Contrastively generative self-expression model for single-cell and spatial multimodal data.

Advances in single-cell multi-omics technology provide an unprecedented opportunity to fully understand cellular heterogeneity. However, integrating omics data from multiple modalities is challenging due to the individual characteristics of each measurement. Here, to solve such a problem, we propose a contrastive and generative deep self-expression model, called single-cell multimodal self-expressive integration (scMSI), which integrates the heterogeneous multimodal data into a unified manifold space. Specifically, scMSI first learns each omics-specific latent representation and self-expression relationship to consider the characteristics of different omics data by deep self-expressive generative model. Then, scMSI combines these omics-specific self-expression relations through contrastive learning. In such a way, scMSI provides a paradigm to integrate multiple omics data even with weak relation, which effectively achieves the representation learning and data integration into a unified framework. We demonstrate that scMSI provides a cohesive solution for a variety of analysis tasks, such as integration analysis, data denoising, batch correction and spatial domain detection. We have applied scMSI on various single-cell and spatial multimodal datasets to validate its high effectiveness and robustness in diverse data types and application scenarios.

Deep latent space fusion for adaptive representation of heterogeneous multi-omics data.

The integration of multi-omics data makes it possible to understand complex biological organisms at the system level. Numerous integration approaches have been developed by assuming a common underlying data space. Due to the noise and heterogeneity of biological data, the performance of these approaches is greatly affected. In this work, we propose a novel deep neural network architecture, named Deep Latent Space Fusion (DLSF), which integrates the multi-omics data by learning consistent manifold in the sample latent space for disease subtypes identification. DLSF is built upon a cycle autoencoder with a shared self-expressive layer, which can naturally and adaptively merge nonlinear features at each omics level into one unified sample manifold and produce adaptive representation of heterogeneous samples at the multi-omics level. We have assessed DLSF on various biological and biomedical datasets to validate its effectiveness. DLSF can efficiently and accurately capture the intrinsic manifold of the sample structures or sample clusters compared with other state-of-the-art methods, and DLSF yielded more significant outcomes for biological significance, survival prognosis and clinical relevance in application of cancer study in The Cancer Genome Atlas. Notably, as a deep case study, we determined a new molecular subtype of kidney renal clear cell carcinoma that may benefit immunotherapy in the viewpoint of multi-omics, and we further found potential subtype-specific biomarkers from multiple omics data, which were validated by independent datasets. In addition, we applied DLSF to identify potential therapeutic agents of different molecular subtypes of chronic lymphocytic leukemia, demonstrating the scalability of DLSF in diverse omics data types and application scenarios.

Constructing NCuS Interface Chemical Bonds over SnS2 for Efficient Solar-Driven Photoelectrochemical Water Splitting.

The restricted charge transfer and slow oxygen evolution reaction (OER) dynamics tremendously hamper the realistic implementation of SnS2 photoanodes for photoelectrochemical (PEC) water splitting. Here, a novel strategy is developed to construct interfacial NCuS bonds between NC skeletons and SnS2 (CuNC@SnS2 ) for efficient PEC water splitting. Compared with SnS2 , the PEC activity of CuNC@SnS2 photoelectrode is tremendously heightened, obtaining a current density of 3.40 mA cm2 at 1.23 VRHE with a negatively shifted onset potential of 0.04 VRHE , which is 6.54 times higher than that of SnS2 . The detailed experimental characterizations and theoretical calculation demonstrate that the interfacial NCuS bonds enhance the OER kinetic, reduce the surface overpotential, facilitate the separation of photon-generated carriers, and provide a fast transmission channel for electrons. This work presents a new approach for modulating charge transfer by interfacial bond design in heterojunction photoelectrodes toward promoting PEC performance and solar energy application.

Unique Tubular BiOBr/g-C3 N4 Heterojunction with Efficient Separation of Charge Carriers for Photocatalytic Nitrogen Fixation.

The industrial ammonia synthesis process consumes a lot of energy and causes serious environmental pollution. As a sustainable approach for ammonia synthesis, photocatalytic nitrogen reduction employing water as the reducing agent has a lot of potential. A simple surfactant-assisted solvothermal method is used to synthesize g-C3 N4 nanotubes with flower-like spherical BiOBr grown inside and outside (BiOBr/g-C3 N4 , BC). The hollow tubular structure realizes the full use of visible light by the multi-scattering effect of light. Large surface areas and more active sites for N2 adsorption and activation are present in the distinctive spatially dispersed hierarchical structures. Particularly, the quick separation and transfer of electrons and holes are facilitated by the sandwich tubular heterojunctions and tight contact interface of BiOBr and g-C3 N4 . The maximal NH3 generation rate of the BiOBr/g-C3 N4 composite catalysts can reach 255.04 µmol⋅ g-1 ⋅ h-1 , and it is 13.9 and 5.8 times that of pure BiOBr and g-C3 N4 . This work provides a novel method for designing and constructing unique heterojunctions for efficient photocatalytic nitrogen fixation.

Different nitrogen acquirement and utilization strategies might determine the ecological competition between ferns and angiosperms.

BACKGROUND AND AIMS: The abundance or decline of fern populations in response to environmental change has been found to be largely dependent on specific physiological properties that distinguish ferns from angiosperms. Many studies have focused on water use efficiency and stomatal behaviours, but the effects of nutrition acquirement and utilization strategies on niche competition between ferns and flowering plants are rarely reported. METHODS: We collected 34 ferns and 42 angiosperms from the Botanic Garden of Hokkaido University for nitrogen (N), sulphur (S), NO3- and SO42- analysis. We then used a hydroponic system to compare the different N and S utilization strategies between ferns and angiosperms under N deficiency conditions. KEY RESULTS: Ferns had a significantly higher NO3--N concentration and NO3--N/N ratio than angiosperms, although the total N concentration in ferns was remarkably lower than that in the angiosperms. Meanwhile, a positive correlation between N and S was found, indicating that nutrient concentration is involved in assimilation. Pteris cretica, a fern species subjected to further study, maintained a slow growth rate and lower N requirement in response to low N stress, while both the biomass and N concentration in wheat (Triticum aestivum) responded quickly to N deficiency conditions. CONCLUSIONS: The different nutritional strategies employed by ferns and angiosperms depended mainly on the effects of phylogenetic and evolutionary diversity. Ferns tend to adopt an opportunistic strategy of limiting growth rate to reduce N demand and store more pooled nitrate, whereas angiosperms probably utilize N nutrition to ensure as much development as possible under low N stress. Identifying the effects of mineral nutrition on the evolutionary results of ecological competition between plant species remains a challenge.

Transcriptional regulator CTR9 promotes hepatocellular carcinoma progression and metastasis via increasing PEG10 transcriptional activity.

Cln Three Requiring 9 (CTR9), a scaffold protein of the polymerase-associated factor-1 (PAF1) complex (PAF1c), is primarily localized in the nucleus of cells. Recent studies show that CTR9 plays essential roles in the development of various human cancers and their occurrence; however, its regulatory roles and precise mechanisms in hepatocellular carcinoma (HCC) remain unclear. In this study, we investigated the roles of CTR9 using in vitro assays and a xenograft mouse model. We found that CTR9 protein is upregulated in tumor tissues from HCC patients. Knockdown of CTR9 substantially reduced HCC cell proliferation, invasion, and migration, whereas its overexpression promoted these activities. In addition, in vitro results revealed that CTR9 silencing dramatically increased cell cycle regulators, p21 and p27, but markedly decreased matrix metalloproteinases, MMP2 and MMP9, with these outcomes reversed upon CTR9 overexpression. Furthermore, the underlying molecular mechanism suggests that CTR9 promoted the oncogene paternally expressed gene 10 (PEG10) transcription via its promoter region. Finally, the oncogenic roles of CTR9 were confirmed in a xenograft mouse model. This study confirms that CTR9, an oncoprotein that promotes HCC cell proliferation, invasion, and migration, increases tumor growth in a xenograft mouse model. CTR9 could be a novel therapeutic target. Further investigation is warranted to verify CTR9 potential in novel therapies for HCC.

The Agronomic Traits, Alkaloids Analysis, FT-IR and 2DCOS-IR Spectroscopy Identification of the Low-Nicotine-Content Nontransgenic Tobacco Edited by CRISPR-Cas9.

In this study, the agricultural traits, alkaloids content and Fourier transform infrared spectroscopy (FT-IR) and two-dimensional correlation infrared spectroscopy (2DCOS-IR) analysis of the tobacco after Berberine Bridge Enzyme-Like Proteins (BBLs) knockout were investigated. The knockout of BBLs has limited effect on tobacco agricultural traits. After the BBLs knockout, nicotine and most alkaloids are significantly reduced, but the content of myosmine and its derivatives increases dramatically. In order to identify the gene editing of tobacco, principal component analysis (PCA) was performed on the FT-IR and 2DCOS-IR spectroscopy data. The results showed that FT-IR can distinguish between tobacco roots and leaves but cannot classify the gene mutation tobacco from the wild one. 2DCOS-IR can enhance the characteristics of the samples due to the increased apparent resolution of the spectra. Using the autopeaks in the synchronous map for PCA analysis, we successfully identified the mutants with an accuracy of over 90%.

IQ motif-containing GTPase-activating protein 1 is essential for the optimal maintenance of lung ILC2s.

Group 2 innate lymphoid cells (ILC2s) play critical roles in type 2 immunity and are crucial for pathogenesis of various types of inflammatory disease. IQ motif-containing GTPase-activating protein 1 (IQGAP1) is a ubiquitously expressed scaffold protein that is involved in multiple cellular functions such as cell survival and trafficking. While the roles for IQGAP1 in T and B lymphocytes have been uncovered, the physiological significance of IQGAP1 in innate lymphocytes remains to be elucidated. In the current study, we demonstrate that using bone marrow chimeras, the deficiency of IQGAP1 caused an impaired survival of lung ILC2s in a cell-intrinsic manner and that Iqgap1-/- mice displayed decreased accumulation of ILC2s after administration of papain and thereby reduced the pathology of the disease. Moreover, Iqgap1-/- ILC2s showed a significantly enhanced apoptosis as compared to wild-type ILC2s under both steady-state and inflammatory conditions. Together these results identify for the first time that IQGAP1 is essential for homeostasis of ILC2s in the lung.

[A new isobenzofuranone derivative from Chaenomeles sinensis and its antibacterial activity].

A new isobenzofuranone derivative was isolated from Chaenomeles sinensis by using various chromatographic techniques,including silica gel,Sephadex LH-20,MCI-gel resin and RP-HPLC. This compound was determined as 2,2-dimethyl-5-( 2-oxopropyl)-2 H-furo[3,4-h]chromen-7( 9 H)-one( 1) by NMR,MS,IR and UV spectra,and was also evaluated for its antibacterial activity. The results showed that it showed prominent antibacterial activity with MIC90 value of( 53. 7±4. 5) mg·L-1 for methicillin resistant Staphylococcus aureus( MRSA) strain. This value is close to that of levofloxacin [with MIC90 value( 50. 2± 4. 2) mg·L-1].

A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification.

BACKGROUND: The advances in target control of complex networks not only can offer new insights into the general control dynamics of complex systems, but also be useful for the practical application in systems biology, such as discovering new therapeutic targets for disease intervention. In many cases, e.g. drug target identification in biological networks, we usually require a target control on a subset of nodes (i.e., disease-associated genes) with minimum cost, and we further expect that more driver nodes consistent with a certain well-selected network nodes (i.e., prior-known drug-target genes). RESULTS: Therefore, motivated by this fact, we pose and address a new and practical problem called as target control problem with objectives-guided optimization (TCO): how could we control the interested variables (or targets) of a system with the optional driver nodes by minimizing the total quantity of drivers and meantime maximizing the quantity of constrained nodes among those drivers. Here, we design an efficient algorithm (TCOA) to find the optional driver nodes for controlling targets in complex networks. We apply our TCOA to several real-world networks, and the results support that our TCOA can identify more precise driver nodes than the existing control-fucus approaches. Furthermore, we have applied TCOA to two bimolecular expert-curate networks. Source code for our TCOA is freely available from http://sysbio.sibcb.ac.cn/cb/chenlab/software.htm or https://github.com/WilfongGuo/guoweifeng . CONCLUSIONS: In the previous theoretical research for the full control, there exists an observation and conclusion that the driver nodes tend to be low-degree nodes. However, for target control the biological networks, we find interestingly that the driver nodes tend to be high-degree nodes, which is more consistent with the biological experimental observations. Furthermore, our results supply the novel insights into how we can efficiently target control a complex system, and especially many evidences on the practical strategic utility of TCOA to incorporate prior drug information into potential drug-target forecasts. Thus applicably, our method paves a novel and efficient way to identify the drug targets for leading the phenotype transitions of underlying biological networks.

[A new naphthaldehyde derivative from Comastoma pulmonarium and its anti-tobacco mosaic virus (anti-TMV) activity].

A new naphthaldehyde derivative has been isolated from Comastoma pulmonarium by using various chromatographic techniques, including silica gel, Sephadex LH-20, MCI-gel resin and RP-HPLC. This compounds was determined as 5-methoxy-2-methyl-7-(2-oxopropyl)naphthalene-1-carbaldehyde(1) by NMR, MS, IR and UV spectra. This compound was also evaluated for its anti-tobacco mosaic virus (anti-TMV) activity. The result showed that it showed high anti-TMV activity with inhibition rate of 32.8%. The inhibition rate is close to that of positive control (ningnanmycin).

Isocoumarins from the fermentation products of a plant entophytic fungus Penicillium oxalicum.

Three new isocoumarins, terrecoumarins A-C (1-3), together with six known isocoumarins (4-9) were isolated from the fermentation products of the fungus Penicillium oxalicum 0403. Their structures were elucidated by spectroscopic methods, including extensive 1D and 2D NMR techniques. The anti-tobacco mosaic virus (anti-TMV) activities of 1-9 were evaluated. The results revealed that compound 1 showed high anti-TMV activity with inhibition rate 25.4 ± 3.5%. Other compounds also showed weak activity with inhibition rate in the range of 11.3-18.9%.

Dihydroxanthenones from the fermentation product of an endophytic fungus Gliomastix murorum.

Three new dihydroxanthones, muroxanthenones A-C (1-3), together with three known dihydroxanthones (4-6) were isolated from the fermentation products of an endophytic fungus Gliomastix murorum. Their structures were elucidated by spectroscopic methods, including extensive 1D and 2D NMR techniques. Compound 3 showed high cytotoxicities against NB4 and PC3 cell with IC(50) values of 2.2 and 2.8 µM. The other compounds also showed moderate cytotoxicities for some tested cell lines with IC(50) values between 4.1 and 9.5 µM.

Flavones from Cassia siamea and their anti-tobacco mosaic virus activity.

Two new flavones, siameflavones A and B (1 and 2), together with five known flavones (3-7) were isolated from the stem of Cassia siamea. Their structures were elucidated by spectroscopic methods including extensive 1D and 2D NMR techniques. Compounds 1-5 were evaluated for their anti-tobacco mosaic virus (Anti-TMV) activity. The results showed that compounds 1-5 showed weak anti-TMV activity with inhibition rates in the range of 11.6-18.5%.

Enhancing remediation efficiency of hyperaccumulators through earthworm addition: Evidence from a pot study on cadmium-contaminated soil.

Soil cadmium (Cd) contamination is an urgent environmental problem, which endangers human health through the food chain. Bioremediation attracted extensive attention around the world due to the high cost-efficiency. However, the remediation efficiency of different plant and earthworm species of soil Cd pollution is still unclear, it is thus of great significance to explore the combined effects of different remediation plants and earthworm species to improve the bioremediation capacity. In the present study, we consequently selected three species of Cd hyperaccumulator plants (vetiver, P. vittata and S. emarginatum) and three species of earthworms (E. fetida P1, E. fetida P2, and P. guillelmi) to compare the differences in Cd accumulation among various earthworm-plant combinations. Results indicated that the changes of soil pH and SOM in plant-animal combined application induced the higher soil Cd removal efficiency. The Cd removal efficiency showed highest in combination groups P. vittata-E. fetida P2 and P. vittata-P. guillelmi. Meanwhile, the improvements of biomass of plants and animals also were consistent with the increasing of Cd concentration in both plants and earthworms after combined application. It showed that the Cd concentrations in P. vittata were the highest while the TFs of Cd in S. emarginatum displays significantly more than that in others. In conclusion, the recommended combined system of earthworm-plant (P. vittata-E. fetida P2 and P. vittata-P. guillelmi) to provide reference for soil Cd bioremediation system in practice.

National-scale 10-m maps of cropland use intensity in China during 2018-2023.

The amount of actively cultivated land in China is increasingly threatened by rapid urbanization and rural population aging. Quantifying the extent and changes of active cropland and cropping intensity is crucial to global food security. However, national-scale datasets for smallholder agriculture are limited in spatiotemporal continuity, resolution, and precision. In this paper, we present updated annual Cropland Use Intensity maps in China (China-CUI10m) with descriptions of the extent of fallow/abandoned, actively cropped fields and cropping intensity at a 10-m resolution in recent six years (2018-2023). The dataset is produced by robust algorithms with no requirements for regional adjustments or intensive training samples, which take full advantage of the Sentinel-1 (S1) SAR and Sentinel-2 (S2) MSI time series. The China-CUI10m maps have achieved high accuracy when compared to ground truth data (Overall accuracy = 90.88%) and statistical data (R2 > 0.94). This paper provides the recent trends in cropland abandonment and agricultural intensification in China, which contributes to facilitating geographic-targeted cropland use control policies towards sustainable intensification of smallholder agricultural systems in developing countries.

TSP-1 increases autophagy level in cartilage by upregulating HSP27 which delays progression of osteoarthritis.

This study aimed to determine whether Thrombospondin-1 (TSP-1) can be used as a biomarker to diagnose early osteoarthritis (OA) and whether it has a chondroprotective effect against OA. We examined TSP-1 expression in cartilage, synovial fluid, and serum at different time points after anterior cruciate ligament transection (ACLT) surgery in rats. Subsequently, TSP-1 was overexpressed or silenced to detect its effects on extracellular matrix (ECM) homeostasis, autophagy level, proliferation and apoptosis in chondrocytes. Adenovirus encoding TSP-1 was injected into the knee joints of ACLT rats to test its effect against OA. Combined with proteomic analysis, the molecular mechanism of TSP-1 in cartilage degeneration was explored. Intra-articular injection of an adenovirus carrying the TSP-1 sequence showed chondroprotective effects against OA. Moreover, TSP-1 expression decreases with OA progression and can effectively promote cartilage proliferation, inhibit apoptosis, and helps to sustain the balance between ECM anabolism and catabolism. Overexpression of TSP-1 also can increase autophagy by upregulating Heat Shock Protein 27 (HSP27, hspb1), thereby enhancing its effect as a stimulator of autophagy. TSP-1 is a hopeful strategy for OA treatment.

The silencing of NREP aggravates OA cartilage damage through the TGF-ß1/Smad2/3 pathway in chondrocytes.

Background: Osteoarthritis (OA) is a common chronic degenerative joint disease. Due to the limited understanding of its complex pathological mechanism, there is currently no effective treatment that can alleviate or even reverse cartilage damage associated with OA. With improvement in public databases, researchers have successfully identified the key factors involved in the occurrence and development of OA through bioinformatics analysis. The aim of this study was to screen for the differentially expressed genes (DEGs) between the normal and OA cartilage through bioinformatics, and validate the function of the TGF-ß1/Smad2/3 pathway-related neuron regeneration related protein (NREP) in the articular cartilage. Methods: The DEGs between the cartilage tissues of OA patients and healthy controls were screened by bioinformatics, and functionally annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The expression levels of the DEG in human and murine OA cartilage was verified by reverse transcription-quantitative PCR (RT-qPCR), Western blotting and immunohistochemistry (IHC). RT-qPCR, Western-blotting, Cell Counting Kit-8(CCK8) and EdU assays were used to evaluate the effects of knocking down NREP in normal chondrocytes, and the molecular mechanisms were investigated by RT-qPCR, Western blotting and IHC. Results: In this study, we identified NREP as a DEG in OA through bioinformatics analysis, and found that NREP was downregulated in the damaged articular cartilage of OA patients and mouse model with surgically-induced OA. In addition, knockdown of NREP in normal chondrocytes reduced their proliferative capacity, which is the pathological basis of OA. At the molecular level, knock-down of NREP inactivated the TGF-ß1/Smad2/3 pathway, resulting in the downregulation of the anabolic markers Col2a1 and Sox9, and an increase in the expression of the catabolic markers MMP3 and MMP13. Conclusion: NREP plays a key role in the progression of OA by regulating the TGF-ß1/Smad2/3 pathway in chondrocytes, and warrants further study as a potential therapeutic target.

Research progress and hotspots on macrophages in osteoarthritis: A bibliometric analysis from 2009 to 2022.

BACKGROUND: Macrophages in the synovium, as immune cells, can be polarized into different phenotypes to play an anti-inflammatory role in the treatment of osteoarthritis. In this study, bibliometric methods were used to search the relevant literature to find valuable research directions for researchers and provide new targets for osteoarthritis prevention and early treatment. METHODS: Studies about the application of macrophages in the treatment of osteoarthritis were searched through the Web of Science core database from 2009 to 2022. Microsoft Excel 2019, VOSviewer, CiteSpace, R software, and 2 online websites were used to analyze the research status and predict the future development of the trend in research on macrophages in osteoarthritis. RESULTS: The number of publications identified with the search strategy was 1304. China and the United States ranked first in the number of publications. Shanghai Jiao Tong University ranked first in the world with 37 papers. Osteoarthritis and Cartilage was the journal with the most publications, and "exosomes," "stem cells," "macrophage polarization," "regeneration," and "innate immunity" may remain the research hotspots and frontiers in the future. CONCLUSION: The findings from the global trend analysis indicate that research on macrophages in the treatment of osteoarthritis is gradually deepening, and the number of studies is increasing. Exosomes may become a research trend and hotspot in the future.

Geographical Origin Determination of Cigar at Different Spatial Scales Based on C and N Metabolites and Mineral Elements Combined with Chemometric Analysis.

In this paper, five C and N metabolites and eighteen mineral elements were used to identify the cigar's geographical origin on a country scale (Dominica, Indonesia, and China) and on a prefecture scale (Yuxi, Puer, and Lincang in China). The results show that the best origin traceability method is the combination of C and N metabolites and mineral elements method. Its. Its accuracy of cross-validation can achieve 95% on a country scale and 94% on a prefecture scale. Determination accuracy is ranked as identification by combination > mineral elements > C and N metabolites. For geo-origin determination of cigars, mineral element identification is better than that metabolite identification. The algorithm and factors for origin determination are selected. The results can be used to guide cigar agricultural practices and monitor and regulate the cigar in production and circulation.