Physical Sciences and Mathematics Commons^™

Integrating And Optimizing Genomic, Weather, And Secondary Trait Data For Multiclass Classification, Vamsi Manthena, Diego Jarquín, Reka Howard

Department of Statistics: Faculty Publications

Modern plant breeding programs collect several data types such as weather, images, and secondary or associated traits besides the main trait (e.g., grain yield). Genomic data is high-dimensional and often over-crowds smaller data types when naively combined to explain the response variable. There is a need to develop methods able to effectively combine different data types of differing sizes to improve predictions. Additionally, in the face of changing climate conditions, there is a need to develop methods able to effectively combine weather information with genotype data to predict the performance of lines better. In this work, we develop a novel …

Mathematical Modeling And Inverse Problems In Applications, Thanh T. Nguyen

College of Science & Mathematics Departmental Research

Mathematical models, based on ordinary or partial differential equations, are widely used to describe physical/chemical/biological processes and can be found in several applications: nondestructive testing, subsurface imaging, defense, medicine, environmental sciences, etc.

Advancing Nanofiber Research: Assessing Non Solvent Contributions To Structure Using Coaxial Electrospinning, Ping Lu

College of Science & Mathematics Departmental Research

Nanofibers play a vital role as precursors for fabricating a wide array of products spanning environmental and energy sustainability, biomedical, and healthcare applications The nanofiber characteristics, such as porosity, domains, and interfaces, are strongly influenced by the phase separation behavior among polymers, solvents, and nonsolvents in the liquid jet during the nanofabrication process However, the precise control and understanding of these phenomena at the level of individual nanofibers still need to be improved due to the need for more current technologies to provide sufficient spatial and temporal resolution To address this challenge, we employed coaxial electrospinning with a nonsolvent core …

Stabilizing G-Quadruplex Dna And Rna Structures With Ionic Liquids, Timothy Vaden

College of Science & Mathematics Departmental Research

Stabilizing DNA and RNA for long-term room-temperature storage is important for many biotechnological applications including oncology pharmaceuticals and mRNA-based vaccines (e.g. Covid vaccines). This poster shows that ionic liquids can improve the thermal stability of G-quadruplex DNA and RNA structures, and motivates further studies of ionic liquid-based materials for DNA / RNA stabilization.

Impact Of Applying Visual Design Principles To Boardwork In A Mathematics Classroom, Jennifer Rose Canizales

Theses and Dissertations

Though black boards and white boards have been a fundamental tool in the classroom for over a century, little research has been done on how to best design and present information using these boards. My study takes visual design principles and applies them to boardwork in a mathematics classroom to better organize and clarify the content. This research shows that students notice boardwork, have strong opinions on what makes boardwork good, and that the application of design principles on boards has a significant impact on students and the teacher. Students felt their cognitive load was lightened and that they were …

Conversion Of Fat To Cellular Fuel—Fatty Acids 𝛽-Oxidation Model, Sylwester M. Kloska, Krzysztof Pałczyński, Tomasz Marciniak, Tomasz Talaśka, Marissa Miller, Beata J. Wysocki, Paul Davis, Tadeusz A. Wysocki

School of Computing: Faculty Publications

𝛽-oxidation of fatty acids plays a significant role in the energy metabolism of the cell. This paper presents a 𝛽-oxidation model of fatty acids based on queueing theory. It uses Michaelis–Menten enzyme kinetics, and literature data on metabolites’ concentration and enzymatic constants. A genetic algorithm was used to optimize the parameters for the pathway reactions. The model enables real-time tracking of changes in the concentrations of metabolites with different carbon chain lengths. Another application of the presented model is to predict the changes caused by system disturbance, such as altered enzyme activity or abnormal fatty acid concentration. The model has …

Statistical Analysis Of Ribonucleotide Incorporation In Human Cells, Tejasvi Channagiri

USF Tampa Graduate Theses and Dissertations

During the DNA replication process, ribonucleotides, the building blocks of RNA, may be occasionally incorporated in the newly synthesized DNA. DNA is primarily composed of deoxyribonucleotides and there exist cellular mechanisms for removing ribonucleotides from DNA, which may point towards ribonucleotide incorporation being a replication error. Further, an excess of these ribonucleotides in the genome has been known to lead to genomic instability and has been implicated in human diseases. However, there are also hypotheses that suggest that ribonucleotides may be beneficial in certain circumstances. In this study we examine ribonucleotide incorporation in the human genome in several human cell …

Population Of Merging Compact Binaries Inferred Using Gravitational Waves Through Gwtc-3, R. Abbott, T. Abbott, F. Acernese, K. Ackley, Teviet Creighton, Mario C. Diaz, Francisco Llamas, Soma Mukherjee, Volker Quetschke, Wen Hui Wang

Physics & Astronomy Faculty Publications

We report on the population properties of compact binary mergers inferred from gravitational-wave observations of these systems during the first three LIGO-Virgo observing runs. The Gravitational-Wave Transient Catalog 3 (GWTC-3) contains signals consistent with three classes of binary mergers: binary black hole, binary neutron star, and neutron star–black hole mergers. We infer the binary neutron star merger rate to be between 10 and 1700  Gpc−3 yr−1 and the neutron star–black hole merger rate to be between 7.8 and 140  Gpc−3 yr−1, assuming a constant rate density in the comoving frame and taking the union of 90% credible intervals for methods …

Urban Mass Transit: New York State And The Mta Sustainability Initiatives On Greenhouse Gas Emission Reduction, Omosehin Moyebi

Sustainability Research & Practice Seminar Presentations

Dr. Omosehin Moyebi, Health - Urban Mass Transit: New York State and the MTA Sustainability Initiatives on Greenhouse Gas Emission Reduction

Comments For The Butte Priority Soils Operable Unit (Bpsou) Draft Final Quarterly Operations And Maintenance Report Butte Treatment Lagoon System – First Quarter 2022 (June 27, 2022), Nikia Greene

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Comment Letter For: Butte Priority Soils Operable Unit (Bpsou) Draft Final Quarterly Operations And Maintenance Report Butte Treatment Lagoons System – Second Quarter 2022 (Dated September 29, 2022), Nikia Greene

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Comment Letter For: Butte Priority Soils Operable Unit (Bpsou) Draft Final Quarterly Operations And Maintenance Report Butte Treatment Lagoons System – Third Quarter 2022 (Dated December 23, 2022), Nikia Greene

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Using Physics-Informed Neural Networks For Multigrid In Time Coarse Grid Equations, Jonathan P. Gutierrez

Mathematics & Statistics ETDs

For parallel-in-time integration methods, the multigrid-reduction-in-time (MGRIT) method has shown promising results in both improved convergence and increased computational speeds when solving evolution problems. However, one problem the MGRIT algorithm currently faces is it struggles solving hyperbolic problems efficiently. In particular, hyperbolic problems are generally solved using explicit methods and this causes issues on the coarser multigrid levels, where larger (coarser) time step sizes can violate the stability condition. In this thesis, physics-informed neural networks (PINNs) are used to evaluate the coarse grid equations in the MGRIT algorithm with the goal to improve convergence for problems with hyperbolic behavior, as …

Lacunary Eta Quotients With Identically Vanishing Coefficients, Timothy Huber, James Mclaughlin, Dongxi Ye

School of Mathematical & Statistical Sciences Faculty Publications

For |q|<1 >, define fi=∏∞n=1(1−qin) , and let (A(q),B(q)) be any of the pairs (f41,f81f22), (f41,f101f23), (f61,f42f21), (f61,f141f42), (f101,f62f21), (f141,f53f1),(f141,f82f21). For any such pair (A(q),B(q)) , define the sequences {a(n)} and {b(n)} to be the coefficients of qn of A(q) and B(q) , respectively. Then for each pair it is shown that a(n) vanishes if and only if b(n) vanishes. In each case, a criterion is given which states precisely when a(n)=b(n)=0 . Moreover, for the pairs (f261,f93f1) , (f261,f162f61) it is shown that a(n)=b(n)=0 if 12n+13 satisfies a criteria of Serre for a(n)=0 .

Virtual And In Vitro Screening Of Natural Products Identifies Indole And Benzene Derivatives As Inhibitors Of Sars-Cov-2 Main Protease (MPro), Dony Ang, Riley Kendall, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with …

Predicting Thermoelectric Power Factor Of Bismuth Telluride During Laser Powder Bed Fusion Additive Manufacturing, Ankita Agarwal, Tanvi Banerjee, Joy Gockel, Saniya Leblanc, Joe Walker, John Middendorf

Computer Science and Engineering Faculty Publications

An additive manufacturing (AM) process, like laser powder bed fusion, allows for the fabrication of objects by spreading and melting powder in layers until a freeform part shape is created. In order to improve the properties of the material involved in the AM process, it is important to predict the material characterization property as a function of the processing conditions. In thermoelectric materials, the power factor is a measure of how efficiently the material can convert heat to electricity. While earlier works have predicted the material characterization properties of different thermoelectric materials using various techniques, implementation of machine learning models …

Damped Oscillating Phosphoryl Transfer Reaction In The Cyanobacterial Circadian Clock, Hye In Jang, Pyonghwa Kim, Yongick Kim

Chemistry Faculty Research

Most organisms have circadian clocks to ensure the metabolic cycle to resonate with the rhythmic environmental changes without “damping,” or losing robustness. Cyanobacteria is the oldest and simplest form of life that is known to harbor this biological intricacy. Its KaiABC-based central oscillator proteins can be reconstituted inside a test tube, and the post-translational modification cycle occurs with 24 h periodicity. KaiC’s two major phosphorylation sites, Ser-431 and Thr-432, become phosphorylated and dephosphorylated by interacting with KaiA and KaiB, respectively. Here, we mutate Thr-432 into Ser to find the oscillatory phosphoryl transfer reaction damps. Previously, this mutant KaiC was reported …

Diverse Portfolios: Investing In Tributaries For Restoration Of Large River Fishes In The Anthropocene, Kristen L. Bouska, Brian D. Healy, Michael J. Moore, Corey G. Dunn, Jonathan J. Spurgeon, Craig P. Paukert

Nebraska Cooperative Fish and Wildlife Research Unit: Staff Publications

Rehabilitation of large Anthropocene rivers requires engagement of diverse stakeholders across a broad range of sociopolitical boundaries. Competing objectives often constrain options for ecological restoration of large rivers whereas fewer competing objectives may exist in a subset of tributaries. Further, tributaries contribute toward building a “portfolio” of river ecosystem assets through physical and biological processes that may present opportunities to enhance the resilience of large river fishes. Our goal is to review roles of tributaries in enhancing mainstem large river fish populations. We present case histories from two greatly altered and distinct large-river tributary systems that highlight how tributaries contribute …

Table Of Contents, The Editors

Coal Geology & Exploration

No abstract provided.

Ecological Environment Assessment Of Shanxi Province And Planned Mining Area Based On Coupling Remote Sensing Ecological Index (Rsei) Model, Ji Xianglin, Yan Yueguan, Guo Wei, Teng Yongjia, Zhao Chuanwu

Coal Geology & Exploration

Ecological environment quality is an important indicator to evaluate the livability, and quantitative assessment on the change rule of regional ecological environment quality could provide scientific basis for the regional ecological environment protection and governance. Taking Shanxi Province and its planned mining area as the research area, the original Remote Sensing Ecology Index (RSEI) is added with Net Primary Productivity (NPP) and Habitat Quality (HQ) to characterize the carbon sink level and habitat suitability respectively based on Google Earth Engine (GEE) platform. Herein, three representative years from 2000 to 2018 were selected for analysis. Specifically, the temporal and spatial heterogeneity …

Influencing Mechanism Of Rock Thermal Resistance On Convective Heat Transfer Of Fracture, Wang Yaning, Lu Chuan, Wang Guiling

Coal Geology & Exploration

The convective heat transfer characteristics between high temperature rocks and fluids in Enhanced Geothermal Systems (EGS) have been an important fundamental element of research on Hot Dry Rock (HDR). The thermal resistance of rock has an important influence on the convective heat transfer characteristics of fracture. In order to study its specific influence, two research methods, i.e., the theoretical analysis and the numerical simulation, were used in combination to study the heat transfer law between two parallel smooth flat plates by discussing the analytical solution and establishing the numerical model. The results show that the local Nusselt number Nu_{x …}

Research On Control System Of Drill Pipe Conveying Device Based On Fuzzy Particle Swarm Optimization, Zhang Ning, Liu Qi, Shao Junjie, Chang Jianghua, Luo Pengping, Zou Zujie

Coal Geology & Exploration

In the tripping operation of large-diameter rescue well construction, the drill pipe conveying device used for large-diameter drilling tool transportation and drill string connection. In view of the problem that it is difficult to quickly and accurately lift the drill pipe to the angle of power head for make-up due to its easy vibration in the process of positioning, the structural characteristics and working principle of the drill pipe conveying device were analyzed at first. The kinematic model for the lifting of drill pipe was deduced with the structural relationship, obtaining the mapping relationship in the motion law of the …

Numerical Simulation Of Co2 Storage In Bedded Salt Rock Storage Cavern In Subei Basin, Zong Shi, Liu Shiqi, Xu Hui, Wang Wenkai, Cao Bo, Huang Fansheng

Coal Geology & Exploration

Underground salt cavern is an effective geological body for CO₂ storage. The leakage of CO₂ along the weak interlayer of salt rock and the interface of salt layer and interlayer is the key to restrict the safe storage of CO₂ in underground salt cavern. A fluid-solid coupling mathematical model of CO₂ storage in bedded salt cavern gas storage was established based on the CO₂ salt cavern storage in Jintan area of Subei basin. On this basis, the leakage and migration law of CO₂ in salt rock and mudstone interlayer, as well as its influence …

Final 2021 Unreclaimed Sites Sampling Ur-40 Site Evaluation Summary Report, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Trait-Based Assembly Of Arbuscular Mycorrhizal Fungal Communities Determines Soil Carbon Formation And Retention, Caitlyn C. A. Horsch, Pedro M. Antunes, Catherine Fahey, A. Stuart Grandy, Cynthia M. Kallenbach

Faculty Publications

Fungi are crucial for soil organic carbon (SOC) formation, especially for the more persistent mineral-associated organic C (MAOC) pool. Yet, evidence for this often overlooks arbuscular mycorrhizal fungi (AMF) communities and how their composition and traits impact SOC accumulation.

We grew sudangrass with AMF communities representing different traits conserved at the family level: competitors, from the Gigasporaceae family; ruderals, from the Glomeraceae family; or both families combined. We labeled sudangrass with 13C-CO2 to assess AMF contributions to SOC, impacts on SOC priming, and fungal biomass persistence in MAOC.

Single-family AMF communities decreased total SOC by 13.8%, likely due to fungal …

Lithium And Lithium Isotope Behavior During High Temperature Solid/Fluid Exchanges: Examples From Iceland And The Izu-Bonin Forearc, Alex Maruszczak

USF Tampa Graduate Theses and Dissertations

The development of a method for lithium isotopic measurement was developed using a quadrupole, single-collector ICP-MS. Measured precision was ±1.00‰ 2σ over a 15-month period based on measurements of international rock standards. A 1-hour leach using cold, HCl was sufficient to remove alteration-related Li in minimally to moderately altered seafloor basalts. Measurements on the Holocene ages lavas from the neovolcanic zones of Iceland suggest no systematic Li isotopic variability among the differing Icelandic sources. Felsic samples from Hekla and Pumice contain elevated Li contents of >18ug/g while the tholeiitic and alkaline basalts are <8ug/g Li. Most of the island lies around MORB values of ~+3 to +5‰ with the exception of Western Volcanic Zone samples that show evidence for seawater inputs. The RN-17 drillcore, which penetrates >3000m through a hydrothermal system in the …

Mechanism Of Coal Fine-Bubble Coupling In The Unsaturated Flow Stage Of Coalbed Methane Drainage, Han Wenlong, Li Yong, Chen Xiangsheng, Zhuo Qiming, Wang Yanbin

Coal Geology & Exploration

To reveal the mechanism of interaction between coal fines and gas in the unsaturated flow stage of coalbed methane (CBM) drainage, it is essential to formulate the drainage system and improve the gas production. The effect of air bubbles with different diameters on coal fines with different particle sizes and densities was systematically experimented through the experiment device for microscopic interaction between the air bubble and the coal fines. Meanwhile, the influence of air bubbles on the migration trajectory and velocity of coal fines and the characteristics of coal fine capturing by air bubbles were also analyzed. The results show …

Optimization Of Cemented Filling Material Ratio Based On Rsm-Bbd Method And Engineering Application, Wang Shushuai, Xu Bin, Li Yang, Yang Zhen

Coal Geology & Exploration

In view of the problems of large stacking of solid waste caused by roof caving method in coal seam mining and imbalance between mining and filling in long-wall cemented backfilling, the No.31 ming area of Chahasu Coal Mine in Inner Monogolia uses continuous mining and filling roadway cemented backfilling mining technology, adopting the “mining at intervals of three” mining method and the “three with high strength filling and one with low strength filling” filling mode. The filling material ratio has an important influence on the filling cost and effect. In order to solve the problems of high cement consumption and …

Mechanical Properties And Mechanism Of Co-Curing Saline Soil With Coal Solid Waste, Dong Chenxi, Wang Nianqin, Li Jiangshan, Chen Xin, Yan Xusheng, Ma Wei

Coal Geology & Exploration

Under the research background of resource utilization of solid wastes in the arid and semiarid regions, a new curing material was developed with the coal wastes (such as the coal gangue (CG) and coal metakaolin (CMK)), the carbide slag (CS) that is a waste material readily available in the arid region, and the ordinary Portland cement (OPC). Besides, its mechanical properties and microscopic change mechanism in curing of saline soil in the arid and semi-arid regions were discussed. Based on the laboratory experiment, the unconfined compressive strength (UCS) characteristics of curing saline soil in different ages were studied by replacing …

Wavefield Separation Of P- And S-Waves Based On Modified Pseudo-Helmholtz Decomposition Operator In Transverse Isotropic Media, Liu Zhaoshun, Du Qizhen, Lyu Wenhao, Zhou Shihao, Fu Liyun

Coal Geology & Exploration

The separation of P- and S-wave fields is a significant step in elastic reverse-time migration (ERTM), which can effectively eliminate the waveform crosstalk and image artifacts, thus improving the precision of imaging. In anisotropic media, nonstationary spatial filters or low-rank approximation methods are commonly used to separate the wavefields. However, the application of multiple Fourier transforms results in the high computation costs of the above wavefield separation methods. Based on the idea of constructing the isotropic decoupling equations of P- and S- waves with the Helmholtz operator, a modified pseudo-Helmholtz decomposition operator was proposed to eliminate the amplitude distortion. Then, …