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The atomic structure and chemistry at metal/oxide interfaces play a crucial role in determining their properties. However, studying semi-coherent metal/oxide interfaces that include misfit dislocations through density functional theory (DFT) is often computationally expensive due to the large number of atoms involved, ranging from hundreds to thousands. In this study, we explore solute segregation behavior at the Fe/Y2O3 interface—an important model interface for cladding applications in nuclear fission reactors—by combining DFT calculations with a machine learning (ML) approach. ML models are trained using DFT-calculated segregation energies (ESeg) to identify the key chemical and geometric factors influencing solute segregation at metal/oxide interfaces, revealing the competition between these features in determining ESeg. Moreover, the segregation behavior at a specific Fe/Y2O3 interface is predicted with high accuracy using ML models trained on data from this interface. Furthermore, it is found that the ML models could also predict solute segregation at a different Fe/Y2O3 interface with a new orientation relationship (OR), at a computational cost of less than 1/45 of that required for similar DFT calculations.

Ectopic activation of rearranged during transfection (RET) has been reported to facilitate lineage differentiation and cell proliferation in different cytogenetic subtypes of acute myeloid leukemia (AML). Herein, we demonstrate that RET is significantly (p < 0.01) upregulated in AML subtypes containing rearrangements of the lysine methyltransferase 2A gene (KMT2A), commonly referred to as KMT2A‐rearranged (KMT2A‐r) AML. Integrating multi‐epigenomics data, we show that the KMT2A‐MLLT3 fusion induces the development of CCCTC‐binding (CTCF)‐guided de novo extrusion enhancer loop to upregulate RET expression in KMT2A‐r AML. Based on the finding that RET expression is tightly correlated with the selective chromatin remodeler and mediator (MED) proteins, we used a small‐molecule inhibitor having dual inhibition against RET and MED12‐associated cyclin‐dependent kinase 8 (CDK8) in KMT2A‐r AML cells. Dual inhibition of RET and CDK8 restricted cell proliferation by producing multimodal oxidative stress responses in treated cells. Our data suggest that epigenetically enhanced RET protects KMT2A‐r AML cells from oxidative stresses, which could be exploited as a potential therapeutic strategy. Rearranged during transfection (RET) proto‐oncogene is epigenetically regulated and highly expressed in KMT2A‐rearranged acute myeloid leukemia subtypes. We developed a novel small‐molecule inhibitor that expressed dual inhibition against RET and mediator protein 12 (MED12)‐associated cyclin‐dependent kinase 8 (CDK8). RET inhibition caused oxidative stress and inhibited leukemic cell growth.

Deep learning tools have recently shown significant potential for accelerating the prediction of microstructure–property linkage in materials. While deep neural networks like convolution neural networks (CNNs) can extract physics information from 3D microstructure images, they often require a large network architecture and substantial training time. In this research, we trained a graph neural network (GNN) using phase field generated microstructures of Ni-Al alloys to predict the evolution of mechanical properties. We found that a single GNN is capable of accurately predicting the strengthening of Ni-Al alloys with microstructures of varying sizes and dimensions, which cannot otherwise be done with a CNN. Additionally, GNN requires significantly less GPU utilization than CNN and offers more interpretable explanation of predictions using saliency analysis as features are manually defined in the graph. We also utilize explainable artificial intelligence tool Bayesian Inference to determine the coefficients in the power law equation that governs coarsening of precipitates. Overall, our work demonstrates the ability of the GNN to accurately and efficiently extract relevant information from material microstructures without having restrictions on microstructure size or dimension and offers an interpretable explanation.

High-risk Multiple Myeloma (MM) patients were found to maintain telomere length (TL), below the margin of short critical length, consistent with proactive overexpression of telomerase. Previously, DNA methylation has been shown as a determinant of telomere-related gene (TRG) expression and TL to assess risk in different types of cancer. We mapped genome-wide DNA methylation in a cohort of newly diagnosed MM (NDMM; n = 53) patients of major molecular subgroups, compared to age-matched healthy donors (n = 4). Differential methylation and expression at TRG-loci were analyzed in combination with overlapping chromatin marks and underlying DNA-sequences. We observed a strong correlation (R2 ≥ 0.5) between DNA methylation and expression amongst selective TRGs, such that demethylation at the promoters of DDX1 and TERF1 were associated to their oncogenic upregulation, while demethylation at the bodies of two key tumor suppressors ZNF208 and RAP1A led to downregulation of the genes. We demonstrated that TRG expression may be controlled by DNA methylation alone or in cooperation with chromatin modifications or CCCTC-binding factor at the regulatory regions. Additionally, we showed that hypomethylated DMRs of TRGs in NDMM are stabilized with G-quadruplex forming sequences, suggesting a crucial role of these epigenetically vulnerable loci in MM pathogenesis. We have identified a panel of five TRGs, which are epigenetically deregulated in NDMM patients and may serve as early detection biomarkers or therapeutic targets in the disease.

Electronic structure calculations were performed to study the role of misfit dislocations on the structure and chemistry of a metal/oxide interface. We found that a chemical imbalance exists at the misfit dislocation which leads to dramatic changes in the point defect content at the interface – stabilizing the structure requires removing as much as 50% of the metal atoms and insertion of a large number of oxygen interstitials. The exact defect composition that stabilizes the interface is sensitive to the external oxygen partial pressure. We relate the preferred defect structure at the interface to a competition between chemical and strain energies as defects are introduced.

Surface-modified sulfur nanoparticles (SNP) of two different sizes were prepared via a modified liquid-phase precipitation method, using sodium polysulfide and ammonium polysulfide as starting material and polyethylene glycol-400 (PEG-400) as the surface stabilizing agent. Surface topology, size distribution, surface modification of SNPs with PEG-400, quantitative analysis for the presence of sulfur in nanoformulations, and thermal stability of SNPs were determined by atomic force microscopy (AFM), dynamic light scattering (DLS) plus high-resolution transmission electron microscopy (HR-TEM), fourier transform infrared (FT-IR) spectroscopy, energy dispersive X-ray (EDX) spectroscopy, and thermogravimetric analysis (TGA), respectively. A simultaneous study with micron-sized sulfur (S^sup 0^) and SNPs was carried out to evaluate their fungicidal efficacy against Aspergillus niger and Fusarium oxysporum in terms of radial growth, sporulation, ultrastructural modifications, and phospholipid content of the fungal strains using a modified poisoned food technique, spore-germination slide bioassay, environmental scanning electron microscopy (ESEM), and spectrometry. SNPs expressed promising inhibitory effect on fungal growth and sporulation and also significantly reduced phospholipid content. [PUBLICATION ABSTRACT]

Stable nanocolloids of monoclinic sulfur (β-SNPs) were prepared through ‘water-in-oil microemulsion technique’ at room temperature after suitable modifications of the surface. The morphology (rod shaped; ~50 nm in diameter) and allotropic nature (monoclinic) of the SNPs were investigated with Transmission Electron Microscopy and X-ray Diffraction technique. The surface modification, colloidal stability, and surface topology of β-SNPs were evaluated with Fourier Transform Infrared Spectroscopy, zeta potential analysis, and Atomic Force Microscopy. Thermal decomposition pattern of these nanosized particles was determined by Thermo Gravimetric Analysis (TGA). β-SNPs-colloids expressed excellent antimicrobial activities against a series of fungal and bacterial isolates with prominent deformities at their surface. In contrast, insignificant cytotoxicity was achieved against the human derived hepatoma (HepG2) cell line upon treatment with β-SNPs. A simultaneous study was performed to determine the stock concentration of β-SNP-colloids using a novel high phase liquid chromatographic method. Cumulative results of this study hence, elucidate the stabilization of nanosized monoclinic sulfur at room temperature and their potential antimicrobial efficacy over micron-sized sulfur.

Background Oncogenic overexpression of integrin-β7 ( ITGB7 ) in cases of high-risk multiple myeloma (MM) was reported to promote enhanced interactions between neoplastic plasma-B cells and stromal cells to develop cell-adhesion mediated drug resistance. Methods Expression profiles of adhesion related genes were analyzed in a cohort of MM patients containing major IgH translocations or hyperdiploidies (HY), diagnosed at the premalignant monoclonal gammopathy of undetermined significance (MGUS; n  = 103), smoldering multiple myeloma; (SMM; n  = 190) or MM (MM; n  = 53) stage. Differential expression was integrated with loci-specific alterations in DNA-methylation and chromatin marks in MM patients. A CRISPR-based targeted induction of DNA-methylation at the ITGB7 super-enhancer (SE) in MM.1S cells was employed to intersect the impact of cis-regulatory elements on ITGB7 expression. Results ITGB7 was significantly ( p  < 0.05) upregulated in patients with t(14;16) and t(14;20) subgroups in all MGUS, SMM and MM stages, but sporadically upregulated in t(4;14) subgroup at the MM stage. We demonstrate a predetermined enhancer state on ITGB7 in primary-B cells that is maintained under bivalent chromatin, which undergoes a process of chromatin-state alterations and develops into an active enhancer in cases of the t(4;14) subgroup or SE in cases of the t(14;16) subgroup. We also demonstrate that while targeted induction of DNA-methylation at the ITGB7 -SE further upregulated the gene, inhibition of ITGB7 -SE-associated transcription factor bromodomain-4 downregulated expression of the gene. Conclusions Our findings suggest an epigenetic regulation of oncogenic overexpression of ITGB7 in MM cells, which could be critical in MM progression and an attractive therapeutic target.

Nanosized elemental sulfur (ES) is already reported to exert superior antimicrobial efficacy than micron-sized ES, which encourages their use in drugs and therapeutics. The aim of the present study is to explore the possible route and mode of antimicrobial action of orthorhombic (α-SNPs) and monoclinic (β-SNPs) allotropes of sulfur, respectively, at their nano-dimensions. The antimicrobial efficacy of α- and β-SNPs was determined against both the conventionally ES-resistant and ES-susceptible fungi and bacteria. Both the SNPs inhibited the microbial growth, irrespective of their resistance profile to ES and caused significant deformities on the microbial cell surfaces. However, the extent of antimicrobial efficacy was found to be optimum for α-SNPs, which can be attributed to their size, shape, and surface modification. Subsequent transcript profiling, metabolite profiling, and enzymatic analyses revealed that α- and β-SNPs impaired a cluster of mitochondrial enzymes involved in cellular respiration and oxidative phosphorylation. ES and SNPs stress were found to elicit the NADPH-dependent glutathione reductase mediated ES-detoxification response in fungi and caused them to undertake the glyoxylate shunt in favor of energy conservation. A simultaneous study was also undertaken to assess the biocompatible or bio-adverse properties of SNPs in terms of their cytotoxic and genotoxic effects against the human derived lung fibroblast cell line (MRC-5). The present study hence explores the antimicrobial physiology of two novel functional materials and demonstrates their compatibility as a future putative antimicrobial drug.

Overexpression of S100B is routinely used for disease-staging and for determining prognostic outcomes in patients with malignant melanoma. Intracellular interactions between S100B and wild-type (WT)-p53 have been demonstrated to limit the availability of free WT-p53 in tumor cells, inhibiting the apoptotic signaling cascade. Herein, we demonstrate that, while oncogenic overexpression of S100B is poorly correlated (R < 0.3; p > 0.05) to alterations in S100B copy number or DNA methylation in primary patient samples, the transcriptional start site and upstream promoter of the gene are epigenetically primed in melanoma cells with predicted enrichment of activating transcription factors. Considering the regulatory role of activating transcription factors in S100B upregulation in melanoma, we stably suppressed S100b (murine ortholog) by using a catalytically inactive Cas9 (dCas9) fused to a transcriptional repressor, Krüppel-associated box (KRAB). Selective combination of S100b-specific single-guide RNAs and the dCas9-KRAB fusion significantly suppressed expression of S100b in murine B16 melanoma cells without noticeable off-target effects. S100b suppression resulted in recovery of intracellular WT-p53 and p21 levels and concomitant induction of apoptotic signaling. Expression levels of apoptogenic factors (i.e., apoptosis-inducing factor, caspase-3, and poly-ADP ribose polymerase) were altered in response to S100b suppression. S100b-suppressed cells also showed reduced cell viability and increased susceptibility to the chemotherapeutic agents, cisplatin and tunicamycin. Targeted suppression of S100b therefore offers a therapeutic vulnerability to overcome drug resistance in melanoma.