Digital Commons Network^™

Techniques In Multi-Omics Data Integration To Develop A Novel Proteogenomics Framework For Identification Of Proteoforms, Kanishka Manna

Theses and Dissertations

Multi-omics experimental approaches are becoming a mainstream practice in systems biology underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of different types of diseases for targeted therapy. Proteogenomics, a sub-field within the broad field of multi-omics incorporates techniques to integrate genomics, transcriptomics and proteomics data for efficient identification of novel proteoforms or protein isoforms. There are multitude of challenges when applying proteogenomics analyses, such as improper integration of each omics data type, missing structural annotations, inefficient identification of splice-junctions, novel genes, etc. This dissertation will outline a novel and integrative proteogenomics pipeline that …

Um Graduate Chosen As 2023 Marshall Scholar, Clara Turnage

University of Mississippi News

OXFORD, Miss. – University of Mississippi alumna Jilkiah Bryant has been awarded a prestigious Marshall Scholarship, making her the third Marshall Scholar in the university’s history.

12.11.2023 Orsp Connect, Liz Williamson

ORED Newsletter

December 11, 2023 Newsletter

Sexually Transmitted Infection Prevention Perspectives In Black Men Who Have Sex With Men Taking Preexposure Prophylaxis In New Orleans, Meredith E. Clement, Jeremy Beckford, Aish Lovett, Julia Siren, Marie Adorno, Sara Legrand, Marsha Bennett, Jamilah Taylor, Emily Hanlen-Rosado, Brian Perry, Amy Corneli

School of Medicine Faculty Publications

INTRODUCTION: Profound sexual health disparities exist for Black men who have sex with men (MSM) in the US South, including a high prevalence of sexually transmitted infections (STIs). Sexually transmitted infection prevention strategies beyond condoms are needed for Black MSM taking preexposure prophylaxis (PrEP). METHODS: We conducted in-depth interviews with Black MSM taking PrEP in New Orleans, Louisiana. Informed by the Health Belief Model, we asked about participants' perceived susceptibility, severity, and concerns regarding STIs, and perceived benefits of STI prevention. We also asked about willingness to use various STI prevention strategies, including antibiotic prophylaxis. Interviews were audio-recorded and analyzed …

Synthesis Of Yaku'amide A Analogues And Progress Toward Synthesis Of Virosine A, Alexander S. Ramos

Theses and Dissertations

The first project in this dissertation endeavors to outline the total synthesis of yaku'amide A and its analogs. Yaku'amide A is a natural product comprised of dehydroamino acids, including E-dehydro isoleucine, and unprecedented Z-dehydro isoleucine. These amino acids present a significant challenge to their synthesis owing to their unsymmetrical nature. To simplify the synthesis process, we synthesized analogs by substituting the E and Z dehydroamino acids with symmetrical subunits. This substitution facilitated the synthesis process and enabled us to obtain a similar three-dimensional structure to that of the natural product. Furthermore, biological testing of the simplified analogs revealed potency similar …

Ultrafast Electronic Relaxation Pathways Of The Molecular Photoswitch Quadricyclane, Kurtis D. Borne, Joseph C. Cooper, Michael N. R. Ashfold, Julien Bachmann, Surjendu Bhattacharyya, Rebecca Boll5, Matteo Bonanomi, Michael Bosch, Carlo Callegari, Martin Centurion, Marcello Coreno, Basile F. E. Curchod, Miltcho B. Danailov, Alexander Demidovich, Michele Di Fraia, Benjamin Erk, Davide Faccialà, Raimund Feifel, Ruaridh J. G. Forbes, Christopher S. Hansen, David M. P. Holland, Rebecca A. Ingle, Roland Lindh, Lingyu Ma, Henry G. Mcghee, Sri Bhavya Muvva, Joao Pedro Figueira Nunes, Asami Odate, Shashank Pathak, Oksana Plekan, Kevin C. Prince, Primoz Rebernik, Arnaud Rouzée, Artem Rudenko, Alberto Simoncig, Richard J. Squibb, Anbu Selvam Venkatachalam, Caterina Vozzi, Peter M. Weber, Adam Kirrander, Daniel Rolles

Martin Centurion Publications

The light-induced ultrafast switching between molecular isomers norbornadiene and quadricyclane can reversibly store and release a substantial amount of chemical energy. Prior work observed signatures of ultrafast molecular dynamics in both isomers upon ultraviolet excitation but could not follow the electronic relaxation all the way back to the ground state experimentally. Here we study the electronic relaxation of quadricyclane after exciting in the ultraviolet (201 nanometres) using time-resolved gas-phase extreme ultraviolet photoelectron spectroscopy combined with non-adiabatic molecular dynamics simulations. We identify two competing pathways by which electronically excited quadricyclane molecules relax to the electronic ground state. The fast pathway (<100 femtoseconds) is distinguished by effective coupling to valence electronic states, while the slow pathway involves initial motions across Rydberg states and takes several hundred femtoseconds. Both pathways facilitate interconversion between the two isomers, albeit on different timescales, and we predict that the branching ratio of norbornadiene/ quadricyclane products immediately after returning to the electronic ground state is approximately 3:2.

Teaching Engineering Design-Based Integrated Stem In Rural Contexts: Nurturing Future Designers, Jung Han, Euisuk Sung, Todd Kelley, John Geoffrey Knowles

Publications and Research

There is a notable shift towards prioritizing the teaching of engineering design within K-12 education, coupled with a strong recommendation for engineering design-based integrated STEM education. This approach underscores the sharing of science and engineering practices as a means to facilitate the learning of various STEM disciplines. Nonetheless, the implementation of integrated STEM education in rural schools poses challenges due to constrained resources and a shortage of high-quality programs. To present a tangible instance of design-based integrated STEM education within a rural setting, this study presents a model lesson that showcases the integration of interdisciplinary problem-solving skills within a genuine …

Response Differences Of Two Maize Hybrid Varieties To The Application Of Bioagent-Ameliorant And Chicken Manure In Fertile Soil, Endang Kantikowati, Karya, Yudi Yusdian, Dian Murti Minangsih, Tien Turmuktini, Erna Yuliani, Fija Faujiah

Jurnal Kultivasi

To ensure adequate nutrition for the growth of maize (Zea mays L.) in sustainable agriculture, it is necessary to apply bio-agent soil conditioner and manure. This study aims to determine the effect of doses of bioagent-ameliorant and chicken manure on growth and yield components. The research was conducted in highland with an altitude 800 m above sea level. This study used an experimental method with two sets of experiments, namely experiments using one and two-cobs maize cultivars. The experiment used a randomized block design (RBD) with two treatment factors and three replications. The first treatment factor was the dose of …

Exploring Policies & Practices For The Private Sector To Advance Women’S Economic Empowerment And Prevent Gender Based Violence In Post-Conflict Countries, Amina Helal

Theses and Dissertations

This study aims to investigate the role of the private sector in advancing women’s economic empowerment and gender-based violence prevention with a focus on post-conflict countries. It explores challenges facing them, and opportunities to be seized by governments and other stakeholders in this regard. The study also sheds light on the gap in the private sector’s awareness and commitment to achieve the UN Sustainable Development Goals (SDGs) and to implement the UN Women, Peace and Security (WPS) agenda in post-conflict countries. It explores the different possible engagements of the private sector in response to the research question. The thesis also …

Advanced Diffusion Mri Technique And Applications In Placenta And Brain, Zhexian Sun

McKelvey School of Engineering Graduate Student Theses & Dissertations

Among a series of contrasts of MRI, diffusion MRI (dMRI) is different from conventional MRI by its ability to capture information about the random movement of water molecules and their interaction with local tissue microstructures. This capability holds the potential to reveal intricate subvoxel microstructural information linked to pathological changes, offering potential imaging biomarkers. A higher-order diffusion analysis model helps to yield more accurate and specific parameters but requires more extensive parameter tuning and higher image quality. In this study, we firstly fine-tuned the previously developed diffusion basis spectrum imaging (DBSI) method to strike a balance between efficiency and accuracy …

Engineering Exosomes To Specifically Target The Mitochondria Of Brain Cells, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Michigan Tech Publications

Mitochondrial dysfunction is associated with various health conditions, including cardiovascular and neurodegenerative diseases. Mitochondrial-targeting therapy aims to restore or enhance mitochondrial function to treat or alleviate these conditions. Exosomes, small vesicles that cells secrete, containing a variety of biomolecules, are critical in cell-to-cell communication and have been studied as potential therapeutic agents. Exosome-based therapy has the potential to treat both cardiovascular and neurodegenerative diseases. Combining these two approaches involves using exosomes as carriers to transport mitochondrial-targeting agents to dysfunctional or damaged mitochondria within target cells. This article presents a new technique for engineering brain-derived exosomes that target mitochondria and has …

Engineering Exosomes To Specifically Target The Mitochondria Of Brain Cells, Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi

Michigan Tech Publications

Mitochondrial dysfunction is associated with various health conditions, including cardiovascular and neurodegenerative diseases. Mitochondrial-targeting therapy aims to restore or enhance mitochondrial function to treat or alleviate these conditions. Exosomes, small vesicles that cells secrete, containing a variety of biomolecules, are critical in cell-to-cell communication and have been studied as potential therapeutic agents. Exosome-based therapy has the potential to treat both cardiovascular and neurodegenerative diseases. Combining these two approaches involves using exosomes as carriers to transport mitochondrial-targeting agents to dysfunctional or damaged mitochondria within target cells. This article presents a new technique for engineering brain-derived exosomes that target mitochondria and has …

Shading The Future: A Gis-Based Approach To Optimal Tree Planting For Urban Heat Mitigation At Northern Michigan University, Mary Kelly

Conspectus Borealis

Increasing tree canopy cover is a powerful tool for mitigating the effects of urban heat on the natural and built environment, specifically the effects of ecosystem stress and air quality. Heat can also place stress on human health. Northern Michigan University (NMU) is proposing to build a new tree nursery on campus, which would help alleviate urban heat in Marquette. Finding suitable areas at NMU to plant new trees from this nursery is an essential component of this effort. A goal of my project was to provide this helpful information. Using GIS and remote sensing techniques in ArcGIS Pro and …

Evaluating Militant Decision-Making With Information Science: The Irish Republican Movement During The "Troubles", Joshua C. Eastin, Emily Kalah Gade, Michael Gabbay

Political Science Faculty Publications and Presentations

Why do militant groups decide to escalate or deescalate their use of violence in conflict? Examining the case of the “Troubles” in Northern Ireland, we analyze groups that adopt violence as a political strategy and evaluate factors that influence its application. To do so, we adopt a novel empirical approach to the study of militant groups. Drawn from information science, this approach enables estimation of variable influence and uncertainty within structured case studies, and is thus ideal for topics such as militant decision-making where systematic data collection is difficult.

Separated Twins Or Just Siblings? A Multiplanet System Around An M Dwarf Including A Cool Sub-Neptune, M. Harris, D. Dragomir, I. Mireles, K. A. Collins, S. Ulmer-Moll, S. B. Howell, K. G. Stassun, G. Zhou, C. Ziegler, F. Bouchy, C. Briceño, D. Charbonneau, K. I. Collins, G. Fűűrész, N. M. Guerrero, J. M. Jenkins, Eric L.N. Jensen, M. H. K. Kristiansen, N. Law, M. Lendl, A. W. Mann, H. P. Osborn, S. N. Quinn, G. R. Ricker, R. P. Schwarz, S. Seager, E. B. Ting, R. Vanderspek, D. Watanabe, J. N. Winn

Physics & Astronomy Faculty Works

We report the discovery of two TESS sub-Neptunes orbiting the early M dwarf TOI-904 (TIC 261257684). Both exoplanets, TOI-904 b and c, were initially observed in TESS Sector 12 with twin sizes of 2.426 (+0.163)/(-0.157) and 2.167 (+0.130)/(-0.118) R_⊕, respectively. Through observations in five additional sectors in the TESS primary mission and the first and second extended missions, the orbital periods of the planets were measured to be 10.887 ± 0.001 and 83.999 ± 0.001 days, respectively. Reconnaissance radial velocity measurements (taken with EULER/CORALIE and SMARTS/CHIRON) and high-resolution speckle imaging with adaptive optics (obtained from SOAR/HRCAM and Gemini …

Examining Steam Education Programs Within Art Museums: “A” Is For Art Museums, Kylie B. Corkern

Art 895 Research Papers

This case study considers the role that art museums can serve while using science, technology, engineering, arts, and math (STEAM) education. Through a qualitative inquiry, cases from literature are examined and opportunities are shared for best practices that art museums can use with STEAM education. This study not only advocates for art museums to include STEAM opportunities but also the collaboration between schools and art museums to be able to create these possibilities. Finding these concepts and ideas will show the unique position that art museums can play in STEAM education. This study will also share the influence in expanding …

A Mathematical Model For Frogeye Leaf Spot Epidemics In Soybean, Chayu Yang, Jin Wang

Department of Mathematics: Faculty Publications

We propose a new mathematical model based on differential equations to investigate the transmission and spread of frogeye leaf spot, a major soybean disease caused by the fungus Cercospora sojina. The model incorporates the primary and secondary transmission routes of the disease as well as the intrinsic dynamics of the pathogen in the contaminated soil. We conduct detailed equilibrium and stability analyses for this model using theories of dynamical systems. We additionally conduct numerical simulations to verify the analytical predictions and to implement the model for a practical application.

Exploring The Nexus Of Cybersecurity Leadership, Human Factors, Emotional Intelligence, Innovative Work Behavior, And Critical Leadership Traits, Sharon L. Burton, Darrell Norman Burrell, Calvin Nobles, Laura A. Jones

Publications

Data shows that 12% of leaders are rated as 'very effective' at leadership. This research emphasizes the importance of understanding human behavior and its impact on leadership effectiveness, innovative work behavior (IWB), and the ability to respond to complex cyber threats, particularly in the realm of cybersecurity leadership. Emotional intelligence (EI), a key human factor, is highlighted as a crucial element that can stimulate cognitive absorption, leading to innovative work behavior and improved innovation efficiency (IE). This underscores the need for leaders to not only be technically proficient but also emotionally intelligent to effectively manage their teams and respond to …

2023-December-10-Illuminating The Path I Want To Take, University Marketing And Communication, East Tennessee State University

ETSU News

Internships are the strength of ETSU’s Applied Data Science grad program

It’s an age-old conundrum. Employers want to hire candidates with experience. But how do you get that experience without someone giving you a chance?

One way is internships, many of which are available to students in academic programs throughout East Tennessee State University. One of those is ETSU’s Applied Data Science Master’s Degree Program, where students are getting valuable experience from the hands-on work they’re doing with entities from local small businesses and government to internationally known companies.

Applied data science is the study of techniques for collecting, …

Electrodeposition Of Giant Magnetostrictive Transducers For A Fabricated Mixed Physics Signal Transmission Device, Mina Faltas

Nanoscience and Microsystems ETDs

Non-intrusive solutions for communication through a sealed metal vessel requires the use of piezoelectric transducers to transmit acoustic waves through the vessel wall. This approach suffers the disadvantage of compromised security because a potential eavesdropper could decipher the correlation between digital and electric signals of both sides of the system. One solution is a mixed physics system employing magnetostrictive transducers.

For a magnetostrictive transducer to work well in this application, it would have to have a high piezomagnetic constant. This is influenced by soft magnetism and saturation magnetostriction. Nickel-Iron-Cobalt alloys are modified to retain their soft magnetic properties while increasing …

The Ppp1r15 Family Of Eif2-Alpha Phosphatase Targeting Subunits (Gadd34 And Crep), Danielle Hicks, Krithika Giresh, Lisa A. Wrischnik, Douglas C. Weiser

Pacific Faculty Work

The vertebrate PPP1R15 family consists of the proteins GADD34 (growth arrest and DNA damage-inducible protein 34, the product of the PPP1R15A gene) and CReP (constitutive repressor of eIF2α phosphorylation, the product of the PPP1R15B gene), both of which function as targeting/regulatory subunits for protein phosphatase 1 (PP1) by regulating subcellular localization, modulating substrate specificity and assembling complexes with target proteins. The primary cellular function of these proteins is to facilitate the dephosphorylation of eukaryotic initiation factor 2-alpha (eIF2α) by PP1 during cell stress. In this review, we will provide a comprehensive overview of the cellular function, biochemistry and pharmacology of …

Revolutionizing Attention Training In Autism Spectrum Disorder: Pioneering Virtual Reality And Artificial Intelligence, Bhavya Sri Sanku, Selena He, Joy Li

Master of Science in Computer Science Theses

In the realm of educational technology, attention training plays a critical role in tailoring learning experiences to individual needs, especially for learners with autism spectrum disorder (ASD). This study presents an advanced framework that provides insights into the efficacy of reinforcement strategies by predicting their impact on attention enhancement in educational virtual reality (VR) settings, utilizing physiological biomarkers such as eye-tracking (ET), heart rate (HR), and electrodermal activity (EDA). A comprehensive comparative analysis was undertaken to evaluate the performance metrics of various machine learning (ML) and deep learning (DL) algorithms. The results showcased the robustness of gradient boosting (GB) and …

Free-Radical Scavenging Activity And Total Phenolic Compounds Of Red And Green Poinsettia Leaves (Euphorbia Pulcherrima Willd.) From Lombok Island, Handa Muliasari, Baiq Sopiah, Emmy Yuanita, Baiq Nila Sari Ningsih

Makara Journal of Science

To determine the free-radical scavenging activity and total phenolic content of the ethanol extract of Poinsettia leaves (Euphorbia pulcherrima Willd.) from Lombok Island, we used the 1,1-diphenyl-2-picrylhydrazyl method and expressed the total phenolic content as gallic acid equivalent (GAE) per gram of ethanol extract. The results show the strong antioxidant activity (79.77 ppm) of the ethanol extract of red Poinsettia leaves and the moderate antioxidant activity of green Poinsettia leaves (118.350 ppm). The ethanol extracts of red and green Poinsettia leaves possessed an average of 63.276 ± 0.228 and 22.715 ± 0.090 mg GAE/g extract total phenolic contents, respectively. …

Oxidation Of Ethanolamine By Potassium Permanganate In The Presence And Absence Of Sodium Dodecyl Sulphate: A Kinetic Study In An Acidic Medium, Dayo Latona

Makara Journal of Science

The kinetics of ethanolamine oxidation by acidified KMnO₄ was investigated in the absence and presence of sodium dodecyl sulfate (SDS) was investigated using a pseudo-first-order kinetics approach, with [ethanolamine]_o >> [KMnO₄]_o. The measurements were conducted at λ_max = 525 nm using an ultraviolet/visible-1800 Shimadzu spectrophotometer. The stoichiometry showed that 2 moles of KMnO₄ were consumed by 5 moles of ethanolamine in the aqueous medium. The reaction orders in both the aqueous and micellar media remained the same with a first-order dependence on [KMnO₄] and [ethanolamine] and a fractional-order dependence on [H …

Histological Study Of The Restorative Effect Of Roselle (Hibiscus Sabdariffa Linn.) Tea On The Digestive Organs Of Monosodium Glutamate-Induced Mice (Mus Musculus Linn.), Kanigara Anupama Sistra, Ngurah Intan Wiratmini, A. A.S.A. Sukmaningsih

Folia Medica Indonesiana

Highlights: • This original study examined the antioxidant compounds derived from naturally sourced Hibiscus sabdariffa calyx. • The findings demonstrated that roselle tea offers a viable and cost-effective solution for repairing histological damage to the digestive organs induced by monosodium glutamate. Abstract Monosodium glutamate (MSG) is a commonly used synthetic additive for enhancing food flavor. Excessive use of MSG can cause cytotoxic effects, which disrupt the balance of oxidative stress and free radicals in the body, particularly in the human digestive system. Roselle (Hibiscus sabdariffa) is a plant with red petals renowned for its abundance of beneficial compounds, including polyphenols, …

Electro-Optical Effect Of 4-N-Alkyl-Sulfanyl-4' Isothiocyanate-Biphenyl Liquid Crystal Homologous Series Under Terahertz Frequency: A Theoretical Approach, Yogesh Kumar, Narinder Kumar

Makara Journal of Science

This work presented the electro-optical effect of the homologous series 4-n-alkyl-sulfanyl-4'-isothiocyanate-biphenyl (N1SC13H8-SH_2n+1C_n) under an electric field with terahertz (THz) frequency. The increase in alkyl sulfanyl chain length reduces the birefringence but increases the order parameter in THz frequency. An inverse relationship exists between the birefringence and order parameter. Meanwhile, the increase in alkyl sulfanyl chain length increases the refractive index with an even–odd effect. Birefringence, refractive index, order parameter, and director angle show an even–odd effect in the THz frequency range. The calculation is performed between 1 and 1,200 THz frequency. The isothiocyanate stretching corresponding to …

Enzymatic Screening And Genotypic Characterization Of Thermophilic Bacteria From The Hot Springs Of Sarawak, Malaysia, Seng Chiew Toh, Samuel Lihan, Sui Sien Leong, Azizul Hakim Lahuri, Wai Cheong Woon, Wing Woh Ng

Makara Journal of Science

Owing to their eccentric thermostable ability, thermophiles are among the most utilized extremophiles in various industries, such as manufacturing, and clinical research. Researchers believe that many unknown thermophiles are yet to be discovered. This study aimed to genotypically characterize the diversity of thermophiles and screen them for the potential production of enzymes in the recreational hot springs located at Northwest Coast of Borneo. Water samples were collected at 45 °C–50 °C from Annah Rais and Panchor hot springs during the sampling period from January 2018 to January 2019. Three samples (water and sediment) were collected twice in a 3-week interval …

The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman

Makara Journal of Science

Fusarium proliferatum decreases the productivity of shallot (Allium cepa L.). Endophytic bacteria are potential biocontrol agents in controlling the growth of F. proliferatum. This study aimed to select and characterize endophytic bacteria producing bioactive compounds that inhibit the growth of F. proliferatum. The endophytic bacteria used were isolated from the roots, stems, leaves, and soil of shallot plants from healthy and diseased shallot farming fields. The endophytic bacteria were selected using the dual culture method and extracted using ethyl acetate solvent. The results of the 16S rRNA identification suggested that isolate ABP5.2 is similar to Pseudomonas …

An Inkjet-Printed Graphene Oxide–Poly(3,4-Ethylenedioxythiophene) Poly(Styrene Sulfonate) Electrode For Nitrite Detection In Water, Budi Riza Putra, Weni Anindya, Mohamad Rafi, Ika Kartika, Yudi Nugraha Thaha, Aga Ridhova, Wulan Tri Wahyuni

Makara Journal of Science

In this study, a screen-printed electrode (SPE) for nitrite (NO₂⁻) sensing was fabricated through an inkjet printing technique using a commercial printer machine and preparing an ink composite solution containing graphene oxide (GO) and poly(3,4 ethylenedioxythiophene) poly(styrene sulfonate) (PEDOT:PSS) as conductive materials. The optimum ink materials for SPE fabrication comprised GO and PEDOT:PSS with binders that resemble the viscosity of commercial ink. The surface topography of the fabricated SPE, which was characterized using scanning electron microscopy and atomic force microscopy, showed a smoother surface compared to the commercial screen-printed carbon electrode, with conductive ink materials deposited primarily …

The Need For Energy Storage On Renewable Energy Generator Outputs To Lessen The Geeth Effect, I.E. Short-Term Variations Mainly Associated With Wind Turbine Active Power Output, Tony Kealy

Articles

Many studies investigating the short-term variations associated with the power output from wind turbine generators utilise simulated or modelled data in the analysis. This current study uses short-term empirical data downloaded directly from operational wind turbines via electrical power quality meters. The empirical data shows that the short-term variations (one-second or sub-one-second timeframe) occur continuously over most of the power output range. A novel name is proposed, the Geeth Effect, for this variability phenomenon. The Geeth Effect is measured using the coefficient of variation mathematical expression and is likely contributing to (i) lower-than-expected financial and environmental benefits associated with …