A multi-rate high-order dynamic twin-latent-variable probabilistic modeling and its process monitoring application.

Quality-relevant process monitoring provides important guarantees for the safety of industrial operation, which is based on the assumption that data collection is complete and low-order autocorrelated. However, real industrial processes always exhibit complex characteristics such as multi-rate sampling and high-order dynamic, which pose great challenges for process monitoring. To this end, a multi-rate high-order dynamic twin-latent-variable probabilistic (MHDTVP) model is presented in this paper to extract data correlations among multi-rate measurements from quality-relevant and irrelevant perspectives. Moreover, to reveal the dynamics in the multi-rate sampling process, an autoregressive twin-latent-variable structure is designed to extract both quality-relevant and quality-irrelevant high-order dynamic features. In the MHDTVP model, parameters are trained through an efficient expectation maximization (EM) iteration framework. Finally, the performance conclusions of MHDTVP are validated with the Tennessee Eastman process (TEP) and Thermal Power Plant (TPP). The experimental results demonstrate that the proposed model exhibits superior monitoring efficiency for multi-rate dynamic processes compared to similar approaches.

Structural transition and migration of incoherent twin boundary in diamond.

Grain boundaries (GBs), with their diversity in both structure and structural transitions, play an essential role in tailoring the properties of polycrystalline materials1-5. As a unique GB subset, {112} incoherent twin boundaries (ITBs) are ubiquitous in nanotwinned, face-centred cubic materials6-9. Although multiple ITB configurations and transitions have been reported7,10, their transition mechanisms and impacts on mechanical properties remain largely unexplored, especially in regard to covalent materials. Here we report atomic observations of six ITB configurations and structural transitions in diamond at room temperature, showing a dislocation-mediated mechanism different from metallic systems11,12. The dominant ITBs are asymmetric and less mobile, contributing strongly to continuous hardening in nanotwinned diamond13. The potential driving forces of ITB activities are discussed. Our findings shed new light on GB behaviour in diamond and covalent materials, pointing to a new strategy for development of high-performance, nanotwinned materials.

Mechanisms, Techniques and Devices of Airborne Virus Detection: A Review.

Airborne viruses, such as COVID-19, cause pandemics all over the world. Virus-containing particles produced by infected individuals are suspended in the air for extended periods, actually resulting in viral aerosols and the spread of infectious diseases. Aerosol collection and detection devices are essential for limiting the spread of airborne virus diseases. This review provides an overview of the primary mechanisms and enhancement techniques for collecting and detecting airborne viruses. Indoor virus detection strategies for scenarios with varying ventilations are also summarized based on the excellent performance of existing advanced comprehensive devices. This review provides guidance for the development of future aerosol detection devices and aids in the control of airborne transmission diseases, such as COVID-19, influenza and other airborne transmission viruses.

Fine Mapping of a Pleiotropic Locus (BnUD1) Responsible for the Up-Curling Leaves and Downward-Pointing Siliques in Brassica napus.

Leaves and siliques are important organs associated with dry matter biosynthesis and vegetable oil accumulation in plants. We identified and characterized a novel locus controlling leaf and silique development using the Brassica napus mutant Bnud1, which has downward-pointing siliques and up-curling leaves. The inheritance analysis showed that the up-curling leaf and downward-pointing silique traits are controlled by one dominant locus (BnUD1) in populations derived from NJAU5773 and Zhongshuang 11. The BnUD1 locus was initially mapped to a 3.99 Mb interval on the A05 chromosome with a BC6F2 population by a bulked segregant analysis-sequencing approach. To more precisely map BnUD1, 103 InDel primer pairs uniformly covering the mapping interval and the BC5F3 and BC6F2 populations consisting of 1042 individuals were used to narrow the mapping interval to a 54.84 kb region. The mapping interval included 11 annotated genes. The bioinformatic analysis and gene sequencing data suggested that BnaA05G0157900ZS and BnaA05G0158100ZS may be responsible for the mutant traits. Protein sequence analyses showed that the mutations in the candidate gene BnaA05G0157900ZS altered the encoded PME in the trans-membrane region (G45A), the PMEI domain (G122S), and the pectinesterase domain (G394D). In addition, a 573 bp insertion was detected in the pectinesterase domain of the BnaA05G0157900ZS gene in the Bnud1 mutant. Other primary experiments indicated that the locus responsible for the downward-pointing siliques and up-curling leaves negatively affected the plant height and 1000-seed weight, but it significantly increased the seeds per silique and positively affected photosynthetic efficiency to some extent. Furthermore, plants carrying the BnUD1 locus were compact, implying they may be useful for increasing B. napus planting density. The findings of this study provide an important foundation for future research on the genetic mechanism regulating the dicotyledonous plant growth status, and the Bnud1 plants can be used directly in breeding.

Fault Monitoring Based on the VLSW-MADF Test and DLPPCA for Multimodal Processes.

Actual industrial processes often exhibit multimodal characteristics, and their data exhibit complex features, such as being dynamic, nonlinear, multimodal, and strongly coupled. Although many modeling approaches for process fault monitoring have been proposed in academia, due to the complexity of industrial data, challenges remain. Based on the concept of multimodal modeling, this paper proposes a multimodal process monitoring method based on the variable-length sliding window-mean augmented Dickey-Fuller (VLSW-MADF) test and dynamic locality-preserving principal component analysis (DLPPCA). In the offline stage, considering the fluctuation characteristics of data, the trend variables of data are extracted and input into VLSW-MADF for modal identification, and different modalities are modeled separately using DLPPCA. In the online monitoring phase, the previous moment's historical modal information is fully utilized, and modal identification is performed only when necessary to reduce computational cost. Finally, the proposed method is validated to be accurate and effective for modal identification, modeling, and online monitoring of multimodal processes in TE simulation and actual plant data. The proposed method improves the fault detection rate of multimodal process fault monitoring by about 14% compared to the classical DPCA method.

Comparative 4D Label-Free Quantitative Proteomic Analysis of Bombus terrestris Provides Insights into Proteins and Processes Associated with Diapause.

Diapause, an adaptative strategy for survival under harsh conditions, is a dynamic multi-stage process. Bombus terrestris, an important agricultural pollinator, is declining in the wild, but artificial breeding is possible by imitating natural conditions. Mated queen bees enter reproductive diapause in winter and recover in spring, but the regulatory mechanisms remain unclear. Herein, we conducted a comparative 4D label-free proteomic analysis of queen bees during artificial breeding at seven timepoints, including pre-diapause, diapause, and post-diapause stages. Through bioinformatics analysis of proteomic and detection of substance content changes, our results found that, during pre-diapause stages, queen bees had active mitochondria with high levels of oxidative phosphorylation, high body weight, and glycogen and TAG content, all of which support energy consumption during subsequent diapause. During diapause stages, body weight and water content were decreased but glycerol increased, contributing to cold resistance. Dopamine content, immune defense, and protein phosphorylation were elevated, while fat metabolism, protein export, cell communication, signal transduction, and hydrolase activity decreased. Following diapause termination, JH titer, water, fatty acid, and pyruvate levels increased, catabolism, synaptic transmission, and insulin signaling were stimulated, ribosome and cell cycle proteins were upregulated, and cell proliferation was accelerated. Meanwhile, TAG and glycogen content decreased, and ovaries gradually developed. These findings illuminate changes occurring in queen bees at different diapause stages during commercial production.

A novel hybrid wind speed interval prediction model based on mode decomposition and gated recursive neural network.

Wind energy has become one of the most efficient renewable energy sources. However, the wind has the characteristics of intermittence and uncontrollability, so it is challenging to predict wind speed accurately. Considering the shortcomings of traditional wind power point predictions, a new hybrid model comprised three main modules used for data preprocessing, deterministic point prediction, and interval prediction is proposed to predict the wind speed interval. The first module, the data preprocessing module, uses variational mode decomposition (VMD), sample entropy (SE), and singular spectrum analysis (SSA) to extract the different frequency components of the initial wind speed series. The second module, the deterministic point prediction module, uses extreme learning machines (ELM), and a gated recursive unit (GRU) model to perform point prediction on the wind speed series. The third module, the interval prediction module, uses the nonparametric kernel density estimation method to construct the upper and lower bounds of the wind speed interval. In addition, the final wind speed prediction interval is obtained by integrating the prediction results of multiple interval prediction results to improve the robustness and generalization of the wind speed interval prediction. Finally, the effectiveness of the prediction performance of the proposed hybrid model is verified based on the data of two actual wind farms. The experimental results show that the proposed hybrid model can obtain the appropriate wind speed interval with high confidence and quality with different confidence levels of 95%, 90%, and 85%.

Transcriptome analysis of the potential molecular mechanism of enteritis in intestine and hepatopancreas of Litopenaeus vannamei.

The prawn, Litopenaeus vannamei (L. vannamei), is the most widely farmed species in the world but the incidence of enteritis in L. vannamei has increased in recent years. However, the pathogenesis of enteritis remains unclear. In this study, high-throughput sequencing was used to analyze the hepatopancreatic and intestinal transcriptome of healthy and enteritis-affected individuals from the same pond. In total, 1209 and 1608 differently-expressed genes (DEGs) were detected in the hepatopancreatic and intestinal transcriptomes, respectively. Significantly changed genes were enriched in the intestinal immune network for IgA Production, Lysosomes, Sphingolipid Metabolism and the Peroxisome Signaling Pathway. Expression of the integrin α4ß7 gene was significantly increased in the intestine of L. vannamei with enteritis, while expression of 38 DEGs associated with the lysosome was significantly down-regulated. Furthermore, the expression of sphingolipid metabolism-related enzymes and superoxide dismutase (SOD) genes was also significantly decreased, indicating that abnormal autoimmune function, weak intestinal resistance to external pathogenic microbial invasion, and self-healing ability were important factors associated with enteritis in L. vannamei. In addition, the expression of trypsin and pancreatic lipase was decreased in the hepatopancreas of L. vannamei with enteritis. This study provided new insights into the possible molecular pathogenesis of enteritis in L. vannamei.

Distribution and density of tertiary lymphoid structures predict clinical outcome in intrahepatic cholangiocarcinoma.

BACKGROUND & AIMS: The prognostic value and clinical relevance of tertiary lymphoid structures (TLSs) in intrahepatic cholangiocarcinoma (iCCA) remain unclear. Thus, we aimed to investigate the prognostic value and functional involvement of TLSs in iCCA. METHODS: We retrospectively included 962 patients from 3 cancer centers across China. The TLSs at different anatomic subregions were quantified and correlated with overall survival (OS) by Cox regression and Kaplan-Meier analyses. Multiplex immunohistochemistry (mIHC) was applied to characterize the composition of TLSs in 39 iCCA samples. RESULTS: A quaternary TLS scoring system was established for the intra-tumor region (T score) and peri-tumor region (P score) respectively. T scores positively correlated with favorable prognosis (p <0.001), whereas a high P score signified worse survival (p <0.001). mIHC demonstrated that both T follicular helper and regulatory T cells were significantly increased in intra-tumoral TLSs compared to peri-tumoral counterparts (p <0.05), and regulatory T cell frequencies within intra-tumoral TLSs were positively associated with P score (p <0.05) rather than T score. Collectively, the combination of T and P scores stratified iCCAs into 4 immune classes with distinct prognoses (p <0.001) that differed in the abundance and distribution pattern of TLSs. Patients displaying an immune-active pattern had the lowest risk, with 5-year OS rates of 68.8%, whereas only 3.4% of patients with an immune-excluded pattern survived at 5 years (p <0.001). The C-index of the immune class was statistically higher than the TNM staging system (0.73 vs. 0.63, p <0.001). These results were validated in an internal and 2 external cohorts. CONCLUSIONS: The spatial distribution and abundance of TLSs significantly correlated with prognosis and provided a useful immune classification for iCCA. T follicular helper and regulatory T cells may play a critical role in determining the functional orientation of spatially different TLSs. LAY SUMMARY: Tertiary lymphoid structures (TLSs) are associated with favorable prognosis in a number of cancers. However, their role in intrahepatic cholangiocarcinoma (iCCA) remains unclear. Herein, we comprehensively evaluated the spatial distribution, abundance, and cellular composition of TLSs in iCCA, and revealed the opposite prognostic impacts of TLSs located within or outside the tumor. This difference could be mediated by the different immune cell subsets present within the spatially distinct TLSs. Based on our analysis, we were able to stratify iCCAs into 4 immune subclasses associated with varying prognoses.

Deep representation features from DreamDIAXMBD improve the analysis of data-independent acquisition proteomics.

We developed DreamDIAXMBD (denoted as DreamDIA), a software suite based on a deep representation model for data-independent acquisition (DIA) data analysis. DreamDIA adopts a data-driven strategy to capture comprehensive information from elution patterns of peptides in DIA data and achieves considerable improvements on both identification and quantification performance compared with other state-of-the-art methods such as OpenSWATH, Skyline and DIA-NN. Specifically, in contrast to existing methods which use only 6 to 10 selected fragment ions from spectral libraries, DreamDIA extracts additional features from hundreds of theoretical elution profiles originated from different ions of each precursor using a deep representation network. To achieve higher coverage of target peptides without sacrificing specificity, the extracted features are further processed by nonlinear discriminative models under the framework of positive-unlabeled learning with decoy peptides as affirmative negative controls. DreamDIA is publicly available at https://github.com/xmuyulab/DreamDIA-XMBD for high coverage and accuracy DIA data analysis.

Land-use changes and ecosystem services under different scenarios in Nansi Lake Basin, China.

Ecosystem services (ESs) have been affected drastically by rapid urban sprawl and significant land-use changes (LUC) in Nansi Lake Basin (NLB) in China. Based on land-use data with a 30-m resolution from 1990 to 2015, we analyzed the process of LUC by atlas analysis and explored the impacts of LUC on ecological service value (ESV) under urban sprawl. The results showed that water area and buildup land increased significantly from 1990 to 2015. The area of cultivated land, forests, grassland, and unutilized land decreased. Land transfer mainly occurred between cultivated land, water area, and grassland. The total amount of land transfer was 4830.64 km2, and the average transfer rate is 185.79 km2/year in 26 years. The most obvious transfer occurred in period IV. The increased buildup land was mainly transferred from cultivated land. The total urban sprawl in the NLB was 1623.37 km2 in the past 26 years, with an average expansion rate of 62.44 km2/year, with the fastest sprawl in period IV. Tengzhou city was the most prominent area of expansion. Its ESV increased by 5.73 × 107 US$ with an increased rate of 2.21 × 106 US$/year. The annual total value of regulating and supporting services in the first-level ESs in the NLB accounted for 54.8 and 25.2% of the total ESV in all years, which were the primary types of ESs. Water area, forests, and cultivated land were the principal contributors to ESV changes. In conclusion, urban sprawl had a significant negative effect on ESV changes. Urban sprawl, water area, forests, and cultivated land were all sensitive factors for ESV changes.

Trichinella spiralis co-infection exacerbates Plasmodium berghei malaria-induced hepatopathy.

BACKGROUND: Although Plasmodium parasites and intestinal helminths share common endemic areas, the mechanisms of these co-infections on the host immune response remain not fully understood. Liver involvement in severe Plasmodium falciparum infections is a significant cause of morbidity and mortality. However, the effect of pre-existing Trichinella spiralis infection on the immune response and liver immune-pathogenesis in P. berghei ANKA (PbANKA)-infected mice needs to be elucidated. METHODS: Outbred Kunming mice were infected with T. spiralis and 9 days later were challenged with P. berghei ANKA (PbANKA), and the investigation occurred at 13 days after co-infection. RESULTS: Compared with PbANKA-mono-infected mice, T. spiralis + PbANKA-co-infected mice had similar survival rate but lower PbANKA parasitaemia; however, there were more severe hepatosplenomegaly, increased liver and spleen indexes, and increased liver pathology observed by hematoxylin and eosin staining; higher expression levels of galectin (Gal)-1, Gal-3, CD68+ macrophages, and elastase-positive neutrophils measured by immunohistochemical staining; upregulated mRNA expression levels of Gal-1, Gal-3, cytokines (interferon-gamma (IFNγ) and interleukin (IL)-6), and M1 macrophage polarization marker (inducible nitric oxide synthase (iNOS)) in the liver, and increased expression levels of Gal-1, IFNγ, IL-6, eosinophil cationic protein, eosinophil protein X, and M1 (IL-1ß and iNOS) and M2 (Ym1) macrophage polarization markers in the spleen of co-infected mice detected by using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). In vitro study showed that compared with PbANKA-mono-infected mice, there were significantly increased expression levels of Gal-1, Gal-3, IL-6, IL-1ß, and iNOS in the peritoneal macrophage isolated from co-infected mice detected by using qRT-PCR. Correlation analysis revealed significant positive correlations between Gal-3 and IL-1ß in the peritoneal macrophages isolated from PbANKA-mono-infected mice, between Gal-3 and IFNγ in the spleen of co-infected mice, and between Gal-1 and Ym1 in the peritoneal macrophages isolated from co-infected mice. CONCLUSIONS: Our data indicate that pre-existing infection of T. spiralis may suppress P. berghei parasitaemia and aggravate malaria-induced liver pathology through stimulating Gal-1 and Gal-3 expression, activating macrophages, neutrophils, and eosinophils, and promoting mediator release and cytokine production.

One-pot preparation of double network hydrogels via enzyme-mediated polymerization and post-self-assembly for wound healing.

Hybrid hydrogels combining polymers and low-molecular-weight gelators (LMWGs) are promising soft materials. Self-assembled LMWG-based supramolecular networks via noncovalent interactions exhibit excellent reversible thixotropy, which are usually incorporated into polymer gel networks generating functional double network hybrid hydrogels. In this study, we used enzyme-mediated polymerization and post-self-assembly for the one-pot preparation of LMWG-based hybrid hydrogels which consist of a covalently cross-linked polyacrylamide as the first chemical network and post-self-assembled DBS-COOH as the second supramolecular network. The gelation processes are monitored by the EPR measurement and 1H NMR characterization. The DBS-COOH gel network endows the hybrid gel with a well-controlled release behaviour of an anti-inflammatory drug-diclofenac sodium (DCF). Further in vivo wound healing experiments elucidated that the hybrid gel is a promising candidate material for biomedical applications. The enzymatic one-pot preparation principle will provide a unique viewpoint for fabricating functional LMWG/polymer hybrid hydrogels.

Remobilization and bioavailability of polycyclic aromatic hydrocarbons from estuarine sediments under the effects of Nereis diversicolor bioturbation.

The effects of Nereis diversicolor bioturbation on the remobilization and bioavailability of polycyclic aromatic hydrocarbons from estuarine sediment were determined after 60 d in a laboratory experiment. The release fluxes and mass transfer coefficients showed that bioturbation by N. diversicolor can lead to a significant remobilization of polycyclic aromatic hydrocarbons (PAHs) from estuarine sediments. Bioturbation enhanced the release of PAHs from sediment to water by accelerating the transport of sediment particles to the sediment-water interface followed by PAHs desorption to the water. The bioavailability of PAHs was described by SPMD-sediment accumulation factors (SSAF). The SSAF of low molecular weight PAHs with bioturbation was significantly higher than that of PAHs without bioturbation, and there were no significant variations in high-molecular-weight PAHs. Our results revealed that N. diversicolor bioturbation significantly increased PAHs release from sediment to water but only increased the bioavailability of low-molecular-weight PAHs.

Method to detect contaminants in heparin using radical depolymerization and liquid chromatography-mass spectrometry.

Heparin is a critically important anticoagulant drug that was contaminated with a persulfonated polysaccharide in 2008, resulting in a number of severe adverse reactions, some leading to death. Controversy remains as to the precise composition of the 2008 contaminant, and new information suggests that heparin may now be subject to adulteration with a new, difficult to detect, contaminant, N-sulfo oversulfated chondroitin sulfate. This study synthesizes this new potential contaminant and describes the use of radical depolymerization followed by liquid chromatography-mass spectrometry to detect N-sulfo oversulfated chondroitin sulfate and to confirm the structure of the 2008 contaminant as oversulfated chondroitin sulfate and not oversulfated heparan sulfate.

Ultrasensitive detection and quantification of acidic disaccharides using capillary electrophoresis and quantum dot-based fluorescence resonance energy transfer.

Rapid and highly sensitive detection of the carbohydrate components of glycoconjugates is critical for advancing glycobiology. Fluorescence (or Förster) resonance energy transfer (FRET) is commonly used in detection of DNA, in protein structural biology, and in protease assays but is less frequently applied to glycan analysis due to difficulties in inserting two fluorescent tags into small glycan structures. We report an ultrasensitive method for the detection and quantification of a chondroitin sulfate disaccharide based on FRET, involving a CdSe-ZnS core-shell nanocrystal quantum dot (QD) streptavidin conjugate donor and a Cy5 acceptor. The disaccharide was doubly labeled with biotin and Cy5. QDs then served to concentrate the target disaccharide, enhancing the overall energy transfer efficiency, with unlinked QDs and Cy5 hydrazide producing nearly zero background signal in capillary electrophoresis using laser-induced fluorescence detection with two different band-pass filters. This method is generally applicable to the ultrasensitive analysis of acidic glycans and offers promise for the high-throughput disaccharide analysis of glycosaminoglycans.

Capillary electrophoresis for the analysis of glycosaminoglycan-derived disaccharides.

Capillary electrophoresis is a common technique used for glycosaminoglycan-derived disaccharide analysis because of its high resolving power, high separation efficiency, high sensitivity, short analysis time, and straightforward operation. CE coupled to laser-induced fluorescence (LIF) detection shows an approximately 100 times higher sensitivity than traditional UV detection at 232 nm. 2-Aminoacridone (AMAC) is a widely used fluorophore for labeling unsaturated disaccharides by deductive amination, which is one of the most important method of derivatization of disaccharides for CE-LIF detection. Outlined in this chapter is a protocol of analyzing glycosaminoglycan-derived disaccharides by CE-LIF with AMAC derivatization.