Separating NADH and NADPH fluorescence in live cells and tissues using FLIM

NAD is a key determinant of cellular energy metabolism. In contrast, its phosphorylated form, NADP, plays a central role in biosynthetic pathways and antioxidant defence. The reduced forms of both pyridine nucleotides are fluorescent in living cells but they cannot be distinguished, as they are spectrally identical. Here, using genetic and pharmacological approaches to perturb NAD(P)H metabolism, we find that fluorescence lifetime imaging (FLIM) differentiates quantitatively between the two cofactors. Systematic manipulations to change the balance between oxidative and glycolytic metabolism suggest that these states do not directly impact NAD(P)H fluorescence decay rates. The lifetime changes observed in cancers thus likely reflect shifts in the NADPH/NADH balance. Using a mathematical model, we use these experimental data to quantify the relative levels of NADH and NADPH in different cell types of a complex tissue, the mammalian cochlea. This reveals NADPH-enriched populations of cells, raising questions about their distinct metabolic roles

Creation and modification of solid-state quantum emitters via charged particle beams

University of Technology Sydney. Faculty of Science.Solid state quantum emitters are building blocks for emerging photonic based quantum technologies. These emitters take the form of atomic scale defects that can be used as sources to generate single photons. Many materials have been identified to host quantum emitters; in particular, diamond and hexagonal boron nitride (hBN) are two promising platforms hosting a number of different defect types. There are many creation methods available but in order to realise real world applications they must be efficient, deterministic and scalable. Charged particle microscopy systems are widespread in research and industry settings and can be utilised to engineer, modify and characterise quantum emitters. This thesis outlines three procedures to create, modify and characterise solid state quantum emitters using charged particle microscopy systems. Firstly, creation of nitrogen vacancy (NV) centres in diamond via recoil implantation of gaseous precursors is presented. The method uses a commercially available focused ion beam (FIB) system to expand and simplify documented methods utilising solid-thin films. Creation of NV centres is demonstrated with three nitrogen containing precursor gases exhibiting the robustness of the method. The next works focus on two defects in hBN; the blue emitter and boron vacancy (VB). Using electron irradiation in a scanning electron microscope (SEM), a technique for site-specific fabrication of single defects is shown. The fabricated emitters demonstrate a single emission energy of 2.8~eV (436~nm), site selectivity and controllable defect density. The ability to fabricate emitters is linked to another existing defect type with emission at 305~nm (4.1~eV). Blue emitter generation is attributed to the fragmentation of carbon clusters by electron impact. The robustness and universality of the emitter fabrication technique is enhanced by a pre-irradiation annealing treatment. These results provide important insights into photophysical properties and structure of defects in hBN, outlining a framework for site-specific fabrication of quantum emitters in hBN. Finally, charge state control of the VB defect is shown using a customised SEM setup with in-situ scanning confocal photoluminescence (PL) microscopy. Charge state switching between the 0 and -1 states is demonstrated under concurrent electron and laser excitation. The switching is shown to be deterministic and reversible. Further control over the charge states is shown using a heterostructure device to adjust the rates of electrons and holes injected into the hBN, stabilising the system to the spin-active -1 charge state

SemEHR:A general-purpose semantic search system to surface semantic data from clinical notes for tailored care, trial recruitment, and clinical research

Objective: Unlocking the data contained within both structured and unstructured components of electronic health records (EHRs) has the potential to provide a step change in data available for secondary research use, generation of actionable medical insights, hospital management, and trial recruitment. To achieve this, we implemented SemEHR, an open source semantic search and analytics tool for EHRs.Methods: SemEHR implements a generic information extraction (IE) and retrieval infrastructure by identifying contextualized mentions of a wide range of biomedical concepts within EHRs. Natural language processing annotations are further assembled at the patient level and extended with EHR-specific knowledge to generate a timeline for each patient. The semantic data are serviced via ontology-based search and analytics interfaces.Results: SemEHR has been deployed at a number of UK hospitals, including the Clinical Record Interactive Search, an anonymized replica of the EHR of the UK South London and Maudsley National Health Service Foundation Trust, one of Europe's largest providers of mental health services. In 2 Clinical Record Interactive Search-based studies, SemEHR achieved 93% (hepatitis C) and 99% (HIV) F-measure results in identifying true positive patients. At King's College Hospital in London, as part of the CogStack program (github.com/cogstack), SemEHR is being used to recruit patients into the UK Department of Health 100 000 Genomes Project (genomicsengland.co.uk). The validation study suggests that the tool can validate previously recruited cases and is very fast at searching phenotypes; time for recruitment criteria checking was reduced from days to minutes. Validated on open intensive care EHR data, Medical Information Mart for Intensive Care III, the vital signs extracted by SemEHR can achieve around 97% accuracy.Conclusion: Results from the multiple case studies demonstrate SemEHR's efficiency: weeks or months of work can be done within hours or minutes in some cases. SemEHR provides a more comprehensive view of patients, bringing in more and unexpected insight compared to study-oriented bespoke IE systems. SemEHR is open source, available at https://github.com/CogStack/SemEHR.</p

Electron Beam Restructuring of Quantum Emitters in Hexagonal Boron Nitride

Hexagonal boron nitride (hBN) holds promise as a solid state, van der Waals host of single photon emitters for on-chip quantum photonics. The B-centre defect emitting at 436 nm is particularly compelling as it can be generated by electron beam irradiation. However, the emitter generation mechanism is unknown, the robustness of the method is variable, and it has only been applied successfully to thick flakes of hBN (>> 10 nm). Here, we use in-situ time-resolved cathodoluminescence (CL) spectroscopy to investigate the kinetics of B-centre generation. We show that the generation of B-centres is accompanied by quenching of a carbon-related emission at ~305 nm and that both processes are rate-limited by electromigration of defects in the hBN lattice. We identify problems that limit the efficacy and reproducibility of the emitter generation method, and solve them using a combination of optimized electron beam parameters and hBN pre- and post-processing treatments. We achieve B-centre quantum emitters in hBN flakes as thin as 8 nm, elucidate the mechanisms responsible for electron beam restructuring of quantum emitters in hBN, and gain insights towards identification of the atomic structure of the B-centre quantum emitter

On-Demand Quantum Light Sources for Underwater Communications

Quantum communication has been at the forefront of modern research for decades, however it is severely hampered in underwater applications, where the properties of water absorb nearly all useful optical wavelengths and prevent them from propagating more than, in most cases, a few metres. This research reports on-demand quantum light sources, suitable for underwater optical communication. The single photon emitters, which can be engineered using an electron beam, are based on impurities in hexagonal boron nitride. They have a zero phonon line at ~ 436 nm, near the minimum value of water absorption and are shown to suffer negligible transmission and purity loss when travelling through water channels. These emitters are also shown to possess exceptional underwater transmission properties compared to emitters at other optical wavelengths and are utilised in a proof of principle underwater communication link with rates of several kbits/s

Framework for engineering of spin defects in hexagonal boron nitride by focused ion beams

Hexagonal boron nitride (hBN) is gaining interest as a wide bandgap van der Waals host of optically active spin defects for quantum technologies. Most studies of the spin-photon interface in hBN focus on the negatively charged boron vacancy (VB-) defect, which is typically fabricated by ion irradiation. However, VB- fabrication methods often lack robustness and reproducibility when applied to thin flakes (less than 10 nm) of hBN. Here we identify mechanisms that both promote and inhibit VB- generation and optimize ion beam parameters for site-specific fabrication of optically active VB- centers. We emphasize conditions accessible by high resolution focused ion beam (FIB) systems, and present a framework for VB- fabrication in hBN flakes of arbitrary thickness for applications in quantum sensing and quantum information processing.Comment: 11 pages, 5 figure

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Optically addressable spin defects coupled to bound states in the continuum metasurfaces

Van der Waals (vdW) materials, including hexagonal boron nitride (hBN), are layered crystalline solids with appealing properties for investigating light-matter interactions at the nanoscale. hBN has emerged as a versatile building block for nanophotonic structures, and the recent identification of native optically addressable spin defects has opened up exciting possibilities in quantum technologies. However, these defects exhibit relatively low quantum efficiencies and a broad emission spectrum, limiting potential applications. Optical metasurfaces present a novel approach to boost light emission efficiency, offering remarkable control over light-matter coupling at the sub-wavelength regime. Here, we propose and realise a monolithic scalable integration between intrinsic spin defects in hBN metasurfaces and high quality (Q) factor resonances leveraging quasi-bound states in the continuum (qBICs). Coupling between spin defect ensembles and qBIC resonances delivers a 25-fold increase in photoluminescence intensity, accompanied by spectral narrowing to below 4 nm linewidth facilitated by Q factors exceeding $10^2$. Our findings demonstrate a new class of spin based metasurfaces and pave the way towards vdW-based nanophotonic devices with enhanced efficiency and sensitivity for quantum applications in imaging, sensing, and light emission.Comment: 13 pages, 4 Figures + 4 Supplementary Figure

Erratum to: Methods for evaluating medical tests and biomarkers

[This corrects the article DOI: 10.1186/s41512-016-0001-y.]

Brachytic2/ZmABCB1 functions in IAA export from intercalary meristems

Dwarfism traits in Zea mays are regulated by multiple factors including the hormone auxin. Dwarf brachytic2 (br2) mutants harbour lesions in the gene encoding an orthologue of Arabidopsis thaliana ABCB1 which functions in auxin efflux out of meristematic regions in the shoot and root. br2 mesocotyls and coleoptiles exhibit reduced auxin transport. However, the dwarf stature of br2 derives from shortened lower internodes whilst the upper portion of the plant is completely normal. As such, it is counter-intuitive to attribute br2 dwarfism exclusively to reduced auxin export out of the shoot apex. Arabidopsis abcb1 mutants exhibit only minor reductions in auxin transport and plant height unless combined with mutations in the ABCB19 auxin transporter. Phylogenetic modelling analysis excludes the possibility that BR2 is more closely related to ABCB19 which has three more closely related orthologues in maize. BR2 is expressed in nodal meristems, and analyses of auxin transport and content indicate that BR2 function in these grass-specific tissues is analogous to ABCB1 function in the shoot and root apex of Arabidopsis. These results indicate that ABCB1/BR2 function is conserved between dicots and monocots, but also suggests that this function must be understood in the context of the segmental organization of grass plants