lncRNASNP v3: an updated database for functional variants in long non-coding RNAs.

Long non-coding RNAs (lncRNAs) act as versatile regulators of many biological processes and play vital roles in various diseases. lncRNASNP is dedicated to providing a comprehensive repository of single nucleotide polymorphisms (SNPs) and somatic mutations in lncRNAs and their impacts on lncRNA structure and function. Since the last release in 2018, there has been a huge increase in the number of variants and lncRNAs. Thus, we updated the lncRNASNP to version 3 by expanding the species to eight eukaryotic species (human, chimpanzee, pig, mouse, rat, chicken, zebrafish, and fruitfly), updating the data and adding several new features. SNPs in lncRNASNP have increased from 11 181 387 to 67 513 785. The human mutations have increased from 1 174 768 to 2 387 685, including 1 031 639 TCGA mutations and 1 356 046 CosmicNCVs. Compared with the last release, updated and new features in lncRNASNP v3 include (i) SNPs in lncRNAs and their impacts on lncRNAs for eight species, (ii) SNP effects on miRNA-lncRNA interactions for eight species, (iii) lncRNA expression profiles for six species, (iv) disease & GWAS-associated lncRNAs and variants, (v) experimental & predicted lncRNAs and drug target associations and (vi) SNP effects on lncRNA expression (eQTL) across tumor & normal tissues. The lncRNASNP v3 is freely available at http://gong_lab.hzau.edu.cn/lncRNASNP3/.

Enhancing the Thermoelectric and Mechanical Properties of p-Type PbS through Band Convergence and Microstructure Regulation.

While lead sulfide shows notable thermoelectric properties, its production costs remain high, and its mechanical hardness is low, which constrains its commercial viability. Herein, we demonstrate a straightforward and cost-effective method to produce PbS nanocrystals at ambient temperature. By introducing controlled amounts of silver, we achieve p-type conductivity and fine-tune the energy band structure and lattice configuration. Computational results show that silver shifts the Fermi level into the valence band, facilitating band convergence and thereby enhancing the power factor. Besides, excess silver is present as silver sulfide, which effectively diminishes the interface barrier and enhances the Seebeck coefficient. Defects caused by doping, along with dislocations and interfaces, reduce thermal conductivity to 0.49 W m-1 K-1 at 690 K. Moreover, the alterations in crystal structure and chemical composition enhance the PbS mechanical properties. Overall, optimized materials show thermoelectric figures of merit approximately 10-fold higher than that of pristine PbS, alongside an average hardness of 1.08 GPa.

Scalar topological photonic nested meta-crystals and skyrmion surface states in the light cone continuum.

Topological photonics is rapidly expanding. However, discovering three-dimensional topological electromagnetic systems can be more challenging than electronic systems for two reasons. First, the vectorial nature of electromagnetic waves results in complicated band dispersions, and simple tight-binding-type predictions usually fail. Second, topological electromagnetic surface modes inside the light cone have very low quality factors (Q factors). Here, we propose the concept of scalar topological photonics to address these challenges. Our approach is experimentally validated by employing a nested meta-crystal configuration using connected coaxial waveguides. They exhibit scalar-wave-like band dispersions, making the search for photonic topological phases an easier task. Their surface states have skyrmion-like electric field distributions, resulting in a whole, bright surface state band inside the light cone continuum. As such, the topological surface states in our three-dimensional nested crystals can be exposed to air, making such systems well-suited for practical applications.

Does growth hormone supplementation of in vitro fertilization/intracytoplasmic sperm injection improve cumulative live birth rates in women with poor embryonic development in the previous cycle?

BACKGROUND: Growth hormone (GH) has been proposed as an adjunct in in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) cycles, especially in women with poor ovarian response. However, it is unclear whether GH supplementation is effective in women with poor embryonic development in the previous IVF cycle. The aim of this study was to evaluate the effectiveness of GH supplementation in IVF/ICSI cycles in women with poor embryonic development in the previous cycle. METHODS: This is a retrospective cohort study from a public fertility center in China, in which we performed propensity score-matching (PSM) for female age and AFC in a ratio of 1:1. We compared the cumulative live birth rate per started cycle, as well as a series of secondary outcomes. We included 3,043 women with poor embryonic development in the previous IVF/ICSI cycle, of which 1,326 had GH as adjuvant therapy and 1,717 had not. After PSM, there were 694 women in each group. RESULTS: After PSM, multivariate analyses showed the cumulative live birth rate to be significantly higher in the GH group than the control group [N = 694, 34.7% vs. N = 694, 27.5%, risk ratio (RR): 1.4 (95%CI: 1.1-1.8)]. Endometrial thickness, number of oocytes retrieved, number of embryos available, and number of good-quality embryos were significantly higher in the GH group compared to controls. Pregnancy outcomes in terms of birth weight, gestational age, fetal sex, preterm birth rate, and type of delivery were comparable. When we evaluated the impact of GH on different categories of female age, the observed benefit in the GH group did not appear to be significant. When we assessed the effect of GH in different AFC categories, the effect of GH was strongest in women with an AFC5-6 (32.2% versus 19.5%; RR 2.0; 95% CI 1.2-3.3). CONCLUSIONS: Women with poor embryonic quality in the previous IVF/ICSI cycles have higher rates of cumulative live birth with GH supplementation.

Animal-eRNAdb: a comprehensive animal enhancer RNA database.

Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from enhancers. As the markers of active enhancers, eRNAs play important roles in gene regulation and are associated with various complex traits and characteristics. With increasing attention to eRNAs, numerous eRNAs have been identified in different human tissues. However, the expression landscape, regulatory network and potential functions of eRNAs in animals have not been fully elucidated. Here, we systematically characterized 185 177 eRNAs from 5085 samples across 10 species by mapping the RNA sequencing data to the regions of known enhancers. To explore their potential functions based on evolutionary conservation, we investigated the sequence similarity of eRNAs among multiple species. In addition, we identified the possible associations between eRNAs and transcription factors (TFs) or nearby genes to decipher their possible regulators and target genes, as well as characterized trait-related eRNAs to explore their potential functions in biological processes. Based on these findings, we further developed Animal-eRNAdb (http://gong_lab.hzau.edu.cn/Animal-eRNAdb/), a user-friendly database for data searching, browsing and downloading. With the comprehensive characterization of eRNAs in various tissues of different species, Animal-eRNAdb may greatly facilitate the exploration of functions and mechanisms of eRNAs.

Analysis of Fever Following Bronchoscopy and Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration.

Objective: Bronchoscopy and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) are two essential methods for obtaining the pathological diagnosis of central lung masses or hilar and mediastinal lymphadenopathy. We can observe that many patients have a fever after examinations, but the pathogenesis is not yet fully clear. We tried to comprehensively assess the occurrence of postoperative fever and bacterial infections in patients undergoing bronchoscopy and endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) procedures. Methods: We retrospectively analyzed 512 patients undergoing bronchoscopy or EBUS-TBNA examination. According to examination methods, all patients were classified into three groups: Only perform bronchoscopy examination (BO) group (122 cases)，both perform bronchoscopy and biopsy (BB) group (262 cases), and EBUS-TBNA after bronchoscopy (EBUS) group (128 cases). Peripheral blood leucocyte, neutrophil count, and serum IL-6 test results were obtained before and after the examination. A blood culture was performed when the body temperature was higher than 38.5°C. Results: Among the three groups, the onset time (5.5h), average duration (6h), and peak temperature (37.7°C) of fever in the BO group were lower than those in the BB and EBUS groups. Still, there was no significant difference in onset time (11.66h, 11.83h), average duration (12.86h, 13.56h), and peak temperature (39.1°C, 39.1°C) between the BB group and EBUS group. There was no significant difference in the peripheral blood leukocyte count, neutrophil count or IL-6 level before the operation (P > .05). Compared with the preoperative, the leukocyte count, neutrophil count and IL-6 level in the three groups were increased after the operation (P < .05). Positive blood cultures were diagnosed as normal oropharyngeal flora. Conclusions: Postoperative fever after bronchoscopy is a relatively common complication, most of which do not require special treatment. Individuals with concomitant diseases such as diabetes may have postoperative infections after EBUS-TBNA, and they should be emphatically observed. The findings could potentially extend to similar diagnostic procedures or situations in pulmonary medicine. Understanding the risk factors associated with postoperative fever can help healthcare providers manage patient expectations and monitor certain groups more closely.

FKF1b controls reproductive transition associated with adaptation to geographical distribution in maize.

Maize (Zea mays subspecies mays) is an important commercial crop across the world, and its flowering time is closely related to grain yield, plant cycle and latitude adaptation. FKF1 is an essential clock-regulated blue-light receptor with distinct functions on flowering time in plants, and its function in maize remains unclear. In this study, we identified two FKF1 homologs in the maize genome, named ZmFKF1a and ZmFKF1b, and indicated that ZmFKF1a and ZmFKF1b independently regulate reproductive transition through interacting with ZmCONZ1 and ZmGI1 to increase the transcription levels of ZmCONZ1 and ZCN8. We demonstrated that ZmFKF1b underwent artificial selection during modern breeding in China probably due to its role in geographical adaptation. Furthermore, our data suggested that ZmFKF1bHap_C7 may be an elite allele, which increases the abundance of ZmCONZ1 mRNA more efficiently and adapt to a wider range of temperature zone than that of ZmFKF1bHap_Z58 to promote maize floral transition. It extends our understanding of the genetic diversity of maize flowering. This allele is expected to be introduced into tropical maize germplasm to enrich breeding resources and may improve the adaptability of maize at different climate zones, especially at temperate region.

Altering the CO2 electroreduction pathways towards C1 or C2+ products via engineering the strength of interfacial Cu-O bond.

Copper (Cu)-based catalysts have established their unique capability for yielding wide value-added products from CO2. Herein, we demonstrate that the pathways of the electrocatalytic CO2 reduction reaction (CO2RR) can be rationally altered toward C1 or C2+ products by simply optimizing the coordination of Cu with O-containing organic species (squarate (C4O4) and cyclohexanhexanone (C6O6)). It is revealed that the strength of Cu-O bonds can significantly affect the morphologies and electronic structures of derived Cu catalysts, resulting in the distinct behaviors during CO2RR. Specifically, the C6O6-Cu catalysts made up from organized nanodomains shows a dominant C1 pathway with a total Faradaic efficiency (FE) of 63.7% at -1.0 V (versus reversible hydrogen electrode, RHE). In comparison, the C4O4-Cu with an about perfect crystalline structure results in uniformly dispersed Cu-atoms, showing a notable FE of 65.8% for C2+ products with enhanced capability of C-C coupling. The latter system also shows stable operation over at least 10 h with a high current density of 205.1 mA cm-2 at -1.0 VRHE, i.e. is already at the boarder of practical relevance. This study sheds light on the rational design of Cu-based catalysts for directing the CO2RR reaction pathway.

A Triplet Iron Carbyne Complex.

Tuning the spin state of metal carbynes, which have broad applications in organic synthesis and material science, presents a formidable challenge for modern chemists as the strong field nature of carbyne ligands dictates low-spin ground spin states (S = 0 or 1/2) for known metal carbynes. Through the oxidative addition reaction of a low-coordinate iron(0) N-heterocyclic carbene complex with the C-S bond of a thioazole-2-ylidene, we synthesized the first triplet (S = 1) metal terminal carbyne, an iron cyclic carbyne complex. Different from the classical metal carbynes, the triplet complex features an LXZ-type carbyne ligand and a weak Fe≡C triple bond, which endow it with the unique reactivity pattern of facile carbyne coupling, weak affinity toward nucleophiles, and facial addition reactions with electrophiles.

Gut Prevotellaceae-GABAergic septohippocampal pathway mediates spatial memory impairment in high-fat diet-fed ovariectomized mice.

Clarifying the risk factors and mechanisms that contribute to the onset of cognitive impairment following estrogen depletion is essential for improving the quality of life of older females. In the current study, using behavioral tests, 16S rDNA sequencing, in vivo and in vitro electrophysiology, optogenetics and chemogenetics, we found that high-fat diet (HFD)-accelerated impairment of hippocampus-dependent memory, gut microbiota, and hippocampal theta rhythmogenesis in ovariectomized (OVX) mice and fecal microbiota transplantation rescued these phenomena. The identification of fasting-activated medial septal neurons showed that PV+ GABAergic neurons in the medial septal area (MSA) respond to gut sensory signals. Optogenetic activation of septohippocampal PV+ GABAergic fibers (but not cholinergic fibers) significantly rescued hippocampal theta rhythmogenesis and spatial memory in HFD-fed OVX mice. Resistant starch supplementation (RSHFD) rectified the gut Prevotellaceae and considerably alleviated reduced septal gut-responsive neurons, decreased hippocampal theta rhythm, and impaired hippocampus-dependent memory in HFD-fed OVX mice. Furthermore, chemogenetic inhibition of septal PV+ GABAergic neurons reversed the neuroprotective effects of resistant starch supplementation. These findings highlight the notable gut-sensory nature of medial septal PV+ GABAergic neurons. A HFD accelerates estrogen deficiency-induced cognitive impairment by disrupting the gut Prevotellaceae-septo-hippocampal pathway. This study contributes to a better understanding of the precise gut-brain control of cognition and cognitive impairment in postmenopausal females.

Surface-Defect-Involved and Eye-Visible Electrochemiluminescence of Unary Copper Nanoclusters for Immunoassay.

A single-stabilizer-capped strategy is proposed for achieving highly efficient and surface-defect-involved electrochemiluminescence (ECL) from unary copper nanoclusters (NCs) via employing l-cysteine (Cys) as a capping agent of luminophore. The Cys-capped CuNCs (Cys-CuNCs) can be electrochemically injected with valence band (VB) holes and exhibit eye-touchable ECL processes around +0.95 and +1.15 V upon employing TPrA as a coreactant. Both accumulated ECL spectra and spooling ECL spectra demonstrated that the two ECL processes are of the same single waveband and spectrally identical to each other with the same maximum emission wavelength of 640 nm. Promisingly, ECL of the Cys-CuNCs/TPrA system is obviously red-shifted for ∼150 nm to PL of Cys-CuNCs, indicating that the bandgap-engineered routes for ECLs of Cys-CuNCs are completely blocked. The oxidative-reduction ECL process of the Cys-CuNCs/TPrA system is a kind of highly efficient, eye-visible, and single-color emission in surface-defect-involved route. The capping agent of Cys can enable the CuNCs/TPrA system with a stronger ECL than other thiol capping agents, so that Cys-CuNCs are utilized as ECL tags for sensitive and selective immunoassays, which exhibit a wide linear response range from 0.05 pg/mL to 0.5 ng/mL and a limit of detection of 0.01 pg/mL (S/N = 3) with carcinoembryonic antigen as the analyte. Moreover, both the luminophore Cys-CuNCs and conjugates Ab2-CuNCs can be safely stored in aqueous media without any protector, which is promising for the evolution and clinic application of metal NC ECL in the surface-defect-involved route.

ATG16L2 inhibits NLRP3 inflammasome activation through promoting ATG5-12-16L1 complex assembly and autophagy.

NLRP3 inflammasome activation is regulated by autophagy, a process tightly controlled by the ATG16L family proteins. However, the inside mechanisms remain elusive. Although the autophagy-related protein ATG16L1 has been well characterized, regulation and biological functions of its close homolog ATG16L2 still remain elusive. Here we report that ATG16L2 deficiency attenuates LPS-induced autophagy flux in macrophages through mediating ATG5-12-16L1 complex assembly. Importantly, NLRP3 inflammasome activation is elevated in ATG16L2-deficient macrophages, which also have defects in mitochondrial integrity and respiration. Finally, ATG16l2 knockout mice are more susceptible to DSS-induced intestinal damage, which can be ameliorated by inhibition of NLRP3. Collectively, our data demonstrate that ATG16L2 positively regulates autophagy and ATG16L2 could be a potential target for manipulating aberrant NLRP3 inflammasome activation induced inflammatory diseases.

A systematic comparison of normalization methods for eQTL analysis.

Expression quantitative trait loci (eQTL) analysis has been widely used in interpreting disease-associated loci through correlating genetic variant loci with the expression of specific genes. RNA-sequencing (RNA-Seq), which can quantify gene expression at the genome-wide level, is often used in eQTL identification. Since different normalization methods of gene expression have substantial impacts on RNA-seq downstream analysis, it is of great necessity to systematically compare the effects of these methods on eQTL identification. Here, by using RNA-seq and genotype data of four different cancers in The Cancer Genome Atlas (TCGA) database, we comprehensively evaluated the effect of eight commonly used normalization methods on eQTL identification. Our results showed that the application of different methods could cause 20-30% differences in the final results of eQTL identification. Among these methods, COUNT, Median of Ratio (MED) and Trimmed Mean of M-values (TMM) generated similar results for identifying eQTLs, while Fragments Per Kilobase Million (FPKM) or RANK produced more differential results compared with other methods. Based on the accuracy and receiver operating characteristic (ROC) curve, the TMM method was found to be the optimal method for normalizing gene expression data in eQTLs analysis. In addition, we also evaluated the performance of different pairwise combinations of these methods. As a result, compared with single normalization methods, the combination of methods can not only identify more cis-eQTLs, but also improve the performance of the ROC curve. Overall, this study provides a comprehensive comparison of normalization methods for identifying eQTLs from RNA-seq data, and proposes some practical recommendations for diverse scenarios.

Conventional photon blockade in the dispersive limit for Tavis-Cummings model.

In the dispersive limit, the conventional photon blockade effect cannot be realized due to the absence of photon nonlinearity. We propose a scheme to recover the photon blockade effect of the dispersive Tavis-Cummings model, which makes it possible to realize the conventional photon blockade effect in the dispersive limit. It is shown that both single-photon and two-photon blockade effects can be recovered at appropriate qubit driving strength. The optimal qubit drive strength and cavity field drive detuning are given analytically. All analyses can be verified by numerical simulation, and the strongest photon blockade effect with the largest average photon number can be produced when the single excitation resonance condition is satisfied. Moreover, we find that the achieved two-photon blockade effect is relatively robust to thermal noise. Our proposal is able to obtain single-photon sources with high purity and high brightness and has great potential for applications in quantum communication processing.

Squeezing-induced nonreciprocal photon blockade in an optomechanical microresonator.

We propose a scheme to generate nonreciprocal photon blockade in a stationary whispering gallery microresonator system based on two physical mechanisms. One of the two mechanisms is inspired by recent work [Phys. Rev. Lett.128, 083604 (2022)10.1103/PhysRevLett.128.083604], where the quantum squeezing caused by parametric interaction not only shifts the optical frequency of propagating mode but also enhances its optomechanical coupling, resulting in a nonreciprocal conventional photon blockade phenomenon. On the other hand, we also give another mechanism to generate stronger nonreciprocity of photon correlation according to the destructive quantum interference. Comparing these two strategies, the required nonlinear strength of parametric interaction in the second one is smaller, and the broadband squeezed vacuum field used to eliminate thermalization noise is no longer needed. All analyses and optimal parameter relations are further verified by numerically simulating the quantum master equation. Our proposed scheme opens a new avenue for achieving the nonreciprocal single photon source without stringent requirements, which may have critical applications in quantum communication, quantum information processing, and topological photonics.

Experimental quantum natural gradient optimization in photonics.

Variational quantum algorithms (VQAs) combining the advantages of parameterized quantum circuits and classical optimizers, promise practical quantum applications in the noisy intermediate-scale quantum era. The performance of VQAs heavily depends on the optimization method. Compared with gradient-free and ordinary gradient descent methods, the quantum natural gradient (QNG), which mirrors the geometric structure of the parameter space, can achieve faster convergence and avoid local minima more easily, thereby reducing the cost of circuit executions. We utilized a fully programmable photonic chip to experimentally estimate the QNG in photonics for the first time, to the best of our knowledge. We obtained the dissociation curve of the He-H+ cation and achieved chemical accuracy, verifying the outperformance of QNG optimization on a photonic device. Our work opens up a vista of utilizing QNG in photonics to implement practical near-term quantum applications.

Quantum generative adversarial learning in photonics.

Quantum generative adversarial networks (QGANs), an intersection of quantum computing and machine learning, have attracted widespread attention due to their potential advantages over classical analogs. However, in the current era of noisy intermediate-scale quantum (NISQ) computing, it is essential to investigate whether QGANs can perform learning tasks on near-term quantum devices usually affected by noise and even defects. In this Letter, using a programmable silicon quantum photonic chip, we experimentally demonstrate the QGAN model in photonics for the first time to our knowledge and investigate the effects of noise and defects on its performance. Our results show that QGANs can generate high-quality quantum data with a fidelity higher than 90%, even under conditions where up to half of the generator's phase shifters are damaged, or all of the generator and discriminator's phase shifters are subjected to phase noise up to 0.04π. Our work sheds light on the feasibility of implementing QGANs on the NISQ-era quantum hardware.

Intrinsic Triple Degeneracy Point Bounded by Nodal Surfaces in Chiral Photonic Crystal.

In periodic systems, band degeneracies are typically protected and classified by spatial symmetries. However, in photonic systems, the Γ point at zero frequency is an intrinsic degeneracy due to the polarization degree of freedom of electromagnetic waves. For chiral photonic crystals, such an intrinsic degeneracy carries ±2 chiral topological charge while having linear band dispersions, different from the general perception of charge-2 nodes being associated with quadratic dispersions. Here, we show that these topological characters originate from the spin-1 Weyl point at zero frequency node of triple degeneracy, due to the existence of an electrostatic flat band. Such a topological charge at zero frequency is usually buried in bulk band projections and has never been experimentally observed. To address this challenge, we introduce space-group screw symmetries in the design of chiral photonic crystal, which makes the Brillouin zone boundary an oppositely charged nodal surface enclosing the Γ point. As a result, the emergent Fermi arcs are forced to connect the projections of these topological singularities, enabling their experimental observation. The number of Fermi arcs then directly reveals the embedded topological charge at zero frequency.

Asteriquinones from Aspergillus sp. GZWMJZ-258 and Their Derivatives.

A new asteriquinone, ochrindole F (1), and five previously reported analogues (2-6) were isolated from the culture of the fungus Aspergillus sp. GZWMJZ-258, an endophyte of Garcinia multiflora. The structure of compound 1 was determined by a spectroscopic analysis. Furthermore, eight new derivatives (7-14) were synthesized from major metabolites 2 and 3. These compounds showed selective antiproliferative activity against the human acute myeloid leukemia (AML) cell line MV4-11, among which compound 12 showed the strongest activity with an IC50 value of 0.14 µM and the highest selectivity with a selectivity index greater than 710. An initial probe of the mechanism of action showed that compounds 12 and 14 could inhibit the expression of FLT-3 in the MV4-11 cell line.

FoxO1 knockdown inhibits RANKL-induced osteoclastogenesis by blocking NLRP3 inflammasome activation.

OBJECTIVES: This study aimed to elucidate the connection between osteoclastic forkhead transcription factor O1 (FoxO1) and periodontitis and explore the underlying mechanism by which FoxO1 knockdown regulates osteoclast formation. MATERIALS AND METHODS: A conventional ligature-induced periodontitis model was constructed to reveal the alterations in the proportion of osteoclastic FoxO1 in periodontitis via immunofluorescence staining. Additionally, RNA sequencing (RNA-seq) was performed to explore the underlying mechanisms of FoxO1 knockdown-mediated osteoclastogenesis, followed by western blotting, quantitative polymerase chain reaction, and enzyme-linked immunosorbent assay. RESULTS: FoxO1+ osteoclasts were enriched in the alveolar bone in experimental periodontitis. Moreover, FoxO1 knockdown led to impaired osteoclastogenesis with low expression of osteoclast differentiation-related genes, accompanied by an insufficient osteoclast maturation phenotype. Mechanistically, RNA-seq revealed that the nuclear factor kappa B (NF-κB) and nucleotide-binding oligomerization domain-like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways were inhibited in FoxO1-knockdown osteoclasts. Consistent with this, MCC950, an effective inhibitor of the NLRP3 inflammasome, substantially attenuated osteoclast formation. CONCLUSIONS: FoxO1 knockdown contributed to the inhibition of osteoclastogenesis by effectively suppressing NF-κB signaling and NLRP3 inflammasome activation. This prospective study reveals the role of FoxO1 in mediating osteoclastogenesis and provides a viable therapeutic target for periodontitis treatment.