Physical Sciences and Mathematics Commons^™

Dat3m: A Data Tracker For Multi-Faceted Management Of Multi-Site Clinical Research Data Submission, Curation, Master Inventorying, And Sharing, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Managing research data is an important and challenging aspect of clinical studies, especially for multi-site collaboratives. To address this challenge, we designed, developed and deployed a multi-faceted, multi-level interactive data tracker (DaT3M) for multi-site clinical research data submission, curation, master inventorying, and sharing. Components of DaT3M include data overview, data portal, data status panel, data query engine, and data downloader. DaT3M managed clinical research data for the Center for SUDEP Research (CSR). The CSR instance of DaT3M includes 2,743 subjects from seven data contributing institutions, 7 data modalities and 10,678 data components: 3,398 Epilepsy Monitoring Unit reports, 3,440 electroencephalography recordings, …

Temporal Cohort Logic

Faculty, Staff and Student Publications

We introduce a new logic, called Temporal Cohort Logic (TCL), for cohort specification and discovery in clinical and population health research. TCL is created to fill a conceptual gap in formalizing temporal reasoning in biomedicine, in a similar role that temporal logics play for computer science and its applications. We provide formal syntax and semantics for TCL and illustrate the various logical constructs using examples related to human health. Relationships and distinctions with existing temporal logical frameworks are discussed. Applications in electronic health record (EHR) and in neurophysiological data resource are provided. Our approach differs from existing temporal logics, in …

Causal Inference Of Genetic Variants And Genes In Amyotrophic Lateral Sclerosis, Yulin Dai, Yin-Ying Wang, Peilin Jia, Fan Liu

Faculty, Staff and Student Publications

Amyotrophic lateral sclerosis (ALS) is a fatal progressive multisystem disorder with limited therapeutic options. Although genome-wide association studies (GWASs) have revealed multiple ALS susceptibility loci, the exact identities of causal variants, genes, cell types, tissues, and their functional roles in the development of ALS remain largely unknown. Here, we reported a comprehensive post-GWAS analysis of the recent large ALS GWAS (n = 80,610), including functional mapping and annotation (FUMA), transcriptome-wide association study (TWAS), colocalization (COLOC), and summary data-based Mendelian randomization analyses (SMR) in extensive multi-omics datasets. Gene property analysis highlighted inhibitory neuron 6, oligodendrocytes, and GABAergic neurons (Gad1/Gad2) as …

Recovery Time, Biomass Characteristics And Recovery Mechanisms Of Seagrass Following Simulated Grazing, Caitlyn O'Dea, Paul Lavery, Chanelle Webster, Kathryn Mcmahon

Research Datasets

The database compiles data published on seagrass recovery time, biomass characteristics, and recovery mechanisms following simulated grazing disturbance experiment in the Swan Canning Estuary, Western Australia. Observations of swans in the vicinity is also included.

Seagrass Species Data Occurrence Recorded In Indonesia's Water, Susi Rahmawati, Udhi Hernawan, Kathryn M. Mcmahon

Research Datasets

This is the dataset of seagrass species occurrence compiled for the research project, titled “Prioritizing areas in Indonesia to conserve and enhance seagrass ecosystem functions under a changing climate”, funded by the 2021/2022 ANU Indonesia Project Research Grants.

Porewater Salinity Influences Germination Of Ruppia Polycarpa In Variable Estuarine Habitats, Chanelle Webster

Research Datasets

Porewater salinity at different depth intervals during different months. Seed, germling and seedling density data in two estuaries and during different months. Seed germination, seedling establishment and growth under experimental conditions.

Changing Snowmelt Conditions In The Western Canadian Arctic, Matthew Y. T. Tsui

Theses and Dissertations (Comprehensive)

Multidecadal Changes in Spring Snowmelt in the Western Canadian Arctic

This study investigates the changes in key aspects of snowmelt in the western Canadian Arctic. Specifically, we will look at changes in the onset of snowmelt and the duration of snowmelt between 1999 and 2019, and extended air temperature between 1957 and 2019. In addition, we will look at changes in eight meteorological variables during the melt period. It was found that the onset of snowmelt occurred 14 days earlier, while the melt period ends 20 days earlier than 20 years ago. As a result, the duration of melt period …

Lake Huron Shoreline Analysis, Shubham Satish Nandanwar

Theses and Dissertations (Comprehensive)

Lake Huron is a popular tourist destination and is home to several businesses and residents. Since the shoreline is dynamic and is subject to change over the years due to several factors such as a change in water level, soil type, human encroachment, etc., these locations tend to encounter floods due to increased water levels and wind speed. This causes erosion and loss to the properties along the shoreline.

This study is based on two areas of interest named Pinery Provincial Park and Sauble Beach which are located on the shoreline of Lake Huron where Pinery Provincial Park is a …

Utilization Of The Yamamoto Cyclotrimerization Reaction Towards The Synthesis Of Polycyclic Aromatic Compounds, Josh Ledrew

Theses and Dissertations (Comprehensive)

The overall theme of this research was to synthesize and study the structure-property relationships of novel polycyclic aromatic compounds capable of self-assembling to form liquid crystalline, and microporous structures, as well as molecules capable of molecular recognition. The unifying theme that connects this research is the utilization of the Yamamoto coupling reaction to access the desired polycyclic aromatic hydrocarbon targets. More specifically, the scope of the Yamamoto coupling reaction was explored for the synthesis of electron-deficient triphenylene derivatives that are otherwise difficult to prepare. The molecules prepared via the Yamamoto coupling reaction are expected to be further utilized as intermediates …

Alpine Shrub Tundra Water Storage And Runoff Dynamics In The Mackenzie Mountains, Sahtú Territory, Nt, Geoffrey Kershaw

Theses and Dissertations (Comprehensive)

Alpine regions receive large volumes of precipitation and are important to local and regional water balances, particularly during baseflow periods of winter cold and summer drought when the larger basin area is frozen and/or water limited. Alpine headwaters in western Canada are expected to warm and receive more precipitation during the coming decades, with implications for groundwater recharge and streamflow generation within these systems and the regional river networks to which they contribute. Throughout the North, thawing peat plateaus and other ice-rich permafrost features are resulting in an increased extent of thermokarst and wetland land cover. This transition places infrastructure …

Coastal Landform Change Influences On Endangered Five-Lined Skink Distribution At Northwest Beach, Point Pelee National Park, Canada, Evan Fortushniok

Theses and Dissertations (Comprehensive)

As park visitation increased to Point Pelee National Park up until its peak in 1963, the installation of infrastructure for the purpose of supporting the recreational interest grew with it. At Northwest Beach, large parking lots were built into the coastal landscape and by the 1970s large areas of sand dunes continued to be heavily impacted by the installation of visitor associated infrastructure. The infrastructure resulted in the stabilization of sand on the beach side of the parking lot, resulting in an artificially stabilized and heavily vegetated dune. Over the last few decades, the park slowly reduced the size and …

Influence Of Dissolved Organic Matter On Phosphate Interactions With Hydrous Ferric Oxides, Alaa Hasan Alsherbi

Theses and Dissertations (Comprehensive)

Phosphorus, iron oxides, and dissolved organic matter (DOM) are components present in all aquatic systems. Excess amounts of phosphorus in aquatic systems have the potential for toxic effects, in particular, contributing to eutrophication. Most of the previous studies performed looked at the surface complexation of inorganic phosphate anions (P) to mineral surfaces such as hydrous ferric oxide (HFO). However, the role of DOM on the interactions between HFO and P is unknown. This study investigates the influence of DOM on the surface complexation of P onto HFO surfaces. Moreover, this study looks at the possibility of cation bridging formation (Ca …

Changes In Lake Drainage In The Western Canadian Arctic, Dilshan Kariyawasam, Philip Marsh Dr

Theses and Dissertations (Comprehensive)

Nearly half of all Pan-Arctic lakes are situated in the Canadian Arctic, with many of these lakes being of thermokarst origin. Thermokarst lakes are sensitive to changes in the surrounding environment, making them useful indicators to examine the condition of hydrological systems in response to rapid climate warming, a trend which has been well observed in the Canadian Western Arctic. In this study, we use aerial photography to quantify lake area and count changes for lakes in the Inuvik-Tuktoyaktuk region, between 1950 and 2004. A combination of aerial photography and Landsat imagery were used in identifying drained thermokarst lake basins …

Exploring Visitor Perceptions And Behaviours Related To Ticks And Lyme Disease Risk In An Ontario Protected Area, Ryan Brady

Theses and Dissertations (Comprehensive)

Lyme disease is the most common vector-borne zoonosis in North America and over the past decade, reported cases of the disease have been rapidly increasing in many regions throughout Canada. The relative novelty of this public health threat presents nature-based tourism and recreation organizations with a range of policy and management challenges. Currently, there is a limited understanding of public perceptions and behaviours associated with tick and Lyme disease risk, especially within a Canadian parks and protected areas visitation and visitor experience context. To address this practical and scholarly knowledge gap, this study utilized in-situ surveys to explore visitor perceptions, …

Enhancing Zero-Shot And Few-Shot Text Classification Using Pre-Trained Language Models, Yanan Chen

Theses and Dissertations (Comprehensive)

In recent years, the community of natural language processing (NLP) has seen amazing progress in the development of pre-trained language models (PLMs). The novel paradigm of PLMs does not require labeled data, allowing us to experiment with increased training scale through employing freely available colossal online self-training corpus to push the limits. Language models (LMs), such as GPT, BERT and T5, have achieved high performance on a wide range of NLP tasks. Meanwhile, research on zero-shot and few-shot text classification has received increasing attention. As labelling can be costly and time-consuming, how to perform data augmentation (DA) and enhance the …

The Kepler Problem On Complex And Pseudo-Riemannian Manifolds, Michael R. Astwood

Theses and Dissertations (Comprehensive)

The motion of objects in the sky has captured the attention of scientists and mathematicians since classical times. The problem of determining their motion has been dubbed the Kepler problem, and has since been generalized into an abstract problem of dynamical systems. In particular, the question of whether a classical system produces closed and bounded orbits is of importance even to modern mathematical physics, since these systems can often be analysed by hand. The aforementioned question was originally studied by Bertrand in the context of celestial mechanics, and is therefore referred to as the Bertrand problem. We investigate the qualitative …

Air Quality: Assessment Of Pollutant Levels And Chemistry In Kitchener, On Using Multisensor Pods, Wisam Mohammed

Theses and Dissertations (Comprehensive)

Air quality is a growing concern amongst governmental bodies worldwide. A large number of scientific studies accumulated over the past 25 years suggest that poor ambient air quality is attributed to adverse health effects, especially in vulnerable communities that exhibit pre-existing conditions. The United Nations Children’s Fund (UNICEF) reported around 600 000 deaths globally in children under the age of 5 as a result of acute lower respiratory infections caused by poor air quality. With the current statistics on air quality impacts, it is clear that more needs to be done. This MSc work aims to put into perspective the …

Orchestration Or Automation: Authentication Flaw Detection In Android Apps, Siqi Ma, Juanru Li, Surya Nepal, Diethelm Ostry, David Lo, Sanjay K. Jha, Robert H. Deng, Elisa Bertino

Research Collection School Of Computing and Information Systems

Passwords are pervasively used to authenticate users' identities in mobile apps. To secure passwords against attacks, protection is applied to the password authentication protocol (PAP). The implementation of the protection scheme becomes an important factor in protecting PAP against attacks. We focus on two basic protection in Android, i.e., SSL/TLS-based PAP and timestamp-based PAP. Previously, we proposed an automated tool, GLACIATE, to detect authentication flaws. We were curious whether orchestration (i.e., involving manual-effort) works better than automation. To answer this question, we propose an orchestrated approach, AUTHEXPLOIT and compare its effectiveness GLACIATE. We study requirements for correct implementation of PAP …

Why Do Smart Contracts Self-Destruct? Investigating The Selfdestruct Function On Ethereum, Jiachi Chen, Xin Xia, David Lo, John C. Grundy

Research Collection School Of Computing and Information Systems

The selfdestruct function is provided by Ethereum smart contracts to destroy a contract on the blockchain system. However, it is a double-edged sword for developers. On the one hand, using the selfdestruct function enables developers to remove smart contracts (SCs) from Ethereum and transfers Ethers when emergency situations happen, e.g., being attacked. On the other hand, this function can increase the complexity for the development and open an attack vector for attackers. To better understand the reasons why SC developers include or exclude the selfdestruct function in their contracts, we conducted an online survey to collect feedback from them and …

Automating App Review Response Generation Based On Contextual Knowledge, Cuiyun Gao, Wenjie Zhou, Xin Xia, David Lo, Qi Xie, Michael R. Lyu

Research Collection School Of Computing and Information Systems

User experience of mobile apps is an essential ingredient that can influence the user base and app revenue. To ensure good user experience and assist app development, several prior studies resort to analysis of app reviews, a type of repository that directly reflects user opinions about the apps. Accurately responding to the app reviews is one of the ways to relieve user concerns and thus improve user experience. However, the response quality of the existing method relies on the pre-extracted features from other tools, including manually labelled keywords and predicted review sentiment, which may hinder the generalizability and flexibility of …

Just-In-Time Defect Prediction On Javascript Projects: A Replication Study, Chao Ni, Xin Xia, David Lo, Xiaohu Yang, Ahmed E. Hassan

Research Collection School Of Computing and Information Systems

Change-level defect prediction is widely referred to as just-in-time (JIT) defect prediction since it identifies a defect-inducing change at the check-in time, and researchers have proposed many approaches based on the language-independent change-level features. These approaches can be divided into two types: supervised approaches and unsupervised approaches, and their effectiveness has been verified on Java or C++ projects. However, whether the language-independent change-level features can effectively identify the defects of JavaScript projects is still unknown. Additionally, many researches have confirmed that supervised approaches outperform unsupervised approaches on Java or C++ projects when considering inspection effort. However, whether supervised JIT defect …

A Survey On Deep Learning For Software Engineering, Yanming Yang, Xin Xia, David Lo

Research Collection School Of Computing and Information Systems

In 2006, Geoffrey Hinton proposed the concept of training "Deep Neural Networks (DNNs)" and an improved model training method to break the bottleneck of neural network development. More recently, the introduction of AlphaGo in 2016 demonstrated the powerful learning ability of deep learning and its enormous potential. Deep learning has been increasingly used to develop state-of-the-art software engineering (SE) research tools due to its ability to boost performance for various SE tasks. There are many factors, e.g., deep learning model selection, internal structure differences, and model optimization techniques, that may have an impact on the performance of DNNs applied in …

Toward Video-Conferencing Tools For Hands-On Activities In Online Teaching, Audrey Labrie, Terrance Mok, Anthony Tang, Michelle Lui, Lora Oehlberg, Lev Poretski

Research Collection School Of Computing and Information Systems

Many instructors in computing and HCI disciplines use hands-on activities for teaching and training new skills. Beyond simply teaching hands-on skills like sketching and programming, instructors also use these activities so students can acquire tacit skills. Yet, current video-conferencing technologies may not effectively support hands-on activities in online teaching contexts. To develop an understanding of the inadequacies of current video-conferencing technologies for hands-on activities, we conducted 15 interviews with university-level instructors who had quickly pivoted their use of hands-on activities to an online context during the early part of the COVID-19 pandemic. Based on our analysis, we uncovered four pedagogical …

An Exploratory Study On The Repeatedly Shared External Links On Stack Overflow, Jiakun Liu, Haoxiang Zhang, Xin Xia, David Lo, Ying Zou, Ahmed E. Hassan, Shanping Li

Research Collection School Of Computing and Information Systems

On Stack Overflow, users reuse 11,926,354 external links to share the resources hosted outside the Stack Overflow website. The external links connect to the existing programming-related knowledge and extend the crowdsourced knowledge on Stack Overflow. Some of the external links, so-called as repeated external links, can be shared for multiple times. We observe that 82.5% of the link sharing activities (i.e., sharing links in any question, answer, or comment) on Stack Overflow share external resources, and 57.0% of the occurrences of the external links are sharing the repeated external links. However, it is still unclear what types of external resources …

Authenticated Data Redaction With Accountability And Transparency, Jinhua Ma, Xinyi Huang, Yi Mu, Robert H. Deng

Research Collection School Of Computing and Information Systems

A common practice in data redaction is removing sensitive information prior to data publication or release. In data-driven applications, one must be convinced that the redacted data is still trustworthy. Meanwhile, the data redactor must be held accountable for (malicious) redaction, which could change/hide the meaning of the original data. Motivated by these concerns, we present a novel solution for authenticated data redaction based on a new Redactable Signature Scheme with Implicit Accountability (RSS - IA). In the event of a dispute, not only the original data signer but also the redactor can generate an evidence tag to unequivocally identify …

Defining Smart Contract Defects On Ethereum, Jiachi Chen, Xin Xia, David Lo, John Grundy, Xiapu Luo, Ting Chen

Research Collection School Of Computing and Information Systems

Smart contracts are programs running on a blockchain. They are immutable to change, and hence can not be patched for bugs once deployed. Thus it is critical to ensure they are bug-free and well-designed before deployment. A Contract defect is an error, flaw or fault in a smart contract that causes it to produce an incorrect or unexpected result, or to behave in unintended ways. The detection of contract defects is a method to avoid potential bugs and improve the design of existing code. Since smart contracts contain numerous distinctive features, such as the gas system. decentralized, it is important …

Perceptions And Needs Of Artificial Intelligence In Health Care To Increase Adoption: Scoping Review, Han Shi Jocelyn Chew, Palakorn Achananuparp

Research Collection School Of Computing and Information Systems

Background: Artificial intelligence (AI) has the potential to improve the efficiency and effectiveness of health care service delivery. However, the perceptions and needs of such systems remain elusive, hindering efforts to promote AI adoption in health care. Objective: This study aims to provide an overview of the perceptions and needs of AI to increase its adoption in health care. Methods: A systematic scoping review was conducted according to the 5-stage framework by Arksey and O’Malley. Articles that described the perceptions and needs of AI in health care were searched across nine databases: ACM Library, CINAHL, Cochrane Central, Embase, IEEE Xplore, …

A Quantum Interpretation Of Separating Conjunction For Local Reasoning Of Quantum Programs Based On Separation Logic, Xuan Bach Le, Shang-Wei Lin, Jun Sun, David Sanan

Research Collection School Of Computing and Information Systems

It is well-known that quantum programs are not only complicated to design but also challenging to verify because the quantum states can have exponential size and require sophisticated mathematics to encode and manipulate. To tackle the state-space explosion problem for quantum reasoning, we propose a Hoare-style inference framework that supports local reasoning for quantum programs. By providing a quantum interpretation of the separating conjunction, we are able to infuse separation logic into our framework and apply local reasoning using a quantum frame rule that is similar to the classical frame rule. For evaluation, we apply our framework to verify various …

On Discovering Motifs And Frequent Patterns In Spatial Trajectories With Discrete Fréchet Distance, Bo Tang, Man Lung Yiu, Kyriakos Mouratidis, Jiahao Zhang, Kai Wang

Research Collection School Of Computing and Information Systems

The discrete Fréchet distance (DFD) captures perceptual and geographical similarity between two trajectories. It has been successfully adopted in a multitude of applications, such as signature and handwriting recognition, computer graphics, as well as geographic applications. Spatial applications, e.g., sports analysis, traffic analysis, etc. require discovering similar subtrajectories within a single trajectory or across multiple trajectories. In this paper, we adopt DFD as the similarity measure, and study two representative trajectory analysis problems, namely, motif discovery and frequent pattern discovery. Due to the time complexity of DFD, these tasks are computationally challenging. We address that challenge with a suite of …

Comparison Of The Mental Burden On Nursing Care Providers With And Without Mat-Type Sleep State Sensors At A Nursing Home In Tokyo, Japan: Quasi-Experimental Study, Sakiko Itoh, Hwee-Pink Tan, Kenichi Kudo, Yasuko Ogata

Research Collection School Of Computing and Information Systems

Background: Increasing need for nursing care has led to the increased burden on formal caregivers, with those in nursing homes having to deal with exhausting labor. Although research activities on the use of internet of things devices to support nursing care for older adults exist, there is limited evidence on the effectiveness of these interventions among formal caregivers in nursing homes. Objective: This study aims to investigate whether mat-type sleep state sensors for supporting nursing care can reduce the mental burden of formal caregivers in a nursing home. Methods: This was a quasi-experimental study at a nursing home in Tokyo, …