Digital Commons Network^™

Fusionpdb:: A Knowledgebase Of Human Fusion Proteins, Himansu Kumar, Lin-Ya Tang, Chengyuan Yang, Pora Kim

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 …

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.

Inpatient Costs Of Treating Patients With Covid-19, Kandice A Kapinos, Richard M Peters, Robert E Murphy, Samuel F Hohmann, 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 …

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 …

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.

Fauna, Flora, And Land Cover Changes Over The Last Two Decades In The Mobile-Tensaw River Delta, Gabriel De Oliveria, Steven R. Schultze, Guilherme Mataveli

Technical Reports

A technical report documenting ecosystem changes to the Mobile-Tensaw River Delta region due to urban expansion over approximately two decades (2001-2019).

Current Challenges And Future Of Agricultural Genomes To Phenomes In The Usa, C. K. Tuggle, J. L. Clarke, B. M. Murdoch, E. Lyons, N. M. Scott, B. Benes, J. D. Campbell, H. Ching, C. L. Daigle, S. D. Choudhury, J.C. M. Dekkers, J.R.R. Dorea, D. S. Erti, B. O. Fragomeni, J. E. Fulton, C. R. Guadagno, D. E. Hagen, A. S. Hess, L. M. Kramer, C. J. Lawrence-Dill, A. E. Lipka, T. Lubberstedt, F. M. Mccarthy, P. S. Schnable

School of Natural Resources: Faculty Publications

No abstract provided.

Enzymatic Degradation Of Plastic Waste: A Review Of Microbial Strategies And Future Perspectives, David Gonçalves

Seton Hall Biochemistry II Annals of Student Reviews

It is said that humans generate 2.01 billion tons of municipal waste every year and this number is projected to explode to a massive 3.40 billion tons annually by the year 2050 (Ellis, 2018). This increase in waste production perfectly underscores a growing reliance on materials that persist in ecosystems long-term. This contamination, generated from large-scale industrial practices to doing your laundry at home, is best exemplified by the proliferation of microplastics throughout the environment.

What are microplastics? The first documented use of the term microplastics can be traced to a 1990 publication in the South African Journal of Science …

Physical, Chemical, And Biological Methods Of Large-Scale Water Decontamination, Belmin Kolenovic

Seton Hall Biochemistry II Annals of Student Reviews

Considering water is the solvent of life, there is a lack of attention to what is added to it and how it impacts not only the environment but also society at large. In recent years, public scrutiny of the actions of individuals and industries concerning their negative actions on the environment has increased. General trends have seen a shift toward reusability and the reduction of pollutants. Examples include the use of reusable water bottles and the shift to biodegradable straws and paper cups. A plastic bottle casually floating atop a river is easily noticeable as a form of pollution but …

15-Yr Biomass Production In Semiarid Nebraska Sandhills Grasslands: Part 1—Plant Functional Group Analysis, B. Zhao, B. M. Stephenson, T. Awada, J. Volesky, B. Wardlow

School of Natural Resources: Faculty Publications

No abstract provided.

Project Final Report Watershed Plan For Crafts Colly, Sand Lick, And Dry Fork, Kentucky Water Resources Research Institute

KWRRI Research Reports

The North Fork: Whitesburg Tributaries Watershed Plan, developed under this project, provides a path to improve waterbodies impacted by poor wastewater treatment, coal mining, and encroachments on floodplain by housing and roadways. Crafts Colly, Sand Lick, and Dry Fork are tributaries to the North Fork of the Kentucky River. They are located just north of the City of Whitesburg, in Letcher County, which is in the coalfields of southeastern Kentucky. The three watersheds encompass 18 square miles of primarily forested lands and about 30 miles of streams, most of which are entrenched. Because of the steep mountain terrain, most of …

Lipschitz Stability For Impulsive Riemann–Liouville Fractional Differential Equations, Martin Bohner, Snezhana Hristova

Mathematics and Statistics Faculty Research & Creative Works

Initial and impulsive conditions for initial value problems of systems of nonlinear impulsive Riemann–Liouville fractional differential equations are introduced. The case when the lower limit of the fractional derivative is changed at each time point of the impulses is studied. In the case studied, the solution has a singularity at the initial time and at any point of the impulses. This leads to the need to appropriately generalize the classical concept of Lipschitz stability. Two derivative types of Lyapunov functions are utilized in order to deduce sufficient conditions for the new stability concept. Three examples are provided for illustration purpose …

Factors Associated With Acoustic Bat Presence During Spring Emergence In The Appalachian Mountains Of Western Virginia, Emily Kirk Pody

Theses, Dissertations and Capstones

Studies of threats that bats face during hibernation have increased in response to white-nose syndrome (WNS), a fungal disease that has ravaged North American bat populations. However, impacts of WNS on bat ecology during spring emergence, when bats are potentially recovering from infection and allocating resources for reproduction, is relatively understudied. As more bat species become listed at the federal and state level, the need to understand the factors associated with spring emergence is critical for improving conservation guidelines and habitat management practices. Acoustic monitoring is an efficient method for monitoring bat presence for prolonged periods of time, giving biologists …

199965, David Kerstetter

PERC Albacore sPAT Data

Datasets (and supporting material) from 4sPAT electronic tags deployed on albacore caught by pelagic longline gear in the western North Atlantic.

199953, David Kerstetter

PERC Albacore sPAT Data

Datasets (and supporting material) from 4sPAT electronic tags deployed on albacore caught by pelagic longline gear in the western North Atlantic.

199949, David Kerstetter

PERC Albacore sPAT Data

Datasets (and supporting material) from 4sPAT electronic tags deployed on albacore caught by pelagic longline gear in the western North Atlantic.

199946, David W. Kerstetter

PERC Albacore sPAT Data

Datasets (and supporting material) from 4sPAT electronic tags deployed on albacore caught by pelagic longline gear in the western North Atlantic.