Digital Commons Network^™

A Privacy-Preserving National Clinical Data Warehouse: Architecture And Analysis, Md Raihan Mia, Abu Sayed Md Latiful Hoque, Shahidul Islam Khan, Sheikh Iqbal Ahamed

Computer Science Faculty Research and Publications

A centralized clinical data repository is essential for inspecting patients’ medical history, disease analysis, population-wide disease research, treatment decision support, and improving existing healthcare policies and services. Bangladesh, a rapidly developing country, poses several unusual challenges for developing such a centralized clinical data repository as the existing Electronic Health Records (EHR) are stored in unconnected, heterogeneous sources with no unique patient identifier and consistency. Data integration with secure record linkage, privacy preservation, quality control, and data standardization are the main challenges for developing a consistent and interoperable centralized clinical data repository. Based on the findings from our previous researches, we …

Exploring And Evaluating The Impact Of Covid-19 On Mobility Changes In Singapore, Aldy Gunawan, Linh Chi Tran, Kar Way Tan, I-Lin Wang

Research Collection School Of Computing and Information Systems

This paper analyzes the changes in mobility trends due to the impact of the COVID-19 pandemic in Singapore in the six different sectors: Retail and Recreation, Grocery and Pharmacy, Parks, Transit Stations, Workplaces and Residential. The period of observation is from 15 February 2020 to 18 August 2021. The observed patterns obtained from the descriptive data analysis sheds light on the effectiveness of social distancing measures in Singapore as well as the level of compliance among the country’s residents. Correlation analysis is used to explore the relationship between different sectors during the pandemic period. The results reveal a strong sense …

Towards Efficient Annotations For A Human-Ai Collaborative, Clinical Decision Support System: A Case Study On Physical Stroke Rehabilitation Assessment, Min Hun Lee, Daniel P. Siewiorek, Asim Smailagic, Alexandre Bernardino, Sergi Bermúdez I Badia

Research Collection School Of Computing and Information Systems

Artificial intelligence (AI) and machine learning (ML) algorithms are increasingly being explored to support various decision-making tasks in health (e.g. rehabilitation assessment). However, the development of such AI/ML-based decision support systems is challenging due to the expensive process to collect an annotated dataset. In this paper, we describe the development process of a human-AI collaborative, clinical decision support system that augments an ML model with a rule-based (RB) model from domain experts. We conducted its empirical evaluation in the context of assessing physical stroke rehabilitation with the dataset of three exercises from 15 post-stroke survivors and therapists. Our results bring …

Wifitrace: Network-Based Contact Tracing For Infectious Diseases Using Passive Wifi Sensing, Amee Trivedi, Camellia Zakaria, Rajesh Krishna Balan, Ann Becker, George Corey, Prashant Shenoy

Research Collection School Of Computing and Information Systems

Contact tracing is a well-established and effective approach for the containment of the spread of infectious diseases. While Bluetooth-based contact tracing method using phones has become popular recently, these approaches suffer from the need for a critical mass adoption to be effective. In this paper, we present WiFiTrace, a network-centric approach for contact tracing that relies on passive WiFi sensing with no client-side involvement. Our approach exploits WiFi network logs gathered by enterprise networks for performance and security monitoring, and utilizes them for reconstructing device trajectories for contact tracing. Our approach is specifically designed to enhance the efficacy of traditional …

The Role Of 3d Ct Imaging In The Accurate Diagnosis Of Lung Function In Coronavirus Patients, Ibrahim Shawky Farahat, Ahmed Sharafeldeen, Mohamed Elsharkawy, Ahmed Soliman, Ali Mahmoud, Mohammed Ghazal, Fatma Taher, Maha Bilal, Ahmed Abdel Khalek Abdel Razek, Waleed Aladrousy, Samir Elmougy, Ahmed Elsaid Tolba, Moumen El-Melegy, Ayman El-Baz

All Works

Early grading of coronavirus disease 2019 (COVID-19), as well as ventilator support machines, are prime ways to help the world fight this virus and reduce the mortality rate. To reduce the burden on physicians, we developed an automatic Computer-Aided Diagnostic (CAD) system to grade COVID-19 from Computed Tomography (CT) images. This system segments the lung region from chest CT scans using an unsupervised approach based on an appearance model, followed by 3D rotation invariant Markov–Gibbs Random Field (MGRF)-based morphological constraints. This system analyzes the segmented lung and generates precise, analytical imaging markers by estimating the MGRF-based analytical potentials. Three Gibbs …

Perceptions Of Drinking Water Access And Quality In Rural Indigenous Villages In Fiji, Sarah Nelson, Jacqueline Thomas, Aaron Jenkins, Kelera Naivalu, Timoci Naivalulevu, Vilisi Naivalulevu, Kinikoto Mailautoka, Shylett Anthony, Mereia Ravoka, Stacy D. Jupiter, Sangeeta Mangubhai, Pierre Horwitz, Seye Abimbola, Joel Negin

Research outputs 2022 to 2026

Poor rural water quality is a health challenge in Fiji. A mixed-methods study in six iTaukei (Indigenous Fijian) villages was conducted to understand local perceptions of drinking water access and quality, how this changes drinking water source choices, and impacts of age and gender. Seventy-two household surveys, 30 key informant interviews (KIIs) and 12 focus group discus-sions (FGDs) were conducted. Household surveys revealed 41.7% of community members perceived their water as dirty and 76.4% perceived their water as clean. Two-thirds of households reported that they always or usually had enough water. FGDs and KIIs revealed water access and quality was …

Effectiveness Of Using Information, Education, And Communication Flowchart Media In Implementation Of Early Breastfeeding Initiation, Rizna Notarianti, Sandra Fikawati, Alifani Faiz Faradhila

Kesmas

Early initiation of breastfeeding (EIB) has many benefits for both the baby and the mother. However, in Bogor City, there are still many babies who do not get EIB when they are born (33.6%). The implementation of EIB is not optimal due to the absence of standard procedures to equalize its theory and perception. This study aimed to investigate the effectiveness of using Information, Education, and Communication (IEC) flowchart media concerning the standard procedure for EIB implementation in the Primary Health Care (PHC) in Bogor City. A quasi-experimental research was conducted on 58 midwives divided into the intervention and control …

Public Perception And Obedience With Social Distancing Policies During The Covid-19 Pandemic In Jakarta, Indonesia, Widyamurti Widyamurti, Edwina Bernita Sitorus, Dewi Susanna, Bambang Wispriyono, Aria Kusuma, Renti Mahkota

Kesmas

The Indonesian Government established a social distancing policy to prevent COVID-19 transmission. However, this implementation will be ineffective without the compliance of the people. This study aimed to analyze the relationship between public perception and obedience with social distancing in terms of the variables based on the Health Belief Model. This study used a cross-sectional design with a population of Daerah Khusus Ibukota (DKI) Jakarta’s indigenes within the productive age of 15-64 years. The sample comprised 408 participants, with the independent variables of sociodemographics (age, gender, occupation, and education) and health beliefs (perceived susceptibility, severity, benefits, barriers, and self-efficacy). Meanwhile, …

Endangered Sustainable Innovation: Indigenous Milk Hygiene And Preservation Techniques By Maasai Too Valuable To Lose, J. Y. Laffa, C. R. Mcculloch, D. Schoder

IGC Proceedings (1977-2023)

The indigenous Parakuyo Maasai communities of Tanzania are traditional pastoralists who depend on fresh cow’s milk as a staple food. However, the arid climate and a lack of clean water challenge milk production and conventional milk hygiene practices.

By conducting informational interviews in eight Parakuyo Maasai regions and 13 districts of Tanzania we sought to identify the key indigenous plants preferred and establish their traditional manner of use. A semi-structured questionnaire was designed to: (i) determine the plants used, (ii) the parts used, (iii) methods of preparation and utensil smoking, (iv) therapeutic applications and associated health benefits of these plants, …

Covid-19 Pandemic Analysis By The Volterra Integral Equation Models: A Preliminary Study Of Brazil, Italy, And South Africa, Yajni Warnapala, Emma Dehetre, Kate Gilbert

Arts & Sciences Faculty Publications

The COVID-19 pandemic has affected many people throughout the world. The objective of this research project was to find numerical solutions through the Gaussian Quadrature Method for the Volterra Integral Equation Model. The non-homogenous Volterra Integral Equation of the second kind is used to capture a broader range of disease distributions. Volterra Integral equation models are used in the context of applied mathematics, public health, and evolutionary biology. The mathematical models of this integral equation gave valid convergence results for the COVID-19 data for 3 countries Italy, South Africa and Brazil. The modeling of these countries was done using the …

Diversity Of Pseudomonas Aeruginosa Temperate Phages, Genevieve Johnson, Swarnali Banerjee, Catherine Putonti

Mathematics and Statistics: Faculty Publications and Other Works

Modern sequencing technologies have provided insight into the genetic diversity of numerous species, including the human pathogen Pseudomonas aeruginosa. Bacterial genomes often harbor bacteriophage genomes (prophages), which can account for upwards of 20% of the genome. Prior studies have found P. aeruginosa prophages that contribute to their host’s pathogenicity and fitness. These advantages come in many different forms, including the production of toxins, promotion of biofilm formation, and displacement of other P. aeruginosa strains. While several different genera and species of P. aeruginosa prophages have been studied, there has not been a comprehensive study of the overall diversity of P. …

New Limit Theorems For Increments Of Birth-And-Death Processes With Linear Rates, Alexander Ya. Kreinin, Vladimir V. Vinogradov

Journal of Stochastic Analysis

No abstract provided.

Women In Stem Fellowship: An Intersectional And Interdisciplinary Approach To Advancing Inclusion In The Sciences, Ina C. Seethaler, Gabriela Perez-Alvarado

Journal of the South Carolina Academy of Science

At our university, women-identified individuals make up 23% of students in STEM fields; less than 15% of them graduate with a STEM degree. Nationally, more than 40% of women who enter a STEM job leave it within fewer than ten years. Gendered issues within STEM industries have been identified, yet we are far from equal opportunities for all genders. In 2018, we—the director of Women’s and Gender Studies (WGS) with colleagues in Math, Computing Sciences, and Chemistry—received a $45,000 grant to create a “Women in STEM Fellowship.” The inclusion of WGS made the fellowship interdisciplinary, intersectional, and informed our decision-making …

Deep-Precognitive Diagnosis: Preventing Future Pandemics By Novel Disease Detection With Biologically-Inspired Conv-Fuzzy Network, Aviral Chharia, Rahul Upadhyay, Vinay Kumar, Chao Cheng, Jing Zhang, Tianyang Wang, Min Xu

Computer Vision Faculty Publications

Deep learning-based Computer-Aided Diagnosis has gained immense attention in recent years due to its capability to enhance diagnostic performance and elucidate complex clinical tasks. However, conventional supervised deep learning models are incapable of recognizing novel diseases that do not exist in the training dataset. Automated early-stage detection of novel infectious diseases can be vital in controlling their rapid spread. Moreover, the development of a conventional CAD model is only possible after disease outbreaks and datasets become available for training (viz. COVID-19 outbreak). Since novel diseases are unknown and cannot be included in training data, it is challenging to recognize them …

Patients With Obesity And A History Of Metformin Treatment Have Lower Influenza Mortality: A Retrospective Cohort Study, Tammy H. Cummings, Joseph Magagnoli Ph.D., Ms, James W. Hardin, S. Scott Sutton

Faculty Publications

Background: Obesity is a risk factor for the development of influenza by leading to a chronic inflammatory state and T-cell dysfunction. Based upon preclinical research, metformin has influenza activity by restoring T-cell function and improving the immune response. Objective: We aimed to evaluate the potential drug repurposing of metformin for the management of influenza among patients with obesity utilizing national claims data in an electronic health record database. Methods: The VA Informatics and Computing Infrastructure (VINCI) was utilized to obtain individual-level information on demographics, administrative claims, and pharmacy dispensation. A cohort was created among individuals with laboratory confirmed diagnosis of …

A Review Of The Impacts Of Invasive Wild Pigs On Native Vertebrates, Matthew T. Mcdonough, Stephen S. Ditchkoff, Mark D. Smith, Kurt C. Vercauteren

United States Department of Agriculture Wildlife Services: Staff Publications

The wild pig (Sus scrofa) is a successful invasive species that has become well established outside of its native range in Eurasia. The invasive wild pig is the result of released or escaped domesticated livestock becoming feral, or Eurasian boar introduced for hunting purposes. The global spread of wild pigs has recently been exacerbated in some areas, such as the USA, by anthropogenically assisted dispersal. Once established in novel ecosystems, wild pigs have the potential to have significant negative impacts on the ecosystem, and the scientific literature is replete with examples. It is generally accepted that wild pigs …

Chemical Reversible Crosslinking Enables Measurement Of Rna 3d Distances And Alternative Conformations In Cells, Ryan Van Damme, Kongpan Li, Minjie Zhang, Jianhui Bai, Wilson H. Lee, Joseph D. Yesselman, Zhipeng Lu, Willem A. Velema

Department of Chemistry: Faculty Publications

Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety of biological processes. However, direct determination of RNA 3D structures in vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present a method, Spatial 2′-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation, and high throughput sequencing, SHARC enables transcriptome-wide tertiary structure contact maps at high accuracy and precision, revealing heterogeneous RNA structures and interactions. SHARC data provide constraints that improves Rosetta-based RNA 3D …

Use Of A Direct, Rapid Immunohistochemical Test For Diagnosis Of Rabies Virus In Bats, Charles E. Rupprecht, Lolita Van Pelt, April D. Davis, Richard B. Chipman, David L. Bergman

United States Department of Agriculture Wildlife Services: Staff Publications

Rabies, a zoonotic encephalitis due to transmission of a lyssavirus, such as rabies virus (RABV), has the highest case fatality of any infectious disease. A global program for the elimination of human rabies caused by dogs is proposed for realization by 2030. Sensitive, specific, and inexpensive diagnostic tests are necessary for enhanced surveillance to detect infection, inform public health and veterinary professionals during risk assessments of exposure, and support overall programmatic goals. Multiple laboratory techniques are used to confirm a suspect case of rabies. One method for the detection of lyssavirus antigens within the brain is the direct rapid immunohistochemical …

Silver Nanoparticles Synthesized By Nd: Yag Laser Ablation Technique: Characterization And Antibacterial Activity, Sahar Naji Rashid Msc., Kadhim A. Aadim Ph.D., Awatif Sabir Jasim Ph.D.

Karbala International Journal of Modern Science

The pulsed laser ablation in liquid (PLAL) technique can produce high purity nanoparticles, it is a top-down physical method based on the principle of dividing metal ion bulk precursors into metal atoms, this method was used in this work to synthesize silver nanoparticles (AgPNs) by using Nd: YAG laser with two wavelengths (355 nm) and (532 nm) at energies (500 mJ) and (600 mJ) respectively, with the number of pulses (500, 600, 700, 800, and 900 pulses) for each wavelength. The properties of the prepared nanoparticles were investigated by UV-Vis, XRD, SEM with EDX, AFM, and FTIR analysis and then …

Summer Distribution And Day Roost Characteristics Of Eastern Small-Footed Bats (Myotis Leibii) In West-Central Arkansas, Valerie Marie Kearny

Student Theses and Dissertations

Information on summer distribution and diurnal roosting is lacking for the imperiled, rock-roosting Myotis leibii, a species threatened by habitat loss and White-nose Syndrome. I aimed to 1) identify diurnal, summer roost locations in the greater Ouachita Mountains of Arkansas, and 2) determine roost habitat characteristics at the local, landscape, and roost-level scales. Using acoustic monitoring, rock searches, mist-netting, and temperature monitoring in 2019 and 2020, I found M. leibii in an aggregated distribution across the landscape roosting either solitarily or in small groups in the Rich Mountain-Black Fork Mountain, Mount Magazine, and Mount Nebo areas under sparse canopy cover, …

Editorial Board

Karbala International Journal of Modern Science

No abstract provided.

Optimizing Management Of Invasions In An Uncertain World Using Dynamic Spatial Models, Kim M. Pepin, Amy J. Davis, Rebecca S. Epanchin-Niell, Andrew M. Gormley, Joslin L. Moore, Timothy J. Smyser, H. Bradley Shaffer, William L. Kendall, Katriona Shea, Michael C. Runge, Sophie Mckee

United States Department of Agriculture Wildlife Services: Staff Publications

Dispersal drives invasion dynamics of nonnative species and pathogens. Applying knowledge of dispersal to optimize the management of invasions can mean the difference between a failed and a successful control program and dramatically improve the return on investment of control efforts. A common approach to identifying optimal management solutions for invasions is to optimize dynamic spatial models that incorporate dispersal. Optimizing these spatial models can be very challenging because the interaction of time, space, and uncertainty rapidly amplifies the number of dimensions being considered. Addressing such problems requires advances in and the integration of techniques from multiple fields, including ecology, …

Phosphomimetic Tyrosine Mutations In Spa47 Inhibit Type Three Secretion Atpase Activity And Shigella Virulence Phenotype, Koleton D. Hardy, Nicholas E. Dickenson

Chemistry and Biochemistry Faculty Publications

Shigella is a highly infectious human pathogen responsible for 269 million infections and 200,000 deaths per year. Shigella virulence is absolutely reliant on the injection of effector proteins into the host cell cytoplasm via its type three secretion system (T3SS). The protein Spa47 is a T3SS ATPase whose activity is essential for the proper function of the Shigella T3SS needle-like apparatus through which effectors are secreted. A phosphoproteomics study recently found several Shigella T3SS proteins, including Spa47, to be tyrosine phosphorylated, suggesting a means of regulating Spa47 enzymatic activity, T3SS function, and overall Shigella virulence. The work presented here employs …

An Efficient Method Of Evaluating Multiple Concurrent Management Actions On Invasive Populations, Amy J. Davis, Randy Farrar, Brad Jump, Parker Hall, Travis Guerrant, Kim M. Pepin

United States Department of Agriculture Wildlife Services: Staff Publications

Evaluating the efficacy of management actions to control invasive species is crucial for maintaining funding and to provide feedback for the continual improvement of management efforts. However, it is often difficult to assess the efficacy of control methods due to limited resources for monitoring. Managers may view effort on monitoring as effort taken away from performing management actions. We developed a method to estimate invasive species abundance, evaluate management effectiveness, and evaluate population growth over time from a combination of removal activities (e.g., trapping, ground shooting) using only data collected during removal efforts (method of removal, date, location, number of …

Marginal Proportional Hazards Models For Clustered Interval-Censored Data With Time-Dependent Covariates, Kaitlyn Cook, Wenbin Lu, Rui Wang

Harvard University Biostatistics Working Paper Series

The Botswana Combination Prevention Project was a cluster-randomized HIV prevention trial whose follow-up period coincided with Botswana’s national adoption of a universal test-and-treat strategy for HIV management. Of interest is whether, and to what extent, this change in policy (i) modified the observed preventative effects of the study intervention and (ii) was associated with a reduction in the population-level incidence of HIV in Botswana. To address these questions, we propose a stratified proportional hazards model for clustered interval-censored data with time-dependent covariates and develop a composite expectation maximization algorithm that facilitates estimation of model parameters without placing parametric assumptions on …

Strict Lyapunov Functions And Feedback Controls For Sir Models With Quarantine And Vaccination, Hiroshi Ito, Michael Malisoff, Frederic Mazenc

Faculty Publications

We provide a new global strict Lyapunov function construction for a susceptible, infected, and recovered (or SIR) disease dynamics that includes quarantine of infected individuals and mass vaccination. We use the Lyapunov function to design feedback controls to asymptotically stabilize a desired endemic equilibrium, and to prove input-to-state stability for the dynamics with a suitable restriction on the disturbances. Our simulations illustrate the potential of our feedback controls to reduce peak levels of infected individuals.

Network-Based Pharmacology Study Reveals Protein Targets For Medical Benefits And Harms Of Cannabinoids In Humans, Xingyu Li, Amit Madhukar Kudke, Felix Joseph Nepveux V, Yan Xu

Chemistry Faculty Publications

This network-based pharmacology study intends to uncover the underlying mechanisms of cannabis leading to a therapeutic benefit and the pathogenesis for a wide range of diseases claimed to benefit from or be caused by the use of the cannabis plant. Cannabis contains more than 600 chemical components. Among these components, cannabinoids are well-known to have multifarious pharmacological activities. In this work, twelve cannabinoids were selected as active compounds through text mining and drug-like properties screening and used for initial protein-target prediction. The disease-associated biological functions and pathways were enriched through GO and KEGG databases. Various biological networks [i.e., protein-protein interaction, …

Economics Of Cormorant Predation On Catfish Farms, Carole Engle, Ganesh Kumar, Terrel Christie, Brian S. Dorr, Brian Davis, Luke Roy, Anita Kelly

United States Department of Agriculture Wildlife Services: Staff Publications

The Double-crested Cormorant is the primary avian predator on catfish farms causing significant economic losses primarily due to 1) on-farm expenditures related to bird-management activities and 2) value of the catfish lost to cormorants. This comprehensive economic study quantified these two economic effects by surveying catfish farms in the delta regions of Mississippi and Arkansas. On-farm expenditures for bird scaring were used to quantify bird-management costs. Economic losses from fish consumed by cormorants were quantified by evaluating data from field studies of the abundance, distribution, and diet of cormorants in the Mississippi delta. This study found that catfish farmers …

Adverse Reactions In A Phase 1 Trial Of The Anti-Malarial Dm1157: An Example Of Pharmacokinetic Modeling And Simulation Guiding Clinical Trial Decisions, Stephen J. Balevic, Shruti M. Raja, Rachel Randall, Gregory A. Deye, Thomas Conrad, Aya Nakamura, David H. Peyton, Sandra Shotwell, Katherine May Liebman, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

Introduction: There is an urgent need to develop new drugs to treat malaria due to increasing resistance to first-line therapeutics targeting the causative organism, Plasmodium falciparum (P. falciparum). One drug candidate is DM1157, a small molecule that inhibits the formation of hemozoin, which protects P. falciparum from heme toxicity. We describe a first-in-human, phase 1 trial of DM1157 in healthy adult volunteers that was halted early because of significant toxicity.

Methods: Adverse events were summarized using descriptive statistics. We used pharmacokinetic modeling to quantitatively assess whether the DM1157 exposure needed for P. falciparum inhibition was achievable at safe doses.

Results: …

A Deep Dive Into The Impact Of Covid-19 On Software Development, Paulo Anselmo Da Mota Silveira Neto, Umme Ayda Mannan, Eduardo Santana De Almeida, Nachiappan Nagappan, David Lo, Pavneet Singh Kochhar, Cuiyun Gao, Iftekhar Ahmed

Research Collection School Of Computing and Information Systems

The COVID-19 pandemic is considered as the most crucial global health calamity of the century. It has impacted different business sectors around the world and software development is not an exception. This study investigates the impact of COVID-19 on software projects and software development professionals. We conducted a mining software repository study based on 100 GitHub projects developed in Java using ten different metrics. Next, we surveyed 279 software development professionals for better understanding the impact of COVID-19 on daily activities and wellbeing. We identified 12 observations related to productivity, code quality, and wellbeing. Our findings highlight that the impact …