Nanophotonic Structures for Coupling to Quantum Emitters in the Visible

This thesis is about the design, fabrication, and characterization of nanophotonic elements in the visible that can enhance light-matter interaction for single quantum emitters. We focus on two material systems: single photon sources based on the nitrogen-vacancy (NV) center in diamond with improved spontaneous emission rates and collection efficiencies, and passive TiO2 devices that comprise a potentially broadband (from the visible to the infrared), low loss photonics platform and that are suitable for probing and manipulating single colloidal quantum dots. We first discuss the requirements for using color center emission in bulk diamond crystals for potential applications in quantum information processing, and provide examples of using nanowire structures and planar resonators made in diamond for engineering the the NV center’s pump and collection efficiencies, and spontaneous emission rates, respectively. We also describe the integration of diamond with plasmonic structures. We have designed and implemented diamond-silver apertures for broadband enhancements of the spontaneous emission rates of NV centers. We show that shallow-implanted NV centers in diamond nanoposts provide a good system for controlling the NV center spontaneous emission rates, allowing for quenched emission with long lifetimes in the bare case, and enhanced emission with fast decay rates (corresponding to a Purcell factor of around 6) when coated with silver. We add plasmonic gratings around the diamond-silver apertures to improve the collection efficiency of the system, and observe over two-fold improvement in collection. We demonstrate the fabrication of chip-scale linear optical elements such as waveguides and racetrack resonators in low-loss $TiO_2$ thin films. The fabricated waveguides operate over a wide bandwidth with propagation losses from from 30 dB/cm in the visible to 4 dB/cm in the IR, while racetrack resonators can critically couple to waveg- uides and have quality factors as high as ~22000 in the red wavelengths. We present the fabrication of dielectric slot waveguides and their integration with colloidal quan- tum dots. Finally, we describe efforts to study and control charge transfer processes between quantum dots and $TiO_2$ on a single emitter level.Engineering and Applied Science

Auditor Choice under Client Information Uncertainty

[[abstract]]This study examines whether companies with financial statements that contain higher degrees of information uncertainty are more inclined to hire specialist auditing firms. We argue that they do so to signal the credibility of the financial statements and improve stakeholders’ perceptions. We develop comprehensive measures of information uncertainty from the auditor’s viewpoint and deconstruct it into fundamental volatility uncertainty and reporting quality uncertainty. We sample U.S. companies that switched auditors from 2001 to 2009 to examine whether information uncertainty influenced their auditor selection. Confirming our conjecture, companies confronting higher information uncertainty prefer to hire specialist auditors. Evidence partially supports that companies confronting higher reporting quality uncertainty are more inclined to hire specialist auditors when compared with those confronting fundamental volatility uncertainty.[[notice]]補正完

Physical interaction and functional coupling between ACDP4 and the intracellular ion chaperone COX11, an implication of the role of ACDP4 in essential metal ion transport and homeostasis

Divalent metal ions such as copper, manganese, and cobalt are essential for cell development, differentiation, function and survival. These essential metal ions are delivered into intracellular domains as cofactors for enzymes involved in neuropeptide and neurotransmitter synthesis, superoxide metabolism, and other biological functions in a target specific fashion. Altering the homeostasis of these essential metal ions is known to connect to a number of human diseases including Alzheimer disease, amyotrophic lateral sclerosis, and pain. It remains unclear how these essential metal ions are delivered to intracellular targets in mammalian cells. Here we report that rat spinal cord dorsal horn neurons express ACDP4, a member of Ancient Conserved Domain Protein family. By screening a pretransformed human fetal brain cDNA library in a yeast two-hybrid system, we have identified that ACDP4 specifically interacts with COX11, an intracellular metal ion chaperone. Ectopic expression of ACDP4 in HEK293 cells resulted in enhanced toxicity to metal ions including copper, manganese, and cobalt. The metal ion toxicity became more pronounced when ACDP4 and COX11 were co-expressed ectopically in HEK293 cells, suggesting a functional coupling between them. Our results indicate a role of ACDP4 in metal ion homeostasis and toxicity. This is the first report revealing a functional aspect of this ancient conserved domain protein family. We propose that ACDP is a family of transporter protein or chaperone proteins for delivering essential metal ions in different mammalian tissues. The expression of ACDP4 on spinal cord dorsal horn neurons may have implications in sensory neuron functions under physiological and pathological conditions

Abiotic and Biotic Stressors Causing Equivalent Mortality Induce Highly Variable Transcriptional Responses in the Soybean Aphid

Environmental stress affects basic organismal functioning and can cause physiological, developmental, and reproductive impairment. However, in many nonmodel organisms, the core molecular stress response remains poorly characterized and the extent to which stress-induced transcriptional changes differ across qualitatively different stress types is largely unexplored. The current study examines the molecular stress response of the soybean aphid (Aphis glycines) using RNA sequencing and compares transcriptional responses to multiple stressors (heat, starvation, and plant defenses) at a standardized stress level (27% adult mortality). Stress-induced transcriptional changes showed remarkable variation, with starvation, heat, and plant defensive stress altering the expression of 3985, 510, and 12 genes, respectively. Molecular responses showed little overlap across all three stressors. However, a common transcriptional stress response was identified under heat and starvation, involved with up-regulation of glycogen biosynthesis and molecular chaperones and down-regulation of bacterial endosymbiont cellular and insect cuticular components. Stressor-specific responses indicated heat affected expression of heat shock proteins and cuticular components, whereas starvation altered a diverse set of genes involved in primary metabolism, oxidative reductive processes, nucleosome and histone assembly, and the regulation of DNA repair and replication. Exposure to host plant defenses elicited the weakest response, of which half of the genes were of unknown function. This study highlights the need for standardizing stress levels when comparing across stress types and provides a basis for understanding the role of general vs. stressor specific molecular responses in aphids

Abiotic and Biotic Stressors Causing Equivalent Mortality Induce Highly Variable Transcriptional Responses in the Soybean Aphid

Environmental stress affects basic organismal functioning and can cause physiological, developmental, and reproductive impairment. However, in many nonmodel organisms, the core molecular stress response remains poorly characterized and the extent to which stress-induced transcriptional changes differ across qualitatively different stress types is largely unexplored. The current study examines the molecular stress response of the soybean aphid (Aphis glycines) using RNA sequencing and compares transcriptional responses to multiple stressors (heat, starvation, and plant defenses) at a standardized stress level (27% adult mortality). Stress-induced transcriptional changes showed remarkable variation, with starvation, heat, and plant defensive stress altering the expression of 3985, 510, and 12 genes, respectively. Molecular responses showed little overlap across all three stressors. However, a common transcriptional stress response was identified under heat and starvation, involved with up-regulation of glycogen biosynthesis and molecular chaperones and down-regulation of bacterial endosymbiont cellular and insect cuticular components. Stressor-specific responses indicated heat affected expression of heat shock proteins and cuticular components, whereas starvation altered a diverse set of genes involved in primary metabolism, oxidative reductive processes, nucleosome and histone assembly, and the regulation of DNA repair and replication. Exposure to host plant defenses elicited the weakest response, of which half of the genes were of unknown function. This study highlights the need for standardizing stress levels when comparing across stress types and provides a basis for understanding the role of general vs. stressor specific molecular responses in aphids

Inter-comparison of Radio-Loudness Criteria for Type 1 AGNs in the XMM-COSMOS Survey

Limited studies have been performed on the radio-loud fraction in X-ray selected type 1 AGN samples. The consistency between various radio-loudness definitions also needs to be checked. We measure the radio-loudness of the 407 type 1 AGNs in the XMM-COSMOS quasar sample using nine criteria from the literature (six defined in the rest-frame and three defined in the observed frame): $R_L=\log(L_{5GHz}/L_B)$, $q_{24}=\log(L_{24\mu m}/L_{1.4GHz})$, $R_{uv}=\log(L_{5GHz}/L_{2500\AA})$, $R_{i}=\log(L_{1.4GHz}/L_i)$, $R_X=\log(\nu L_{\nu}(5GHz)/L_X)$, $P_{5GHz}=\log(P_{5GHz}(W/Hz/Sr))$, $R_{L,obs}=\log(f_{1.4GHz}/f_B)$ (observed frame), $R_{i,obs}=\log(f_{1.4GHz}/f_i)$ (observed frame), and $q_{24, obs}=\log(f_{24\mu m}/f_{1.4GHz})$ (observed frame). Using any single criterion defined in the rest-frame, we find a low radio-loud fraction of $\lesssim 5\%$ in the XMM-COSMOS type 1 AGN sample, except for $R_{uv}$. Requiring that any two criteria agree reduces the radio-loud fraction to $\lesssim 2\%$ for about 3/4 of the cases. The low radio-loud fraction cannot be simply explained by the contribution of the host galaxy luminosity and reddening. The $P_{5GHz}=\log(P_{5GHz}(W/Hz/Sr))$ gives the smallest radio-loud fraction. Two of the three radio-loud fractions from the criteria defined in the observed frame without k-correction ($R_{L,obs}$ and $R_{i,obs}$) are much larger than the radio-loud fractions from other criteria.Comment: 12 pages, 7 figures, MNRAS submitte

Single-Color Centers Implanted in Diamond Nanostructures

The development of material-processing techniques that can be used to generate optical diamond nanostructures containing a single-color center is an important problem in quantum science and technology. In this work, we present the combination of ion implantation and top-down diamond nanofabrication in two scenarios: diamond nanopillars and diamond nanowires. The first device consists of a 'shallow' implant (similar to 20 nm) to generate nitrogen-vacancy (NV) color centers near the top surface of the diamond crystal prior to device fabrication. Individual NV centers are then mechanically isolated by etching a regular array of nanopillars in the diamond surface. Photon anti-bunching measurements indicate that a high yield (> 10%) of the devices contain a single NV center. The second device demonstrates 'deep' (similar to $1 \mu m$) implantation of individual NV centers into diamond nanowires as a post-processing step. The high single-photon flux of the nanowire geometry, combined with the low background fluorescence of the ultrapure diamond, allowed us to observe sustained photon anti-bunching even at high pump powers.Engineering and Applied SciencesPhysic

Twelve years of SAMtools and BCFtools.

BACKGROUND: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. FINDINGS: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. CONCLUSION: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org

Crosstalk between Integrin αvβ3 and Estrogen Receptor-α Is Involved in Thyroid Hormone-Induced Proliferation in Human Lung Carcinoma Cells

A cell surface receptor for thyroid hormone that activates extracellular regulated kinase (ERK) 1/2 has been identified on integrin αvβ3. We have examined the actions of thyroid hormone initiated at the integrin on human NCI-H522 non-small cell lung carcinoma and NCI-H510A small cell lung cancer cells. At a physiologic total hormone concentration (10−7 M), T4 significantly increased proliferating cell nuclear antigen (PCNA) abundance in these cell lines, as did 3, 5, 3′-triiodo-L-thyronine (T3) at a supraphysiologic concentration. Neutralizing antibody to integrin αvβ3 and an integrin-binding Arg-Gly-Asp (RGD) peptide blocked thyroid hormone-induced PCNA expression. Tetraiodothyroacetic acid (tetrac) lacks thyroid hormone function but inhibits binding of T4 and T3 to the integrin receptor; tetrac eliminated thyroid hormone-induced lung cancer cell proliferation and ERK1/2 activation. In these estrogen receptor-α (ERα)-positive lung cancer cells, thyroid hormone (T4>T3) caused phosphorylation of ERα; the specific ERα antagonist ICI 182,780 blocked T4-induced, but not T3-induced ERK1/2 activation, as well as ERα phosphorylation, proliferating-cell nuclear antigen (PCNA) expression and hormone-dependent thymidine uptake by tumor cells. Thus, in ERα-positive human lung cancer cells, the proliferative action of thyroid hormone initiated at the plasma membrane is at least in part mediated by ERα. In summary, thyroid hormone may be one of several endogenous factors capable of supporting proliferation of lung cancer cells. Activity as an inhibitor of lung cancer cell proliferation induced at the integrin receptor makes tetrac a novel anti-proliferative agent

Evaluating 'Prefer not to say' Around Sensitive Disclosures

As people's offline and online lives become increasingly entwined, the sensitivity of personal information disclosed online is increasing. Disclosures often occur through structured disclosure fields (e.g., drop-down lists). Prior research suggests these fields may limit privacy, with non-disclosing users being presumed to be hiding undesirable information. We investigated this around HIV status disclosure in online dating apps used by men who have sex with men. Our online study asked participants (N=183) to rate profiles where HIV status was either disclosed or undisclosed. We tested three designs for displaying undisclosed fields. Visibility of undisclosed fields had a significant effect on the way profiles were rated, and other profile information (e.g., ethnicity) could affect inferences that develop around undisclosed information. Our research highlights complexities around designing for non-disclosure and questions the voluntary nature of these fields. Further work is outlined to ensure disclosure control is appropriately implemented around online sensitive information disclosures