41 research outputs found

    Table1_Identification of oxidative stress-related genes and potential mechanisms in atherosclerosis.DOCX

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    Atherosclerosis (AS) is the main cause of death in individuals with cardiovascular and cerebrovascular diseases. A growing body of evidence suggests that oxidative stress plays an essential role in Atherosclerosis pathology. The aim of this study was to determine genetic mechanisms associated with Atherosclerosis and oxidative stress, as well as to construct a diagnostic model and to investigate its immune microenvironment. Seventeen oxidative stress-related genes were identified. A four-gene diagnostic model was constructed using the least absolute shrinkage and selection operator (LASSO) algorithm based on these 17 genes. The area under the Receiver Operating Characteristic (ROC) curve (AUC) was 0.967. Based on the GO analysis, cell-substrate adherens junction and focal adhesion were the most enriched terms. KEGG analysis revealed that these overlapping genes were enriched in pathways associated with Alzheimer’s disease and Parkinson’s disease, as well as with prion disease pathways and ribosomes. Immune cell infiltration correlation analysis showed that the immune cells with significant differences were CD4 memory activated T cells and follicular helper T cells in the GSE43292 dataset and CD4 naïve T cells and CD4 memory resting T cells in the GSE57691 dataset. We identified 17 hub genes that were closely associated with oxidative stress in AS and constructed a four-gene (aldehyde dehydrogenase six family member A1 (ALDH6A1), eukaryotic elongation factor 2 kinase (EEF2K), glutaredoxin (GLRX) and l-lactate dehydrogenase B (LDHB)) diagnostic model with good accuracy. The four-gene diagnostic model was also found to have good discriminatory efficacy for the immune cell infiltration microenvironment of AS. Overall, these findings provide valuable information and directions for future research into Atherosclerosis diagnosis and aid in the discovery of biological mechanisms underlying AS with oxidative stress.</p

    Beyond Kitaev physics in strong spin-orbit coupled magnets

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    We review the recent advances and current challenges in the field of strong spin-orbit coupled Kitaev materials, with a particular emphasis on the physics beyond the exactly-solvable Kitaev spin liquid point. To this end, we present a comprehensive overview of the key exchange interactions in candidate materials with a specific focus on systems featuring effective Jeff = 1/2 magnetic moments. This includes, but not limited to, 5d5 iridates, 4d5 ruthenates and 3d7 cobaltates. Our exploration covers the microscopic origins of these interactions, along with a systematic attempt to map out the most intriguing correlated regimes of the multi-dimensional parameter space. Our approach is guided by robust symmetry and duality transformations as well as insights from a wide spectrum of analytical and numerical studies. We also survey higher spin Kitaev models and recent exciting results on quasi-one-dimensional models and discuss their relevance to higher-dimensional models. Finally, we highlight some of the key questions in the field as well as future directions.</p

    Relative frequencies of contact pairs.

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    <p><b>A.</b> Observed relative frequencies of different types of contact pairs at the interface. B. Ratios between the observed relative frequencies of pair types at the interface and their background relative frequencies on the surface.</p

    Scores against l_rmsd.

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    <p>Scores established by the profiles of the local network patterns given by heterodimer interfaces. l_rmsd: the RMSD of the backbone atoms of the interface residues after they have been optimally superimposed. r-1_182529 has a near-native interface and has the highest iScore, and r-1_51 is a poor decoy and has the lowest iScore.</p

    Structures of the interfaces.

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    <p>The structures have two chains, chain A and chain B, marked in green and red, respectively. In the interface, the contact sites on chain A are highlighted in blue, while those on chain B are in magenta. (A)r-l_51; (B)1KU6;(C)r-l_182529.</p

    Comparison of distributions of intra-protein 4-tuples and inter-protein 4-tuples.

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    <p>From the left to right the 4-tuples are named from ‘A’ to ‘F’ respectively. The relative frequencies for intra-protein 4-tuples are relative to the total number of the occurrences of all types of 4-tuples in the protein interior. The relative frequencies for inter-protein 4-tuple are relative to the total number of the occurrences of all types of 4-tuples in the protein-protein interface.</p

    Scatter plots of observed relative frequencies and their background relative frequencies.

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    <p><b>A.</b> Contact pairs; <b>B.</b> Contact triangles. The label ‘HA’ means the contact pair which consists of hydrophobic residue and aromatic residue, and the label ‘HAA’ is hydrophobic-aromatic-aromatic triangle type.</p

    Complex list.

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    <p>Complexes selected from DOCKGROUND to demonstrate the use of the observed local network pattern at the interface.</p><p>Class.: (1) enzyme/inhitor, (0) others.</p><p>Rec.: pdb code of unbound structure of protein 1; Lig.: pdb code of unbound structure of protein 2.</p><p>Chains before colon are in unbound structure; chains after colon are in co-crystallized structure.</p><p>RMSD: C_alpha rmsd of unbound and co-crystallized structure.</p><p>Res.: crystal structure resolution.</p><p>Hits: the number of near-native solution kept in each decoy set.</p

    Counting of inter-protein 4-tuples in contact.

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    <p>Scatter plot for observed relative frequencies and their background relative frequencies for 4-tuples. The insert is an enlargement of a particular area of the graph, and the corresponding dots are marked with red circles. ‘AAAA’ is short for the aromatic-aromatic-aromatic-aromatic 4-tuple type. ‘SHNP’ stands for the small-hydrophobic-negative-polar 4-tuple type. ‘SHHH’ and ‘HHSA’ are the small-hydrophobic-hydrophobic-hydrophobic and hydrophobic-hydrophobic-small-aromatic 4-tuple types, respectively. The 4-tuples of ‘HHSA’ and ‘SHHH’ have the highest relative frequency to be contact 4-tuples, while ‘SHNP’ is expected to be the most frequent one at interface according to the background frequencies of S, H, N, and P on the surface. ‘AAAA’ is the type of contact 4-tuples with the largest divergence angle from the diagonal line.</p

    Comparison of the best performance achieved by iScore on three datasets.

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    <p>The best performance was defined by selecting the top N scored structures to reach the highest possible specificity and sensitivity at the same time.</p
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