Thought Graph: Generating Thought Process for Biological Reasoning

We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for bioinformatics and precision medicine.Comment: 4 pages. Accepted by Web Conf 202

Beta-informativeness-diffusion multilayer graph embedding for brain network analysis

Brain network analysis provides essential insights into the diagnosis of brain disease. Integrating multiple neuroimaging modalities has been demonstrated to be more effective than using a single modality for brain network analysis. However, a majority of existing brain network analysis methods based on multiple modalities often overlook both complementary information and unique characteristics from various modalities. To tackle this issue, we propose the Beta-Informativeness-Diffusion Multilayer Graph Embedding (BID-MGE) method. The proposed method seamlessly integrates structural connectivity (SC) and functional connectivity (FC) to learn more comprehensive information for diagnosing neuropsychiatric disorders. Specifically, a novel beta distribution mapping function (beta mapping) is utilized to increase vital information and weaken insignificant connections. The refined information helps the diffusion process concentrate on crucial brain regions to capture more discriminative features. To maximize the preservation of the unique characteristics of each modality, we design an optimal scale multilayer brain network, the inter-layer connections of which depend on node informativeness. Then, a multilayer informativeness diffusion is proposed to capture complementary information and unique characteristics from various modalities and generate node representations by incorporating the features of each node with those of their connected nodes. Finally, the node representations are reconfigured using principal component analysis (PCA), and cosine distances are calculated with reference to multiple templates for statistical analysis and classification. We implement the proposed method for brain network analysis of neuropsychiatric disorders. The results indicate that our method effectively identifies crucial brain regions associated with diseases, providing valuable insights into the pathology of the disease, and surpasses other advanced methods in classification performance

Current-driven magnetization switching in a van der Waals ferromagnet Fe3GeTe2

The recent discovery of ferromagnetism in two-dimensional (2D) van der Waals (vdW) materials holds promises for novel spintronic devices with exceptional performances. However, in order to utilize 2D vdW magnets for building spintronic nanodevices such as magnetic memories, key challenges remain in terms of effectively switching the magnetization from one state to the other electrically. Here, we devise a bilayer structure of Fe3GeTe2/Pt, in which the magnetization of few-layered Fe3GeTe2 can be effectively switched by the spin-orbit torques (SOTs) originated from the current flowing in the Pt layer. The effective magnetic fields corresponding to the SOTs are further quantitatively characterized using harmonic measurements. Our demonstration of the SOT-driven magnetization switching in a 2D vdW magnet could pave the way for implementing low-dimensional materials in the next-generation spintronic applications

Metakaolin-Reinforced Sulfoaluminate-Cement-Solidified Wasteforms of Spent Radioactive Resins—Optimization by a Mixture Design

Cement solidification is a main technique for radioactive waste treatment to reduce its risk to the environment and human health. However, this method underperforms when dealing with spent radioactive ion-exchange resin, taking much space, and costing much money for final disposal. In this work, simulated spent radioactive resin was solidified using a metakaolin-reinforced sulfoaluminate cement system, which was optimized by a mixture design based on the effects of components and parameters, and the durability of solidified wasteforms was assessed in terms of strength and Cs(I) leaching. Solidified by an optimized formula of 40 wt.% spent resin, 55.8 wt.% sulfoaluminate cement, 2.2 wt.% metakaolin, and 2 wt.% water reducer, the resin loading in wasteforms reached 64% and the compressive strength 13.7 MPa. The dominant mineral phases of hydration products were ettringite crystalline of acicular and columnar morphology, with small amounts of scattered amorphous clusters of aluminum gels and C–S–H gels. Metakaolin, a source of aluminum, promoted the growth of ettringite, which facilitated (1) the encapsulation of resin beads with high strengths, even in acidic environments or during frequent freezing-thawing, and (2) the retention of Cs(I), with a 42 day leaching rate of 2.3 × 10−4 cm/day. This work offers a technical justification for spent resin solidification in the metakaolin-reinforced sulfoaluminate cement system, which is an applicational solution for the efficient treatment of radioactive waste

Efficient Iodine Removal by Porous Biochar-Confined Nano-Cu2O/Cu0: Rapid and Selective Adsorption of Iodide and Iodate Ions

Iodine is a nuclide of crucial concern in radioactive waste management. Nanomaterials selectively adsorb iodine from water; however, the efficient application of nanomaterials in engineering still needs to be developed for radioactive wastewater deiodination. Artemia egg shells possess large surface groups and connecting pores, providing a new biomaterial to remove contaminants. Based on the Artemia egg shell-derived biochar (AES biochar) and in situ precipitation and reduction of cuprous, we synthesized a novel nanocomposite, namely porous biochar-confined nano-Cu2O/Cu0 (C-Cu). The characterization of C-Cu confirmed that the nano-Cu2O/Cu0 was dispersed in the pores of AES biochar, serving in the efficient and selective adsorption of iodide and iodate ions from water. The iodide ion removal by C-Cu when equilibrated for 40 min exhibited high removal efficiency over the wide pH range of 4 to 10. Remarkable selectivity towards both iodide and iodate ions of C-Cu was permitted against competing anions (Cl−/NO3−/SO42−) at high concentrations. The applicability of C-Cu was demonstrated by a packed column test with treated effluents of 1279 BV. The rapid and selective removal of iodide and iodate ions from water is attributed to nanoparticles confined on the AES biochar and pore-facilitated mass transfer. Combining the advantages of the porous biochar and nano-Cu2O/Cu0, the use of C-Cu offers a promising method of iodine removal from water in engineering applications

Nrf2 Ablation Promotes Alzheimer’s Disease-Like Pathology in APP/PS1 Transgenic Mice: The Role of Neuroinflammation and Oxidative Stress

Introduction. Alzheimer’s disease (AD), the most common neurodegenerative disorder, is characterized by the accumulation of amyloid-β (Aβ) peptide and hyperphosphorylated tau protein. Accumulating evidence has revealed that the slow progressive deterioration of AD is associated with oxidative stress and chronic inflammation in the brain. Nuclear factor erythroid 2- (NF-E2-) related factor 2 (Nrf2), which acts through the Nrf2/ARE pathway, is a key regulator of the antioxidant and anti-inflammatory response. Although recent data show a link between Nrf2 and AD-related cognitive decline, the mechanism is still unknown. Thus, we explored how Nrf2 protects brain cells against the oxidative stress and inflammation of AD in a mouse model of AD (APP/PS1 transgenic (AT) mice) with genetic removal of Nrf2. Methods. The spatial learning and memory abilities of 12-month-old transgenic mice were evaluated using a Morris water maze test. Hippocampal levels of Nrf2, Aβ, and p-tauS404 and of astrocytes and microglia were determined by immunostaining. Inflammatory cytokines were determined by ELISA and quantitative real-time polymerase chain reaction (qRT-PCR). Oxidative stress was measured by 8-hydroxydeoxyguanosine immunohistochemistry, and the antioxidant response was determined by qRT-PCR. Results. The spatial learning and memory abilities of AT mice were impaired after Nrf2 deletion. Aβ and p-tauS404 accumulation was increased in the hippocampus of AT/Nrf2-KO mice. Astroglial and microglial activation was exacerbated, followed by upregulation of the proinflammatory cytokines IL-1β, IL-6, and TNF-α. Conclusion. Our present results show that Nrf2 deficiency aggravates AD-like pathology in AT mice. This phenotype was associated with increased levels of oxidative and proinflammatory markers, which suggests that the Nrf2 pathway may be a promising therapeutic target for AD

DataSheet_1_Evaluation of dendritic cell-targeting T7 phages as a vehicle to deliver avian influenza virus H5 DNA vaccine in SPF chickens.docx

IntroductionThere is a growing demand for effective technologies for the delivery of antigen to antigen-presenting cells (APCs) and their immune-activation for the success of DNA vaccines. Therefore, dendritic cell (DC)-targeting T7 phages were used as a vehicle to deliver DNA vaccine.MethodsIn this study, a eukaryotic expression plasmid pEGFP-C1-HA2-AS containing the HA2 gene derived from the avian H5N1 virus and an anchor sequence (AS) gene required for the T7 phage packaging process was developed. To verify the feasibility of phage delivery, the plasmid encapsulated in DC-targeting phage capsid through the recognition of AS was evaluated both in vitro and in vivo. The pEGFP-C1-HA2-AS plasmid could evade digestion by DNase I by becoming encapsulated into the phage particles and efficiently expressed the HA2 antigen in DCs with the benefit of DC-targeting phages.ResultsFor chickens immunized with the DC-targeting phage 74 delivered DNA vaccine, the levels of IgY and IgA antibodies, the concentration of IFN-γ and IL-12 cytokines in serum, the proliferation of lymphocytes, and the percentage of CD4+/CD8+ T lymphocytes isolated from peripheral blood were significantly higher than chickens which were immunized with DNA vaccine that was delivered by non-DC-targeting phage or placebo (pConclusionThis study provides a strategy for development of a novel avian influenza DNA vaccine and demonstrates the potential of DC-targeting phage as a DNA vaccine delivery vehicle.</p