUAK1 and CKAP4, for the first time, which involved in breast development and other related functions by gene annotation. Overall, this study provides new molecular markers for the breeding of teat number in pigs.

Toward a10†dB net-gain waveguide amplifier in an Er3+-Yb3+ co-doped phosphate glass.

High-gain materials and high-quality structures are the two main conditions that determine the amplification performance of optical waveguides. However, it has been hard to balance each other, to date. In this work, we demonstrate breakthroughs in both glass optical gain and optical waveguide structures. We propose a secondary melting dehydration technique that prepares high-quality Er3+-Yb3+ co-doped phosphate glass with low absorption loss. Additionally, we propose a femtosecond laser direct-writing technique that allows controlling the cross section, size, and mode field of waveguides written in glass with high accuracy, leveraging submicron-resolution multi-scan direct-writing optical waveguide technology, which is beneficial for reducing insertion loss. As a proof of concept demonstration, we designed and fabricated two kinds of waveguides, namely, LP01- and LP11-mode waveguides in the Er3+-Yb3+ co-doped phosphate glass, enabling insertion loss as low as 0.9 dB for a waveguide length of 2 mm. Remarkably, we successfully achieved an optical amplification for both the waveguides with a net gain of >7 dB and a net-gain coefficient of >3.5 dB/mm, which is approximately one order of magnitude larger than that in the Er3+-Yb3+ co-doped phosphate glass fabricated by the traditional melt-quenching method. This will open new avenues toward the development of integrated photonic chips.

High-order mode waveguide amplifier with high mode extinction ratio written in an Er3+-doped phosphate glass.

Inscription of fiber-compatible active waveguides in high-gain glass, followed by direct interconnection with few-mode fibers, is one of the most promising solutions for all-optical mode-division multiplexing. In this work, based on the femtosecond laser writing technique, we propose a general fabrication scheme for inscribing high-order mode waveguides in glass, by carefully tailoring the cross-section of the waveguides to match the mode intensity distribution via an improved multi-scan approach. Specifically, we design and fabricate two kinds of waveguides, namely, LP01-mode waveguide and LP11-mode waveguide in a highly Er3+-doped phosphate glass, enabling the insertion loss of the waveguides to be as low as 1.88 dB, and the mode extraction factor of the LP11-mode waveguide up to ∼24 dB. Importantly, we have successfully achieved optical amplification of the waveguides, with an on-off gain as high as 3.52 dB. This novel high-order mode waveguide amplifier has broad application prospects in monolithic on-chip integrated photonic light sources and optical interconnection with few-mode fiber and/or silicon-based waveguide.

One-step generation of composite soybean plants with transgenic roots by Agrobacterium rhizogenes-mediated transformation.

BACKGROUND: Agrobacterium rhizogenes-mediated (ARM) transformation is a highly efficient technique for generating composite plants composed of transgenic roots and wild-type shoot, providing a powerful tool for studying root biology. The ARM transformation has been established in many plant species, including soybean. However, traditional transformation of soybean, transformation efficiency is low. Additionally, the hairy roots were induced in a medium, and then the generated composite plants were transplanted into another medium for growth. This two-step operation is not only time-consuming, but aggravates contamination risk in the study of plant-microbe interactions. RESULTS: Here, we report a one-step ARM transformation method with higher transformation efficiency for generating composite soybean plants. Both the induction of hairy roots and continuous growth of the composite plants were conducted in a single growth medium. The primary root of a 7-day-old seedling was decapitated with a slanted cut, the residual hypocotyl (maintained 0.7-1 cm apical portion) was inoculated with A. rhizogenes harboring the gene construct of interest. Subsequently, the infected seedling was planted into a pot with wet sterile vermiculite. Almost 100% of the infected seedlings could produce transgenic positive roots 16 days post-inoculation in 7 tested genotypes. Importantly, the transgenic hairy roots in each composite plant are about three times more than those of the traditional ARM transformation, indicating that the one-step method is simpler in operation and higher efficiency in transformation. The reliability of the one-step method was verified by CRISPR/Cas9 system to knockout the soybean Rfg1, which restricts nodulation in Williams 82 (Nod-) by Sinorhizobium fredii USDA193. Furthermore, we applied this method to analyze the function of Arabidopsis YAO promoter in soybean. The activity of YAO promoter was detected in whole roots and stronger in the root tips. We also extended the protocol to tomato. CONCLUSIONS: We established a one-step ARM transformation method, which is more convenient in operation and higher efficiency (almost 100%) in transformation for generating composite soybean plants. This method has been validated in promoter functional analysis and rhizobia-legume interactions. We anticipate a broad application of this method to analyze root-related events in tomato and other plant species besides soybean.

Nonuniform fast Fourier transform method for numerical diffraction simulation on tilted planes.

The method, based on the rotation of the angular spectrum in the frequency domain, is generally used for the diffraction simulation between the tilted planes. Due to the rotation of the angular spectrum, the interval between the sampling points in the Fourier domain is not even. For the conventional fast Fourier transform (FFT)-based methods, a spectrum interpolation is needed to get the approximate sampling value on the equidistant sampling points. However, due to the numerical error caused by the spectrum interpolation, the calculation accuracy degrades very quickly as the rotation angle increases. Here, the diffraction propagation between the tilted planes is transformed into a problem about the discrete Fourier transform on the uneven sampling points, which can be evaluated effectively and precisely through the nonuniform fast Fourier transform method (NUFFT). The most important advantage of this method is that the conventional spectrum interpolation is avoided and the high calculation accuracy can be guaranteed for different rotation angles, even when the rotation angle is close to π/2. Also, its calculation efficiency is comparable with that of the conventional FFT-based methods. Numerical examples as well as a discussion about the calculation accuracy and the sampling method are presented.

Research on beam characteristics in a large-Fresnel-number unstable-waveguide hybrid resonator with parabolic mirrors.

Large-Fresnel-number unstable-waveguide hybrid resonators employing spherical resonator mirrors suffer from spherical aberration, which adversely affects beam quality and alignment sensitivity. In this paper, we present experimental and numerical wave-optics simulations of the beam characteristics of a negative-branch hybrid resonator having parabolic mirrors with a large equivalent Fresnel number in the unstable direction. These results are compared with a resonator using spherical mirrors. Using parabolic mirrors, the output beam has a smaller beam spot size and higher power density at the focal plane. We found that the power extraction efficiency is 3.5% higher when compared with a resonator using spherical mirrors as the cavity length was varied between -1 and 1 mm from the ideal confocal resonator. In addition, the power extraction efficiency is 5.6% higher for mirror tilt angles varied between -6 and 6 mrad. Furthermore, the output propagating field is similar to a converging wave for a spherical mirror resonator and the output beam direction deviates 3.5 mrad from the optical axis. The simulation results are in good agreement with the experimental results.

Beam shaping characteristics of an unstable-waveguide hybrid resonator.

The unstable-waveguide hybrid resonator emits a rectangular, simple astigmatic beam with a large number of high-spatial-frequency oscillations in the unstable direction. To equalize the beam quality, in this paper, a beam shaping system with a spatial filter for the hybrid resonator was investigated by numerical simulation and experimental method. The high-frequency components and fundamental mode of the output beam of the hybrid resonator in the unstable direction are separated by a focus lens. The high-frequency components of the beam are eliminated by the following spatial filter. A nearly Gaussian-shaped beam with approximately equal beam propagation factor M² in the two orthogonal directions was obtained. The effects of the width of the spatial filter on the beam quality, power loss, and intensity distribution of the shaped beam were investigated. The M² factor in the unstable direction is changed from 1.6 to 1.1 by optimum design. The power loss is only 9.5%. The simulation results are in good agreement with the experimental results.

Genetic variation between two Tibetan macaque (Macaca thibetana) populations in the eastern China based on mitochondrial DNA control region sequences.

Tibetan macaque (Macaca thibetana) is a threatened primate species endemic to China. Population genetic and phylogenetic analyses were conducted in 66 Tibetan individuals from Sichuan (SC), Huangshan (HS), and Fujian (FJ) based on a 477-bp fragment of mitochondrial DNA control region. Four new haplotypes were defined, and a relatively high level of genetic diversity was first observed in FJ populations (Hd = 0.7661). Notably, a continuous approximately 10 bp-fragment deletion was observed near the 5' end of the mtDNA control region of both HS and FJ populations when compared with that of SC population, and a sharing haplotype was found between the two populations, revealing a closer genetic relationship. However, significant genetic differentiation (FST = 0.8700) and more poor gene exchange (Nm < 1) had occurred among three populations. This study mainly provide a further insight into the genetic relationship between HS and FJ Tibetan macaque populations, but it may be necessary to carry out further study with extra samples from other locations in the geographic coverage of the two subspecies (M. thibetana pullus and M. thibetana huangshanensis).

Calibration of multiplexed fiber-optic spectroscopy.

Large-scale commercial bioprocesses that manufacture biopharmaceutical products such as monoclonal antibodies generally involve multiple bioreactors operated in parallel. Spectra recorded during in situ monitoring of multiple bioreactors by multiplexed fiber-optic spectroscopies contain not only spectral information of the chemical constituents but also contributions resulting from differences in the optical properties of the probes. Spectra with variations induced by probe differences cannot be efficiently modeled by the commonly used multivariate linear calibration models or effectively removed by popular empirical preprocessing methods. In this study, for the first time, a calibration model is proposed for the analysis of complex spectral data sets arising from multiplexed probes. In the proposed calibration model, the spectral variations introduced by probe differences are explicitly modeled by introducing a multiplicative parameter for each optical probe, and then their detrimental effects are effectively mitigated through a "dual calibration" strategy. The performance of the proposed multiplex calibration model has been tested on two multiplexed spectral data sets (i.e., MIR data of ternary mixtures and NIR data of bioprocesses). Experimental results suggest that the proposed calibration model can effectively mitigate the detrimental effects of probe differences and hence provide much more accurate predictions than commonly used multivariate linear calibration models (such as PLS) with and without empirical data preprocessing methods such as orthogonal signal correction, standard normal variate, or multiplicative signal correction.

Maintaining the predictive abilities of multivariate calibration models by spectral space transformation.

In quantitative on-line/in-line monitoring of chemical and bio-chemical processes using spectroscopic instruments, multivariate calibration models are indispensable for the extraction of chemical information from complex spectroscopic measurements. The development of reliable multivariate calibration models is generally time-consuming and costly. Therefore, once a reliable multivariate calibration model is established, it is expected to be used for an extended period. However, any change in the instrumental response or variations in the measurement conditions can render a multivariate calibration model invalid. In this contribution, a new method, spectral space transformation (SST), has been developed to maintain the predictive abilities of multivariate calibration models when the spectrometer or measurement conditions are altered. SST tries to eliminate the spectral differences induced by the changes in instruments or measurement conditions through the transformation between two spectral spaces spanned by the corresponding spectra of a subset of standardization samples measured on two instruments or under two sets of experimental conditions. The performance of the method has been tested on two data sets comprising NIR and MIR spectra. The experimental results show that SST can achieve satisfactory analyte predictions from spectroscopic measurements subject to spectrometer/probe alteration, when only a few standardization samples are used. Compared with the existing popular methods designed for the same purpose, i.e. global PLS, univariate slope and bias correction (SBC) and piecewise direct standardization (PDS), SST has the advantages of implementation simplicity, wider applicability and better performance in terms of predictive accuracy.