Diffusion probabilistic model for bike-sharing demand recovery with factual knowledge fusion.

The mining of diverse patterns from bike flow has attracted widespread interest from researchers and practitioners. Prior arts concentrate on forecasting the flow evolution from bike demand records. Nevertheless, a tricky reality is the frequent occurrence of missing bike flow, which hinders us from accurately understanding flow patterns. This study investigates an interesting task, i.e., Bike-sharing demand recovery (Biker). Biker is not a simple time-series imputation problem, rather, it confronts three concerns: observation uncertainty, complex dependencies, and environmental facts. To this end, we present a novel diffusion probabilistic solution with factual knowledge fusion, namely DBiker. Specifically, DBiker is the first attempt to extend the diffusion probabilistic models to the Biker task, along with a conditional Markov decision-making process. In contrast to existing probabilistic solutions, DBiker forecasts missing observations through progressive steps guided by an adaptive prior. Particularly, we introduce a Flow Conditioner with step embedding and a Factual Extractor to explore the complex dependencies and multiple environmental facts, respectively. Additionally, we devise a self-gated fusion layer that adaptively selects valuable knowledge to act as an adaptive prior, guiding the generation of missing observations. Finally, experiments conducted on three real-world bike systems demonstrate the superiority of DBiker against several baselines.

H-NS involved in positive regulation of glycerol dehydratase gene expression in Klebsiella pneumoniae 2e.

Glycerol dehydratase is the key and rate-limiting enzyme in the 1,3-propanediol synthesis pathway of Klebsiella pneumoniae, which determined the producing rate and yield of 1,3-propanediol. However, the expression regulation mechanism of glycerol dehydratase gene dhaB remains poorly unknown. In this study, a histone-like nucleoid-structuring (H-NS) protein was identified and characterized as the positive transcription regulator for dhaB expression in K. pneumoniae 2e, which exhibited high tolerance against crude glycerol in our previous study. Deletion of hns gene significantly decreased the transcription level of dhaB in K. pneumoniae 2e, which led to a remarkable defect on strain growth, glycerol dehydratase activity, and 3-hydroxypropanal production during glycerol fermentation. The transcription level of dhaB was significantly up-regulated in crude glycerol relative to pure glycerol, while the inactivation of H-NS resulted in more negative effect for transcription level of dhaB in the former. Though the H-NS expression level was almost comparable in both substrates, its multimer state was reduced in crude glycerol relative to pure glycerol, suggesting that the oligomerization state of H-NS might have contributed for positive regulation of dhaB expression. Furthermore, electrophoretic mobility shift and DNase I footprinting assays showed that H-NS could directly bind to the upstream promoter region of dhaB by recognizing the AT-rich region. These findings provided new insight into the transcriptional regulation mechanism of H-NS for glycerol dehydratase expression in K. pneumoniae, which might offer new target for engineering bacteria to industrially produce 1,3-propanediol.IMPORTANCEThe biological production of 1,3-propanediol from glycerol by microbial fermentation shows great promising prospect on industrial application. Glycerol dehydratase catalyzes the penultimate step in glycerol metabolism and is regarded as one of the key and rate-limiting enzymes for 1,3-propanediol production. H-NS was reported as a pleiotropic modulator with negative effects on gene expression in most studies. Here, we reported for the first time that the expression of glycerol dehydratase gene is positively regulated by the H-NS. The results provide insight into a novel molecular mechanism of H-NS for positive regulation of glycerol dehydratase gene expression in K. pneumoniae, which holds promising potential for facilitating construction of engineering highly efficient 1,3-propanediol-producing strains.

Digital light processing printed hydrogel scaffolds with adjustable modulus.

Hydrogels are extensively explored as biomaterials for tissue scaffolds, and their controlled fabrication has been the subject of wide investigation. However, the tedious mechanical property adjusting process through formula control hindered their application for diverse tissue scaffolds. To overcome this limitation, we proposed a two-step process to realize simple adjustment of mechanical modulus over a broad range, by combining digital light processing (DLP) and post-processing steps. UV-curable hydrogels (polyacrylamide-alginate) are 3D printed via DLP, with the ability to create complex 3D patterns. Subsequent post-processing with Fe3+ ions bath induces secondary crosslinking of hydrogel scaffolds, tuning the modulus as required through soaking in solutions with different Fe3+ concentrations. This innovative two-step process offers high-precision (10 µm) and broad modulus adjusting capability (15.8-345 kPa), covering a broad range of tissues in the human body. As a practical demonstration, hydrogel scaffolds with tissue-mimicking patterns were printed for cultivating cardiac tissue and vascular scaffolds, which can effectively support tissue growth and induce tissue morphologies.

Intestinal IL-33 promotes microbiota-derived trimethylamine N -oxide synthesis and drives metabolic dysfunction-associated steatotic liver disease progression by exerting dual regulation on HIF-1α.

BACKGROUND AND AIMS: Gut microbiota plays a prominent role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). IL-33 is highly expressed at mucosal barrier sites and regulates intestinal homeostasis. Herein, we aimed to investigate the role and mechanism of intestinal IL-33 in MASLD. APPROACH AND RESULTS: In both humans and mice with MASLD, hepatic expression of IL-33 and its receptor suppression of tumorigenicity 2 (ST2) showed no significant change compared to controls, while serum soluble ST2 levels in humans, as well as intestinal IL-33 and ST2 expression in mice were significantly increased in MASLD. Deletion of global or intestinal IL-33 in mice alleviated metabolic disorders, inflammation, and fibrosis associated with MASLD by reducing intestinal barrier permeability and rectifying gut microbiota dysbiosis. Transplantation of gut microbiota from IL-33 deficiency mice prevented MASLD progression in wild-type mice. Moreover, IL-33 deficiency resulted in a decrease in the abundance of trimethylamine N -oxide-producing bacteria. Inhibition of trimethylamine N -oxide synthesis by 3,3-dimethyl-1-butanol mitigated hepatic oxidative stress in mice with MASLD. Nuclear IL-33 bound to hypoxia-inducible factor-1α and suppressed its activation, directly damaging the integrity of the intestinal barrier. Extracellular IL-33 destroyed the balance of intestinal Th1/Th17 and facilitated Th1 differentiation through the ST2- Hif1a - Tbx21 axis. Knockout of ST2 resulted in a diminished MASLD phenotype resembling that observed in IL-33 deficiency mice. CONCLUSIONS: Intestinal IL-33 enhanced gut microbiota-derived trimethylamine N -oxide synthesis and aggravated MASLD progression through dual regulation on hypoxia-inducible factor-1α. Targeting IL-33 and its associated microbiota may provide a potential therapeutic strategy for managing MASLD.

Research trends in vascular chips from 2012 to 2022: a bibliometrix and visualized analysis.

Objective: The vascular chip has emerged as a significant research tool, garnering increasing interest and exploration. We utilize bibliometric techniques to analyze literature from the Web of Science (WOS) database, focusing on core journal publications. The aim is to provide a systematic review and prospective outlook on research trends within the vascular chip field, delving into current dynamics and highlighting areas for further investigation. Methods: We retrieved articles, proceedings papers, and early-access publications related to vascular chips published between January 2012 and December 2022 reported by Web of Science Core Collection (WoSCC) in 2023. Scientific bibliometric analysis was performed using R-bibliometrix, CiteSpace, VOSviewer, and Microsoft Excel software tools. Results: A total of 456 publications were obtained, including 444 articles, 11 proceedings papers, and one early-access article. These originated from 167 academic journals and 751 research institutions across 44 countries/regions. The United States contributed the majority of publications (41%), with Harvard University leading in contributions (6.6%). Lab on a Chip was the top journal in terms of publications. Notably, authors Jeon NL and Huh D wielded significant influence, with the former being the most prolific author and the latter garnering the most citations. Recent research has predominantly focused on angiogenesis in relation to endothelial cells. Conclusion: This scientometric investigation comprehensively surveys literature on vascular chips over past decade, providing valuable insights for scholars in the field. Our study reveals global increases in publications, with endothelial cells and angiogenesis being primary research focuses. This trend will persist, drawing continued attention from researchers.

Ganospirones A-G, seven undescribed spiro-meroterpenoids from Ganoderma lucidum and their biological activities.

Ganoderma lucidum, a medicinal mushroom with a long history in traditional Chinese medicine, is widely used for chronic diseases. Ganospirones A-G (1-7), seven pairs of undescribed spiro-meroterpenoids, were isolated from the fruiting bodies of G. lucidum. Their structures including absolute configurations were characterized by using NMR spectroscopic data, ECD computational and X-ray diffraction methods. The anti-inflammatory and anti-renal fibrosis activities of the meroterpenoids 1-7 were tested, and the results revealed that (-)-2 and (+)-2 could inhibit iNOS expression in lipopolysaccharide-induced RAW264.7 cells at 20 µM.

Mining the interpretable prognostic features from pathological image of intrahepatic cholangiocarcinoma using multi-modal deep learning.

BACKGROUND: The advances in deep learning-based pathological image analysis have invoked tremendous insights into cancer prognostication. Still, lack of interpretability remains a significant barrier to clinical application. METHODS: We established an integrative prognostic neural network for intrahepatic cholangiocarcinoma (iCCA), towards a comprehensive evaluation of both architectural and fine-grained information from whole-slide images. Then, leveraging on multi-modal data, we conducted extensive interrogative approaches to the models, to extract and visualize the morphological features that most correlated with clinical outcome and underlying molecular alterations. RESULTS: The models were developed and optimized on 373 iCCA patients from our center and demonstrated consistent accuracy and robustness on both internal (n = 213) and external (n = 168) cohorts. The occlusion sensitivity map revealed that the distribution of tertiary lymphoid structures, the geometric traits of the invasive margin, the relative composition of tumor parenchyma and stroma, the extent of necrosis, the presence of the disseminated foci, and the tumor-adjacent micro-vessels were the determining architectural features that impacted on prognosis. Quantifiable morphological vector extracted by CellProfiler demonstrated that tumor nuclei from high-risk patients exhibited significant larger size, more distorted shape, with less prominent nuclear envelope and textural contrast. The multi-omics data (n = 187) further revealed key molecular alterations left morphological imprints that could be attended by the network, including glycolysis, hypoxia, apical junction, mTORC1 signaling, and immune infiltration. CONCLUSIONS: We proposed an interpretable deep-learning framework to gain insights into the biological behavior of iCCA. Most of the significant morphological prognosticators perceived by the network are comprehensible to human minds.

Magnetic excitations in strained infinite-layer nickelate PrNiO2 films.

Strongly correlated materials respond sensitively to external perturbations such as strain, pressure, and doping. In the recently discovered superconducting infinite-layer nickelates, the superconducting transition temperature can be enhanced via only ~ 1% compressive strain-tuning with the root of such enhancement still being elusive. Using resonant inelastic x-ray scattering (RIXS), we investigate the magnetic excitations in infinite-layer PrNiO2 thin films grown on two different substrates, namely SrTiO3 (STO) and (LaAlO3)0.3(Sr2TaAlO6)0.7 (LSAT) enforcing different strain on the nickelates films. The magnon bandwidth of PrNiO2 shows only marginal response to strain-tuning, in sharp contrast to the enhancement of the superconducting transition temperature Tc in the doped superconducting samples. These results suggest the bandwidth of spin excitations of the parent compounds is similar under strain while Tc in the doped ones is not, and thus provide important empirics for the understanding of superconductivity in infinite-layer nickelates.

Multi-model analysis of gallbladder cancer reveals the role of OxLDL-absorbing neutrophils in promoting liver invasion.

BACKGROUND: Gallbladder cancer (GBC) is the most common and lethal malignancy of the biliary tract that lacks effective therapy. In many GBC cases, infiltration into adjacent organs or distant metastasis happened long before the diagnosis, especially the direct liver invasion, which is the most common and unfavorable way of spreading. METHODS: Single-cell RNA sequencing (scRNA-seq), spatial transcriptomics (ST), proteomics, and multiplexed immunohistochemistry (mIHC) were performed on GBC across multiple tumor stages to characterize the tumor microenvironment (TME), focusing specifically on the preferential enrichment of neutrophils in GBC liver invasion (GBC-LI). RESULTS: Multi-model Analysis reveals the immunosuppressive TME of GBC-LI that was characterized by the enrichment of neutrophils at the invasive front. We identified the context-dependent transcriptional states of neutrophils, with the Tumor-Modifying state being associated with oxidized low-density lipoprotein (oxLDL) metabolism. In vitro assays showed that the direct cell-cell contact between GBC cells and neutrophils led to the drastic increase in oxLDL uptake of neutrophils, which was primarily mediated by the elevated OLR1 on neutrophils. The oxLDL-absorbing neutrophils displayed a higher potential to promote tumor invasion while demonstrating lower cancer cytotoxicity. Finally, we identified a neutrophil-promoting niche at the invasive front of GBC-LI that constituted of KRT17+ GBC cells, neutrophils, and surrounding fibroblasts, which may help cultivate the oxLDL-absorbing neutrophils. CONCLUSIONS: Our study reveals the existence of a subset of pro-tumoral neutrophils with a unique ability to absorb oxLDL via OLR1, a phenomenon induced through cell-cell contact with KRT17+ GBC cells in GBC-LI.

A high-performance organic fluorescent probe with aggregation-induced emission properties for long-term tumor monitoring.

Near-infrared organic fluorescent probes have great need in biological sciences and medicine but most of them are still largely unable to meet demand. In this work, a delicate multipurpose organic fluorescent probe (DPPM-TPA) with aggregation-induced emission performances is designed and prepared by facile method to reflect fluorescence labeling, two-photon imaging, and long-term fluorescent tracking. Specifically, DPPM-TPA NPs was constructed from 4-(diphenylamino)phenylboronic acid and DPPM-Br by classical Suzuki coupling reaction and then coated with F127. Such nanoprobe possessed high stability in diverse medium under ambient temperatures, low cytotoxicity, and brilliant fluorescence performance. More importantly, DPPM-TPA NPs showed excellent two-photon imaging and extraordinary long-term fluorescence tracing capacity to malignant tumor, and it can last up to 9 days. These results indicated that DPPM-TPA NPs is expected to serve as a fluorescent probe for photodiagnostic and providing a new idea for the development of long-term fluorescent tracker.

Regulation and Response Mechanism of Acute Low-Salinity Stress during Larval Stages in Macrobrachium rosenbergii Based on Multi-Omics Analysis.

Macrobrachium rosenbergii is an essential species for freshwater economic aquaculture in China, but in the larval process, their salinity requirement is high, which leads to salinity stress in the water. In order to elucidate the mechanisms regulating the response of M. rosenbergii to acute low-salinity exposure, we conducted a comprehensive study of the response of M. rosenbergii exposed to different salinities' (0‱, 6‱, and 12‱) data for 120 h. The activities of catalase, superoxide dismutase, and glutathione peroxidase were found to be significantly inhibited in the hepatopancreas and muscle following low-salinity exposure, resulting in oxidative damage and immune deficits in M. rosenbergii. Differential gene enrichment in transcriptomics indicated that low-salinity stress induced metabolic differences and immune and inflammatory dysfunction in M. rosenbergii. The differential expressions of MIH, JHEH, and EcR genes indicated the inhibition of growth, development, and molting ability of M. rosenbergii. At the proteomic level, low salinity induced metabolic differences and affected biological and cellular regulation, as well as the immune response. Tyramine, trans-1,2-Cyclohexanediol, sorbitol, acetylcholine chloride, and chloroquine were screened by metabolomics as differential metabolic markers. In addition, combined multi-omics analysis revealed that metabolite chloroquine was highly correlated with low-salt stress.

Realizing color transitions for three copper (I) cluster organic-inorganic hybrid materials by adjusting reaction conditions.

Copper iodide organic-inorganic hybrid materials have been favored by many researchers in the field of solid-state lighting (SSL) due to their structural diversity and optical adjustability. In this paper, three isomeric copper iodide cluster hybrid materials, Cu4I6(L)2(1), Cu5I4.5Cl2.5(L)2(2) and Cu5I7(L)2) (3) (L=1-(4-methylpyrimidin-2-yl)-1,4-diazabicyclo[2.2.2]octan-1-ium), were achieved by adjusting the reaction conditions. The crystal color transit from green, yellow to orange and the internal quantum yield (IQY) increase from 57% to 88%. All three complexes have good thermal stability, good solution processability, and high quantum yield. And origin and mechanism of luminescence of complexes were further studied. This study can provide ideas and theoretical basis for the regulation of cuprous iodide cluster luminescent materials.

The characteristics and environmental significance of BVOCs released by aquatic macrophytes.

Biogenic volatile organic compounds (BVOCs) emitted by plants serve crucial biological functions and potentially impact atmospheric environment and global carbon cycling. Despite their significance, BVOC emissions from aquatic macrophytes have been relatively understudied. In this study, for the first time we identified there were 68 major BVOCs released from 34 common aquatic macrophytes, and these compounds referred to alcohols, aldehydes, alkanes, alkenes, arenes, ethers, furans, ketones, phenol. For type of BVOC emissions from different life form and phylogenetic group of aquatic macrophytes, 34 of the 68 BVOCs from emergent and submerged macrophytes are classified into alkene and alcohol compounds, over 50% BVOCs from dicotyledon and monocotyledon belong to alcohol and arene compounds. Charophyte and pteridophyte emitted significantly fewer BVOCs than dicotyledon and monocotyledon, and each of them only released 12 BVOCs. These BVOCs may be of great importance for the growth and development of macrophytes, because many BVOCs, such as azulene, (E)-ß-farnesene, and dimethyl sulfide are proved to play vital roles in plant growth, defense, and information transmission. Our results confirmed that both life form and phylogenetic group of aquatic macrophytes had significantly affected the BVOC emissions form macrophytes, and suggested that the intricate interplay of internal and external factors that shape BVOC emissions from aquatic macrophytes. Thus, further studies are urgently needed to investigate the influence factors and ecological function of BVOCs released by macrophytes within aquatic ecosystem.

lncRNA Gm20257 alleviates pathological cardiac hypertrophy by modulating the PGC-1α-mitochondrial complex IV axis.

Pathological cardiac hypertrophy, a major contributor to heart failure, is closely linked to mitochondrial function. The roles of long noncoding RNAs (lncRNAs), which regulate mitochondrial function, remain largely unexplored in this context. Herein, a previously unknown lncRNA, Gm20257, was identified. It markedly increased under hypertrophic stress in vivo and in vitro. The suppression of Gm20257 by using small interfering RNAs significantly induced cardiomyocyte hypertrophy. Conversely, the overexpression of Gm20257 through plasmid transfection or adeno-associated viral vector-9 mitigated angiotensin II-induced hypertrophic phenotypes in neonatal mouse ventricular cells or alleviated cardiac hypertrophy in a mouse TAC model respectively, thus restoring cardiac function. Importantly, Gm20257 restored mitochondrial complex IV level and enhanced mitochondrial function. Bioinformatics prediction showed that Gm20257 had a high binding score with peroxisome proliferator-activated receptor coactivator-1 (PGC-1α), which could increase mitochondrial complex IV. Subsequently, Western blot analysis results revealed that Gm20257 substantially affected the expression of PGC-1α. Further analyses through RNA immunoprecipitation and immunoblotting following RNA pull-down indicated that PGC-1α was a direct downstream target of Gm20257. This interaction was demonstrated to rescue the reduction of mitochondrial complex IV induced by hypertrophic stress and promote the generation of mitochondrial ATP. These findings suggest that Gm20257 improves mitochondrial function through the PGC-1α-mitochondrial complex IV axis, offering a novel approach for attenuating pathological cardiac hypertrophy.

Effect of Frequency-Amplitude Parameter and Aspect Ratio on Propulsion Performance of Underwater Flapping-Foil.

The propulsion system is the core component of unmanned underwater vehicles. The flapping propulsion method of marine animals' flippers, which allows for flexibility, low noise, and high energy utilization at low speeds, can provide a new perspective for the development of new propulsion technology. In this study, a new experimental flapping propulsion apparatus that can be installed in both directions has been constructed. The guide rail slider mechanism can achieve the retention of force in the direction of movement, thereby decoupling thrust, lift, and torque. Subsequently, the motion parameters of frequency-amplitude related to the thrust and lift of a bionic flapping-foil are scrutinized. A response surface connecting propulsion efficiency and these motion parameters is formulated. The highest efficiency of the flapping-foil propulsion is achieved at a frequency of 2 Hz and an amplitude of 40°. Furthermore, the impact of the installation mode and the aspect ratio of the flapping-foil is examined. The reverse installation of the swing yields a higher thrust than the forward swing. As the chord length remains constant and the span length increases, the propulsive efficiency gradually improves. When the chord length is extended to a certain degree, the propulsion efficiency exhibits a parabolic pattern, increasing initially and then diminishing. This investigation offers a novel perspective for the bionic design within the domain of underwater propulsion. This research provides valuable theoretical guidance for bionic design in the underwater propulsion field.

A potyvirus provides an efficient viral vector for gene expression and functional studies in Asteraceae plants.

Plant virus-derived vectors are rapid and cost-effective for protein expression and gene functional studies in plants, particularly for species that are difficult to genetically transform. However, few efficient viral vectors are available for functional studies in Asteraceae plants. Here, we identified a potyvirus named zinnia mild mottle virus (ZiMMV) from common zinnia (Zinnia elegans Jacq.) through next-generation sequencing. Using a yeast homologous recombination strategy, we established a full-length infectious cDNA clone of ZiMMV under the control of the cauliflower mosaic virus 35S promoter. Furthermore, we developed an efficient expression vector based on ZiMMV for the persistent and abundant expression of foreign proteins in the leaf, stem, root, and flower tissues with mild symptoms during viral infection in common zinnia. We showed that the ZiMMV-based vector can express ZeMYB9, which encodes a transcript factor inducing dark red speckles in leaves and flowers. Additionally, the expression of a gibberellic acid (GA) biosynthesis gene from the ZiMMV vector substantially accelerated plant height growth, offering a rapid and cost-effective method. In summary, our work provides a powerful tool for gene expression, functional studies, and genetic improvement of horticultural traits in Asteraceae plant hosts.

Pan-cancer proteogenomics expands the landscape of therapeutic targets.

Fewer than 200 proteins are targeted by cancer drugs approved by the Food and Drug Administration (FDA). We integrate Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomics data from 1,043 patients across 10 cancer types with additional public datasets to identify potential therapeutic targets. Pan-cancer analysis of 2,863 druggable proteins reveals a wide abundance range and identifies biological factors that affect mRNA-protein correlation. Integration of proteomic data from tumors and genetic screen data from cell lines identifies protein overexpression- or hyperactivation-driven druggable dependencies, enabling accurate predictions of effective drug targets. Proteogenomic identification of synthetic lethality provides a strategy to target tumor suppressor gene loss. Combining proteogenomic analysis and MHC binding prediction prioritizes mutant KRAS peptides as promising public neoantigens. Computational identification of shared tumor-associated antigens followed by experimental confirmation nominates peptides as immunotherapy targets. These analyses, summarized at https://targets.linkedomics.org, form a comprehensive landscape of protein and peptide targets for companion diagnostics, drug repurposing, and therapy development.

Molecular Engineering of Metal-Organic Frameworks for Boosting Photocatalytic Hydrogen Peroxide Production.

The development of novel metal-organic frameworks (MOFs) as efficient photocatalysts for hydrogen peroxide production from water and oxygen is particularly interesting, yet remains a challenge. Herein, we have prepared four cyclic trinuclear units (CTUs) based MOFs, exhibiting good light absorption ability and suitable bandgaps for photosynthesis of H2O2. However, Cu-CTU-based MOFs are not able to photocatalyzed the formation of H2O2, while the alteration of metal nodes from Cu-CTU to Ag-CTU dramatically enhances the photocatalytic performance for H2O2production and the production rates can reach as high as 17476 µmol g-1 h-1 with an apparent quantum yield of 9.51%, at 420 nm, which is much higher than most reported MOFs. The photocatalytic mechanism is comprehensively studied by combining the isotope labeling experiments and DFT calculation. This study provides new insights into the preparation of MOF photocatalysts with high activity for H2O2 production through molecular engineering.