Structural and optical performance of NiV/Ti multilayer mirrors for Z-pinch plasma diagnostic at the wavelength region of 350-450†eV.

This Letter reports on investigations of novel, to the best of our knowledge, NiV(Ni93V7)/Ti multilayer mirrors for the operation in the wavelength region of 350-450 eV. Such mirrors are promising optical components for the Z-pinch plasma diagnostic. The NiV/Ti multilayers show superior structural and optical performance compared to conventional Ni/Ti multilayers. Replacing Ni with NiV in multilayers decreases interface widths and enhances the contrast of the refractive index between the absorber and spacer layers. The improvement of interface quality contributes to the enhancement in reflectance. Under the grazing incidence of 13°, a peak reflectivity of 25.1% at 429 eV is achieved for NiV/Ti multilayers, while 17.7% at 427 eV for Ni/Ti.

scSemiAAE: a semi-supervised clustering model for single-cell RNA-seq data.

BACKGROUND: Single-cell RNA sequencing (scRNA-seq) strives to capture cellular diversity with higher resolution than bulk RNA sequencing. Clustering analysis is critical to transcriptome research as it allows for further identification and discovery of new cell types. Unsupervised clustering cannot integrate prior knowledge where relevant information is widely available. Purely unsupervised clustering algorithms may not yield biologically interpretable clusters when confronted with the high dimensionality of scRNA-seq data and frequent dropout events, which makes identification of cell types more challenging. RESULTS: We propose scSemiAAE, a semi-supervised clustering model for scRNA sequence analysis using deep generative neural networks. Specifically, scSemiAAE carefully designs a ZINB adversarial autoencoder-based architecture that inherently integrates adversarial training and semi-supervised modules in the latent space. In a series of experiments on scRNA-seq datasets spanning thousands to tens of thousands of cells, scSemiAAE can significantly improve clustering performance compared to dozens of unsupervised and semi-supervised algorithms, promoting clustering and interpretability of downstream analyses. CONCLUSION: scSemiAAE is a Python-based algorithm implemented on the VSCode platform that provides efficient visualization, clustering, and cell type assignment for scRNA-seq data. The tool is available from https://github.com/WHang98/scSemiAAE .

Current understanding on antibacterial mechanisms and research progress of tea polyphenols as a supplementary disinfectant for drinking water.

Disinfection by-products (DBPs) generated during the disinfection of drinking water have become an urgent problem. So, tea polyphenol, a natural green disinfectant, has attracted widespread attention in recent years. This review summarizes the antibacterial mechanism of tea polyphenols and the recent findings on tea polyphenols as disinfectants for drinking water. These studies show that tea polyphenol is an antibacterial agent that works through different mechanisms and can be used as a supplementary disinfectant because of its higher lasting effect and economical cost. The dosage of tea polyphenols as a disinfectant of ultrafiltration effluent is the lowest among all the tea polyphenols disinfection methods, which can ensure the microbial safety of drinking water. This application of tea polyphenols is deemed a practical solution to solving the issue of disinfecting drinking water and reducing DBPs. However, it is necessary to further explore the influence of factors such as pipeline materials on the disinfection process and efficacy to expand the application scope of tea polyphenols. The large-scale application of tea polyphenols still needs to be fine-tuned but with new developments in tea polyphenol purification technology and the long-term need for drinking water that is safe for human consumption, tea polyphenols have good prospects for further development.

Reinforcement learning to boost molecular docking upon protein conformational ensemble.

Intrinsically disordered proteins (IDPs) are widely involved in human diseases and thus are attractive therapeutic targets. In practice, however, it is computationally prohibitive to dock large ligand libraries to thousands and tens of thousands of conformations. Here, we propose a reversible upper confidence bound (UCB) algorithm for the virtual screening of IDPs to address the influence of the conformation ensemble. The docking process is dynamically arranged so that attempts are focused near the boundary to separate top ligands from the bulk accurately. It is demonstrated in the example of transcription factor c-Myc that the average docking number per ligand can be greatly reduced while the performance is merely slightly affected. This study suggests that reinforcement learning is highly efficient in solving the bottleneck of virtual screening due to the conformation ensemble in the rational drug design of IDPs.

A simple and rapid immunochromatography test based on readily available filter paper modified with chitosan to screen for 13 sulfonamides in milk.

In this study, we developed a novel, simple, rapid, and low-cost colloidal gold-based immunochromatography method, with filter paper replacing nitrocellulose membrane as the substrate. To obtain adequately immobilized protein, chitosan was used to functionalize the filter paper. After conditions and parameters were optimized, the novel immunochromatography method was applied for detection of sulfonamide residues in milk. Quantitative detection was accomplished using a smartphone and Photoshop software (Adobe Inc., San Jose, CA), allowing us to screen 13 sulfonamides with a limit of detection ranging from 0.42 to 8.64 µg/L and recovery ranging from 88.2 to 116.9% in milk. The proposed novel method performed similarly to the conventional method that uses a nitrocellulose membrane as the transport medium, and it had lower cost and better usability because of the inexpensive and easily available filter paper.

Fluorescent lateral flow immunoassay based on gold nanocluster for detection of pyrrolizidine alkaloids.

An ultrasensitive and rapid fluorescent immunoassay based on a broad-spectrum monoclonal antibody (mAb) was developed to detect pyrrolizidine alkaloids (PAs) in honey samples. First, Discovery Studio software was used to analyze and predict the target hapten, and retrorsine (RTS) was selected to react with succinic anhydride (HS) for hapten synthesization. A sensitive and broad-spectrum monoclonal antibody (mAb 13E1) was obtained for nine PAs. Then, fluorescent gold nanoclusters (AuNCs) were conjugated with mAb as a label probe and used in establishing a qualitative and quantitative lateral flow immunoassay (AuNCs-LFIA) for the determination of four PAs (retrorsine, platyphylline, senecionine, integerrimine) in honey within 14 min. The limits of detection (LOD) were 0.083 µg/kg. The recovery in spiked honey samples were 87.98-119.57%, with coefficients of variation of ≤ 11.5%. A total of 45 commercial import honey samples from nine different countries were tested through AuNCs-LFIA and UPLC-MS/MS method, and satisfactory consistency (R2 = 0.995) was obtained. The rates of positive samples were 55.56% (25/45), and the average concentrations of four PAs were 3.24-46.47 µg/kg. This ultrasensitive multi-PA method provides an alternative analytical tool for evaluating the human risk posed by the consumption of PA-contaminated honey.

Highly sensitive chromatographic time-resolved fluoroimmunoassay for rapid onsite detection of streptomycin in milk.

Antibiotic residues are major contaminants in milk because of their use in agriculture and animal husbandry. In particular, streptomycin, an aminoglycoside antibiotic, is a potential risk to consumers because of its ototoxicity, anaphylaxis, and growth inhibition. Herein, monoclonal antibodies for streptomycin were conjugated with europium microspheres to serve as detection probes for the development of a chromatographic time-resolved fluoroimmunoassay to detect streptomycin residues in milk. The method had a low detection limit of 0.58 µg/kg, a linear range of 0.8 to 6.25 µg/kg, and substantial recovery, from 85.6 to 108.3%. It showed slight cross-reactivity with another aminoglycoside analog. Strong correlations between the results of established chromatographic time-resolved fluoroimmunoassay and ultra-performance liquid chromatography-tandem mass spectrometry indicated that the established fluoroimmunoassay is a reliable method for rapid onsite detection of streptomycin in milk and it has great potential in food safety monitoring.

Pharmacokinetics and bioavailability of tildipirosin in rabbits following single-dose intravenous and intramuscular administration.

The objective of this study was to determine the pharmacokinetics of tildipirosin in rabbits after a single intravenous (i.v.) and intramuscular (i.m.) injection at a dose of 4 mg/kg. Twelve white New Zealand rabbits were assigned to a randomized, parallel trial design. Blood samples were collected prior to administration and up to 14 days postadministration. Plasma concentrations of tildipirosin were quantified using a validated ultra-high-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method. The pharmacokinetic parameters were calculated using a noncompartmental model in WinNonlin 5.2 software. Following i.v. and i.m. administration, the elimination half-life (T1/2λ ) was 81.17 ± 9.28 and 96.68 ± 15.37 hr, respectively, and the mean residence time (MRTlast ) was 65.44 ± 10.89 and 67.06 ± 10.49 hr, respectively. After i.v. injection, the plasma clearance rate (Cl) and volume of distribution at steady state (Vdss ) were 0.28 ± 0.10 L kg-1  h-1 and 17.78 ± 5.15 L/kg, respectively. The maximum plasma concentration (Cmax ) and time to reach maximum plasma concentration (Tmax ) after i.m. administration were 836.2 ± 117.9 ng/ml and 0.33 ± 0.17 hr, respectively. The absolute bioavailability of i.m. administration was 105.4%. Tildipirosin shows favorable pharmacokinetic characteristics in rabbits, with fast absorption, extensive distribution, and high bioavailability. These findings suggest that tildipirosin might be a potential drug for the prevention and treatment of respiratory diseases in rabbits.

Fluctuation correlations as major determinants of structure- and dynamics-driven allosteric effects.

Allosteric control is essential for regulating biological functions whereby stimuli such as ligand binding at one site on a protein cause a response at a distant functional site. Correlations between different sites in proteins have been used widely in identifying allosteric sites and pathways, and in designing allosteric drugs. However, the deterministic connection between correlations and allostery remains unsolved, especially considering that there are various types of correlations. Here, we combine perturbation-theory analysis and numerical calculations to study both structure- and dynamics-driven allosteric effects in an anisotropic network model (ANM). The results reveal that the allosteries are determined by the correlation (covariance) of distance fluctuations, but are irrelevant to the usual displacement correlations or time-delayed correlations. Dynamics-driven allostery is weaker than structure-driven allostery by at least one to two orders of magnitude. The intrinsic allostery capacity decays with distance by an exponential law, with the resulting characteristic distance parameter lying in the range of 7-10 Å for structure-driven allostery and 4-5 Å for dynamics-driven allostery. The importance of the cutoff distance of the ANM is also addressed.

Different neural mechanisms for nonsalient trained stimuli and physically salient stimuli in visual processing.

Previous studies have shown that nonsalient trained stimuli could capture attention and would be actively suppressed when served as distractors. However, it was unclear whether nonsalient trained stimuli and physically salient stimuli operate through the same attentional neural mechanism. In the current study, we investigated this question by recording event-related potentials (ERPs) of searching for the two stimuli separately after matching the difficulty. The present results provided additional evidence for the function of the suppression in that it may terminate a shift of attention. For the N1 component, the nonsalient trained stimuli had a shorter latency and larger amplitude than the physically salient stimuli whether presented as targets or distractors. It indicated that the nonsalient trained stimuli had an earlier sensory processing and greater visual attention orienting. The N2 posterior-contralateral (N2pc) amplitude of the physically salient target was larger than the nonsalient trained target. This suggested that physically salient stimuli had a stronger ability to capture attention. However, when they presented as distractors, only the nonsalient trained stimuli could elicit the PD component. Therefore, active suppression of the physically salient stimuli was more difficult than the nonsalient trained stimulus with the same difficulty. For the P3 component, the amplitude of the physically salient stimuli was larger than that of the nonsalient trained stimuli, both as targets and distractors, which indicated that the top-down controlled process of outcome evaluation for the salient triangle was stronger. Overall, these results suggested that they were processed via different neural mechanisms in the early sensory processing, attentional selection, active suppression, and the outcome-evaluation process.

scVSC: Deep variational subspace clustering for single-cell transcriptome data.

Single-cell RNA sequencing (scRNA-seq) is a potent advancement for analyzing gene expression at the individual cell level, allowing for the identification of cellular heterogeneity and subpopulations. However, it suffers from technical limitations that result in sparse and heterogeneous data. Here, we propose scVSC, an unsupervised clustering algorithm built on deep representation neural networks. The method incorporates the variational inference into the subspace model, which imposes regularization constraints on the latent space and further prevents overfitting. In a series of experiments across multiple datasets, scVSC outperforms existing state-of-the-art unsupervised and semi-supervised clustering tools regarding clustering accuracy and running efficiency. Moreover, the study indicates that scVSC could visually reveal the state of trajectory differentiation, accurately identify differentially expressed genes, and further discover biologically critical pathways.

Four birds with one stone: Aggregation-induced emission-type zeolitic imidazolate framework-8 based bionic nanoreactor for portable detection of olaquindox in environmental water and swine urine by smartphone.

The abuse of olaquindox (OLA) as both an antimicrobial agent and a growth promoter poses significant threats to the environment and human health. While nanoreactors have proven effective in hazard detection, their widespread adoption has been hindered by tedious chemical processes and limited functionality. In this study, we introduce a novel green self-assembly strategy utilizing invertase, horseradish peroxidase, antibodies, and gold nanoclusters to form an aggregation-induced emission-type zeolitic imidazolate framework-8 nanoreactor. The results demonstrate that the lateral flow immunoassay not only allows for qualitative naked eye detection but also enables optical analysis through the fluorescence generated by aggregated gold nanoclusters and enzyme-catalyzed enhancement of visible colorimetric signals. To accommodate more detection scenarios, the photothermal effects and redox reactions of the nanoreactor can fulfill the requirements of thermal sensing and electrochemical analysis for smartphone applications. Remarkably, the proposed approach achieves a detection limit 17 times lower than conventional methods. Besides, the maximum linear range spans from 0.25 to 5 µg/L with high specificity, and the recovery is 85.2-112.9% in environmental water and swine urine. The application of this high-performance nanoreactor opens up avenues for the construction of multifunctional biosensors with great potential in monitoring hazardous materials.

Generation of broad-spectrum recombinant antibody and construction of colorimetric immunoassay for tropane alkaloids: Recognition mechanism and application.

Tropane alkaloids (TAs) have emerged as plant toxins, related to poisoning events. The development of stable antibodies is crucial to ensure the effectiveness of immunological methods in quickly and accurately monitoring these alkaloids. In this study, based on hybridoma, the variable region gene of monoclonal antibody (mAb) was amplified, and the recombinant antibody (rAb) gene sequence (VH-Linker-VL) was successfully constructed and expressed in HEK293F. The obtained rAb has kept the same performance as mAb, and the IC50 of 29 TAs ranged from 0.12 to 2642.78 ng/mL. In the recognition mechanism, the docking and dynamics model identified hydrophobic interaction as the most critical force. Substituent will impact recognition by influencing the spatial structure and hydrophobic properties. Then, a colorimetric immunoassay based on rAb was established, five types of water and thirty-nine nectars of honey were tested. The results demonstrated the absence of TAs in environmental water, whereas atropine was detected in more than 13.47% of honey samples at concentrations exceeding 1 µg/kg. The results show a good correlation with UHPLC-MS/MS, suggesting that the immunoassay has excellent screening ability. The data on TAs in honey and water could serve as a foundation for developing relevant policies.

The effects of UiO-66 ultrafine particles on the rapid detection of sulfonamides in milk: Adsorption performance and mechanism.

Nanoscale MOFs particles possess both excellent adsorption and dispersion properties. In this study, ultrafine particles UiO-66 (UP/UiO-66) with a particle size below 50 nm were synthesised by a template-controlled method. UP/UiO-66 was able to achieve a maximum adsorption capacity of 139.64 mg/g for 5 methoxylated sulfonamides. Adsorption studies showed that UP/UiO-66 adsorption of sulfonamides can be classified as a pseudo-secondary kinetic adsorption model for single molecular layer adsorption. ELISA (validated by Raman and molecular docking) showed that the sulfonamide molecule was still immunoreactive with antibodies after adsorption by UP/UiO-66. In 15 min, UP/UiO-66 could be used directly in the ELISA test for sulfonamides in milk without elution and separation. The LOQ (IC20) of UP/UiO-66-ELISA for sulfonamides in milk was 0.21-2.05 ng/mL. The ultrafine particle strategy of UiO-66 is expected to be applied to other MOFs and used as a general pretreatment material for residue monitoring in complex matrices.

Novel Label-Free Nanocrystalline Gold Interdigitated Microelectrode Immunosensor for the Rapid and Ultrasensitive Detection of SARS-CoV-2.

Waves of COVID-19 outbreaks have dragged down the global economy and endangered human life. There is an urgent need for timeliness and sensitive SARS-CoV-2 detection techniques to complement the existing PCR assay. Herein, the controllable growth of gold crystalline grains was achieved by applying the reverse current during pulse electrochemical deposition (PED) interval. The proposed method validates the effects of pulse reverse current (PRC) on the atomic arrangement, crystal structures, orientations, and film characteristics in Au PED. The gap between the gold grains on the surface of the nanocrystalline gold interdigitated microelectrodes (NG-IDME) fabricated by the PED+PRC process matches the size of the antiviral antibody. Immunosensors are prepared by binding a large number of antiviral antibodies on the surface of NG-IDME. The NG-IDME immunosensor has a high specific capture ability for SARS-CoV-2 nucleocapsid protein (SARS-CoV-2/N-Pro) and completes ultrasensitive and quantification of SARS-CoV-2/N-Pro in humans and pets within 5 min (the LOQ as low as 75 fg/mL). The specificity, accuracy, stability, and actual blind sample tests show that the NG-IDME immunosensor is suitable for the detection of SARS-CoV-2 in humans and animals. This approach assists in monitoring the transmission of SARS-CoV-2-infected animals to humans.

Attentional disengagement effect based on relevant features.

In visual search tasks, distractors similar to the target can attract our attention and affect the speed of attentional disengagement. The attentional disengagement refers to shifting attention away from stimuli that are not relevant to the task. Previous studies mainly focused on the attentional disengagement of one feature dimension. However, the mechanisms of different feature dimensions on attentional disengagement in single and conjunction visual search remain unclear. In the current study, we adopted the oculomotor disengagement paradigm and used saccade latency as an indicator to explore the effects of different feature dimensions of center stimuli on attentional disengagement. In both single and conjunction feature search tasks, participants began each search by fixating on a center stimulus that appeared simultaneously with search display but would not be the target. Participants were instructed to ensure the first saccade to the target location. In Experiments 1A (single feature search) and 1B (conjunction feature search), we found that the attentional disengagement was significantly delayed or accelerated when center stimuli shared color features with the target or salient distractor, but not in shape feature. Moreover, we found that the difference between the two feature dimensions might be caused by their different search difficulty (Experiment 1C). Therefore, in Experiment 2, we matched the difficulty of searching for color and shape tasks before exploring whether there were differences in the effects of different feature dimensions on attentional disengagement. However, the results in Experiment 2 were similar to those in Experiment 1A, indicating that the different effects of feature dimensions on attentional disengagement were caused by feature asymmetry. Therefore, in Experiment 3, we improved the salient discernibility of shape dimension and matched color search to it. The results showed that although the attentional disengagement was delayed in shape dimension, it was still smaller than that in color dimension. Our results supported that goal-oriented attention sets were the main cause of delayed attentional disengagement. By series of experiments, we found that the utilization of different feature dimensions was associated with task difficulty and the features asymmetry in both single and conjunction visual search.

Control of phase ordering and elastic properties in phase field crystals through three-point direct correlation.

Effects of three-point direct correlation on properties of the phase field crystal (PFC) modeling are examined for the control of various ordered and disordered phases and their coexistence in both three-dimensional and two-dimensional systems. Such effects are manifested via the corresponding gradient nonlinearity in the PFC free-energy functional that is derived from classical density functional theory. Their significant impacts on the stability regimes of ordered phases, phase diagrams, and elastic properties of the system, as compared to those of the original PFC model, are revealed through systematic analyses and simulations. The nontrivial contribution from three-point direct correlation leads to the variation of the critical point of order-disorder transition to which all the phase boundaries in the temperature-density phase diagram converge. It also enables the variation and control of system elastic constants over a substantial range as needed in modeling different types of materials with the same crystalline structure but different elastic properties. The capability of this PFC approach in modeling both solid and soft matter systems is further demonstrated through the effect of three-point correlation on controlling the vapor-liquid-solid coexistence and transitions for body-centered cubic phase and on achieving the liquid-stripe or liquid-lamellar phase coexistence. All these provide a valuable and efficient method for the study of structural ordering and evolution in various types of material systems.

Recombinant Antibody-Based and Computer-Aided Comprehensive Analysis of Antibody's Equivalent Recognition Mechanism of Alternariol and Alternariol Monomethyl Ether.

Alternariol (AOH) and alternariol monomethyl ether (AME) are two main Alternaria mycotoxins that endanger human health. In this study, a single-chain antibody fragment (scFv) capable of equivalently and specifically recognizing AOH and AME was first expressed, and its equivalent recognition mechanism was discussed. According to molecular docking and dynamic simulation, the C9 site, which was always exposed outside the binding cavity, made the structural differences between AOH and AME negligible. Due to the high similarity of structures, AOH and AME interacted with almost the same amino acids on the scFv; thus, the same interaction mode and interaction force were produced. This was considered to be the most critical reason for the equivalent recognition. Thus, the exposure of common structures was considered a potential strategy to obtain the equivalent recognition antibodies, and C9 was considered the key site in the process of hapten modification. These results laid a theoretical foundation for further research on antibodies against Alternaria mycotoxins. It could promote the rapid detection of AOH and AME in food and provide a new idea for targeted preparation of antibodies that could recognize multiple hazards with similar structures.

Dual-readout fluorescence quenching immunochromatographic test strips for highly sensitive simultaneous detection of chloramphenicol and amantadine based on gold nanoparticle-triggered photoluminescent nanoswitch control.

Herein, a novel fluorescence quenching immunochromatographic test strip (FQICTS) for simultaneous detection of chloramphenicol (CAP) and amantadine (AMD) was developed on the basis of inner filter effect (IFE), with the combination of gold nanoparticles (AuNPs) and highly luminescent green-emitting gold nanoclusters (AuNCs) as the IFE quencher/donor pair. The AuNPs could quench the excitation light and emission light of AuNCs and achieve a high IFE efficiency due to dual spectral overlapping. Under optimal conditions, the "turn-on" mode of the AuNCs-based dual-readout FQICTS showed good linearity for CAP detection in chicken samples from 0.05 ng/g to 10 ng/g, with a limit of detection (LOD) of 0.043 ng/g. The linear range of AMD is 0.5-50 ng/g, with LOD of 0.45 ng/g. The visual LODs of CAP and AMD in "turn-on" mode were 200 and 10 times lower than that in "turn-off" mode, respectively. The "turn-on" mode of FQICTS showed high recovery for detecting CAP (82.5-94.5%) and AMD (81.9-110.7%) spiked into chicken samples. The performance and practicability of the established method were verified with commercial enzyme-immunoassay kits, and good correlations were observed. Overall, the newly developed AuNCs-based dual-readout FQICTS is a promising on-site screening tool for rapid, high-sensitivity detection of multiple food contaminants in practical applications.

Progress in Immunoassays of Toxic Alkaloids in Plant-Derived Medicines: A Review.

Plants are the cradle of the traditional medicine system, assuaging human or animal diseases, and promoting health for thousands of years. However, many plant-derived medicines contain toxic alkaloids of varying degrees of toxicity that pose a direct or indirect threat to human and animal health through accidental ingestion, misuse of plant materials, or through the food chain. Thus, rapid, easy, and sensitive methods are needed to effectively screen these toxic alkaloids to guarantee the safety of plant-derived medicines. Antibodies, due to their inherent specificity and high affinity, have been used as a variety of analytical tools and techniques. This review describes the antigen synthesis and antibody preparation of the common toxic alkaloids in plant-derived medicines and discusses the advances of antibody-based immunoassays in the screening and detection of toxic alkaloids in plants or other related matrices. Finally, the limitations and prospects of immunoassays for toxic alkaloids are discussed.