Biological and Chemical Physics Commons^™

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Somatic Inhibition By Microscopic Magnetic Stimulation, Hui Ye

Biology: Faculty Publications and Other Works

Electric currents can produce quick, reversible control of neural activity. Externally applied electric currents have been used in inhibiting certain ganglion cells in clinical practices. Via electromagnetic induction, a miniature-sized magnetic coil could provide focal stimulation to the ganglion neurons. Here we report that high-frequency stimulation with the miniature coil could reversibly block ganglion cell activity in marine mollusk Aplysia californica, regardless the firing frequency of the neurons, or concentration of potassium ions around the ganglion neurons. Presence of the ganglion sheath has minimal impact on the inhibitory effects of the coil. The inhibitory effect was local to the …

Recovery Of High Specific Activity Molybdenum-99 From Accelerator-Induced Fission On Low-Enriched Uranium For Technetium-99m Generators, M. Alex Brown, Nathan Johnson, Artem V. Gelis, Milan Stika, Anna G. Servis, Alex Bakken, Christine Krizmanich, Kristin Shannon, Peter Kozak, Amanda Barnhart, Chad Denbrock, Nicolas Luciani, Terry Grimm, Peter Tkac

Chemistry and Biochemistry Faculty Research

A new process was developed to recover high specific activity (no carrier added) 99Mo from electron-accelerator irradiated U3O8 or uranyl sulfate targets. The process leverages a novel solvent extraction scheme to recover Mo using di(2-ethylhexyl) phosphoric acid following uranium and transuranics removal with tri-n-butyl phosphate. An anion-exchange concentration column step provides a final purification, generating pure 99Mo intended for making 99Mo/99mTc generators. The process was demonstrated with irradiated uranium targets resulting in more than 95% 99Mo recovery and without presence of fission products or actinides in the product.

The Early Medieval Transition: Diet Reconstruction, Mobility, And Culture Contact In The Ravenna Countryside, Northern Italy, Anastasia Temkina

USF Tampa Graduate Theses and Dissertations

This research project evaluates the effects of increased mobility and culture contact on dietary practices, and on dietary variation among people buried at two northern Italian sites, Chiunsano di Ficarolo and Chiesazza di Ficarolo, located near the ancient Roman capital of Ravenna and dating 4th to 7th century CE. The Early Medieval period was a time of change, political instability, migration and invasion of the “barbarian” tribes, and diet was not unaffected. In particular, it is hypothesized that a new staple crop, millet, was introduced and that meat consumption had increased. The goal of this research is to use stable …

Protein Motifs For Proton Transfers That Build The Transmembrane Proton Gradient, Divya Kaur, Umesh Khaniya, Yingying Zhang, M. R. Gunner

Publications and Research

Biological membranes are barriers to polar molecules, so membrane embedded proteins control the transfers between cellular compartments. Protein controlled transport moves substrates and activates cellular signaling cascades. In addition, the electrochemical gradient across mitochondrial, bacterial and chloroplast membranes, is a key source of stored cellular energy. This is generated by electron, proton and ion transfers through proteins. The gradient is used to fuel ATP synthesis and to drive active transport. Here the mechanisms by which protons move into the buried active sites of Photosystem II (PSII), bacterial RCs (bRCs) and through the proton pumps, Bacteriorhodopsin (bR), Complex I and Cytochrome …

Electrochemical And Spectroscopic Characterization Of Cerium Salts And Nanoceria Material, Emily Velarde, Wei Zhou

Symposium of Student Scholars

The nanoscale form of cerium oxide, nanoceria (nano-CeO_x), has drawn great attention in recent years in electrochemical, nanomaterial research and medicinal studies due to its antibacterial properties, UV absorption, and its biochemical function as possible radical scavenger. Many new synthesis methods have achieved uniform and biocompatible nanoceria particles, and our lab has created cerium oxide particles that shows UV/Vis. absorption and X-ray patterns similar to the commercial nanoceria and nanoceria made in other research laboratories with novel synthetic methods.

This study focuses on charactering and comparing electrochemical properties of cerium inorganic salts and synthesized nanoceria. Preliminary results …

Photochemistry Of Nh2No2 And Implications For Chemistry In The Atmosphere, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Recent studies have indicated that nitramide (NH₂NO₂) may be formed more plentifully in the atmosphere than previously thought, while also being a missing source of the greenhouse gas nitrous oxide (N₂O) via catalyzed isomerization. To validate the importance of NH₂NO₂ in the Earth’s atmosphere, the ground and first electronic excited states of NH₂NO₂ were characterized and its photochemistry was investigated using multireference and coupled cluster methods. NH₂NO₂ is non-planar and of singlet multiplicity in the ground state while exhibiting large out-of-plane rotation in the triplet …

Raman Spectroscopic Characterisation Of Non Stimulated And Stimulated Human Whole Saliva, Genecy Calado, Isha Behl, Hugh Byrne, Fiona Lyng

Articles

Human saliva is a unique biofluid which can reflect the physiopathological state of an individual. The wide spectrum of molecules present in saliva, compounded by the close association of salivary composition to serum metabolites, can provide valuable information for clinical diagnostic applications through highly sensitive vibrational spectroscopic techniques such as Raman spectroscopy. However, the nature of saliva, in terms of collection and patient-related characteristics, can be considered factors which may strongly affect the Raman spectral profile of salivary samples and disrupt the search for specific salivary biomarkers in the detection of diseases. The main objective of this study was to …

Abhd5 Induced Morphological Changes On Model Membrane Systems, Nasser S. Junedi

Honors College Theses

Proper regulation of neutral lipid storage (lipogenesis) and release (lipolysis) are critical molecular processes localized to an organelle called the Lipid Droplet (LD). The LD consists of a core with neutral lipids such as triacylglycerols (TAGs) and sterol esters surrounded by a phospholipid monolayer. Dysregulation of the processes localized to the LD are involved in the pathology of various diseases such as Neutral Lipid Storage Disease, diabetes, stroke and cancer. The non-enzymatic protein ABHD5 (α-β Hydrolase Domain-Containing Protein 5), is thought to play a key role in the process of lipolysis by forming homo-oligomers on the surface of the LD …

Identifying Skeletal Puberty Stages In A Modern Sample From The United States, Jordan T. Wright

USF Tampa Graduate Theses and Dissertations

Investigating the onset and progression of puberty can provide insight and evidence for social changes regarding the transition to adulthood. There are also many social factors that can lead to variation in the timing of the onset and progression of puberty. Methods created by Mary Lewis and Fiona Shapland for assessing changes in skeletal development associated with pubertal timing were applied to computerized tomography scans (n=400) from the New Mexico Decedent Image Database and recorded in an attempt to identify adolescent growth trends in a modern skeletal sample from the United States. This is a novel study using the methods …

Pregnancy And Fertility Amongst Women With The Mthfr C677t Polymorphism: An Anthropological Review, Caroline A. Maclean

USF Tampa Graduate Theses and Dissertations

Effects of the MTHFR C677T allele on reproduction include multiple complications. The frequency of births with neural tube defects, Down Syndrome, or recurrent pregnancy loss of CC, CT, and TT mothers was measured using data collected from existing literature. Total participants n=2605 (n=1111 cases, n=1494 controls). Results show that folic acid supplementation did not prevent the incidence of NTD pregnancy in CT women. Furthermore, CT women are more fecund overall, producing more pregnancies than CC and TT women. While CT case women did have higher incidences of RPL, NTD pregnancy and DS pregnancy, this is due to the overall greater …

Listening To Women: Using A Mixed-Methods Approach To Understanding Women’S Desires And Experience During Childbirth, Nicole Loraine Falk Smith

USF Tampa Graduate Theses and Dissertations

This dissertation is based on evolutionary medicine and applied anthropological research where the narratives and biology of modern women are used to inform evolutionary theory, specifically obligate midwifery, and modern birth practices. Improvements to the US maternity care systems are needed as rates of maternal mortality and morbidity are continually higher than rates in other technologically advanced nations. Additionally, women birthing under the technocratic model of care, as is predominant in the US, report trauma and post-traumatic stress disorders due to their birthing experience, and more women are experiencing postpartum depression. Thus, I seek to use an evolutionary medicine perspective …

Remotely Controlled Enzyme Behavior Using Localized Thermal Gradients, Sarah Brown

UNO Student Research and Creative Activity Fair

No existing model describes an identified special case of enzyme behavior when directly stimulated with thermal energy via an RF field.

The ability to remotely influence cellular functions and outcomes is a new approach to targeted medicine. Nano-medicine and biotechnology are the future of medical diagnostics and treatment. The ability to remotely influence cellular functions and outcomes is a new approach to targeted medicine. Direct heating of an enzyme vs bulk heating changes the enzyme activity.

I tested how direct transfer of thermal energy changes rates of enzyme reactions. We created samples of enzymes, attached to ferrous (magnetic) nano-particles, and …

Alternative View Of Oxygen Reduction On Porous Carbon Electrocatalysts: The Substance Of Complex Oxygen-Surface Interactions, Giacomo De Falco, Marc Florent, Jacek Jagiello, Yongqiang Cheng, Luke L. Daemen, Anibal J. Ramirez-Cuesta, Teresa J. Bandosz

Publications and Research

Electrochemical oxygen reduction reaction (ORR) is an important energy-related process requiring alternative catalysts to expensive platinum-based ones. Although recently some advancements in carbon catalysts have been reported, there is still a lack of understanding which surface features might enhance their efficiency for ORR. Through a detailed study of oxygen adsorption on carbon molecular sieves and using inelastic neutron scattering, we demonstrated here that the extent of oxygen adsorption/interactions with surface is an important parameter affecting ORR. It was found that both the strength of O2 physical adsorption in small pores and its specific interactions with surface ether functionalities in the …

Diagnostics Of A Large Volume Pin-To-Plate Atmospheric Plasma Source For The Study Of Plasma Species Interactions With Cancer Cell Cultures, Laurence Scally, Chaitanya Sarangapani, Brijesh Tiwari, Renee Malone, Hugh Byrne, James Curtin, P.J. Cullen

Articles

A large gap pin-to-plate, atmospheric pressure plasma reactor is demonstrated as means of in vitro study of plasma species interactions with cell cultures. By employing optical emission and optical absorption spectroscopy, we report that the pin-to-pate plasma array had an optimal discharge frequency for cell death of 1000 Hz in ambient air for the target cancer cell line; human glioblastoma multiform (U-251MG). The detected plasma chemistry contained reactive oxygen and nitrogen species including OH, N₂, N₂⁺, and O₃. We show that, by varying the plasma discharge frequency, the plasma chemistry can be tailored …

Impact Of Dynamic Sub-Populations Within Grafted Chains On The Protein Binding And Colloidal Stability Of Pegylated Nanoparticles, Delyan Hristov, Hender Lopez, Yannick Ortin, Kate O'Sullivan, Kenneth A. Dawson, Dermot F. Brougham

Articles

Polyethylene glycol grafting has played a central role in preparing the surfaces of nano-probes for biological interaction, to extend blood circulation times and to modulate protein recognition and cellular uptake. However, the role of PEG graft dynamics and conformation in determining surface recognition processes is poorly understood primarily due to the absence of a microscopic picture of the surface presentation of the polymer. Here a detailed NMR analysis reveals three types of dynamic ethylene glycol units on PEG-grafted SiO2 nanoparticles (NPs) of the type commonly evaluated as long-circulating theranostic nano-probes; a narrow fraction with fast dynamics associated with the chain …

Coarse-Grained Simulation Of Pegylated And Tethered Protein Devices At All Experimentally Accessible Surface Residues On Β-Lactamase For Stability Analysis And Comparison, Addison K. Smith, Mehran Sultani, Joshua Wilkerson, Brandon Timmerman, Emily Long Zhao, Bradley C. Bundy, Thomas A. Knotts

Faculty Publications

PEGylated and surface-tethered proteins are used in a variety of biotechnological applications, but traditional methods offer little control over the placement of the functionalization sites on the protein. Fortunately, recent experimental methods functionalize the protein at any location on the amino acid sequence, so the question becomes one of selecting the site that will result in the best protein function. This work shows how molecular simulation can be used to screen potential attachment sites for surface tethering or PEGylation. Previous simulation work has shown promise in this regard for a model protein, but these studies are limited to screening only …

Determination Of The Rydberg Constant From The Emission Spectra Of H And He+, Kyle D. Shaffer

Ramifications

Abstract

In this experiment, the Rydberg constants for the hydrogen atom and He⁺ were determined by analysis of the emission spectra of Hand He, respectively, in comparison to the principal quantum numbers of each transition. Using both a hydrogen and then a helium atomic lamp attached to a 0.5 m grating spectrometer and a photomultiplier detector (PMT), a change in voltage detected by the PMT can be paired with a corresponding wavelength passing through the spectrometer from each emission peak in the visible to ultraviolet range. The peaks acquired from this change in voltage were analyzed to find their …

The Potential Of Raman Spectroscopy In The Diagnosis Of Dysplastic And Malignant Oral Lesions, Ola Ibrahim, M. Toner, Steven Flint, Hugh Byrne, Fiona Lyng

Articles

Early diagnosis, treatment and/or surveillance of oral premalignant lesions are important in preventing progression to oral squamous cell carcinoma (OSCC). The current gold standard is through histopathological diagnosis, which is limited by inter and intra observer and sampling errors. The objective of this work was to use Raman spectroscopy to discriminate between benign, mild, moderate and severe dysplasia and OSCC in formalin fixed paraffin preserved (FFPP) tissues. The study included 72 different pathologies from which 17 were benign lesions, 20 mildly dysplastic, 20 moderately dysplastic, 10 severely dysplastic and 5 invasive OSCC. The glass substrate and paraffin wax background were …

Using The Marcus Inverted Region And Artificial Cofactors To Create A Charge Separated State In De Novo Designed Proteins, Eskil Me Andersen

Dissertations, Theses, and Capstone Projects

To create an efficient de novo photosynthetic protein it is important to create long lived charge separated states. Achieving stable charge separation leads to an increase in the efficiency of the photosynthetic reaction which in turn leads to higher yields of end products, such as biofuels, electrical charge, or synthetic chemicals. In an attempt to create charge separated states in de novo proteins we hypothesized that we could engineer the free energy gaps in the proteins from excited primary donor (PD) to acceptor (A), and A back to ground state PD such that the forward electron transfer (ET) would be …