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  1. Tumor subtype and menopausal status are strong predictors of breast cancer (BC) prognosis. We aimed to find and validate subtype- or menopausal-status-specific changes in tumor DNA methylation (DNAm) associated with all-cause mortality or BC progression. Associations between site-specific tumor DNAm and BC prognosis were estimated among The Cancer Genome Atlas participants ( n = 692) with Illumina Infinium HumanMethylation450 BeadChip array data. All-cause mortality and BC progression were modeled using Cox proportional hazards models stratified by tumor subtypes, adjusting for age, race, stage, menopausal status, tumor purity, and cell type proportion. Effect measure modification by subtype and menopausal status were evaluated by incorporating a product term with DNAm. Site-specific inference was used to identify subtype- or menopausal-status-specific differentially methylated regions (DMRs) and functional pathways. The validation of the results was carried out on an independent dataset (GSE72308; n = 180). We identified a total of fifteen unique CpG probes that were significantly associated ( P ≤ 1 × 10 − 7 with survival outcomes in subtype- or menopausal-status-specific manner. Seven probes were associated with overall survival (OS) or progression-free interval (PFI) for women with luminal A subtype, and four probes were associated with PFI for women with luminal B subtype.more »Five probes were associated with PFI for post-menopausal women. A majority of significant probes showed a lower risk of OS or BC progression with higher DNAm. We identified subtype- or menopausal-status-specific DMRs and functional pathways of which top associated pathways differed across subtypes or menopausal status. None of significant probes from site-specific analyses met genome-wide significant level in validation analyses while directions and magnitudes of coefficients showed consistent pattern. We have identified subtype- or menopausal-status-specific DNAm biomarkers, DMRs and functional pathways associated with all-cause mortality or BC progression, albeit with limited validation. Future studies with larger independent cohort of non-post-menopausal women with non-luminal A subtypes are warranted for identifying subtype- and menopausal-status-specific DNAm biomarkers for BC prognosis.« less
    Free, publicly-accessible full text available March 2, 2024
  2. Free, publicly-accessible full text available August 9, 2024
  3. The oxides of platinum group metals are promising for future electronics and spintronics due to the delicate interplay of spin-orbit coupling and electron correlation energies. However, their synthesis as thin films remains challenging due to their low vapour pressures and low oxidation potentials. Here we show how epitaxial strain can be used as a control knob to enhance metal oxidation. Using Ir as an example, we demonstrate the use of epitaxial strain in engineering its oxidation chemistry, enabling phase-pure Ir or IrO2 films despite using identical growth conditions. The observations are explained using a density-functional-theory-based modified formation enthalpy framework, which highlights the important role of metal-substrate epitaxial strain in governing the oxide formation enthalpy. We also validate the generality of this principle by demonstrating epitaxial strain effect on Ru oxidation. The IrO2 films studied in our work further revealed quantum oscillations, attesting to the excellent film quality. The epitaxial strain approach we present could enable growth of oxide films of hard-to-oxidize elements using strain engineering.
    Free, publicly-accessible full text available May 22, 2024
  4. Free, publicly-accessible full text available January 1, 2024
  5. Abstract

    The oscillatory bubble pulses generated by airguns in seawater are known to produce artefacts in seismic images. Although such artefacts are suppressible by employing larger airgun arrays in acquisition, small airgun arrays are used more often now to minimize the environmental impacts, thus raising the need for further suppressing bubble pulses at data processing stage. For a deep marine reflection dataset recently acquired by a small airgun array, we compare the effectiveness of three popular debubbling methods that estimate the far‐field source signature based on theoretical simulation and wavelets extracted from seafloor reflections and direct arrivals, respectively. In this case, due to the lack of near‐field measurements for calibration, the debubbling via simulation underperforms the two wavelet extraction methods. Overlapping events in the noisy response of seafloor sediments lead to the failure of the wavelet extraction from primary seafloor reflections. The estimated source signature based on direct arrivals achieves the best bubble suppression result, indicating the importance of signal‐to‐noise ratio and a low level of directionality of the small airgun array source.

    Free, publicly-accessible full text available July 20, 2024
  6. ABSTRACT The circular-crack model has been widely used in seismology to infer earthquake stress drop. A common assumption is that the background medium is isotropic, although many earthquakes occur in geologically anisotropic settings. In this article, we study the effect of anisotropy on stress drop for a circular crack model and present explicit formalism in both static and kinematic cases. In the static case, we obtain the relationship between stress drop and slip for a circular crack model in an arbitrarily anisotropic medium. Special attention is given to the transversely isotropic (TI) medium. The static formalism is useful in understanding stress drop, but not all quantities are observables. Therefore, we resort to the kinematic case, from which we can infer stress drop using recorded far-field body waves. In the kinematic case, we assume that the crack ruptures circularly and reaches the final displacement determined by the static solutions. The far-field waveforms show that the corner frequency will change with different anisotropic parameters. Finally, we calculate the stress drops for cracks in isotropic and anisotropic media using the far-field waveforms. We find that in an isotropic medium, only shear stress acting on the crack surface contributes to shear slip. However, inmore »a TI medium, if the anisotropy symmetry axis is not perpendicular or parallel to the crack surface, a normal stress (normal to the crack surface) can produce a shear slip. In calculating stress drop for an earthquake in an anisotropic medium using far-field body waves, a large error may be introduced if we ignore the possible anisotropy in the inversion. For a TI medium with about 18% anisotropy, the misfit of inferred stress drop could be up to 41%. Considering the anisotropic information, we can further improve the accuracy of stress-drop inversion.« less
    Free, publicly-accessible full text available November 15, 2023
  7. Abstract

    Solid-state control of the thermal conductivity of materials is of exceptional interest for novel devices such as thermal diodes and switches. Here, we demonstrate the ability tocontinuouslytune the thermal conductivity of nanoscale films of La0.5Sr0.5CoO3-δ(LSCO) by a factor of over 5, via a room-temperature electrolyte-gate-induced non-volatile topotactic phase transformation from perovskite (withδ≈ 0.1) to an oxygen-vacancy-ordered brownmillerite phase (withδ= 0.5), accompanied by a metal-insulator transition. Combining time-domain thermoreflectance and electronic transport measurements, model analyses based on molecular dynamics and Boltzmann transport equation, and structural characterization by X-ray diffraction, we uncover and deconvolve the effects of these transitions on heat carriers, including electrons and lattice vibrations. The wide-range continuous tunability of LSCO thermal conductivity enabled by low-voltage (below 4 V) room-temperature electrolyte gating opens the door to non-volatile dynamic control of thermal transport in perovskite-based functional materials, for thermal regulation and management in device applications.

  8. Free, publicly-accessible full text available February 1, 2024
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  10. Free, publicly-accessible full text available March 9, 2024