Faithful rule extraction for differentiable rule learning models

There is increasing interest in methods for extracting interpretable rules from ML models trained to solve a wide range of tasks over knowledge graphs (KGs), such as KG completion, node classification, question answering and recommendation. Many such approaches, however, lack formal guarantees establishing the precise relationship between the model and the extracted rules, and this lack of assurance becomes especially problematic when the extracted rules are applied in safety-critical contexts or to ensure compliance with legal requirements. Recent research has examined whether the rules derived from the influential Neural-LP model exhibit soundness (or completeness), which means that the results obtained by applying the model to any dataset always contain (or are contained in) the results obtained by applying the rules to the same dataset. In this paper, we extend this analysis to the context of DRUM, an approach that has demonstrated superior practical performance. After observing that the rules currently extracted from a DRUM model can be unsound and/or incomplete, we propose a novel algorithm where the output rules, expressed in an extension of Datalog, ensure both soundness and completeness. This algorithm, however, can be inefficient in practice and hence we propose additional constraints to DRUM models facilitating rule extraction, albeit at the expense of reduced expressive power

Interaction of Flavonoids from Woodwardia unigemmata with Bovine Serum Albumin (BSA): Application of Spectroscopic Techniques and Molecular Modeling Methods

Phytochemical investigation on the methanol extract of Woodwardia unigemmata resulted in the isolation of seven flavonoids, including one new flavonol acylglycoside (1). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison of literature data. The multidrug resistance (MDR) reversing activity was evaluated for the isolated compounds using doxorubicin-resistant K562/A02 cells model. Compound 6 showed comparable MDR reversing effect to verapamil. Furthermore, the interaction between compounds and bovine serum albumin (BSA) was investigated by spectroscopic methods, including steady-state fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular docking approach. The experimental results indicated that the seven flavonoids bind to BSA by static quenching mechanisms. The negative ∆H and ∆S values indicated that van der Waals interactions and hydrogen bonds contributed in the binding of compounds 2–6 to BSA. In the case of compounds 1 and 7 systems, the hydrophobic interactions play a major role. The binding of compounds to BSA causes slight changes in the secondary structure of BSA. There are two binding sites of compound 6 on BSA and site I is the main site according to the molecular docking studies and the site marker competitive binding assayThis work was supported by the Natural Science Foundation of China (81502921) and the Young Scholars Program of Shandong University (2015WLJH50).Peer Reviewe

Stability and asynchrony of local communities but less so diversity increase regional stability of Inner Mongolian grassland

Extending knowledge on ecosystem stability to larger spatial scales is urgently needed because present local-scale studies are generally ineffective in guiding management and conservation decisions of an entire region with diverse plant communities. We investigated stability of plant productivity across spatial scales and hierarchical levels of organization and analyzed impacts of dominant species, species diversity, and climatic factors using a multisite survey of Inner Mongolian grassland. We found that regional stability across distant local communities was related to stability and asynchrony of local communities. Using only dominant instead of all-species dynamics explained regional stability almost equally well. The diversity of all or only dominant species had comparatively weak effects on stability and synchrony, whereas a lower mean and higher variation of precipitation destabilized regional and local communities by reducing population stability and synchronizing species dynamics. We demonstrate that, for semi-arid temperate grassland with highly uneven species abundances, the stability of regional communities is increased by stability and asynchrony of local communities and these are more affected by climate rather than species diversity. Reduced amounts and increased variation of precipitation in the future may compromise the sustainable provision of ecosystem services to human well-being in this region

Identification of biomarkers co-associated with M1 macrophages, ferroptosis and cuproptosis in alcoholic hepatitis by bioinformatics and experimental verification

BackgroundsAlcoholic hepatitis (AH) is a major health problem worldwide. There is increasing evidence that immune cells, iron metabolism and copper metabolism play important roles in the development of AH. We aimed to explore biomarkers that are co-associated with M1 macrophages, ferroptosis and cuproptosis in AH patients.MethodsGSE28619 and GSE103580 datasets were integrated, CIBERSORT algorithm was used to analyze the infiltration of 22 types of immune cells and GSVA algorithm was used to calculate ferroptosis and cuproptosis scores. Using the “WGCNA” R package, we established a gene co-expression network and analyzed the correlation between M1 macrophages, ferroptosis and cuproptosis scores and module characteristic genes. Subsequently, candidate genes were screened by WGCNA and differential expression gene analysis. The LASSO-SVM analysis was used to identify biomarkers co-associated with M1 macrophages, ferroptosis and cuproptosis. Finally, we validated these potential biomarkers using GEO datasets (GSE155907, GSE142530 and GSE97234) and a mouse model of AH.ResultsThe infiltration level of M1 macrophages was significantly increased in AH patients. Ferroptosis and cuproptosis scores were also increased in AH patients. In addition, M1 macrophages, ferroptosis and cuproptosis were positively correlated with each other. Combining bioinformatics analysis with a mouse model of AH, we found that ALDOA, COL3A1, LUM, THBS2 and TIMP1 may be potential biomarkers co-associated with M1 macrophages, ferroptosis and cuproptosis in AH patients.ConclusionWe identified 5 potential biomarkers that are promising new targets for the treatment and diagnosis of AH patients

Research progress on the role of lncRNA–miRNA networks in regulating adipogenic and osteogenic differentiation of bone marrow mesenchymal stem cells in osteoporosis

Osteoporosis (OP) is characterized by a decrease in osteoblasts and an increase in adipocytes in the bone marrow compartment, alongside abnormal bone/fat differentiation, which ultimately results in imbalanced bone homeostasis. Bone marrow mesenchymal stem cells (BMSCs) can differentiate into osteoblasts and adipocytes to maintain bone homeostasis. Several studies have shown that lncRNAs are competitive endogenous RNAs that form a lncRNA–miRNA network by targeting miRNA for the regulation of bone/fat differentiation in BMSCs; this mechanism is closely related to the corresponding treatment of OP and is important in the development of novel OP-targeted therapies. However, by reviewing the current literature, it became clear that there are limited summaries discussing the effects of the lncRNA–miRNA network on osteogenic/adipogenic differentiation in BMSCs. Therefore, this article provides a review of the current literature to explore the impact of the lncRNA–miRNA network on the osteogenic/adipogenic differentiation of BMSCs, with the aim of providing a new theoretical basis for the treatment of OP

Resistance Switching Behavior in Rectangle-Nano-Pattern SrTiO3 Induced by Simple Annealing.

The tunability of semi-conductivity in SrTiO3 single crystal substrates has been realized by a simple encapsulated annealing method under argon atmosphere. This high temperature annealing-induced property changes are characterized by the transmission spectra, scanning electron microscopy (SEM) and synchrotron-based X-ray absorption (XAS). We find the optical property is strongly influenced by the annealing time (with significant decrease of transmittance). A sub gap absorption at ~427 nm is detected which is attributed to the introduction of oxygen vacancy. Interestingly, in the SEM images, annealing-induced regularly rectangle nano-patterns are directly observed which is contributed to the conducting filaments. The XAS of O K-edge spectra shows the changes of electronic structure by annealing. Very importantly, resistance switching response is displayed in the annealed SrTiO3 single crystal. This suggests a possible simplified route to tune the conductivity of SrTiO3 and further develop novel resistance switching materials

Volumetric-modulated arc therapy as an alternative to intensity-modulated radiotherapy for primary tumors of advanced non–small-cell lung cancer: A multicenter retrospective analysis based on propensity score matching

Purpose: To investigate the effect of volumetric-modulated arc therapy (VMAT) versus intensity-modulated radiotherapy (IMRT) for advanced non–small-cell lung cancer (NSCLC). Methods: Cases in which the primary tumors were treated with IMRT or VMAT as initial intervention in stages III and IV NSCLC patients from September 2008 to March 2020 were retrospectively analyzed. Propensity Score Matching (PSM) was used to assess the efficacy and toxicity of the two radiotherapy techniques. Results: A total of 637 patients were included, out of which 483 cases were treated with IMRT, while 154 received VMAT. A total of 308 patients were selected after PSM. Patients who were having acute radiation esophagitis and pneumonia treated with VMAT had a lower percentage than those treated with IMRT (p < 0.05) before PSM. However, there was no significant difference in grades 3 - 4 toxicity (χ2 = 2.77, p = 0.096). There were also no significant differences in the primary endpoints between the two groups after PSM (p > 0.05), while for secondary endpoints, all lung V5, and V20, mean lung dose and heart V30, heart V40, mean heart dose in all patients and stage N2 patients in VMAT after PSM were significantly lower than those of IMRT (p < 0.05). Conclusion: Radiation therapy of A-NSCLC primary tumors using VMAT and IMRT seem to produce similar efficacy. The volume parameters of normal tissues and organs is significantly lower in VMAT, especially in patients with stage N2. Therefore, VMAT may be more beneficial for reducing radiation damage in normal tissues and organs

Antifungal effects and biocontrol potential of lipopeptide-producing Streptomyces against banana Fusarium wilt fungus Fusarium oxysporum f. sp. cubense

Fusarium wilt of banana (FWB), caused by Fusarium oxysporum f. sp. cubense (Foc), especially tropical race 4 (TR4), presents the foremost menace to the global banana production. Extensive efforts have been made to search for efficient biological control agents for disease management. Our previous study showed that Streptomyces sp. XY006 exhibited a strong inhibitory activity against several phytopathogenic fungi, including F. oxysporum. Here, the corresponding antifungal metabolites were purified and determined to be two cyclic lipopeptide homologs, lipopeptin A and lipopeptin B. Combined treatment with lipopeptin complex antagonized Foc TR4 by inhibiting mycelial growth and conidial sporulation, suppressing the synthesis of ergosterol and fatty acids and lowering the production of fusaric acid. Electron microscopy observation showed that lipopeptide treatment induced a severe disruption of the plasma membrane, leading to cell leakage. Lipopeptin A displayed a more pronounced antifungal activity against Foc TR4 than lipopeptin B. In pot experiments, strain XY006 successfully colonized banana plantlets and suppressed the incidence of FWB, with a biocontrol efficacy of up to 87.7%. Additionally, XY006 fermentation culture application improved plant growth parameters and induced peroxidase activity in treated plantlets, suggesting a possible role in induced resistance. Our findings highlight the potential of strain XY006 as a biological agent for FWB, and further research is needed to enhance its efficacy and mode of action in planta

Spectroscopic methodologies and molecular docking studies on the interaction of the soluble guanylate cyclase stimulator riociguat with human serum albumin

Publisher's version (útgefin grein)Abstract Interaction of riociguat with human serum albumin (HSA) is extremely important in understanding the drug's disposition and efficiency. In the current study, the binding of riociguat to HSA was explored using spectroscopic methods and molecular docking. The quenching constant, the binding constant, the number of binding sites, thermodynamic parameters, and the secondary structure of protein were determined. A fluorescence study revealed that riociguat quenched HSA fluorescence via static quenching with a binding constant of 1.55 × 104 L mol-1 at 298 K. The calculated thermodynamic parameters indicated that the binding process was spontaneous and that the main interaction force was hydrophobic interaction. Site marker competitive binding experiments and molecular docking studies suggested that riociguat was inserted into the subdomain IIA (site I) of HSA. Alterations in the protein secondary structure after drug complexation were predicted. Results indicated that the protein a-helix structure increased with an increasing concentration of riociguat. This indicated that a riociguat-HSA complex was formed and that the protein secondary structure was altered by the addition of riociguat.This work was supported by the Natural Science Foundation of China (81502921 and 81503251), the Key Research and Development Program of Shandong Province (2017GSF218049), and Young Scholars Program of Shandong University (2015WLJH50).Peer Reviewe