Evolutionary analysis of a complete chicken genome.

Microchromosomes are prevalent in nonmammalian vertebrates [P. D. Waters et al., Proc. Natl. Acad. Sci. U.S.A. 118 (2021)], but a few of them are missing in bird genome assemblies. Here, we present a new chicken reference genome containing all autosomes, a Z and a W chromosome, with all gaps closed except for the W. We identified ten small microchromosomes (termed dot chromosomes) with distinct sequence and epigenetic features, among which six were newly assembled. Those dot chromosomes exhibit extremely high GC content and a high level of DNA methylation and are enriched for housekeeping genes. The pericentromeric heterochromatin of dot chromosomes is disproportionately large and continues to expand with the proliferation of satellite DNA and testis-expressed genes. Our analyses revealed that the 41-bp CNM repeat frequently forms higher-order repeats (HORs) at the centromeres of acrocentric chromosomes. The centromere core regions where the kinetochore attaches often encompass telomeric sequence (TTAGGG)n, and in a one of the dot chromosomes, the centromere core recruits an endogenous retrovirus (ERV). We further demonstrate that the W chromosome shares some common features with dot chromosomes, having large arrays of hypermethylated tandem repeats. Finally, using the complete chicken chromosome models, we reconstructed a fine picture of chordate karyotype evolution, revealing frequent chromosomal fusions before and after vertebrate whole-genome duplications. Our sequence and epigenetic characterization of chicken chromosomes shed insights into the understanding of vertebrate genome evolution and chromosome biology.

Single-molecule optofluidic microsensor with interface whispering gallery modes.

Label-free sensors are highly desirable for biological analysis and early-stage disease diagnosis. Optical evanescent sensors have shown extraordinary ability in label-free detection, but their potentials have not been fully exploited because of the weak evanescent field tails at the sensing surfaces. Here, we report an ultrasensitive optofluidic biosensor with interface whispering gallery modes in a microbubble cavity. The interface modes feature both the peak of electromagnetic-field intensity at the sensing surface and high-Q factors even in a small-sized cavity, enabling a detection limit as low as 0.3 pg/cm2 The sample consumption can be pushed down to 10 pL due to the intrinsically integrated microfluidic channel. Furthermore, detection of single DNA with 8 kDa molecular weight is realized by the plasmonic-enhanced interface mode.

Feedback insensitivity in a self-chaotic microcavity laser.

Insensitivity to external optical feedback is experimentally demonstrated in a self-chaotic deformed square microcavity laser for the first time, to the best of our knowledge. Both the optical and radio frequency (RF) spectra of the microlaser remain unaffected for external optical feedback with feedback strength as high as 9.9 dB. In addition, the autocorrelation function curve exhibits no time-delayed peaks. The insensitivity makes the self-chaotic microcavity laser promising for applications in feedback-insensitive optical sources.

Phase-Transition Microcavity Laser.

Liquid-crystal microcavity lasers have attracted considerable attention because of their extraordinary tunability and sensitive response to external stimuli, and because they operate generally within a specific phase. Here, we demonstrate a liquid-crystal microcavity laser operated in the phase transition in which the reorientation of liquid-crystal molecules occurs from aligned to disordered states. A significant wavelength shift of the microlaser is observed, resulting from the dramatic changes in the refractive index of liquid-crystal microdroplets during the phase transition. This phase-transition microcavity laser is then exploited for sensitive thermal sensing, enabling a two-order-of-magnitude enhancement in sensitivity compared with the nematic-phase microlaser operated far from the transition point. Experimentally, we demonstrate an exceptional sensitivity of -40 nm/K and an ultrahigh resolution of 320 µK. The phase-transition microcavity laser features compactness, softness, and tunability, showing great potential for high-performance sensors, optical modulators, and soft matter photonics.

Narrow linewidth optical frequency comb based on a directly modulated microcavity laser with optical feedback.

A narrow linewidth optical frequency comb (OFC) based on a directly modulated microcavity laser with external optical feedback is investigated numerically and demonstrated experimentally. Based on the numerical simulations with rate equations, the evolution of the optical and electrical spectra is presented for the direct-modulated microcavity laser with increased feedback strength, and the linewidth property is improved at suitable feedback conditions. The simulation results also show good robustness for the generated OFC in terms of feedback strength and phase. Moreover, the OFC generation experiment is performed by combining with the dual-loop feedback structure to suppress the side mode, and an OFC with a side-mode suppression ratio of 31 dB is realized. Thanks to the high electro-optical response of the microcavity laser, a 15-tone OFC with a frequency interval of 10 GHz is obtained. Finally, the linewidth of each comb tooth is measured to be around 7 kHz under the feedback power of 47 µW, which indicates an enormous compression of approximately 2000 times compared with the free-running continuous-wave microcavity laser.

Unidirectional light emission in a deformed circular-side triangular microresonator.

A waveguide-connected deformed circular-side triangular microresonator is proposed and fabricated. Room temperature unidirectional light emission is experimentally demonstrated in the far-field pattern with a divergence angle of 38°. Single mode lasing at 1545.4 nm is realized at an injection current of 12 mA. The emission pattern changes drastically upon the binding of a nanoparticle with radius down to several nanometers, predicting applications in electrically pumped, cost-effective, portable and highly sensitive far-field detection of nanoparticles.

Wideband multiwavelength Brillouin fiber laser with switchable channel spacing.

A multiwavelength Brillouin fiber laser (MBFL) with a switchable channel spacing is demonstrated using a 1.55-µm single-mode AlGaInAs/InP hybrid square-rectangular laser as a seeding source. The scheme employs a highly nonlinear fiber loop with a feedback path to generate a 10-GHz-spacing MBFL. Then, assisted by a tunable optical bandpass filter, MBFLs with spacing from 20 GHz to 100 GHz at a step of 10 GHz are generated in another highly nonlinear fiber loop based on the cavity-enhanced four-wave mixing. More than 60 lasing lines with an optical signal-to-noise ratio over 10 dB are obtained successfully in all the switchable spacings. The total output power and the channel spacing of the MBFLs are proved to be stable.

Spatio-temporal dynamic diversity of bacterial alkaline phosphatase phoD gene and its environmental drivers in sediments during algal blooms: A case study of shallow Lake Taihu.

Bacterial alkaline phosphatase encoded by the phoD gene is essential for phosphorus (P) cycling in ecosystems. Until now, knowledge of the phoD gene diversity in shallow lake sediments is still lacking. In this study, from early to late stage of cyanobacterial blooms, we investigated the dynamic changes of the abundance of phoD gene (hereafter phoD abundance) and phoD-harboring bacterial community composition (hereafter phoD-harboring BCC) in sediments from different ecological regions of Lake Taihu, the third-largest shallow freshwater lake in China, as well as explored their environmental driving factors. Results showed that phoD abundance in the sediments of Lake Taihu showed spatiotemporal heterogeneity. The highest abundance was found in macrophyte-dominated area (mean 3.25*106copies/g DW), where Haliangium and Aeromicrobium were identified as the major contributors. Due to the negative impact of Microcystis species, phoD abundance decreased significantly (by 40.28% on average) during cyanobacterial blooms in all other regions except the estuary area. The phoD abundance in sediment was positively correlated with total organic carbon (TOC) and total nitrogen (TN). However, the relationship between phoD abundance and alkaline phosphatase activity (APA) varied with time, showing positive correlation (R2 = 0.763, P < 0.01) in the early stage of cyanobacterial blooms, but not (R2 = -0.052, P = 0.838) in the later stage. The predominant phoD-harboring genera in sediments were Kribbella, Streptomyces and Lentzea, all of which belong to Actinobacteria. Non-metric multidimensional scaling (NMDS) analysis revealed that the spatial heterogeneity of phoD-harboring BCC in the sediments of Lake Taihu was significantly higher than the temporal heterogeneity. TP and sand were the principle environmental factors affecting the phoD-harboring BCC in the sediments of the estuary area, while DO, pH, organic phosphorus (Po) and diester phosphorus were the key driving factors for other lake regions. We concluded that the C, N, and P cycles in sediments might work in concert. This study extends the understanding of the phoD gene diversity in shallow lake sediments.

Single-mode lasing in an AlGaInAs/InP dual-port square microresonator.

Mode selection is crucial to achieving stable single-mode lasing in microlasers. Here, we demonstrate experimentally a dual-port square microresonator for single-mode lasing with a side-mode-suppression ratio (SMSR) exceeding 40 dB. By connecting waveguides at two opposite vertices, the quality factor for the antisymmetric mode (ASM) is much higher than that of the symmetric mode (SM), enabling single-mode lasing. Furthermore, far-field interference patterns similar to Young's two-slit interference are observed. This microlaser is capable of providing two optical sources simultaneously for optical signal processing in high-density integrated photonic circuits.

Nonlinear Sensing with Whispering-Gallery Mode Microcavities: From Label-Free Detection to Spectral Fingerprinting.

Optical microresonators have attracted intense interests in highly sensitive molecular detection and optical precision measurement in the past decades. In particular, the combination of a high quality factor with a small mode volume significantly enhances the nonlinear light-matter interaction in whispering-gallery mode (WGM) microresonators, which greatly boost nonlinear optical sensing applications. Nonlinear WGM microsensors not only allow for label-free detection of molecules with an ultrahigh sensitivity but also support new functionalities in sensing such as the specific spectral fingerprinting of molecules with frequency conversion involved. Here, we review the mechanisms, sensing modalities, and recent progresses of nonlinear optical sensors along with a brief outlook on the possible future research directions of this rapidly advancing field.

Unidirectional emission and nanoparticle detection in a deformed circular square resonator.

We propose a novel deformed square resonator which has four asymmetric circular sides. Photons leak out from specific points, depending on the interplay between stable islands and unstable manifolds in phase space. By carefully breaking the mirror reflection symmetry, optical modes with strong chirality approaching 1 and unidirectional emission can be achieved simultaneously. Upon binding of a nanoparticle, the far-field emission pattern of the deformed microcavity changes drastically. Due to the EP point of the degenerate mode pairs in the deformed cavity, chirality-based far-field detection of nanoparticles with ultra-small size can be realized.

[Development of expert diagnostic system for common respiratory diseases].

OBJECTIVE: To develop an internet-based expert diagnostic system for common respiratory diseases. METHODS: SaaS system was used to build architecture; pattern of forward reasoning was applied for inference engine design; ASP.NET with C# from the tool pack of Microsoft Visual Studio 2005 was used for website-interview medical expert system.The database of the system was constructed with Microsoft SQL Server 2005. RESULTS: The developed expert system contained large data memory and high efficient function of data interview and data analysis for diagnosis of various diseases.The users were able to perform this system to obtain diagnosis for common respiratory diseases via internet. CONCLUSION: The developed expert system may be used for internet-based diagnosis of various respiratory diseases,particularly in telemedicine setting.

Parametric down-conversion and polariton pair generation in optomechanical systems.

We demonstrate that the nonlinear optomechanical interaction leads to parametric down-conversion, capable of generating polariton pairs formed by photons and phonons. The nonlinearity is resonantly enhanced through frequency matching, and such parametric down-conversion does not require the stringent condition that the single-photon optomechanical coupling strength g be on the order of the mechanical resonance frequency ω(m). We provide analytical results for the frequency matching condition and derive the nonlinear coefficient. Numerical simulations on polariton pair generation are presented, showing that photonlike polaritons, phononlike polaritons, and mixed photon-phonon polaritons can be selectively generated. Such nonlinear interaction offers a promising way for harnessing the optomechanical nonlinearity to manipulate photons and phonons.

Trapping photons with optical black hole.

An optical black-hole cavity based on transformation optics enables Q-factor enhancement and strong field confinement, by eliminating the intrinsic radiation loss of the conventional whispering-gallery modes, holding potential for applications in energy harvesting and optoelectronics.

Bright semiconductor single-photon sources pumped by heterogeneously integrated micropillar lasers with electrical injections.

The emerging hybrid integrated quantum photonics combines the advantages of different functional components into a single chip to meet the stringent requirements for quantum information processing. Despite the tremendous progress in hybrid integrations of III-V quantum emitters with silicon-based photonic circuits and superconducting single-photon detectors, on-chip optical excitations of quantum emitters via miniaturized lasers towards single-photon sources (SPSs) with low power consumptions, small device footprints, and excellent coherence properties is highly desirable yet illusive. In this work, we present realizations of bright semiconductor SPSs heterogeneously integrated with on-chip electrically-injected microlasers. Different from previous one-by-one transfer printing technique implemented in hybrid quantum dot (QD) photonic devices, multiple deterministically coupled QD-circular Bragg Grating (CBG) SPSs were integrated with electrically-injected micropillar lasers at one time via a potentially scalable transfer printing process assisted by the wide-field photoluminescence (PL) imaging technique. Optically pumped by electrically-injected microlasers, pure single photons are generated with a high-brightness of a count rate of 3.8 M/s and an extraction efficiency of 25.44%. Such a high-brightness is due to the enhancement by the cavity mode of the CBG, which is confirmed by a Purcell factor of 2.5. Our work provides a powerful tool for advancing hybrid integrated quantum photonics in general and boosts the developments for realizing highly-compact, energy-efficient and coherent SPSs in particular.

Low-threshold nanolasers based on miniaturized bound states in the continuum.

The pursuit of compact lasers with low thresholds has imposed strict requirements on tight light confinements with minimized radiation losses. Bound states in the continuum (BICs) have been recently demonstrated as an effective mechanism to trap light. However, most reported BIC lasers are still bulky due to the absence of in-plane light confinement. Here, we combine BICs and photonic bandgaps to realize three-dimensional light confinements, as referred to miniaturized BICs (mini-BICs). We demonstrate highly compact active mini-BIC resonators with a record high-quality (Q) factor of up to 32,500, which enables single-mode lasing with the lowest threshold of 80 W/cm2 among the reported BIC lasers. In addition, photon statistics measurements further confirm the occurrence of the stimulated emission in our devices. Our work reveals a path toward compact BIC lasers with ultralow power consumption and potentially boosts the applications in cavity quantum electrodynamics, nonlinear optics, and integrated photonics.

Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots.

The karyotype of most birds has remained considerably stable during more than 100 million years' evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of four parrot genomes, we uncover frequent chromosome fusions and fissions, with most of them occurring independently among lineages. The increased activities of chromosomal rearrangements in parrots are likely associated with parrot-specific loss of two genes, ALC1 and PARP3, that have known functions in the repair of double-strand breaks and maintenance of genome stability. We further find that the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. Together, the combination of our genomic and cytogenetic analyses characterizes the complex evolutionary history of chromosomal rearrangements and sex chromosomes in parrots.

Chiral emission and Purcell enhancement in a hybrid plasmonic-photonic microresonator.

A high-Q hybrid plasmonic-photonic microresonator, which consists of a dielectric microdisk hybridized with a plasmonic nanoantenna dimer, enables an enlarged local density of states of the optical field and chiral propagation of photons inside the cavity.

Fabrication and Analysis of Chemically-Derived Graphene/Pyramidal Si Heterojunction Solar Cells.

In the study, the chemically-derived reduced graphene oxide flakes on the pyramidal Si substrate to construct the heterojunction solar cells via simple spin-coating process have been presented. The total reflectance of chemically-derived graphene on pyramidal Si is ~12% at the wavelength of 550 nm which is remarkably reduced compared with that of reduced graphene oxide on planar Si. By modifying the density and distribution of reduced graphene oxide flakes on Si, the power conversion efficiency of 5.20% is achieved. Additionally, the simulated absorbance of different-thick graphene is implemented to optimize the performance of graphene/pyramidal Si devices. The fabrication technique for rGO-based devices has the merits of simplicity, large scale, high throughput and low cost, which is a new starting point in the direction of graphene-based material for the applications of next generation optoelectronics.

Low serum selenium level is associated with low muscle mass in the community-dwelling elderly.

OBJECTIVES: Elderly persons with low muscle mass (LMM) or sarcopenia are prone to frailty and functional decline. This study aimed to investigate the relationship between serum selenium level and skeletal muscle mass in community-dwelling elderly. DESIGN: Cross-sectional observational study. SETTING AND PARTICIPANTS: A total of 327 elderly Taipei citizens (mean age 71.5 ± 4.7 years) were recruited from the community. MEASUREMENTS: Skeletal muscle mass was measured by bioelectrical impedance analysis. LMM was defined by low skeletal muscle index (SMI: muscle mass (kg)/[height (m)](2)). All participants were further divided into quartiles by serum selenium level and the risk for LMM among these quartiles was examined using multivariate logistic regression analyses. Estimated serum selenium levels for the LMM group vs the normal group and estimated SMI in the quartiles of serum selenium were computed by least square method in linear regression models. RESULTS: The estimated mean (±standard deviation) of serum selenium level was significantly lower in the LMM group compared with the normal group after adjusting for confounders (1.01 ± 0.03 µmol/L vs 1.14 ± 0.02 µmol/L, P < .001). After adjusting for age, sex, lifestyle, and physical and metabolic factors, the odds ratios (95% confidence interval, P value) of LMM in the bottom, second, and third selenium quartile groups were 4.62 (95% CI 2.11-10.10, P < .001), 2.30 (95% CI 1.05-5.03, P < .05) and 1.51 (95% CI 0.66-3.46, P = .327), respectively, compared with the top quartile group of serum selenium level. The least square mean of SMI increased with the quartiles of serum selenium (P < .001). CONCLUSIONS: This is the first study to demonstrate that low serum selenium is independently associated with low muscle mass in the elderly. The causality and underlying mechanism between selenium and low muscle mass or sarcopenia warrant further research.