A Computationally Efficient Hybrid Neural Network Architecture for Porous Media: Integrating CNNs and GNNs for Improved Permeability Prediction

Subsurface fluid flow, essential in various natural and engineered processes, is largely governed by a rock's permeability, which describes its ability to allow fluid passage. While convolutional neural networks (CNNs) have been employed to estimate permeability from high-resolution 3D rock images, our novel visualization technology reveals that they occasionally miss higher-level characteristics, such as nuanced connectivity and flow paths, within porous media. To address this, we propose a novel fusion model to integrate CNN with the graph neural network (GNN), which capitalizes on graph representations derived from pore network model to capture intricate relational data between pores. The permeability prediction accuracy of the fusion model is superior to the standalone CNN, whereas its total parameter number is nearly two orders of magnitude lower than the latter. This innovative approach not only heralds a new frontier in the research of digital rock property predictions, but also demonstrates remarkable improvements in prediction accuracy and efficiency, emphasizing the transformative potential of hybrid neural network architectures in subsurface fluid flow research

Bovine PrPC directly interacts with αB-crystalline

AbstractWe used a bovine brain cDNA library to perform a yeast two-hybrid assay with bovine mature PrPC as bait. The screening result showed that αB-crystalline interacted with PrPC. The interaction was further evaluated both in vivo and in vitro with different methods, such as immunofluorescent colocalization, native polyacrylamide-gel electrophoresis, and IAsys biosensor assays. The results suggested that αB-crystalline may have the ability to refold denatured prion proteins, and provided first evidence that αB-crystalline is directly associated with prion protein

Correlation and entanglement of two-component Bose-Einstein condensates in a double well

We consider a novel system of two-component atomic Bose-Einstein condensate in a double-well potential. Based on the well-known two-mode approximation, we demonstrate that there are obvious avoided level-crossings when both interspecies and intraspecies interactions of two species are increased. The quantum dynamics of the system exhibits revised oscillating behaviors compared with a single component condensate. We also examine the entanglement of two species. Our numerical calculations show the onset of entanglement can be signed as a violation of Cauchy-Schwarz inequality of second-order cross correlation function. Consequently, we use Von Neumann entropy to quantity the degree of entanglement

Ethyne Reducing Metal-Organic Frameworks to Control Fabrications of Core/shell Nanoparticles as Catalysts

An approach using cobalt metal-organic frameworks (Co-MOF) as precursors is established for the fabrication of cobalt nanoparticles in porous carbon shells (core/shell Co@C). Chemical vapor deposition of ethyne is used for controlling the reduction of cobalt nanoclusters in the MOF and the spontaneous formation of the porous carbon shells. The metallic cobalt cores formed are up to 4 - 6 nm with the crystal phase varying between hexagonally-close-packed (hcp) and face-centre-packed (fcc). The porous carbon shells change from amorphous to graphene with the ethyne deposition temperature increasing from 400 to 600 oC. The core/shell Co@C nanoparticles exhibit high catalytic activity in selectively converting syngas (CTY: 254.1 - 312.1 μmolCO·gCo-1·s-1) into hydrocarbons (4.0 - 5.2 gHC·g-cat-1·h-1) at 260 oC. As well as the crystal size and phase, the coordination numbers of the cobalt to oxygen and to other cobalt atoms on the surface of the cobalt nanoparticles, and the permeability of the porous carbon shell have been related to the catalytic performance in FTS reactions

MqsR/MqsA Toxin/Antitoxin System Regulates Persistence and Biofilm Formation in Pseudomonas putida KT2440

Bacterial toxin/antitoxin (TA) systems have received increasing attention due to their prevalence, diverse structures, and important physiological functions. In this study, we identified and characterized a type II TA system in a soil bacterium Pseudomonas putida KT2440. This TA system belongs to the MqsR/MqsA family. We found that PP_4205 (MqsR) greatly inhibits cell growth in P. putida KT2440 and Escherichia coli, the antitoxin PP_4204 (MqsA) neutralizes the toxicity of the toxin MqsR, and the two genes encoding them are co-transcribed. MqsR and MqsA interact with each other directly in vivo and MqsA is a negative regulator of the TA operon through binding to the promoter. Consistent with the MqsR/MqsA pair in E. coli, the binding of the toxin MqsR to MqsA inhibits the DNA binding ability of MqsA in P. putida KT2440. Disruption of the mqsA gene which induces mqsR expression increases persister cell formation 53-fold, while overexpressing mqsA which represses mqsR expression reduces persister cell formation 220-fold, suggesting an important role of MqsR in persistence in P. putida KT2440. Furthermore, both MqsR and MqsA promote biofilm formation. As a DNA binding protein, MqsA can also negatively regulate an ECF sigma factor AlgU and a universal stress protein PP_3288. Thus, we revealed an important regulatory role of MqsR/MqsA in persistence and biofilm formation in P. putida KT2440

Bioengineered human tissue regeneration and repair using endogenous stem cells

We describe a general approach to produce bone and cartilaginous structures utilizing the self-regenerative capacity of the intercostal rib space to treat a deformed metacarpophalangeal joint and microtia. Anatomically precise 3D molds were positioned on the perichondro-periosteal or perichondral flap of the intercostal rib without any other exogenous elements. We find anatomically precise metacarpal head and auricle constructs within the implanted molds after 6 months. The regenerated metacarpal head was used successfully to surgically repair the deformed metacarpophalangeal joint. Auricle reconstructive surgery in five unilateral microtia patients yielded good aesthetic and functional results. Long-term follow-up revealed the auricle constructs were safe and stable. Single-cell RNA sequencing analysis reveal early infiltration of a cell population consistent with mesenchymal stem cells, followed by IL-8-stimulated differentiation into chondrocytes. Our results demonstrate the repair and regeneration of tissues using only endogenous factors and a viable treatment strategy for bone and tissue structural defects.</p

Comprehensive investigation and regulatory function of lncRNAs engaged in western honey bee larval immune response to Ascosphaera apis invasion

Ascosphaera apis is a fungal pathogen that exclusively infects bee larvae, causing chalkbrood disease, which results in severe damage for beekeeping industry. Long non-coding RNAs (lncRNAs) are versatile regulators in various biological processes such as immune defense and host-pathogen interaction. However, expression pattern and regulatory role of lncRNAs involved in immune response of bee host to A. apis invasion is still very limited. Here, the gut tissues of Apis mellifera ligustica 4-, 5-, and 6-day-old larvae inoculated by A. apis spores (AmT1, AmT2, and AmT3 groups) and corresponding un-inoculated larval guts (AmCK1, AmCK2, and AmCK3 groups) were prepared and subjected to deep sequencing, followed by identification of lncRNAs, analysis of differentially expressed lncRNAs (DElncRNAs), and investigation of competing endogenous RNA (ceRNA) network. In total, 3,746 A. m. ligustica lncRNAs were identified, including 78 sense lncRNAs, 891 antisense lncRNAs, 1,893 intergenic lncRNAs, 346 bidirectional lncRNAs, and 210 intronic lncRNAs. In the 4-, 5-, and 6- comparison groups, 357, 236, and 505 DElncRNAs were discovered. Additionally, 217, 129, and 272 DElncRNAs were respectively predicted to regulate neighboring genes via cis-acting manner, and these targets were associated with a series of GO terms and KEGG pathways of great importance, such as response to stimulus and Jak-STAT signaling pathway. Moreover, 197, 95, and 356 DElncRNAs were observed to target 10, eight, and 21 DEmiRNAs and further target 147, 79, and 315 DEmRNAs, forming complex regulatory networks. Further investigation suggested that these targets were engaged in several key cellular and humoral immune pathways, such as phagosome and MAPK signaling pathway. Ultimately, the expression trends of nine randomly selected DElncRNAs were verified by RT-qPCR, confirming the authenticity and reliability of our transcriptome data. Findings in this current work not only provide candidate DElncRNAs for functional study, but also lay a foundation for unclosing the mechanism underlying DElncRNA-regulated larval immune responses to A. apis invasion

The Involvement of Renin-Angiotensin System in Lipopolysaccharide-Induced Behavioral Changes, Neuroinflammation, and Disturbed Insulin Signaling

Brain insulin signaling is accounted for the development of a variety of neuropsychiatric disorders, such as anxiety and depression, whereas both inflammation and the activated renin-angiotensin system (RAS) are two major contributors to insulin resistance. Intriguingly, inflammation and RAS can activate each other, forming a positive feedback loop that would result in exacerbated unwanted tissue damage. To further examine the interrelationship among insulin signaling, neuroinflammation and RAS in the brain, the effect of repeated lipopolysaccharide (LPS) exposure and co-treatment with the angiotensin II (Ang II) receptor type 1 (AT1) blocker, candesartan (Cand), on anxiety and depression-like behaviors, RAS, neuroinflammation and insulin signaling was explored. Our results demonstrated that prolonged LPS challenge successfully induced the rats into anxiety and depression-like state, accompanied with significant neural apoptosis and neuroinflammation. LPS also activated RAS as evidenced by the enhanced angiotensin converting enzyme (ACE) expression, Ang II generation and AT1 expression. However, blocking the activated RAS with Cand co-treatment conferred neurobehavioral protective properties. The AT1 blocker markedly ameliorated the microglial activation, the enhanced gene expression of the proinflammatory cytokines and the overactivated NF-κB signaling. In addition, Cand also mitigated the LPS-induced disturbance of insulin signaling with the normalized phosphorylation of serine 307 and tyrosine 896 of insulin receptor substrate-1 (IRS-1). Collectively, the present study, for the first time, provided the direct evidence indicating that the inflammatory condition may interact with RAS to impede brain insulin pathway, resulting in neurobehavioral damage, and inhibiting RAS seems to be a promising strategy to block the cross-talk and cut off the vicious cycle between RAS and immune system