THE MECHANISM OF PRL-3 SIGNALLING UNDER CELLULAR STRESS

Ph.DDOCTOR OF PHILOSOPH

Enhanced flux pinning in YBa2Cu3O7-d films by nano-scaled substrate surface roughness

Nano-scaled substrate surface roughness is shown to strongly influence the critical current density Jc in YBCO films made by pulse-laser-deposition on the crystalline LaAlO3 substrates consisting of two separate twin-free and twin-rich regions. The nano-scaled corrugated surface was created in the twin-rich region during the deposition process. Using magneto-optical imaging techniques coupled with optical and atomic force microscopy, we observed an enhanced flux pinning in the YBCO films in the twin-rich region, resulted in \~30% increase in Jc, which was unambiguously confirmed by the direct transport measurement.Comment: 16 pages, 3 figures, accepted by Applied Physics Letter

Discriminative multi-task feature selection for multi-modality classification of Alzheimer’s disease

Recently, multi-task based feature selection methods have been used in multi-modality based classification of Alzheimer’s disease (AD) and its prodromal stage, i.e., mild cognitive impairment (MCI). However, in traditional multi-task feature selection methods, some useful discriminative information among subjects is usually not well mined for further improving the subsequent classification performance. Accordingly, in this paper, we propose a discriminative multitask feature selection method to select the most discriminative features for multi-modality based classification of AD/MCI. Specifically, for each modality, we train a linear regression model using the corresponding modality of data, and further enforce the group-sparsity regularization on weights of those regression models for joint selection of common features across multiple modalities. Furthermore, we propose a discriminative regularization term based on the intra-class and inter-class Laplacian matrices to better use the discriminative information among subjects. To evaluate our proposed method, we perform extensive experiments on 202 subjects, including 51 AD patients, 99 MCI patients, and 52 healthy controls (HC), from the baseline MRI and FDG-PET image data of the Alzheimer’s Disease Neuroimaging Initiative (ADNI). The experimental results show that our proposed method not only improves the classification performance, but also has potential to discover the disease-related biomarkers useful for diagnosis of disease, along with the comparison to several state-of-the-art methods for multi-modality based AD/MCI classification

Quasi-Floquet prethermalization in a disordered dipolar spin ensemble in diamond

Floquet (periodic) driving has recently emerged as a powerful technique for engineering quantum systems and realizing non-equilibrium phases of matter. A central challenge to stabilizing quantum phenomena in such systems is the need to prevent energy absorption from the driving field. Fortunately, when the frequency of the drive is significantly larger than the local energy scales of the many-body system, energy absorption is suppressed. The existence of this so-called prethermal regime depends sensitively on the range of interactions and the presence of multiple driving frequencies. Here, we report the observation of Floquet prethermalization in a strongly interacting dipolar spin ensemble in diamond, where the angular dependence of the dipolar coupling helps to mitigate the long-ranged nature of the interaction. Moreover, we extend our experimental observation to quasi-Floquet drives with multiple incommensurate frequencies. In contrast to a single-frequency drive, we find that the existence of prethermalization is extremely sensitive to the smoothness of the applied field. Our results open the door to stabilizing and characterizing non-equilibrium phenomena in quasi-periodically driven systems.Comment: 7+13 pages, 3+8 figure

Using Supercomputing Resources in Genomic Research

TACC resources have proven to be critical and enabling to mine cancer genomic data, genomic variants associated with human disease and polymorphic human traits, addressing biological questions otherwise non-approachable by conventional experiments. We have developed computational scripts that we use in a parallel environment to harness the capabilities of TACC HPCs, and which we have made publicly available on GitHub. In selected peer-review publications acknowledging TACC support, we have reported the association of DNA sequences able to form alternative DNA structures (or non-B DNA) with sites of chromosomal breaks leading to gross chromosomal translocations in cancer genomes, with sites of gene duplication predisposing to Parkinson’s disease, and most recently with regions of increased polymorphism in the human population. We found an exquisite correlation between the expression of selected genes and the mutational burden in cancer patients. While solving the crystal structure of a poorly characterized exonuclease, named EXO5, TACC resources enabled the assignment of a role for EXO5 in the cellular response to DNA damage, a vital pathway used by tumors to survive and grow, along with key genes whose high expression is linked to poor survival in cancer patients. Most recently, during the discovery of a nuclear role for GRB2, an adaptor protein previously thought to act only in the cytoplasm, TACC resources enabled us to test hypotheses derived from laboratory data. We were gratified to confirm the laboratory prediction that high expression of GRB2, together with its binding partner the MRE11 nuclease, carries accurate prognostic power for poor patient survival in breast cancer patients proficient in DNA homology-directed repair. These composite findings, significantly facilitated by TACC resources, have been critical to further our understanding in biological processes relevant to human disease, and to provide knowledge for the development of more precise therapeutic tools aimed at improving human health

Novel hypoglycemic injury mechanism: N-methyl-D-aspartate receptor-mediated white matter damage

Objective: Hypoglycemia is a common adverse event and can injure central nervous system (CNS) white matter (WM). We determined if glutamate receptors were involved in hypoglycemic WM injury. Methods: Mouse optic nerves (MON), CNS WM tracts, were maintained at 37°C with oxygenated artificial cerebrospinal fluid (ACSF) containing 10 mM glucose. Aglycemia was produced by switching to 0 glucose ACSF. Supra-maximal compound action potentials (CAPs) were elicited using suction electrodes and axon function was quantified as the area under the CAP. Amino acid release was measured using HPLC. Extracellular [lactate] was measured using an enzyme electrode. Results: About 50% of MON axons were injured after 60 min of aglycemia (90% after 90 min); injury was not affected by animal age. Blockade of NMDA-type glutamate receptors improved recovery after 90 min of aglycemia by 250%. Aglycemic injury was increased by reducing [Mg2+]o or increasing [glycine]o, and decreased by lowering pHo, expected results for NMDA receptor-mediated injury. Extracellular pH increased during aglycemia, due to a drop in [lactate-]o. Aglycemic injury was dramatically reduced in the absence of [Ca2+]o. Extracellular aspartate, a selective NMDA receptor agonist, increased during aglycemia. Interpretation: Aglycemia injured WM by a unique excitotoxic mechanism involving NMDA receptors (located primarily on oligodendrocytes). During WM aglycemia, the selective NMDA agonist, aspartate, is released, probably from astrocytes. Injury is mediated by Ca2+ influx through aspartate-activated NMDA receptors made permeable by an accompanying alkaline shift in pHo caused by a fall in [lactate-]o. These insights have important clinical implications

Isotope engineering for spin defects in van der Waals materials

Spin defects in van der Waals materials offer a promising platform for advancing quantum technologies. Here, we propose and demonstrate a powerful technique based on isotope engineering of host materials to significantly enhance the coherence properties of embedded spin defects. Focusing on the recently-discovered negatively charged boron vacancy center ($\mathrm{V}_{\mathrm{B}}^-$) in hexagonal boron nitride (hBN), we grow isotopically purified $\mathrm{h}{}^{10}\mathrm{B}{}^{15}\mathrm{N}$ crystals for the first time. Compared to $\mathrm{V}_{\mathrm{B}}^-$ in hBN with the natural distribution of isotopes, we observe substantially narrower and less crowded $\mathrm{V}_{\mathrm{B}}^-$ spin transitions as well as extended coherence time $T_2$ and relaxation time $T_1$. For quantum sensing, $\mathrm{V}_{\mathrm{B}}^-$ centers in our $\mathrm{h}{}^{10}\mathrm{B}{}^{15}\mathrm{N}$ samples exhibit a factor of $4$ ($2$) enhancement in DC (AC) magnetic field sensitivity. For quantum registers, the individual addressability of the $\mathrm{V}_{\mathrm{B}}^-$ hyperfine levels enables the dynamical polarization and coherent control of the three nearest-neighbor ${}^{15}\mathrm{N}$ nuclear spins. Our results demonstrate the power of isotope engineering for enhancing the properties of quantum spin defects in hBN, and can be readily extended to improving spin qubits in a broad family of van der Waals materials.Comment: 8+4+8 pages, 4+4+6 figure