Medicine and Health Sciences Commons^™

Msdrp: A Deep Learning Model Based On Multisource Data For Predicting Drug Response, Haochen Zhao, Xiaoyu Zhang, Qichang Zhao, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Cancer heterogeneity drastically affects cancer therapeutic outcomes. Predicting drug response in vitro is expected to help formulate personalized therapy regimens. In recent years, several computational models based on machine learning and deep learning have been proposed to predict drug response in vitro. However, most of these methods capture drug features based on a single drug description (e.g. drug structure), without considering the relationships between drugs and biological entities (e.g. target, diseases, and side effects). Moreover, most of these methods collect features separately for drugs and cell lines but fail to consider the pairwise interactions between drugs and cell …

Progenitor Cell Isolation From Mouse Epididymal Adipose Tissue And Sequencing Library Construction, Qianglin Liu, Chaoyang Li, Yuxia Li, Leshan Wang, Xujia Zhang, Buhao Deng, Peidong Gao, Mohammad Shiri, Fozi Alkaifi, Junxing Zhao, Jacqueline M. Stephens, Constantine A. Simintiras, Joseph Francis, Jiangwen Sun, Xing Fu

Computer Science Faculty Publications

Here, we present a protocol to isolate progenitor cells from mouse epididymal visceral adipose tissue and construct bulk RNA and assay for transposase-accessible chromatin with sequencing (ATAC-seq) libraries. We describe steps for adipose tissue collection, cell isolation, and cell staining and sorting. We then detail procedures for both ATAC-seq and RNA sequencing library construction. This protocol can also be applied to other tissues and cell types directly or with minor modifications.

For complete details on the use and execution of this protocol, please refer to Liu et al. (2023).¹

*¹ Liu, Q., Li, C., Deng, B., Gao, P., …

Comparison Of Physics-Based Deformable Registration Methods For Image-Guided Neurosurgery, Nikos Chrisochoides, Yixun Liu, Fotis Drakopoulos, Andriy Kot, Panos Foteinos, Christos Tsolakis, Emmanuel Billias, Olivier Clatz, Nicholas Ayache, Andrey Fedorov, Alex Golby, Peter Black, Ron Kikinis

Computer Science Faculty Publications

This paper compares three finite element-based methods used in a physics-based non-rigid registration approach and reports on the progress made over the last 15 years. Large brain shifts caused by brain tumor removal affect registration accuracy by creating point and element outliers. A combination of approximation- and geometry-based point and element outlier rejection improves the rigid registration error by 2.5 mm and meets the real-time constraints (4 min). In addition, the paper raises several questions and presents two open problems for the robust estimation and improvement of registration error in the presence of outliers due to sparse, noisy, and incomplete …

A Mathematical Model Of Juvenile Delinquency In The New York State, Oluwasegun Micheal Ibrahim

Articles

This report presents a mathematical model of juvenile delinquency in the New York State. In particular, we develop a juvenile delinquency system of non-linear differential equations using the mathematical epidemiology framework. In constructing this model, we assume that juvenile delinquency can be studied as a socially infectious disease. The stability of the juvenile delinquency-free equilibrium of the model is examined using the standard non-linear dynamical systems theory technique. We carried out a data fitting based on real-life data from the New York State Criminal Justice Services. The research result reveals that the formulated model conforms with the available data and …

Split Catalytic Probes For The Detection Of Monkeypox Virus, Jaehyun Ahn

Honors Undergraduate Theses

The COVID-19 outbreak highlighted the important role that diagnostic tests play in the healthcare system. To reduce the impact of infectious disease outbreaks, the development of rapid and cost-effective point-of-care-tests (POCTs) is crucial. With the dissemination of the Monkeypox (Mpox) virus, it became a necessity to produce POCTS that are inexpensive and easy to use. This work explored the construction of two colorimetric assays that aim to detect Mpox genetic signatures. One is based on the split-peroxidase-like deoxyribozyme probes (sPDz), while the other utilizes a cascade system of split RNA-cleaving deoxyribozyme (sDz) and peroxidase-like deoxyribozyme (PDz). Both rely on catalytic …

Winona State University News Blog: 2015-February 2023, Winona State University

Winona State University Blogs

This PDF document includes Winona State University (WSU) News Blog articles and entries for the university from 2015-May 2023.

S-Methyl Cysteine Sulfoxide And Its Potential Role In Human Health: A Scoping Review, Caroline R. Hill, Alex Haoci Liu, Lyn Mccahon, Liezhou Zhong, Armaghan Shafaei, Lois Balmer, Joshua R. Lewis, Jonathan M. Hodgson, Lauren C. Blekkenhorst

Research outputs 2022 to 2026

Higher intakes of cruciferous and allium vegetables are associated with a lower risk of cardiometabolic-related outcomes in observational studies. Whilst acknowledging the many healthy compounds within these vegetables, animal studies indicate that some of these beneficial effects may be partially mediated by S-methyl cysteine sulfoxide (SMCSO), a sulfur-rich, non-protein, amino acid found almost exclusively within cruciferous and alliums. This scoping review explores evidence for SMCSO, its potential roles in human health and possible mechanistic action. After systematically searching several databases (EMBASE, MEDLINE, SCOPUS, CINAHL Plus Full Text, Agricultural Science), we identified 21 original research articles meeting our inclusion criteria. These …

Development Of A Scoring Tool For Australian Rural Food Retail Environments, Tracy L. Schumacher, Carissa A. Alderton, Leanne J. Brown, Susan Heaney, Laura Alston, Katherine Kent, Stephanie L. Godrich

Research outputs 2022 to 2026

Current tools scoring the healthiness of food retail outlets do not reflect outlets found in rural locations. This study aimed to adapt pre-existing Australian scoring tools to represent non-metropolitan areas. Rural nutrition experts were identified, and a modified Delphi technique was used to adapt two pre-existing, food-scoring tools in five iterative stages. Stages included identifying all relevant outlets, providing a description and score for each, ensuring consistency between outlet scores and pre-existing, metro-centric tools, and providing instructions for correct use. Six rural nutrition experts were identified and engaged in the modified Delphi technique. The final tool consisted of 12 categories …

Readiness For Transfer: A Mixed-Methods Study On Icu Transfers Of Care, Soo-Hoon Lee, Clarice Wee, Phillip Phan, Yanika Kowitlawakul, Chee-Kiat Tan, Amartya Mukhopadhyay

Management Faculty Publications

Objective Past studies on intensive care unit (ICU) patient transfers compare the efficacy of using standardised checklists against unstructured communications. Less studied are the experiences of clinicians in enacting bidirectional (send/receive) transfers. This study reports on the differences in protocols and data elements between receiving and sending transfers in the ICU, and the elements constituting readiness for transfer.

Methods Mixed-methods study of a 574-bed general hospital in Singapore with a 74-bed ICU for surgical and medical patients. Six focus group discussions (FGDs) with 34 clinicians comprising 15 residents and 19 nurses, followed by a structured questionnaire survey of 140 clinicians …

Stem Education And Retention For Black Women Using High-Impact Practices: Historically Black Colleges And Universities Vs. Predominantly White Liberal Arts Colleges, Annette Njei

CMC Senior Theses

Black women are significantly underrepresented within the fields of science, technology, engineering, and mathematics (STEM). To address this, the Association of American Colleges & Universities crafted ten high-impact practices to increase student engagement and promote retention. This research paper examines how three specific high-impact practices (learning communities, mentoring, and undergraduate research experience) are utilized in STEM education.This research paper explores and compares the best high impact approaches that successfully teach and retain Black women within the various fields of STEM within the differing academic environments of historically Black colleges & universities ( HBCUs) and predominantly white liberal art colleges (PWLACs). …

Enhancing Health Data Representation For Older Adults: Unlocking Opportunities, Peterson Jean

Academic Posters Collection

The prevalence of off-the-shelf wearable devices increases the monitoring and measurement of critical physiological parameters like activity, sleep, heart rate, and blood pressure. However, the accessibility of health data representations poses challenges for older adults, who often struggle to understand the criticality of their own health data without assistance. This poster highlights the challenges older adults face in accessing their health data from wearable technologies, specifically focusing on data representations.

To address these challenges, it proposes a methodology that involves a heuristic evaluation of existing data representations with experts and accessibility studies with older adults using a mixed methods approach …

Thermodynamic Analysis Of Digestate Pyrolysis Coupled With Co2 Sorption, Antonella Dimotta, Cesare Freda

Conference papers

To date the management of digestate is a crucial task for anaerobic digestion process. In the present work a strategy for digestate management is thermodynamically analyzed by a commercial software for process simulation called CHEMCAD®. Pyrolysis of digestate is simulated by a minimization of the free Gibbs energy. The sequestration of the carbon dioxide (CO2) released by the pyrolysis is investigated by the addition of calcium oxide, in order to reduce CO2 emissions. The effect of the pyrolysis temperature between 400–900 °C and of the CaO/digestate mass ratio between 0–0.5 was discussed, as well. The CHEMCAD application allowed to investigate …

Autodocking Studies Of Oxygenated Fullerenes As Inhibitors Of The Hiv Protease, Michael Kaminski

All Student Theses

In a previous study, several oxygenated fullerene compounds were produced by ozonation of C60 (Buckminsterfullerene) and were identified by elemental analysis and by SALI (surface analysis by laser ionization). Some of these compounds, especially a batch, SK-5, a mixture of C60O1-8, were shown to inhibit activities of HIV-Protease with IC50 (concentration for 50% inhibition) of 1 mg/mol in the in-vitro studies. The oxygenated fullerenes were shown to have epoxide, ketones, and hydroxyl functionalities. As expected, C60 interacted with ozone with alkene functionality and not as an aromatic compound. It was postulated that C60O had epoxide functionality, as a product of …

An Approach To Developing Benchmark Datasets For Protein Secondary Structure Segmentation From Cryo-Em Density Maps, Thu Nguyen, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

More and more deep learning approaches have been proposed to segment secondary structures from cryo-electron density maps at medium resolution range (5--10Å). Although the deep learning approaches show great potential, only a few small experimental data sets have been used to test the approaches. There is limited understanding about potential factors, in data, that affect the performance of segmentation. We propose an approach to generate data sets with desired specifications in three potential factors - the protein sequence identity, structural contents, and data quality. The approach was implemented and has generated a test set and various training sets to study …

Detecting Deceptive Dark-Pattern Web Advertisements For Blind Screen-Reader Users, Satwick Ram Kodandaram, Mohan Sunkara, Sampath Jayarathna, Vikas Ashok

Computer Science Faculty Publications

Advertisements have become commonplace on modern websites. While ads are typically designed for visual consumption, it is unclear how they affect blind users who interact with the ads using a screen reader. Existing research studies on non-visual web interaction predominantly focus on general web browsing; the specific impact of extraneous ad content on blind users' experience remains largely unexplored. To fill this gap, we conducted an interview study with 18 blind participants; we found that blind users are often deceived by ads that contextually blend in with the surrounding web page content. While ad blockers can address this problem via …

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

Enabling Customization Of Discussion Forums For Blind Users, Mohan Sunkara, Yash Prakash, Hae-Na Lee, Sampath Jayarathna, Vikas Ashok

Computer Science Faculty Publications

Online discussion forums have become an integral component of news, entertainment, information, and video-streaming websites, where people all over the world actively engage in discussions on a wide range of topics including politics, sports, music, business, health, and world affairs. Yet, little is known about their usability for blind users, who aurally interact with the forum conversations using screen reader assistive technology. In an interview study, blind users stated that they often had an arduous and frustrating interaction experience while consuming conversation threads, mainly due to the highly redundant content and the absence of customization options to selectively view portions …

Modification Of Hyaluronic Acid To Enable Click Chemistry Photo-Crosslinking Of Hydrogels With Tailorable Degradation Profiles, Ciara Buckley

Articles

Hyaluronic acid (HA) is a naturally occurring mucopolysaccharide that, due to its inherent bioactivity and extracellular matrix-like structure, has the potential to be utilised extensively in tissue engineering. However, this glycosaminoglycan lacks the properties required for cellular adhesion and photo-crosslinking by UV light, which significantly hinders this polymers applicability. This research presents a method for modifying hyaluronic acid via thiolation and methacrylation to generate a novel photo-crosslinkable polymer with improved physicochemical properties, biocompatibility and the potential to customize biodegradability according to the ratio of monomers used. A decrease in stiffness proportional to increasing thiol concentration was observed when testing the …

Analysis Of Biologically Effective Dose For Retroactive Yttrium-90 Trans-Arterial Radioembolization Treatment Optimization, Mj Lindsey

CMC Senior Theses

Trans-arterial radioembolization (TARE) is a protracted modality of radiation therapy where radionuclides labeled with Yttrium-90 (⁹⁰Y) are inserted inside a patient's hepatic artery to treat hepatocellular carcinoma (HCC). While TARE has been shown to be a clinically effective and safe treatment, there is little understanding of the radiobiological relationship between absorbed dose and tissue response, and thus there is no dosimetric standard for treatment planning. The Biologically Effective Dose (BED) formalism, derived from the Linear-Quadratic model of radiobiology, is used to weigh the absorbed dose by the time pattern of delivery. BED is a virtual dose that can …

Knowledge Discovery On The Integrative Analysis Of Electrical And Mechanical Dyssynchrony To Improve Cardiac Resynchronization Therapy, Zhuo He

Dissertations, Master's Theses and Master's Reports

Cardiac resynchronization therapy (CRT) is a standard method of treating heart failure by coordinating the function of the left and right ventricles. However, up to 40% of CRT recipients do not experience clinical symptoms or cardiac function improvements. The main reasons for CRT non-response include: (1) suboptimal patient selection based on electrical dyssynchrony measured by electrocardiogram (ECG) in current guidelines; (2) mechanical dyssynchrony has been shown to be effective but has not been fully explored; and (3) inappropriate placement of the CRT left ventricular (LV) lead in a significant number of patients.

In terms of mechanical dyssynchrony, we utilize an …

Nutrient Pollution And Chlorophyll-A As A Precursor To Harmful Algal Blooms And Cyanotoxins In Rehabilitated Machado Lake, California, Michael E. Shiang

Walden Dissertations and Doctoral Studies

Algal blooms result in the formation of cyanotoxic conditions in a freshwater lake causing severe detrimental impacts to community and public health. Nitrogen, phosphorous, and ammonia stimulate the growth of phytoplankton biomass and algae, as measured by chlorophyll. This retrospective quantitative research study, grounded in the socioecological model, examined the relationship between nutrient pollutants and chlorophyll-a (Chl-a) that forecast harmful algal blooms, a precursor to cyanotoxins. A former impaired lake, Machado Lake in California, provided an ideal setting to assess relationships among nutrient indicators and Chl-a post-lake rehabilitation. Correlation and multiple regression analyses were performed to determine if a relationship …

Lessons Learned From Interdisciplinary Efforts To Combat Covid-19 Misinformation: Development Of Agile Integrative Methods From Behavioral Science, Data Science, And Implementation Science, Sahiti Myneni, Paula Cuccaro, Sarah Montgomery, Vivek Pakanati, Jinni Tang, Tavleen Singh, Olivia Dominguez, Trevor Cohen, Belinda Reininger, Lara S Savas, Maria E Fernandez

Journal Articles

BACKGROUND: Despite increasing awareness about and advances in addressing social media misinformation, the free flow of false COVID-19 information has continued, affecting individuals' preventive behaviors, including masking, testing, and vaccine uptake.

OBJECTIVE: In this paper, we describe our multidisciplinary efforts with a specific focus on methods to (1) gather community needs, (2) develop interventions, and (3) conduct large-scale agile and rapid community assessments to examine and combat COVID-19 misinformation.

METHODS: We used the Intervention Mapping framework to perform community needs assessment and develop theory-informed interventions. To supplement these rapid and responsive efforts through large-scale online social listening, we developed a …

Potential Alzheimer's Disease Plasma Biomarkers, Taylor Estepp

Theses and Dissertations--Epidemiology and Biostatistics

In this series of studies, we examined the potential of a variety of blood-based plasma biomarkers for the identification of Alzheimer's disease (AD) progression and cognitive decline. With the end goal of studying these biomarkers via mixture modeling, we began with a literature review of the methodology. An examination of the biomarkers with demographics and other health factors found evidence of minimal risk of confounding along the causal pathway from biomarkers to cognitive performance. Further study examined the usefulness of linear combinations of biomarkers, achieved via partial least squares (PLS) analysis, as predictors of various cognitive assessment scores and clinical …

Evaluation Of Roost Culling As A Management Strategy For Reducing Invasive Rose‑Ringed Parakeet (Psittacula Krameri) Populations, C. Janes Anderson, Leonard A. Brennan, William P. Bukoski, Steven C. Hess, Clayton D. Hilton, Aaron B. Shiels, Shane Siers, Bryan M. Kluever, Page E. Klug

USDA Wildlife Services: Staff Publications

Rose-ringed parakeets (Psittacula krameri) are one of the most widespread invasive avian species worldwide. This species was introduced to the island of Kaua‘i, Hawai‘i, USA, in the 1960s. The rapidly increasing population has caused substantial economic losses in the agricultural and tourism industries. We evaluated the efficacy of a roost culling program conducted by an independent contractor from March 2020 to March 2021. We estimated island-wide minimum abundance was 10,512 parakeets in January 2020 and 7,372 in April 2021. Over 30 nights of culling at four roost sites, approximately 6,030 parakeets were removed via air rifles with 4,415 …

Predicting Dispersal And Conflict Risk For Wolf Recolonization In Colorado, Mark A. Ditmer, George Wittemyer, Katherine A. Zeller, Stewart W. Breck, Robert J. Fletcher Jr., Kevin R. Crooks

USDA Wildlife Services: Staff Publications

1. The colonization of suitable yet unoccupied habitat due to natural dispersal or human introduction can benefit recovery of threatened species. Predicting habitat suitability and conflict potential of colonization areas can facilitate conservation planning.

2. Planning for reintroduction of gray wolves (Canis lupus) to the United States state of Colorado is underway. Assessing which occupancy sites minimize the likelihood of human-wolf conflict during dispersal events and seasonal movements is critical to the success of this initiative.

3. We used a spatial absorbing Markov chain (SAMC) framework, which extends random walk theory and probabilistically accounts for both movement behavior …

High Winds And Melting Sea Ice Trigger Landward Movement In A Polar Bear Population Of Concern, Annie Kellner, Todd C. Atwood, David C. Douglas, Stewart W. Breck, Colorado State University - Fort Collins

USDA Wildlife Services: Staff Publications

Some animal species are responding to climate change by altering the timing of events like mating and migration. Such behavioral plasticity can be adaptive, but it is not always. Polar bears (Ursus maritimus) from the southern Beaufort Sea subpopulation have mostly remained on ice year-round, but as the climate warms and summer sea ice declines, a growing proportion of the subpopulation is summering ashore. The triggers of this novel behavior are not well understood. Our study uses a parametric time-to-event model to test whether biological and/or time-varying environmental variables thought to influence polar bear movement and habitat selection …

Deriving Spatially Explicit Direct And Indirect Interaction Networks From Animal Movement Data, Anni Yang, Mark Q. Wilber, Kezia R. Manlove, Ryan S. Miller, Raoul Boughton, James Beasley, Joseph Northrup, Kurt C. Vercauteren, George Wittemyer, Kim Pepin

USDA Wildlife Services: Staff Publications

Quantifying spatiotemporally explicit interactions within animal populations facilitates the understanding of social structure and its relationship with ecological processes. Data from animal tracking technologies (Global Positioning Systems [“GPS”]) can circumvent longstanding challenges in the estimation of spatiotemporally explicit interactions, but the discrete nature and coarse temporal resolution of data mean that ephemeral interactions that occur between consecutive GPS locations go undetected. Here, we developed a method to quantify individual and spatial patterns of interaction using continuous-time movement models (CTMMs) fit to GPS tracking data. We first applied CTMMs to infer the full movement trajectories at an arbitrarily fine temporal scale …

H7n9 Influenza A Virus Transmission In A Multispecies Barnyard Model, Angela M. Bosco-Lauth, Anna Rodriguez, Rachel M. Maison, Stephanie M. Porter, J. Jeffrey Root

USDA Wildlife Services: Staff Publications

Influenza A viruses are a diverse group of pathogens that have been responsible for millions of human and avian deaths throughout history. Here, we illustrate the transmission potential of H7N9 influenza A virus between Coturnix quail (Coturnix sp.), domestic ducks (Anas platyrhynchos domesticus), chickens (Gallus gallus domesticus), and house sparrows (Passer domesticus) co-housed in an artificial barnyard setting. In each of four replicates, individuals from a single species were infected with the virus. Quail shed virus orally and were a source of infection for both chickens and ducks. Infected chickens transmitted the virus to quail but not to ducks or …

Raccoon Rabies Control And Elimination In The Northeastern Usa And Southern Québec, Canada, Amy J. Davis, Marianne Gagnier, Ariane Massé, Kathleen M. Nelson, Jordona D. Kirby, Ryan Wallace, Xiaoyue Ma, Christine Fehlner-Gardiner, Richard B. Chipman, Amy Gilbert

USDA Wildlife Services: Staff Publications

Rabies virus (RABV) is a deadly zoonosis that circulates in wild carnivore populations in North America. Intensive management within the USA and Canada has been conducted to control the spread of the raccoon (Procyon lotor) variant of RABV and work towards elimination. We examined RABV occurrence across the northeastern USA and southeastern Québec, Canada during 2008–2018 using a multi-method, dynamic occupancy model. Using a 10 km× 10 km grid overlaid on the landscape, we examined the probability that a grid cell was occupied with RABV and relationships with management activities (oral rabies vaccination (ORV) and trap-vaccinate-release efforts), habitat, neighbour effects …

Transmission Of Sars-Cov-2 In Free-Ranging White-Tailed Deer In The United States, Aijing Feng, Sarah Bevins, Jeff Chandler, Thomas J. Deliberto, Ria Ghai, Kristina Lantz, Julianna Lenoch, Adam Retchless, Susan A. Shriner, Cynthia Y. Tang, Suxiang Sue Tong, Mia Torchetti, Anna Uehara, Xiu-Feng Wan

USDA Wildlife Services: Staff Publications

SARS-CoV-2 is a zoonotic virus with documented bi-directional transmission between people and animals. Transmission of SARS-CoV-2 from humans to free-ranging white-tailed deer (Odocoileus virginianus) poses a unique public health risk due to the potential for reservoir establishment where variantsmay persist and evolve. We collected 8,830 respiratory samples from free-ranging white-tailed deer across Washington, D.C. and 26 states in the United States between November 2021 and April 2022. We obtained 391 sequences and identified 34 Pango lineages including the Alpha, Gamma, Delta, and Omicron variants. Evolutionary analyses showed these white-tailed deer viruses originated fromat least 109 independent spillovers fromhumans,which resulted in …