scDAC: deep adaptive clustering of single-cell transcriptomic data with coupled autoencoder and Dirichlet process mixture model.

MOTIVATION: Clustering analysis for single-cell RNA sequencing (scRNA-seq) data is an important step in revealing cellular heterogeneity. Many clustering methods have been proposed to discover heterogenous cell types from scRNA-seq data. However, adaptive clustering with accurate cluster number reflecting intrinsic biology nature from large-scale scRNA-seq data remains quite challenging. RESULTS: Here, we propose a single-cell Deep Adaptive Clustering (scDAC) model by coupling the Autoencoder (AE) and the Dirichlet Process Mixture Model (DPMM). By jointly optimizing the model parameters of AE and DPMM, scDAC achieves adaptive clustering with accurate cluster numbers on scRNA-seq data. We verify the performance of scDAC on five subsampled datasets with different numbers of cell types and compare it with 15 widely used clustering methods across nine scRNA-seq datasets. Our results demonstrate that scDAC can adaptively find accurate numbers of cell types or subtypes and outperforms other methods. Moreover, the performance of scDAC is robust to hyperparameter changes. AVAILABILITY AND IMPLEMENTATION: The scDAC is implemented in Python. The source code is available at https://github.com/labomics/scDAC.

MetaLogo: a heterogeneity-aware sequence logo generator and aligner.

Sequence logos are used to visually display conservations and variations in short sequences. They can indicate the fixed patterns or conserved motifs in a batch of DNA or protein sequences. However, most of the popular sequence logo generators are based on the assumption that all the input sequences are from the same homologous group, which will lead to an overlook of the heterogeneity among the sequences during the sequence logo making process. Heterogeneous groups of sequences may represent clades of different evolutionary origins, or genes families with different functions. Therefore, it is essential to divide the sequences into different phylogenetic or functional groups to reveal their specific sequence motifs and conservation patterns. To solve these problems, we developed MetaLogo, which can automatically cluster the input sequences after multiple sequence alignment and phylogenetic tree construction, and then output sequence logos for multiple groups and aligned them in one figure. User-defined grouping is also supported by MetaLogo to allow users to investigate functional motifs in a more delicate and dynamic perspective. MetaLogo can highlight both the homologous and nonhomologous sites among sequences. MetaLogo can also be used to annotate the evolutionary positions and gene functions of unknown sequences, together with their local sequence characteristics. We provide users a public MetaLogo web server (http://metalogo.omicsnet.org), a standalone Python package (https://github.com/labomics/MetaLogo), and also a built-in web server available for local deployment. Using MetaLogo, users can draw informative, customized and publishable sequence logos without any programming experience to present and investigate new knowledge on specific sequence sets.

Integration of N, P-doped carbon quantum dots with hydrogel as a solid-phase fluorescent probe for adsorption and detection of Fe3.

In this work, a novel nitrogen-phosphorus co-doped carbon quantum dots (N, P-CQDs) hydrogel was developed utilizing the as-synthesized N, P-CQDs and acrylamide (AM) with the existence of ammonium persulfate and N, N'-methylene bisacrylamide (N-MBA). In consistent with pure N, P-CQDs, the N, P-CQDs hydrogel also shows a dramatic fluorescence property with maximum emission wavelength of 440 nm, which can also be quenched after adsorbing iron ions (Fe3+). When the concentration of Fe3+is 0-6 mmol l-1, a better linear relationship between Fe3+concentration and the fluorescence intensities can be easily obtained. Additionally, the N, P-CQDs hydrogel exhibits better recyclability. This confirms that the N, P-CQDs hydrogel can be used for adsorbing and detecting Fe3+in aqueous with on-off-on mode. The fluorescence quenching mainly involves three procedures including the adsorption of Fe3+by hydrogel, integration of Fe3+with N, P-CQDs and the transportation of conjugate electrons in N, P-CQDs to the vacant orbits of Fe3+and the adsorption process follows a pseudo-second-order kinetic model confirmed in the Freundlich isotherm model. In conclusion, this work provides a novel route for synchronously removing and detecting the metal ions in aqueous by integrating N, P-CQDs with hydrogel with better recyclability.

Tip-Induced In-Plane Ferroelectric Superstructure in Zigzag-Wrinkled BaTiO3 Thin Films.

The complex micro-/nanoscale wrinkle morphology primarily fabricated by elastic polymers is usually designed to realize unique functionalities in physiological, biochemical, bioelectric, and optoelectronic systems. In this work, we fabricated inorganic freestanding BaTiO3 ferroelectric thin films with zigzag wrinkle morphology and successfully modulated the ferroelectric domains to form an in-plane (IP) superstructure with periodic surface charge distribution. Our piezoresponse force microscopy (PFM) measurements and phase-field simulation demonstrate that the self-organized strain/stress field in the zigzag-wrinkled BaTiO3 film generates a corresponding pristine domain structure. These domains can be switched by tip-induced strain gradient (flexoelectricity) and naturally form a robust and unique "braided" in-plane domain pattern, which enables us to offer an effective and convenient way to create a microscopic ferroelectric superstructure. The corresponding periodic surface potential distribution provides an extra degree of freedom in addition to the morphology that could regulate cells or polar molecules in physiological and bioelectric applications.

Maize starch derived boron doped carbon spheres via facile solvothermal route as the photoluminescence sensor for determination of pH and Cr(VI).

In this work, a kind of boron doped carbon spheres (B-CSs) was successfully synthesized utilizing maize starch as carbon source and boric acid as dopant via facile solvothermal method. The chemical structure of the prepared B-CSs was systemically investigated by TEM, FT-IR, XRD, XPS and EDS. The synthesized B-CSs feature spherical structure with average size of ∼254 nm and exhibit strong photoluminescence (PL) with maximum emission at a wavelength of ∼453 nm under irradiation at 350 nm, leading to a quantum yield of 6.2%. Furthermore, the aqueous pH and Cr(VI) has a significantly various impact on the PL intensity of B-CSs, which can be flexibly utilized as the PL sensor for detection aqueous pH and Cr(VI) in aqueous. Particularly, the B-CSs have a desirable sensitivity and selectivity for detection of Cr(VI) with a low detection limit of ∼0.34µmol l-1. Conclusively, our work provides a novel and dual-functional fluorescent sensor for detection of the pH and toxic metal ions in water environment.

Design Appropriate Incision Length for Uniportal Video-Assisted Thoracoscopic Lobectomy: Take into Account Safety and Minimal Invasiveness.

BACKGROUND: There is no criterion on the length of the uniportal video-assisted thoracoscopic surgery (UVATS) incision when performing lobectomy. We aimed to develop a nomogram to assist surgeons in designing incision length for different individuals. METHODS: A cohort consisting of 290 patients were enrolled for nomogram development. Univariate and multivariate logistic regression analyses were performed to identify candidate variables among perioperative characteristics. C-index and calibration curves were utilized for evaluating the performance of the nomogram. Short-term outcomes of nomogram-predicted high-risk patients were compared between long incision group and conventional incision group. RESULTS: Of 290 patients, 150 cases (51.7%) were performed incision extension during the surgery. Age, tumor size, and tumor location were identified as candidate variables related with intraoperative incision extension and were incorporated into the nomogram. C-index of the nomogram was 0.75 (95% confidence interval: 0.6961-0.8064), indicating the good predictive performance. Calibration curves presented good consistency between the nomogram prediction and actual observation. Of high-risk patients identified by the nomogram, the long incision group (n = 47) presented shorter duration of operation (p = 0.03), lower incidence of total complications (p = 0.01), and lower incidence of prolonged air leak (p = 0.03) compared with the conventional incision group (n = 55). CONCLUSION: We developed a novel nomogram for predicting the risk of intraoperative incision extension when performing uniportal video-assisted thoracoscopic lobectomy. This model has the potential to assist clinicians in designing the incision length preoperatively to ensure both safety and minimal invasiveness.

Large asymmetric anomalous reflection in bilayer gradient metasurfaces.

Gradient metasurfaces have attracted much attention due to intriguing wavefront and polarization manipulation. Here, a bilayer gradient metasurface is constructed by use of a rectangular nanorod layer and its complementary nanoaperture. It reveals asymmetric anomalous reflection and symmetric anomalous transmission for two counter-propagating directions. The dependence of the anomalous reflection and transmission phenomena on nanostructure thickness are numerically studied in optical frequencies. The increasing metallic layer thickness of the gradient metasurface greatly enhances anomalous reflection of the left-handed circularly polarized wave (LCP) for the nanorod side and suppresses anomalous reflection for the other side. Both resonant frequencies of anomalous reflection and transmission linearly shift with the refractive index. The bilayer gradient metasurface is important for realizing wavefront modulation and optical sensing.

Switchable dual-band to broadband terahertz metamaterial absorber incorporating a VO2 phase transition.

We design and demonstrate a thermally switchable terahertz metamaterial absorber consisting of an array of orthogonal coupled split-ring metal resonators involving a VO2 phase transition. Numerical results indicate that the active metamaterial always absorbs the TE wave in dual-band regardless of insulating and metallic VO2, while the insulator-to-metal phase transition enables a switchable effect between dual-band and broadband absorption of the TM wave with the resonant frequency tunability of 33%. Especially under the metallic VO2 state, the absorption properties are polarization-dependent and exhibit a switching effect between dual-band and broadband absorption with the increase of the polarization angle. The tunable absorption mechanism can be explained by effective impedance theory and electric energy density distributions. The proposed dual-band to broadband metamaterial switching absorber may have broad applications in sensors, imaging and emitters.

Angle enhanced circular dichroism in bilayer 90°-twisted metamaterial.

Intrinsic and extrinsic chiral responses have been widely investigated in metamaterials, however the relationship between them has been seldom discussed. We numerically and experimentally demonstrate angle enhanced chiral dichroism and study the separation between intrinsic and extrinsic chiral responses in metamaterial with asymmetrically split aperture dimers. The metamaterial exhibits triple-band resonant circular dichroism at normal incidence. The oblique incidence leads to giant enhancement of circular dichroism at two low-frequency resonances while yields an obvious resonance split of the circular dichroism in the vicinity of the high-frequency resonance. The whole circular dichroism response results from the balance between intrinsic and extrinsic chirality and the circular dichroism spectra at positive and negative angles of incidence exhibit an asymmetry due to the existence of intrinsic chirality. Importantly, the intrinsic chirality in the metamaterial may be individually investigated since extrinsic chiral response may be removed from the total circular dichroism by superimposing two circular dichroism spectra at positive and negative incident angles. The metamaterial will be promising to achieve enhanced chiral response and also separately utilize intrinsic and extrinsic chirality for manipulating the polarization state of light.

Tunable chiroptical response of graphene achiral metamaterials in mid-infrared regime.

We numerically investigate a tunable and extrinsic chiroptical response of a graphene achiral metamaterial in mid-infrared regime. The achiral metamaterial is composed of cascaded metallic split ring apertures and complementary graphene rings patterned on a dielectric layer. The strong extrinsic chiroptical responses of the metamaterial are allowed at oblique incidence and the integrated graphene can dynamically modulate extrinsic chirality by changing its Fermi level. The spectra of the chiroptical responses will show a blue shift with increasing the Fermi level of the patterned graphene. The maximal values of circular dichroism in the reflection and transmission modes can reach 80% and 50%, respectively. The maximal values of polarization rotation angle in the reflection and transmission modes can reach 80° and 60°, respectively. This graphene-based metamaterial design paves a way for a myriad of important terahertz (THz) and mid-infrared applications, such as optical modulators, absorbers and polarizers.

High-efficiency Huygens' metasurface for terahertz wave manipulation.

A fair amount of theoretical work has shown that Huygens' metasurfaces well modulate electromagnetic waves by properly designing electrical impedance Zes and magnetic admittance Yms; however, the transmissive Huygens' metasurface is still challenging in the terahertz band. In this work, a transmission-type Huygens' metasurface with bilayer metallic patches has been proposed and theoretically demonstrated to show a reflectionless phase modulation for a linearly polarized terahertz wave. The simulation results show that the metasurface can achieve 2π phase coverage, and importantly the phase change can be simply achieved by changing a single geometric parameter of the metamolecule, along with a similar transmission effect. We design a high-efficiency beam deflector to realize an anomalous refraction with an angle of 19.8°. The proposed metasurface will provide a simple and direct way to realize efficient terahertz devices for wavefront manipulation.

HONH3Cl optimized CH3NH3PbI3 films for improving performance of planar heterojunction perovskite solar cells via a one-step route.

Planar heterojunction perovskite solar cells (PHJ-PSCs) constructed with one-step precursor solution spin-coating deposition (OPSSD) usually give an extremely low performance mainly due to the poor morphology and low crystallinity of the perovskite films. In this work, by incorporating a suitable HONH3Cl additive in the perovskite precursor solution, a high quality perovskite film with improved morphology and crystallinity was obtained. The UV-vis measurement of the CH3NH3I solutions without and with HONH3Cl demonstrates that the improved quality of the perovskite film can be easily attributed to a combined effect of N2, I2, H2O and CH3NH3Cl originating from the oxidation of CH3NH3I triggered by the HONH3Cl additive, which can manipulate the crystallization process of the perovskite. Accordingly, the improved performance for the HONH3Cl-induced PHJ-PSCs can also be demonstrated. At the optimized molar ratio of 1 : 1 : 0.1 for PbI2 : CH3NH3I : HONH3Cl, the PHJ-PSCs exhibit an average power conversion efficiency (PCE) of 10.61 ± 0.51%, which is much higher than that of pristine 1 : 1 : 0 based cells without additive (7.21 ± 0.61%), and the best performing HONH3Cl-induced device can yield a PCE as high as 11.12% with a Jsc of 18.42 mA cm-2, Voc of 0.95 V and FF of 0.63. Introducing suitable HONH3Cl as an additive into the perovskite precursor solution is really an effective route to enhance the performance of the PHJ-PSCs via OPSSD.

Preparation and characterization of slow-release urea fertilizer encapsulated by a blend of starch derivative and polyvinyl alcohol with desirable biodegradability and availability.

In this study, a novel double-layer slow-release fertilizer (SRF) was developed utilizing stearic acid (SA) as a hydrophobic inner coating and a blend of starch phosphate carbamate (abbreviated as SPC) and polyvinyl alcohol (PVA) as a hydrophilic outer coating (designated as SPCP). The mass ratios of SPC and PVA in the SPCP matrices were systematically optimized by comprehensively checking the water absorbency, water contact angle (WCA), water retention property (WR), and mechanical properties such as percentage elongation at break and tensile strength with FTIR, XRD, EDS, and XPS techniques, etc. Moreover, the optimal SPCP/5:5 demonstrated superior water absorbency with an 80.2 % increase for the total mass compared to natural starch/PVA(NSP), along with desirable water retention capacity in the soil, exhibiting a weight loss of only 48 % over 13 d. Relative to pure urea and SA/NSPU/5:5, SA/SPCPU/5:5 released 50.3 % of its nutrient within 15 h, leading to nearly complete release over 25 h in the aqueous phase, while only 46.6 % of urea was released within 20 d in soil, extending to approximately 30 d. The slow release performance of urea reveals that the diffusion rate of urea release shows a significant decrease with an increase in coating layers. Consequently, this work demonstrated a prospective technology for the exploration of environmentally friendly SRF by integrating biodegradable starch derivatives with other polymers.

Advancing overall water splitting via phase-engineered amorphous/crystalline interface: A novel strategy to accelerate proton-coupled electron transfer.

Traditional phase engineering enhances conductivity or activity by fully converting electrocatalytic materials into either a crystalline or an amorphous state, but this approach often faces limitations. Thus, a practical solution entails balancing the dynamic attributes of both phases to maximize an electrocatalyst's functionality is urgently needed. Herein, in this work, Co/Co2C crystals have been assembled on the amorphous N, S co-doped porous carbon (NSPC) through hydrothermal and calcination processes. The stable biphase structure and amorphous/crystalline (A/C) interface enhance conductivity and intrinsic activity. Moreover, the adsorption ability of water molecules and intermediates is improved significantly attributed to the rich oxygen-containing groups, unsaturated bonds, and defect sites of NSPC, which accelerates proton-coupled electron transfer (PCET) and overall water splitting. Consequently, A/C-Co/Co2C/NSPC (Co/Co2C/NSPC with amorphous/crystalline interface) exhibits outstanding behavior for oxygen evolution reaction (OER) and hydrogen evolution reaction (HER), requiring the overpotential of 240.0 mV and 70.0 mV to achieve 10 mA cm-2. Moreover, an electrolyzer assembled by A/C-Co/Co2C/NSPC-3 (anode) and A/C-Co/Co2C/NSPC-2 (cathode) demonstrates a low drive voltage of 1.54 V during overall water splitting process. Overall, this work has pioneered the coexistence of crystalline/amorphous phases in electrocatalysts and provided new insights into phase engineering.

Engineering hierarchical snowflake-like multi-metal selenide catalysts anchored on Ni foam for high-efficiency and stable overall water splitting.

The development of excellent bifunctional electrocatalysts is an effective way to promote the industrial application of electrolytic water. In this work, a free-standing W-doped cobalt selenide (W-CoSe300/NF) electrocatalyst with a snowflake-like structure supported on nickel foam was prepared by a hydrothermal-selenization strategy. Benefiting from the high specific surface area of the 3D snowflake-like structure and the regulation of tungsten doping on the electronic structure of the metal active center, W-CoSe300/NF shows remarkable electrocatalytic water decomposition performance. In 1.0 M KOH, the W-CoSe300/NF electrocatalyst achieved an efficient HER and OER at a current density of 50 mA cm-2 with overpotentials as low as 84 mV and 283 mV, respectively. More importantly, W-CoSe300/NF acts as both the anode and cathode of the electrolytic tank, requiring only a potential of 1.54 V to obtain 10 mA cm-2 and can operate continuously for more than 120 hours at this current density. This study proposes a new way for the design of high efficiency and affordable bifunctional electrocatalysts.

Greatly Improved the Tunable Amplitude of Ferromagnetism Based on Interface Effect of Flexible Pt/YIG Heterojunctions.

Flexible quantum spin electronic devices based on ferromagnetic insulators have attracted wide attention due to their outstanding advantages of low-power dissipation and noncontact sensing. However, ferromagnetic insulators, such as monocrystalline yttrium iron garnet (Y3Fe5O12, YIG), hve weak stress effects with a small magnetostrictive coefficient (λ110, 10 ppm), making it difficult to achieve a large magnetic tunable amplitude. In this paper, large-scale (with a diameter of 40 mm), flexible Pt/YIG heterojunctions were obtained by double-cavity magnetron sputtering technology, indicating typical soft magnetism and good bending fatigue characteristics. Here, the 3 nm thickness of the Pt layer triggers an obvious magnetic proximity effect, in which the in-plane ferromagnetic resonance field is decreased by 70 Oe compared to flexible Cu/YIG heterojunctions. Meanwhile, it shows a wide tunable amplitude of 110 Oe under the flexible bending stresses, which is induced by the sensitive interface effect of Pt (3 nm)/YIG heterojunctions. The saturation magnetization of Pt/YIG heterojunctions is negatively correlated with Pt thickness rather than the relative stability of Cu/YIG heterojunctions, depending on the magnetic proximity effect. It brings greater application possibilities for flexible stress-sensitive magnetic oxides in spin logic electronic devices.

Remarkable flexibility in freestanding single-crystalline antiferroelectric PbZrO3 membranes.

The ultrahigh flexibility and elasticity achieved in freestanding single-crystalline ferroelectric oxide membranes have attracted much attention recently. However, for antiferroelectric oxides, the flexibility limit and fundamental mechanism in their freestanding membranes are still not explored clearly. Here, we successfully fabricate freestanding single-crystalline PbZrO3 membranes by a water-soluble sacrificial layer technique. They exhibit good antiferroelectricity and have a commensurate/incommensurate modulated microstructure. Moreover, they also have good shape recoverability when bending with a small radius of curvature (about 2.4 µm for the thickness of 120 nm), corresponding to a bending strain of 2.5%. They could tolerate a maximum bending strain as large as 3.5%, far beyond their bulk counterpart. Our atomistic simulations reveal that this remarkable flexibility originates from the antiferroelectric-ferroelectric phase transition with the aid of polarization rotation. This study not only suggests the mechanism of antiferroelectric oxides to achieve high flexibility but also paves the way for potential applications in flexible electronics.

Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS.

Integrating single-cell datasets produced by multiple omics technologies is essential for defining cellular heterogeneity. Mosaic integration, in which different datasets share only some of the measured modalities, poses major challenges, particularly regarding modality alignment and batch effect removal. Here, we present a deep probabilistic framework for the mosaic integration and knowledge transfer (MIDAS) of single-cell multimodal data. MIDAS simultaneously achieves dimensionality reduction, imputation and batch correction of mosaic data by using self-supervised modality alignment and information-theoretic latent disentanglement. We demonstrate its superiority to 19 other methods and reliability by evaluating its performance in trimodal and mosaic integration tasks. We also constructed a single-cell trimodal atlas of human peripheral blood mononuclear cells and tailored transfer learning and reciprocal reference mapping schemes to enable flexible and accurate knowledge transfer from the atlas to new data. Applications in mosaic integration, pseudotime analysis and cross-tissue knowledge transfer on bone marrow mosaic datasets demonstrate the versatility and superiority of MIDAS. MIDAS is available at https://github.com/labomics/midas .

Discriminative Geometric-Structure-Based Deep Hashing for Large-Scale Image Retrieval.

Deep hashing reaps the benefits of deep learning and hashing technology, and has become the mainstream of large-scale image retrieval. It generally encodes image into hash code with feature similarity preserving, that is, geometric-structure preservation, and achieves promising retrieval results. In this article, we find that existing geometric-structure preservation manner inadequately ensures feature discrimination, while improving feature discrimination of hash code essentially determines hash learning retrieval performance. This fact principally spurs us to propose a discriminative geometric-structure-based deep hashing method (DGDH), which investigates three novel loss terms based on class centers to induce the so-called discriminative geometrical structure. In detail, the margin-aware center loss assembles samples in the same class to the corresponding class centers for intraclass compactness, then a linear classifier based on class center serves to boost interclass separability, and the radius loss further puts different class centers on a hypersphere to tentatively reduce quantization errors. An efficient alternate optimization algorithm with guaranteed desirable convergence is proposed to optimize DGDH. We theoretically analyze the robustness and generalization of the proposed method. The experiments on five popular benchmark datasets demonstrate superior image retrieval performance of the proposed DGDH over several state of the arts.

Twisted Integration of Complex Oxide Magnetoelectric Heterostructures via Water-Etching and Transfer Process.

HIGHLIGHTS: The (001)-oriented ferromagnetic La0.67Sr0.33MnO3 films are stuck onto the (011)-oriented ferroelectric single-crystal 0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 substrate with 0° and 45° twist angle. By applying a 7.2 kV cm-1 electric field, the coexistence of uniaxial and fourfold in-plane magnetic anisotropy is observed in 45° Sample, while a typical uniaxial anisotropy is found in 0° Sample. Manipulating strain mode and degree that can be applied to epitaxial complex oxide thin films have been a cornerstone of strain engineering. In recent years, lift-off and transfer technology of the epitaxial oxide thin films have been developed that enabled the integration of heterostructures without the limitation of material types and crystal orientations. Moreover, twisted integration would provide a more interesting strategy in artificial magnetoelectric heterostructures. A specific twist angle between the ferroelectric and ferromagnetic oxide layers corresponds to the distinct strain regulation modes in the magnetoelectric coupling process, which could provide some insight in to the physical phenomena. In this work, the La0.67Sr0.33MnO3 (001)/0.7Pb(Mg1/3Nb2/3)O3-0.3PbTiO3 (011) (LSMO/PMN-PT) heterostructures with 45º and 0º twist angles were assembled via water-etching and transfer process. The transferred LSMO films exhibit a fourfold magnetic anisotropy with easy axis along LSMO < 110 >. A coexistence of uniaxial and fourfold magnetic anisotropy with LSMO [110] easy axis is observed for the 45° Sample by applying a 7.2 kV cm-1 electrical field, significantly different from a uniaxial anisotropy with LSMO [100] easy axis for the 0° Sample. The fitting of the ferromagnetic resonance field reveals that the strain coupling generated by the 45° twist angle causes different lattice distortion of LSMO, thereby enhancing both the fourfold and uniaxial anisotropy. This work confirms the twisting degrees of freedom for magnetoelectric coupling and opens opportunities for fabricating artificial magnetoelectric heterostructures.