Physical Sciences and Mathematics Commons^™

Usf Jamovi Tutorial Project: Open Education Resource, Aline Hitti, Saera Khan

USF OER Faculty Grant

Jamovi is an open source free software that USF staff, faculty and student can download to carry out any statistical analyses. The current report summarizes the progress made on an Open Education Resource Grant funded project, which aimed to created Jamovi tutorials. In this report, student feedback and faculty reaction are summarized after one semester of using the tutorials created.

A Numerical Solution Of Water Flow In Unsaturated Soil With Evapotraspiration, Andrei Ludu, Harihar Khanal, Ramesh Chandra Timsina, Kedar Nath Uprety

Publications

Flow movement in unsaturated soil can be expressed by Richards equation. This equation can be obtained by applying the mass conversation law and the Darcy law. In this work, we solve one-dimensional Kirchhoff transformed Richards equation with loss of water due to the evaporation of unsaturated porous media (soils) and transpiration of plants numerically using Crank-Nicolson method. The result has compared with evapotranspiration function and without it in the governing equation. It has found that an additional work in time and flow movement is needs to reach the given boundary condition for the model without evapotranspiration.

Evaluating Technology-Mediated Collaborative Workflows For Telehealth, Christopher Bondy Ph.D., Pengcheng Shi, Pamela Grover Md, Vicki Hanson, Linlin Chen, Rui Li

Articles

Goals: This paper discusses the need for a predictable method to evaluate gains and gaps of collaborative technology-mediated workflows and introduces an evaluation framework to address this need. Methods: The Collaborative Space Analysis Framework (CS-AF), introduced in this research, is a cross-disciplinary evaluation method designed to evaluate technology-mediated collaborative workflows. The 5-step CS-AF approach includes: (1) current-state workflow definition, (2) current-state (baseline) workflow assessment, (3) technology-mediated workflow development and deployment, (4) technology-mediated workflow assessment, (5) analysis, and conclusions. For this research, a comprehensive, empirical study of hypertension exam workflow for telehealth was conducted using the CS-AF approach. Results: The CS-AF …

Silver Bow Creek/Butte Area Npl Site, Trec Inc., A Woodard And Curran Company

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

The Smooth 4-Genus Of (The Rest Of) The Prime Knots Through 12 Crossings, Mark Brittenham, Susan Hermiller

Department of Mathematics: Faculty Publications

We compute the smooth 4-genera of the prime knots with 12 crossings whose values, as reported on the KnotInfo website, were unknown. This completes the calculation of the smooth 4-genus for all prime knots with 12 or fewer crossings.

Silver Bow Creek/Butte Area Npl Site, Trec Inc., A Woodard And Curran Company

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Silver Bow Creek Butte Area Npl Site 2022 Draft Butte Priority Soils Operable Unit Interim Site-Wide Groundwater Monitoring Qapp. Consent Decree- Civil Action No. Cv 89-039-Bu-She, Josh Bryson

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

A Framework Of Web-Based Dark Patterns That Can Be Detected Manually Or Automatically, Ioannis Stavrakakis, Andrea Curley, Dympna O'Sullivan, Damian Gordon, Brendan Tierney

Articles

This research explores the design and development of a framework for the detection of Dark Patterns, which are a series of user interface tricks that manipulate users into actions that they do not intend to do, for example, share more data than they want to, or spend more money than they plan to. The interface does this using either deception or other psychological nudges. User Interface experts have categorized a number of these tricks that are commonly used and have called them Dark Patterns. They are typically varied in their form and what they do, and the goal of this …

Numerical Investigation On The Effect Of Spectral Radiative Heat Transfer Within An Ablative Material, Raghava S. C. Davuluri, Rui Fu, Kaveh A. Tagavi, Alexandre Martin

Mechanical Engineering Faculty Publications

The spectral radiative heat flux could impact the material response. In order to evaluate it, a coupling scheme between KATS - MR and P1 approximation model of radiation transfer equation (RTE) is constructed and used. A Band model is developed that divides the spectral domain into small bands of unequal widths. Two verification studies are conducted: one by comparing the simulation computed by the Band model with pure conduction results and the other by comparing with similar models of RTE. The comparative results from the verification studies indicate that the Band model is computationally efficient and can be used to …

On The Documentation Of Refactoring Types, Eman Abdullah Alomar, Jiaqian Liu, Kenneth Addo, Mohamed Wiem Mkaouer, Christian D. Newman, Ali Ouni, Zhe Yu

Articles

Commit messages are the atomic level of software documentation. They provide a natural language description of the code change and its purpose. Messages are critical for software maintenance and program comprehension. Unlike documenting feature updates and bug fixes, little is known about how developers document their refactoring activities. Specifically, developers can perform multiple refactoring operations, including moving methods, extracting classes, renaming attributes, for various reasons, such as improving software quality, managing technical debt, and removing defects. Yet, there is no systematic study that analyzes the extent to which the documentation of refactoring accurately describes the refactoring operations performed at the …

Dynamic Relationship Study Between The Observed Seismicity And Spatiotemporal Pattern Of Lineament Changes In Palghar, North Maharashtra (India), Biswajit Nath, Ramesh P. Singh, Vineet K. Gahalaut, Ajay P. Singh

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The Palghar region (north Maharashtra, India), located in the northwestern part of the stable continental region of India, experienced a low magnitude earthquake swarm, which was initiated in September 2018 and is continuing to date (as of October 2021). From December 2018 to December 2020, ~5000 earthquakes with magnitudes from M1.2 to M3.8 occurred in a small region of 20 × 10 km². These earthquakes were probably triggered by fluid migration during seasonal rainfall. In this study, we have used multi-temporal Landsat satellite data of the year 2000, 2015, 2018, 2019, and 2020, extracted lineaments, and studied the …

The Sonora Substellar Atmosphere Models. Ii. Cholla: A Grid Of Cloud-Free, Solar Metallicity Models In Chemical Disequilibrium For The Jwst Era, Theodora Karalidi, Mark Marley, Jonathan J. Fortney, Caroline Morley, Didier Saumon, Roxana Lupu, Channon Visscher, Richard Freedman

Faculty Work Comprehensive List

Exoplanet and brown dwarf atmospheres commonly show signs of disequilibrium chemistry. In the James Webb Space Telescope (JWST) era, high-resolution spectra of directly imaged exoplanets will allow the characterization of their atmospheres in more detail, and allow systematic tests for the presence of chemical species that deviate from thermochemical equilibrium in these atmospheres. Constraining the presence of disequilibrium chemistry in these atmospheres as a function of parameters such as their effective temperature and surface gravity will allow us to place better constraints on the physics governing these atmospheres. This paper is part of a series of works presenting the Sonora …

Topics In Analytic Number Theory And Consecutive Primitive Roots, Nelson Carella

Publications and Research

This monograph proves the existence of various configurations of $(k+1)$-tuples of consecutive and quasi consecutive primitive roots $n+a_0, n+a_1, n+a_2, ,,,, n+a_k$ in the finite field $\F_p$, where $a_0,a_1, \ldots, a_k$ is a fixed $(k+1)$-tuples of distinct integers.

Exploring The Relationships Among Stoichiometric Coefficients, Number Of Transferred Electrons, Mean Oxidation Number Of Carbons, And Oxidative Ratio In Organic Combustion Reactions, Pong Kau Yuen, Cheng Man Diana Lau

Faculty Publications

Combustion reactions, stoichiometry, and redox reactions are some of the basic contents in chemistry curriculum. Although the counting of transferred electrons is critical in redox reactions, assigning mean oxidation number of organic carbons (ONc) is not always easy. Even though the relationship between the oxidative ratio (OR) and ONc is known, the relationship between the number of transferred electrons (Te−) and OR has not been thoroughly studied. The H-atom method has already been developed to balance and deduct organic combustion reactions. It can be used further to help establish the relationships among the stoichiometric coefficients (SC), the number of transferred …

Solution-Processed Flexible Broadband Zno Photodetector Modified By Ag Nanoparticles, N. P. Klochko, K. S. Klepikova, I. V. Khrypunova, V. R. Kopach, I. I. Tyukhov, S. I. Petrushenko, S. V. Dukarov, V. M. Sukhov, M. V. Kirichenko, A. L. Khrypunova

Faculty Research, Scholarly, and Creative Activity

In this work, we present flexible broadband photodetectors (PDs) fabricated by a deposition of nanostructured zinc oxide (ZnO) films on polyimide (PI) substrates by using cheap and scalable aqueous method Successive Ionic Layer Adsorption and Reaction (SILAR). In order to increase the long-wavelength absorption of the nanostructured ZnO layer, we created its intrinsic defects, including oxygen vacancies by post-treatment at 300 °C in vacuum and thus the light-sensitive material ZnO/PI was obtained. Then we applied silver nanoparticles (Ag NPs) from a silver sol onto a nanostructured ZnO film, which were visualized using SEM in the form of spheres up to …

A Mathematical Model For Transport And Growth Of Microbes In Unsaturated Porous Soil, Harihar Khanal, Andrei Ludu, Ramesh Chandra Timsina, Kedar Nath Uprety

Publications

In this work, we develop a mathematical model for transport and growth of microbes by natural (rain) water infiltration and flow through unsaturated porous soil along the vertical direction under gravity and capillarity by coupling a system of advection diffusion equations (for concentration of microbes and their growth-limiting substrate) with the Richards equation. (e model takes into consideration several major physical, chemical, and biological mechanisms. (e resulting coupled system of PDEs together with their boundary conditions is highly nonlinear and complicated to solve analytically. We present both a partial analytic approach towards solving the nonlinear system and finding the main …

A Nanoscale Shape-Discovery Framework Supporting Systematic Investigations Of Shape-Dependent Biological Effects And Immunomodulation, Wei Zhang, Hender Lopez, Luca Boselli, Paolo Bigini, André Perez-Potti, Zengchun Xie, Valentina Castagnola, Qi Cai, Camila P. Silveira, Joao M. De Araujo, Laura Talamini, Nicolò Panini, Giuseppe Ristagno, Martina B. Violatto, Stéphanie Devineau, Marco P. Monopoli, Mario Salmona, Valeria A. Giannone, Sandra Lara, Kenneth A. Dawson, Yan Yan

Articles

Since it is now possible to make, in a controlled fashion, an almost unlimited variety of nanostructure shapes, it is of increasing interest to understand the forms of biological control that nanoscale shape allows. However, a priori rational investigation of such a vast universe of shapes appears to present intractable fundamental and practical challenges. This has limited the useful systematic investigation of their biological interactions and the development of innovative nanoscale shape-dependent therapies. Here, we introduce a concept of biologically relevant inductive nanoscale shape discovery and evaluation that is ideally suited to, and will ultimately become, a vehicle for machine …

The Circle Of Life: The Mathematics Of Predator-Prey Dynamics, John Butler, Rebecca Brady

Articles

Some animals hunt other animals to feed themselves; these animals are called predators. Animals who are hunted and eaten are known as prey. What do you think would happen if a predator were introduced to an ecosystem where the prey previously lived without fear of being hunted? Would the new predator eat all the prey animals until they go extinct? Actually, the relationship between predator and prey is far more interesting than this. In this article, we show what the predator-prey relationship looks like over time and explain how scientists can make predictions about future population levels, all using basic …

Response To Agency Comments Received December 15 On Silver Bow Creek Butte Area Npl Site 2022 Draft Butte Priority Soils Operable Unit Interim Site-Wide Surface Water Monitoring Quality Assurance Project Plan. Consent Decree- Civil Action No. Cv 89-039-Bu-She, Josh Bryson

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Silver Bow Creek/Butte Area Npl Site, Trec Inc., A Woodard And Curran Company

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Measurement Of Differential Branching Fractions Of Inclusive B →Xuℓ+Νℓ Decays, L. Cao, W. Sutcliffe, R. Van Tonder, F. U. Bernlochner, I. Adachi, H. Aihara, D. M. Asner, T. Aushev, R. Ayad, V. Babu, S. Bahinipati, P. Behera, K. Belous, J. Bennett, M. Bessner, T. Bilka, J. Biswal, A. Bobrov, M. Bračko

Faculty and Student Publications

The first measurements of differential branching fractions of inclusive semileptonic B→Xuℓ+νℓ decays are performed using the full Belle data set of 711 fb-1 of integrated luminosity at the (4S) resonance and for ℓ=e, μ. With the availability of these measurements, new avenues for future shape-function model-independent determinations of the Cabibbo-Kobayashi-Maskawa matrix element |Vub| can be pursued to gain new insights in the existing tension with respect to exclusive determinations. The differential branching fractions are reported as a function of the lepton energy, the four-momentum-transfer squared, light-cone momenta, the hadronic mass, and the hadronic mass squared. They are obtained by subtracting …

Negative Order Kdv Equation With No Solitary Traveling Waves, Miguel Rodriguez, Jing Li, Zhijun Qiao

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

We consider the negative order KdV (NKdV) hierarchy which generates nonlinear integrable equations. Selecting different seed functions produces different evolution equations. We apply the traveling wave setting to study one of these equations. Assuming a particular type of solution leads us to solve a cubic equation. New solutions are found, but none of these are classical solitary traveling wave solutions.

Splashing Of Large Helium Nanodroplets Upon Surface Collisions, Paul Martini, Simon Albertini, Felix Laimer, Miriam Meyer, Michael Gatchell, Olof E. Echt, Fabio Zappa, Paul Scheier

Faculty Publications

In the present work we observe that helium nanodroplets colliding with surfaces can exhibit splashing in a way that is analogous to classical liquids. We use transmission electron microscopy and mass spectrometry to demonstrate that neutral and ionic dopants embedded in the droplets are efficiently backscattered in such events. High abundances of weakly bound He-tagged ions of both polarities indicate a gentle extraction mechanism of these ions from the droplets upon collision with a solid surface. This backscattering process is observed for dopant particles with masses up to 400 kilodaltons, indicating an unexpected mechanism that effectively lowers deposition rates of …

Explaining Deep Learning Models For Tabular Data Using Layer-Wise Relevance Propagation, Ihsan Ullah, Andre Rios, Vaibhov Gala, Susan Mckeever

Articles

Trust and credibility in machine learning models are bolstered by the ability of a model to explain its decisions. While explainability of deep learning models is a well-known challenge, a further challenge is clarity of the explanation itself for relevant stakeholders of the model. Layer-wise Relevance Propagation (LRP), an established explainability technique developed for deep models in computer vision, provides intuitive human-readable heat maps of input images. We present the novel application of LRP with tabular datasets containing mixed data (categorical and numerical) using a deep neural network (1D-CNN), for Credit Card Fraud detection and Telecom Customer Churn prediction use …

All-Sky Search For Short Gravitational-Wave Bursts In The Third Advanced Ligo And Advanced Virgo Run, R. Abbott, T. Abbott, F. Acernese, K. Ackley, Teviet Creighton, Mario C. Diaz, F. Llamas, Soma Mukherjee, Volker Quetschke, Wenhui Wang

Physics and Astronomy Faculty Publications and Presentations

This paper presents the results of a search for generic short-duration gravitational-wave transients in data from the third observing run of Advanced LIGO and Advanced Virgo. Transients with durations of milliseconds to a few seconds in the 24–4096 Hz frequency band are targeted by the search, with no assumptions made regarding the incoming signal direction, polarization, or morphology. Gravitational waves from compact binary coalescences that have been identified by other targeted analyses are detected, but no statistically significant evidence for other gravitational wave bursts is found. Sensitivities to a variety of signals are presented. These include updated upper limits on …

Workflow Critical Path: A Data-Oriented Critical Path Metric For Holistic Hpc Workflows, Daniel D. Nguyen, Karen L. Karavanic

Computer Science Faculty Publications and Presentations

Current trends in HPC, such as the push to exascale, convergence with Big Data, and growing complexity of HPC applications, have created gaps that traditional performance tools do not cover. One example is Holistic HPC Workflows — HPC workflows comprising multiple codes, paradigms, or platforms that are not developed using a workflow management system. To diagnose the performance of these applications, we define a new metric called Workflow Critical Path (WCP), a data-oriented metric for Holistic HPC Workflows. WCP constructs graphs that span across the workflow codes and platforms, using data states as vertices and data mutations as edges. …

Sharing The Salt Bowl: Counterion Identity Drives N-Alkyl Resorcinarene Affinity For Pyrophosphate In Water, Kwaku Twum, Seyed Iraj Sadraei, Jordan Feder, S. Maryamdokht Taimoory, Kari Rissanen, John F. Trant, Ngong Kodiah Beyeh

Chemistry and Biochemistry Publications

N-Alkyl ammonium resorcinarene chloride receptors, NARX4, have been shown to act as high-sensitivity detectors of pyrophosphate (PPi), a biomarker of disease, in aqueous media through the chloride-to-PPi exchange [NAR(Cl)4 to NARPPi]. The nature of the anion of the macrocyclic NARX4 (X = Cl−, Br−, triflate OTf−) receptor greatly influences the PPi-affinity in aqueous media. The binding affinity for [NAR (Cl)4] is 3.61 × 105 M−1, while the NAR (Br)4 and NAR (OTf)4 show stronger binding of 5.30 × 105 M−1, and 6.10 × 105 M−1, respectively. The effects of upper rim ammonium cation, –N+H2R substituents (R = 3-hydroxypropyl, cyclohexyl, …

High-Resolution Cryo-Electron Microscopy Structure Of Photosystem Ii From The Mesophilic Cyanobacterium, Synechocystis Sp. Pcc 6803, Christopher J. Gisriel, Jimin Wang, Jinchan Liu, David A. Flesher, Krystle M. Reiss, Hao-Li Huang, Ke R. Yang, William H. Armstrong, M. R. Gunner, Victor S. Batista, Richard J. Debus, Gary W. Brudvig

Publications and Research

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a highresolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the …

Genetic Contributors Of Incident Stroke In 10,700 African Americans With Hypertension: A Meta-Analysis From The Genetics Of Hypertension Associated Treatments And Reasons For Geographic And Racial Differences In Stroke Studies, Nicole D. Armstrong, Vinodh Srinivasasainagendra, Amit Patki, Rikki M. Tanner, Bertha A. Hidalgo, Hemant K. Tiwari, Nita A. Limdi, Ethan M. Lange, Leslie A. Lange, Donna K. Arnett, Marguerite R. Irvin

Epidemiology and Environmental Health Faculty Publications

Background: African Americans (AAs) suffer a higher stroke burden due to hypertension. Identifying genetic contributors to stroke among AAs with hypertension is critical to understanding the genetic basis of the disease, as well as detecting at-risk individuals.

Methods: In a population comprising over 10,700 AAs treated for hypertension from the Genetics of Hypertension Associated Treatments (GenHAT) and Reasons for Geographic and Racial Differences in Stroke (REGARDS) studies, we performed an inverse variance-weighted meta-analysis of incident stroke. Additionally, we tested the predictive accuracy of a polygenic risk score (PRS) derived from a European ancestral population in both GenHAT and REGARDS AAs …

Dysregulation Of Dna Methylation And Epigenetic Clocks In Prostate Cancer Among Puerto Rican Men, Anders Berglund, Jaime Matta, Jarline Encarnación-Medina, Carmen Ortiz-Sanchéz, Julie Dutil, Raymond Linares, Joshua Marcial, Caren Abreu-Takemura, Natasha Moreno, Ryan Putney, Ratna Chakrabarti, Hui Yi Lin, Kosj Yamoah, Carlos Diaz Osterman, Liang Wang, Jasreman Dhillon, Youngchul Kim, Seung Joon Kim, Gilberto Ruiz-Deya, Jong Y. Park

School of Public Health Faculty Publications

In 2021, approximately 248,530 new prostate cancer (PCa) cases are estimated in the United States. Hispanic/Latinos (H/L) are the second largest racial/ethnic group in the US. The objective of this study was to assess DNA methylation patterns between aggressive and indolent PCa along with ancestry proportions in 49 H/L men from Puerto Rico (PR). Prostate tumors were classified as aggressive (n = 17) and indolent (n = 32) based on the Gleason score. Genomic DNA samples were extracted by macro-dissection. DNA methylation patterns were assessed using the Illumina EPIC DNA methylation platform. We used ADMIXTURE to estimate global ancestry proportions. …