Digital Commons Network^™

Seeing Eye To Eye? Comparing Faculty And Student Perceptions Of Biomolecular Visualization Assessments, Josh T. Beckham, Daniel R. Dries, Bonnie L. Hall, Rarchel M. Mitton-Fry, Shelly Engelman, Charmita Burch, Roderico Acevedo, Pamela S. Mertz, Didem Vardar-Ulu, Swati Agrawal, Kristin M. Fox, Shane Austin, Margaret A. Franzen, Henry V. Jakubowski, Walter R. P. Novak, Rebecca Roberts, Alberto I. Roca, Kristen Procko

Chemistry Faculty Publications

While visual literacy has been identified as a foundational skill in life science education, there are many challenges in teaching and assessing biomolecular visualization skills. Among these are the lack of consensus about what constitutes competence and limited understanding of student and instructor perceptions of visual literacy tasks. In this study, we administered a set of biomolecular visualization assessments, developed as part of the BioMolViz project, to both students and instructors at multiple institutions and compared their perceptions of task difficulty. We then analyzed our findings using a mixed-methods approach. Quantitative analysis was used to answer the following research questions: …

Draft Final 2023 Residential Metals Abatement Program (Rmap) Whitehall Borrow Submittal #2, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Qiditangshen Granules Alleviates Diabetic Nephropathy Podocyte Injury: A Network Pharmacology Study And Experimental Validation In Vivo And Vitro, Yang Shi, Xianhui Zhang, Hongfang Liu

Faculty, Staff and Student Publications

BACKGROUND: QiDiTangShen granules (QDTS), a traditional Chinese medicine (TCM) compound prescription, have remarkable efficacy in diabetic nephropathy (DN) patients, and their pharmacological mechanism needs further exploration.

METHODS: According to the active ingredients and targets of the QDTS in the TCMSP database, the network pharmacology of QDTS was investigated. The potential active ingredients were chosen based on the oral bioavailability and the drug similarity index. At the same time, targets for DN-related disease were obtained from GeneCards, OMIM, PharmGKB, TTD, and DrugBank. The TCM-component-target network and the protein-protein interaction (PPI) network were constructed with the Cytoscape and STRING platforms, respectively, and …

Market Analysis And Bidding Strategy Of Hybrid Renewable Energy Systems Considering Emissions, Fatma Elzahraa, Mohamed Elnemr, Samir Dawoud

Journal of Engineering Research

The competition in the electricity markets makes it difficult to choose a suitable strategy for maximizing profit while reducing harmful emissions. To have an adequate energy price for consumers while minimizing the harmful emissions to the atmosphere and maximizing profits of all participants in the electricity market needs an aggressive bidding strategy. Developing these bidding strategies with the integration of renewable energy (RE) in the electricity market became important. This research studies various bidding strategies for maximizing profits in the deregulated energy market since participants are keen on developing bidding strategies considering emissions. These bidding strategies will consider the integration …

Treatment Of Oil Refinery Wastewater Polluted By Heavy Metal Ions Via Adsorption Technique Using Non-Valuable Media: Cadmium Ions And Buckthorn Leaves As A Study Case, Salem Jawad Alhamd, Mohammed Nsaif Abbas, Mehrdad Manteghian, Thekra Atta Ibrahim, Karar Dawood Salman Jarmondi

Karbala International Journal of Modern Science

This study focuses on the removal of cadmium ions generated by oil refinery wastewater, employing an agricultural by-product. Buckthorn leaves, sourced from Baghdad and Diyala provinces, underwent preparation, including washing, drying, crushing, and sieving before being utilized in experiments. Batch experiments were conducted using simulated solutions to assess the impact of six key adsorption design parameters: pH, cadmium concentration, agitation speed, contact time, adsorbent dosage, and temperature. The highest adsorption efficiency, reaching 94.4367%, was directly correlated with contact time, adsorbent dosage, pH value, and agitation speed, and inversely related to other variables. Morphological studies on the treated adsorbent, indicated structural …

Compartmental Modeling For The Neophyte: An Application Of Berkeley Madonna, Olcay Akman, Siddharth Bhumpelli, Cody Cline, Christopher Hay-Jahans

Spora: A Journal of Biomathematics

Compartmental modeling serves as a necessary framework in many fields, especially biomathematics and ecology. This article introduces readers to a user-friendly approach to constructing compartmental models and solving the resulting systems of differential equations to simulate real-world applications. The platform used is Berkeley Madonna, a software package that has an intuitive graphical interface which empowers users—even those with limited mathematical and programming backgrounds—to focus on modeling concepts rather than mathematical or programming intricacies. This makes Berkeley Madonna an ideal platform for students, educators, and researchers.

Cambrian Trilobites From The Nounan Dolomite And Lower St. Charles Formation (Upper Marjuman To Lower Sunwaptan; Miaolingian To Furongian Series), Smithfield Canyon, Northern Utah, Frederick A. Sundberg, Hannah R. Cothren, Carol M. Dehler

Geosciences Faculty Publications

The trilobite faunas that occur with the Steptoean Positive Isotope Carbon Excursion (SPICE) at Smithfield Canyon, Utah, have been reported, but not illustrated. Given the importance of the SPICE at this section for international correlations, the trilobites from new collections from the upper Nounan Dolomite to lower St. Charles Formation at Smithfield Canyon are reported herein and integrated with the previously reported taxa. Trilobite assemblages indicate that the upper Cedaria to the Ellipsocephaloides biozones (Miaolingian Series, Guzhangian Stage to Furongian Series, Jiangshanian Stage) are present stratigraphically below or above the SPICE.

Some of the taxa reported herein may represent new …

Group 14 Metallocene Catalysts For Carbonyl Hydroboration And Cyanosilylation, Haley J. Robertson, Mallory N. Fujiwara, Allegra L. Liberman-Martin

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

A series of six Group 14 metallocene compounds (M = Ge, Sn, Pb) were studied as catalysts for carbonyl hydroboration and cyanosilylation reactions at room temperature. Both bis(pentamethylcyclopentadienyl) and tetramethyldisiloxa[3]metallocenophane compounds were compared. The tin and lead metallocenophanes exhibited the highest reactivity in hydroboration and cyanosilylation reactions. Hammett analysis of aldehyde hydroboration provided a ρ value of 0.73, suggesting a buildup of negative charge during the turnover-limiting step, consistent with the transition state for hydride transfer to the carbonyl center. NMR studies of Lewis acidity indicate that the Ge, Sn, and Pb tetramethyldisiloxa[3]metallocenophane compounds are weak Lewis acids.

Forecasting Foreign Tourist Arrivals In India: A Strategic Analysis For Sustainable Religious Tourism Growth, Vishwajeet Singh, Dr. Taruna, Tarushree Bari, Subhash Kumar Yadav

International Journal of Religious Tourism and Pilgrimage

The exponential growth of the tourism industry in India significantly impacts the nation’s economic landscape. This study presents an analysis of tourism arrival trends from 2000 to 2019 to forecast foreign tourist arrivals, aligning with the broader scope of religious tourism and pilgrimage. Employing the Box-Jenkins methodology, the research aims to project short-term forecasts for inbound tourism. Diverse modelling techniques are explored to capture the nuances of the time series data, including the assessment of stationarity using the Dickey-Fuller Test to discern underlying trends. The study culminates in identifying the A.R.I.M.A (0, 1, 1) model with drift as the most …

Young Professionals: Fireside Chat With Jacques Lewiner And J. Keith Nelson At The Ieee Conference On Electrical Insulation And Dielectric Phenomena, Mattewos Tefferi, Allen Andersen, Sneha Hedge, Moein Borghei

Journal Articles

At the IEEE Conference on Electrical Insulation and Dielectric Phenomena (CEIDP), the Dielectrics and Electrical Insulation Society’s Young Professionals (DEIS-YP) Committee has initiated a YP luncheon event. This event aims to feature keynote speakers who share insights into their career trajectories with young professionals. In the current CEIDP edition, we had the privilege of hosting two distinguished speakers: Jacques Lewiner, the 2023 Whitehead Memorial Lecturer, and J. Keith Nelson, the 2022 recipient of the Dakin Award who also presented his award lecture at the CEIDP 2023. The fire- side chat was moderated by Allen Andersen, who began with initial questions …

Fusionpdb:: A Knowledgebase Of Human Fusion Proteins

Faculty, Staff and Student Publications

Tumorigenic functions due to the formation of fusion genes have been targeted for cancer therapeutics (i.e. kinase inhibitors). However, many fusion proteins involved in various cellular processes have not been studied for targeted therapeutics. This is because the lack of complete fusion protein sequences and their whole 3D structures has made it challenging to develop new therapeutic strategies. To fill these critical gaps, we developed a computational pipeline and a resource of human fusion proteins named FusionPDB, available at https://compbio.uth.edu/FusionPDB. FusionPDB is organized into four levels: 43K fusion protein sequences (14.7K in-frame fusion genes, Level 1), over 2300 + 1267 …

Ageannomo: A Knowledgebase Of Multi-Omics Annotation For Animal Aging, Haixia Xu, Qingxuan Li, Yuhao Jia, Liyu Huang, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes …

Drmref: Comprehensive Reference Map Of Drug Resistance Mechanisms In Human Cancer, Kexin Huang, Jiajia Liu, Grant Wang, Pora Kim, Qianqian Song, Xiaobo Zhou

Faculty, Staff and Student Publications

Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in …

Fitting A Covid-19 Model Incorporating Senses Of Safety And Caution To Local Data From Spartanburg County, South Carolina, D. Chloe Griffin, Amanda Mangum

CODEE Journal

Common mechanistic models include Susceptible-Infected-Removed (SIR) and Susceptible-Exposed-Infected-Removed (SEIR) models. These models in their basic forms have generally failed to capture the nature of the COVID-19 pandemic's multiple waves and do not take into account public policies such as social distancing, mask mandates, and the ``Stay-at-Home'' orders implemented in early 2020. While the Susceptible-Vaccinated-Infected-Recovered-Deceased (SVIRD) model only adds two more compartments to the SIR model, the inclusion of time-dependent parameters allows for the model to better capture the first two waves of the COVID-19 pandemic when surveillance testing was common practice for a large portion of the population. We find …

Response Of Water Resources To The Kahramanmaraş Earthquakes (Mw 7.7 And Mw 7.6) That Occurred On February 6, 2023, On The East Anatolian Fault Zone (Türkiye), Celaletti̇n Şi̇mşek, Görkem Akinci, Okan Fistikoğlu, Kerem Canli, Hasan Sözbi̇li̇r, Azi̇ze Ayol, Efem Bi̇lgi̇ç

Turkish Journal of Earth Sciences

On February 6, 2023, two destructive earthquakes of 7.7 MW and 7.6 MW occurred in Pazarcık (Kahramanmaraş) and Elbistan (Kahramanmaraş) at 04:17 and 13:24 hours, respectively. These earthquakes caused a surface rupture with a total length of 450 km in the region with an average displacement of 3 m between the Arabian and Anatolian plates. This study was conducted to investigate the physical deformation of the aquifer system and the current water quality characteristics in the affected region utilizing field observations and on-site analysis of water sources and tap water. The study revealed significant physical changes in the karstic springs …

Nonlinear Dynamics Of Mountain Pine Beetle Populations: Discussion Of Forestry Policy, A Survey Of Existing Mathematical Models, And Code Base Demonstration, Scott A. Strong, Maya Maes-Johnson

CODEE Journal

This article presents existing mathematical models associated with mountain pine beetle populations in lodgepole pine forests, whose reproductive cycle requires the destruction of colonized host trees, decreasing timber availability/quality, and providing fuel sources for wildfires. With the existence of a positive-feedback loop with environmental warming, the need for intervention and management is clear. However, the legislative responses to the focusing events from our 2000-2010 North American epidemics are characterized as under-leveraged. While the reasons for this are multifaceted, increasing the capacity of STEM-informed individuals to take part in quantitative modeling of the underlying ecosystem generates awareness and provides pathways connecting …

Applying The Sir Model: Can Students Advise The Mayor Of A Small Community?, Carrin Goosen, Mark I. Nelson, Mahime Watanabe

CODEE Journal

This is an account of a modelling scenario that uses the sir epidemic model. It was used in a third year applied mathematics subject. All students were enrolled in a mathematics degree of some type. Students are presented with the results of a test carried out on 100 individuals in a community containing 3000 people. From this they determined the number of infectious and recovered individuals in the population. Given the per capita recovery rate and making a suitable assumption about the number of infectious individuals at the start of the epidemic, they then estimate the infectious contact rate and …

Splitfed-Based Patient Severity Prediction And Utility Maximization In Industrial Healthcare 4.0, Himanshu Singh, Biken Moirangthem, Ajay Pratap, Shilpi Kumari, Abhishek Kumar, Sajal K. Das

Computer Science Faculty Research & Creative Works

The healthcare industry has transitioned from traditional healthcare 1.0 to AI-powered healthcare 4.0. However, overall cost for patient treatment remains high and challenging to manage due to the absence of a centralized cost evaluation mechanism before hospital visits. Therefore, in this paper, we devise a cloud-based mechanism to calculate hospitals' star rating based on questionnaire with the application of Z-score and K∗clustering algorithm. To evaluate disease severity at cloud, splitfed technique is utilized in coordination with Wireless Body Area Network (WBAN). Finally, the cloud calculates provisional treatment costs and finds a preferable hospital with a low payable treatment cost and …

Fish Assemblage Structure In Great Lakes Coastal Wetlands Over Ten Years, Matthew S. Silverhart

Masters Theses

Coastal wetlands in the Laurentian Great Lakes are important habitats for many fish species. The geographic scale of the watershed and the diversity of land uses in the region result in substantial environmental variation among coastal wetlands. During 2011-2020, annual surveys were conducted as part of the Great Lakes Coastal Wetland Monitoring Program (GLCWMP) to better understand the status and trends of coastal wetlands. Fish sampling consisted of fyke netting in monodominant vegetation zones. During this time, 1225 unique monodominant plant zones in coastal wetlands were sampled, resulting in 584,125 fishes captured that consisted of 113 different species. Yellow Perch …

Enrichment Of Polycyclic Aromatic Hydrocarbon Metabolizing Microorganisms On The Oral Mucosa Of Tobacco Users, James V. Defrancesco, Lin Tao, M Paul Chiarelli, Sylvia Pavlova, Antonia Kolokythas, Joel Schwartz, Benjamin Salameh, Stefan J. Green, Guy Adami

Chemistry: Faculty Publications and Other Works

Certain soil microbes resist and metabolize polycyclic aromatic hydrocarbons (PAHs). The same is true for a subset of skin microbes. In the human mouth, oral microbes have the potential to oxidize tobacco PAHs, thereby increasing these chemicals' ability to cause cancer of adjacent epithelium. We hypothesized that we could identify, in smokers, the oral mucosal microbes that can metabolize PAH. We isolated bacteria and fungi that survived long-term in minimal media with PAHs as the sole carbon source, under aerobic conditions, from the oral mucosa in 17 of 26 smokers and two of 14 nonsmokers. Of bacteria genera that survived …

Integrating External Controls By Regression Calibration For Genome-Wide Association Study, Lirong Zhu, Shijia Yan, Xuewei Cao, Shuanglin Zhang, Qiuying Sha

Michigan Tech Publications

Genome-wide association studies (GWAS) have successfully revealed many disease-associated genetic variants. For a case-control study, the adequate power of an association test can be achieved with a large sample size, although genotyping large samples is expensive. A cost-effective strategy to boost power is to integrate external control samples with publicly available genotyped data. However, the naive integration of external controls may inflate the type I error rates if ignoring the systematic differences (batch effect) between studies, such as the differences in sequencing platforms, genotype-calling procedures, population stratification, and so forth. To account for the batch effect, we propose an approach …

On Water Arrangements In Right- And Left-Handed Dna Structures, Liliya A. Yatsunyk, S. Neidle

Chemistry & Biochemistry Faculty Works

DNA requires hydration to maintain its structural integrity. Crystallographic analyses have enabled patterns of water arrangements to be visualized. We survey these water motifs in this review, focusing on left- and right-handed duplex and quadruplex DNAs, together with the i-motif. Common patterns of linear spines of water organization in grooves have been identified and are widely prevalent in right-handed duplexes and quadruplexes. By contrast, a left-handed quadruplex has a distinctive wheel of hydration populating the almost completely circular single groove in this structure.

Attochemistry Regulation Of Charge Migration, Aderonke Folorunso

LSU Doctoral Dissertations

Charge migration (CM) is a coherent attosecond process that involves the movement of localized holes across a molecule. This phenomenon is potentially useful to understand the fundamental principles of photochemistry, such as light harvesting. The first part of this dissertation discusses the molecular modes of attosecond charge migration. In this work, we used first-principles calculations to investigate the modes of charge migration (CM) in halogenated hydrocarbon chains at attosecond timescales. We have simulated the creation of a localized hole on the halogen atom using constrained density functional theory (DFT) and then tracked its subsequent dynamics with time-dependent DFT (TDDFT). Our …

Inpatient Costs Of Treating Patients With Covid-19, Ankita Podichetty, Raymond S Greenberg

Faculty, Staff and Student Publications

IMPORTANCE: With more than 6.2 million hospitalizations due to COVID-19 in the US, recognition of the average hospital costs to provide inpatient care during the pandemic is necessary to understanding the national medical resource use and improving public health readiness and related policies.

OBJECTIVE: To examine the mean cost to provide inpatient care to treat COVID-19 and how it varied through the pandemic waves and by important sociodemographic patient characteristics.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used inpatient-level data from March 1, 2020, to March 31, 2022, extracted from a repository of clinical, administrative, and financial information covering 97% …

Innovative Cyanine-Based Fluorescent Dye For Targeted Mitochondrial Imaging And Its Utility In Whole-Brain Visualization, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Michigan Tech Publications

Conducting in vivo brain imaging can be a challenging task due to the complexity of brain tissue and the strict requirements for safe and effective imaging agents. However, a new fluorescent dye called Cy5-PEG2 has been developed that selectively accumulates in mitochondria, enabling the visualization of these essential organelles in various cell lines. This dye is versatile and can be used for the real-time monitoring of mitochondrial dynamics in living cells. Moreover, it can cross the blood-brain barrier, making it a promising tool for noninvasive in vivo brain imaging. Based on the assessment of glial cell responses in the hippocampus …

Time Scale Theory On Stability Of Explicit And Implicit Discrete Epidemic Models: Applications To Swine Flu Outbreak, Gülşah Yeni, Elvan Akın, Naveen K. Vaidya

Mathematics and Statistics Faculty Research & Creative Works

Time scales theory has been in use since the 1980s with many applications. Only very recently, it has been used to describe within-host and between-hosts dynamics of infectious diseases. In this study, we present explicit and implicit discrete epidemic models motivated by the time scales modeling approach. We use these models to formulate the basic reproduction number, which determines whether an outbreak occurs, or the disease dies out. We discuss the stability of the disease-free and endemic equilibrium points using the linearization method and Lyapunov function. Furthermore, we apply our models to swine flu outbreak data to demonstrate that the …

Microstructure-Based Modeling Of Primary Cilia Mechanics, Nima Mostafazadeh, Andrew Resnick, Y.-N. Young, Zhangli Peng

Physics Faculty Publications

A primary cilium, made of nine microtubule doublets enclosed in a cilium membrane, is a mechanosensing organelle that bends under an external mechanical load and sends an intracellular signal through transmembrane proteins activated by cilium bending. The nine microtubule doublets are the main load-bearing structural component, while the transmembrane proteins on the cilium membrane are the main sensing component. No distinction was made between these two components in all existing models, where the stress calculated from the structural component (nine microtubule doublets) was used to explain the sensing location, which may be totally misleading. For the first time, we developed …

Habitat Characteristics, Distribution, And Abundance Of Cicindelidia Haemorrhagica (Leconte) (Coleoptera: Cicindelidae) In Yellowstone National Park, K. A. Willemssens, J. L. Bowley, L. Cavallini, E. Oberg, R.K.D. Peterson, Leon G. Higley

School of Natural Resources: Faculty Publications

No abstract provided.

Dynamic Rates Of Freshwater Drum Near The Northern Extent Of Their Range: Evidence Of Environment-Recruitment Relationships, M. Stuart, N. Kludt, M. A. Pegg, F. Montesanto, C. Lyon, C. J. Chance-Ossowski

School of Natural Resources: Faculty Publications

No abstract provided.

Long-Term Croplands Water Productivity In Response To Management And Climate In The Western Us Corn Belt, M. Khorchani, Tala Awada, M. Schmer, V. Jin, G. Birru, S.R.S. Dangal, Andrew E. Suyker, A. Freidenreich

School of Natural Resources: Faculty Publications

No abstract provided.