Access beyond geographic accessibility: understanding opportunities to human needs in a physical-virtual world

Access to basic human needs, such as food and healthcare, is conceptually understood to be comprised of multiple spatial and aspatial dimensions. However, research in this area has traditionally been explored with spatial accessibility measures that almost exclusively focus on just two dimensions. Namely, the availability of resources, services, and facilities, and the accessibility or ease to which locations of these opportunities can be reached with existing land-use and transport systems under temporal constraints and considering individual characteristics of people. These calculated measures are insufficient in holistically capturing available opportunities as they ignore other components, such as the emergence of virtual space to carry out activities and interactions enabled by modern information and communication technologies (ICT). Human dynamics today exist in a hybrid physical-virtual space, and recent research has highlighted the importance of understanding ICT, individual behavior, local context, social relations, and human perceptions in identifying opportunities available to people. However, there lacks a holistic approach that relates these different aspects to access research. This dissertation addresses this gap by proposing a new conceptual framework for the geography of access for various kinds of human needs, using food access as a case study to illustrate how the proposed framework can be applied to address critical societal issues. An interactive multispace geographic information system (GIS) web application is developed to better understand and visualize individual potential food access based on the conceptual framework. This dissertation contributes to the body of research with a proposed conceptual framework of access in a hybrid physical-virtual world, integration of various big and small data sources to reveal information relating to the access of people, and novel development of a multi-space GIS to analyze and visualize access to opportunities

Citrate inhibition of cisplatin reaction with DNA studied using fluorescently labeled oligonucleotides: implication for selectivity towards guanine

The reaction between cisplatin and DNA is conveniently studied using fluorescently labeled oligonucleotides and gel electrophoresis; as an example of application, the inhibition of this reaction by citrate is demonstrated, which might increase selectivity of cisplatin towards guanine over adenine.University of Waterloo || Canadian Foundation for Innovation || Natural Sciences and Engineering Research Council || Ontario Ministry of Research, Innovation and Science |

A Cleavable Molecular Beacon for Hg2+ Detection based on Phosphorothioate RNA Modifications

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/ 10.1021/acs.analchem.5b01362Mercury is a highly toxic heavy metal, and detection of Hg2+ by biosensors has attracted extensive research interest in the past decade. In particular, a number of DNA-based sensing strategies have been developed. Well-known examples include thymine-Hg2+ interactions and Hg2+-activated DNAzymes. However, these mechanisms are highly dependent on buffer conditions or require hybridization with another DNA strand. Herein, we report a new mechanism based on Hg2+-induced cleavage of phosphorothioate (PS) modified RNA. Among the various metal ions tested, Hg2+ induced the most significant cleavage (∼16%), while other metals cleaved less than 2% of the same substrate. The uncleaved substrate undergoes desulfurization in the presence of Hg2+. This cleavage reaction yields a similar amount of product from pH 3.5 to 7 and in the temperature range between 20 and 90 °C. Various PS RNA junctions can be cleaved with a similar efficiency, but PS DNA junctions cannot be cleaved. A molecular beacon containing three PS RNA modifications is designed, detecting Hg2+ down to 1.7 nM with excellent selectivity. This sensor can also detect Hg2+ in the Lake Ontario water sample, although its response is significantly masked by fish tissues.Ontario Ministry of Research & Innovation || Natural Sciences and Engineering Research Council |

Thermal Dissipation and Variability in Electrical Breakdown of Carbon Nanotube Devices

We study high-field electrical breakdown and heat dissipation from carbon nanotube (CNT) devices on SiO2 substrates. The thermal "footprint" of a CNT caused by van der Waals interactions with the substrate is revealed through molecular dynamics (MD) simulations. Experiments and modeling find the CNT-substrate thermal coupling scales proportionally to CNT diameter and inversely with SiO2 surface roughness (~d/{\Delta}). Comparison of diffuse mismatch modeling (DMM) and data reveals the upper limit of thermal coupling ~0.4 W/K/m per unit length at room temperature, and ~0.7 W/K/m at 600 C for the largest diameter (3-4 nm) CNTs. We also find semiconducting CNTs can break down prematurely, and display more breakdown variability due to dynamic shifts in threshold voltage, which metallic CNTs are immune to; this poses a fundamental challenge for selective electrical breakdowns in CNT electronics

A Two Hour Quasi-Period in an Ultra-luminous X-Ray source in NGC628

Quasi-periodic oscillations and X-ray spectroscopy are powerful probes of black hole masses and accretion disks, and here we apply these diagnostics to an ultraluminous X-ray source (ULX) in the spiral galaxy NGC628 (M74). This object was observed four times over two years with the Chandra X-ray Observatory and XMM-Newton, with three long observations showing dramatic variability, distinguished by a series of outbursts with a quasi-period (QPO) of 4,000-7,000 seconds. This is unique behavior among both ULXs and Galactic X-ray binaries due to the combination of its burst-like peaks and deep troughs, its long quasi-periods, its high variation amplitudes of $>90$%, and its substantial variability between observations. The X-ray spectra is fitted by an absorbed accretion disk plus a power-law component, suggesting the ULX was in a spectral state analogous to the Low Hard state or the Very High state of Galactic black hole X-ray binaries. A black hole mass of $\sim2$--$20\times10^3 M_\odot$ is estimated from the $f_b$--$M_\bullet$ scaling relation found in the Galactic X-ray binaries and active galactic nuclei.Comment: 12 pages, 3 figures. accepted for publication in ApJ Lette

Rationally Designed Nucleobase and Nucleotide Coordinated Nanoparticles for Selective DNA Adsorption and Detection

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Wang, F., Liu, B., Huang, P.-J. J., & Liu, J. (2013). Rationally Designed Nucleobase and Nucleotide Coordinated Nanoparticles for Selective DNA Adsorption and Detection. Analytical Chemistry, 85(24), 12144–12151. https://doi.org/10.1021/ac4033627Nanomaterials for DNA adsorption are useful for sequence-specific DNA detection. Current materials for DNA adsorption employ electrostatic attraction, hydrophobic interaction, or π–π stacking, none of which can achieve sequence specificity. Specificity might be improved by involving hydrogen bonding and metal coordination. In this work, a diverse range of nucleobase/nucleotide (adenine, adenosine, adenosine 5′-triphosphate (ATP), adenosine 5′-monophosphate (AMP), and guanosine 5′-triphosphate (GTP)) coordinated materials containing various metal ions (Au(III), Ag(I), Ce(III), Gd(III), and Tb(III)) are prepared. In most cases, nanoparticles are formed. These materials have different surface charges, and positively charged particles only show nonspecific DNA adsorption. Negatively charged materials give different adsorption kinetics for different DNA sequences, where complementary DNA homopolymers are adsorbed faster than other sequences. Therefore, the bases in the coordinated materials can still form base pairs with the DNA. The adsorption strength is mainly controlled by the metal ions, where Au shows the strongest adsorption while lanthanides are weaker. These materials can be used as sensors for DNA detection and can also deliver DNA into cells with no detectable toxicity. By tuning the nanoparticle formulation, enhanced detection can be achieved. This study is an important step toward rational design of materials to achieve specific interactions between biomolecules and synthetic nanoparticle surfaces.University of Waterloo || Canadian Foundation for Innovation || Ontario Ministry of Research & Innovation || Natural Sciences and Engineering Research Council |

Efficient Deep Image Denoising via Class Specific Convolution

Deep neural networks have been widely used in image denoising during the past few years. Even though they achieve great success on this problem, they are computationally inefficient which makes them inappropriate to be implemented in mobile devices. In this paper, we propose an efficient deep neural network for image denoising based on pixel-wise classification. Despite using a computationally efficient network cannot effectively remove the noises from any content, it is still capable to denoise from a specific type of pattern or texture. The proposed method follows such a divide and conquer scheme. We first use an efficient U-net to pixel-wisely classify pixels in the noisy image based on the local gradient statistics. Then we replace part of the convolution layers in existing denoising networks by the proposed Class Specific Convolution layers (CSConv) which use different weights for different classes of pixels. Quantitative and qualitative evaluations on public datasets demonstrate that the proposed method can reduce the computational costs without sacrificing the performance compared to state-of-the-art algorithms.Comment: The Thirty-Fifth AAAI Conference on Artificial Intelligence(AAAI-21

Ultra-luminous X-ray Sources in nearby galaxies from ROSAT HRI observations II. statistical properties

The statistical properties of the ultra-luminous X-ray source (ULX) populations extracted from the ROSAT HRI survey of X-ray point sources in nearby galaxies in Paper I are studied to reveal connections between the ULX phenomenon and survey galaxy properties. The $logN$--$logS$ relation is used to calculate and remove the influence of false ULXs from the background and/or foreground objects. Study of the luminosity functions shows that the regular ULXs below $10^{40}$ erg/sec are an extension of the ordinary HMXB/LMXB population below $10^{39}$ erg/sec in the late-type galaxies, and that the extreme ULXs above $10^{40}$ erg/sec might be a different population from the regular ULXs. This survey confirms statistically that the ULX phenomenon is closely connected to star formation activities, since ULXs preferentially occur in late-type galaxies rather than in early-typTwo ULX populations, the HMXB-like ULXs as an extension of the ordinary HMXB population associated with the young stellar population and the LMXB-like ULXs as an extension of the ordinary LMXB population associated with the old stellar population, are both required to account for the total ULX population. It is found that the LMXB-like ULXs dominate the ULX population at low star formation rates, while HMXB-like ULXs dominate at high star formation rates. However, an accurate quantitative description of the relative fractions of HMXB-like ULXs and LMXB-like ULXs is impossible in the current HRI survey due to the source blending effects, and a Chandra survey of the X-ray point sources in nearby galaxies would be required for this purpose. e galaxies, and ULXs in late-type galaxies tend to trace the spiral arms.Comment: 45 pages, 14 figures, 5 tables. submitted to Ap