Digital Commons Network^™

Quantitative Proteomics For The Investigation Of Phosphoprotein Phosphatase 1 And 3 Substrate Specificities, Galini Poimenidou

Dartmouth College Ph.D Dissertations

Reversible phosphorylation is a crucial post-translational modification (PTM) that modulates a variety of signaling pathways intracellularly, with aberrant protein phosphorylation being a hallmark of many human diseases. Kinases, which catalyze phosphorylation of their substrates, have been extensively studied in the context of the signaling pathways they regulate and their effects on cellular processes. In contrast, phosphoprotein phosphatases (PPPs), which catalyze the removal of phosphate groups from substrate proteins, have only recently come to the research spotlight. For a long time, protein phosphatases were deemed unspecific housekeeping enzymes, but they are now known to display exquisite substrate specificity. Phosphoprotein phosphatase 1 …

Res-Mnd: Motor Neuron Disease Detection Using Res4net–Convolutional Block Attention Module ​, Shuriya Balusamy, Rakesh Sivalingam, Shobana Rooben, Sony Helen

Turkish Journal of Medical Sciences

Background/aim: Motor neuron diseases (MNDs) are progressive neurological disorders that cause muscle weakness and wasting as a result of ongoing neurodegeneration. MNDs require comprehensive diagnostic approaches that integrate clinical symptoms, laboratory findings, and multimodal imaging data.

Materials and methods: In this study, a novel residual network for motor neuron disease detection (RES-MND) framework is proposed for detecting MNDs using multimodal imaging data. Initially, the input multimodal images, including MRI, CT, PET, and DTI, are preprocessed using adaptive dynamic histogram equalization and the total variation bilateral filter. The preprocessed multimodal images are processed through Res4Net-CBAM for feature extraction to enhance image …

Role Of Novel Renal Biomarkers In Prognosticating Patients With Chronic Kidney Disease: A Prospective Cohort Study, Raghavan Padmanabhan, Kaviya Manoharan, Melina Sahay, Pooja Bhujangarao, Luxitaa Goenka, Solai Priya, Kumaraswamy Subramaniyan, Damal Kandadai Sriram, Melvin George

Turkish Journal of Medical Sciences

Background/aim: Several biomarkers have been assessed for the diagnosis of chronic kidney disease (CKD). However, limited data are available regarding their ability to predict mortality in CKD. The aim of this study was to assess the ability of lipocalin-2, receptor for advanced glycation end products (RAGE), tissue inhibitor of metalloproteinase 1 (TIMP-1), osteopontin, and trefoil factor 3 (TFF-3) in predicting the prognosis of patients with CKD.

Materials and methods: We included patients with CKD as defined by an estimated glomerular filtration rate of <60 mL/min/1.73 m2 of either sex who were above the age of 18 years. Patients with a history of acute-on-chronic kidney disease were excluded. The novel markers of interest were estimated from patients’ plasma samples using the multiplex enzyme-linked immunosorbent assay. These patients were followed for 1 year to assess mortality.

Results: The median (with interquartile range) plasma concentrations of lipocalin-2, RAGE, TIMP-1, osteopontin, and TFF-3 were 56.9 …

Diversity, Complexity, And Beauty, Jeff Ploegstra

Faculty Work Comprehensive List

"A pile of Lego pieces might be interesting, but it’s nothing compared to what those pieces can become when they’re arranged with intention."

Posting about what makes something beautiful from In All Things, an online hub that offers insight into maintaining and faithful and orthodox Reformed Christian worldview while fearlessly engaging in every aspect of contemporary life – until all is made new.

Diversity, Complexity, and Beauty

Artificial Intelligence-Assisted Neuropharmacology: Reshaping Drug Discovery And Translational Strategies For Neurological Diseases ​, Pri̇yanka Rathee, Suni̇thi̇ Lohan, Sari̇ta Khatkar, Neelam Mali̇k, Esra Akkol, Renu Sehrawat, Pooja Rathee, Anurag Khatkar

Turkish Journal of Medical Sciences

The rapid expansion of data-driven technologies, particularly machine learning (ML) and artificial intelligence (AI), has substantially influenced biomedical research and drug discovery. In neuropharmacology, the availability of large-scale genomic, proteomic, chemical, and clinical datasets has stimulated the adoption of AI-based approaches to address persistent challenges in neurological drug development, including high attrition rates and the scarcity of disease-modifying therapies. Unlike prior reviews that broadly discuss AI applications in drug discovery or neurology, this narrative review focuses specifically on neuropharmacology, with an emphasis on translational relevance, disease-oriented examples, and real-world constraints. We critically examine the application of AI and ML across …

Analysis Of Calr-Mutated Essential Thrombocythemia As A Distinct Disease Entity Compared With Jak2 V617f-Mutated And Triple-Negative Patients ​, Gökhan Sami̇ Aydin, Eli̇f Aksoy, İpek Yönal Hi̇ndi̇lerden, Aynur Dağlar Aday, Emi̇ne Gültürk, Meli̇ha Nalçaci, Fehmi̇ Hi̇ndi̇lerden

Turkish Journal of Medical Sciences

Background/aim: Calreticulin (CALR) mutations in essential thrombocythemia (ET) are associated with younger age, higher platelet counts, and lower thrombosis rates. The present study analyzes the demographic, laboratory, and clinical features of the CALR mutation and its prognostic impact.

Materials and methods: The clinical impact of CALR mutations was assessed in 391 ET patients.

Results: CALR-mutation patients were more commonly male than JAK2 V617F-positive and triple-negative patients. Age at diagnosis was similar across all groups, although patients with type 2 CALR mutations were younger than those with nontype 1/nontype 2 mutations. Compared with JAK2 V617F-positive patients, CALR-mutation patients had lower leukocyte …

Comprehensive Profiling Of Gut Microbiota In Postmenopausal Osteoporosis ​, Gülsemi̇n Ertürk Çeli̇k, Sedat Yildiz, Münevver Aksoy Bektaş, Yaprak Engi̇n-Üstün

Turkish Journal of Medical Sciences

Background/aim: Osteoporosis is a multifactorial skeletal disease that predominantly affects postmenopausal women and is characterized by reduced bone mass and an increased risk of fractures. Growing evidence suggests that the gut microbiota plays a pivotal role in bone metabolism through immunological, endocrine, and metabolic pathways, forming the basis of the so-called gut– bone axis. This study aimed to characterize gut microbiota composition in postmenopausal women with osteoporosis compared with healthy controls.

Materials and methods: Forty postmenopausal women aged 55–65 years were classified into osteoporosis (n = 20) and healthy control (n = 20) groups based on dual-energy X-ray absorptiometry T-scores. …

Johnson & Johnson V. Samsung Bioepis Co Ltd

2026 Decisions

USDC for the District of New Jersey

Front Matter

Texas A&M Law Review

Front Matter.

The Unexplored Future Of State Copyrights And Patents In Ai-Generated Creations, Timothy J. Mcfarlin

Texas A&M Law Review

This is the first article to broadly explore the possibility of state copyrights and patents in AI-generated creations and what it could portend for the future of intellectual property law.

The U.S. Constitution delegates to Congress, via Article I, the power to pass laws “securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries.” It reserves to the states or to the people, via the Tenth Amendment, certain unspecified powers not delegated to the federal government. These could include the power to recognize exclusive rights in “writings and discoveries” generated by artificially intelligent …

Regulating Data Monetization, Peter Ormerod

Texas A&M Law Review

Companies today generate hundreds of billions of dollars each year by collecting massive amounts of information about human activity and wringing predictive insights from it. The scale of these influence activities is stunning: your driving habits dictate your car insurance rates, buying the wrong thing will increase your borrowing costs, and the information ecosystem you inhabit is finely tuned for keeping your attention available to the highest bidder.

States have recently enacted new consumer privacy laws that confer on individuals a series of generally applicable rights over their personal information. But this approach has proven ineffective at disciplining firms’ data …

Hybrid Bermudagrass Dormancy Management In A Cool-Season Climate, Clarissa H. Peterson

Theses and Dissertations

Hybrid bermudagrass (Cynodon dactylon [L.] Pers. × C. transvaalensis Burtt Davy) (HBG) is a water efficient warm-season turfgrass increasingly adopted in cool-season and semi-arid regions due to climate change and the demand for reduced irrigation inputs. However, prolonged winter dormancy limits its visual quality (verdure) and seasonal performance. This thesis evaluated multiple management strategies to modify dormancy dynamics and improve off-season turf quality in a cool-season environment. Field experiments assessed the effects of growth covers, fertilizers, colorants, surfactants, organic acids, and overseeding with cool-season species on HBG dormancy over two seasons. Dormancy responses were quantified using normalized difference vegetation index …

My Four Years Of Animal Care Through Community Service, Margaret Reed '26

Senior Presentation of Learning

I joined DePauw as a Bonner Scholar with little knowledge about the program, but ready to continue my work in community service. I was unaware of the long term impacts and relationships that I would build over the course of the four years. I bounced around many service sites, but one, the Putnam County Humane Society. I began regularly volunteering at the shelter entering my second semester of freshman year. In my final semester, I am the intern and coordinate for other new volunteers like myself all those semesters ago. I also am a volunteer at the Lakeland Center, Inc., …

Living In Service: Mia's Bonner Journey, Mia Martin-Fuller '26

Senior Presentation of Learning

During my time, I have been allowed to learn a lot about myself and the communities I have had the privilege of serving. One of the biggest lessons I have learned is that I do not always have the answer, and that's okay. Going into areas where individuals may think or act differently than I do, I have found it is most useful to approach with a humble attitude and an open mind.

Regulatory Role Of Il-1Β And Cxcl8 In Inflammatory Cell Dynamics And Gingival Inflammation In Gingivitis, Dhuha Mahmood Ali

Muthanna Medical Journal

Background: Gingivitis is a common inflammatory disease of the periodontal tissues characterized by immune responses triggered by microbial biofilm. The inflammatory process involves the release of several cytokines and chemokines, including interleukin-1 beta (IL-1β ) and chemokine CXCL8, which play crucial roles in regulating leukocyte recruitment and inflammatory signaling within the gingival tissues. These biomarkers are considered important indicators of periodontal inflammation and may reflect the progression of periodontal diseases.

Aim: This study aimed to evaluate the levels of inflammatory biomarkers IL-1β and CXCL8 and investigate their role in gingival inflammation.

Materials and Methods: This case-control study included subjects diagnosed …

Secondary Contact Dynamics In White-Breasted Nuthatches (Sitta Carolinensis) Across The Pine Ridge Of Nebraska, Eugene A. Huryn

Biology Theses, Dissertations, and Student Creative Activity

Populations’ interactions in contact zones are important for understanding divergence dynamics of closely related taxa. Such interactions may vary from inter-population divergence being reinforced to secondary contact resulting in the creation of a hybrid swarm. The ecology of each lineage, and different factors like behavior and ecological niches, may impact the outcome of such contact. However, there is little current research on how habitat choice at local scales might reflect distinct populations, particularly in cryptic species. To study how niche dynamics affect diversification, we studied the White-breasted Nuthatch (Sitta carolinensis) complex in northwestern Nebraska. Two members of this …

Neural Signaling Contributes To Heart Formation And Growth In The Invertebrate Chordate, Ciona Robusta, Hannah N. Gruner, C. J. Pickett, Jasmine Yimeng Bao , '24, Richard Garcia , '24, A. Hozumi, T. D. Scully, Sydney Popsuj, Shaoyang Ning, Mavis Gao , '26, Gia Bautista , '23, Keren Meze , '24, Haeun Karissa Lim , '25, T. Osugi, Mae Collins-Doijode , '26, Ofubofu Cairns , '24, Gabriel Levis , '23, Shu Yi Chen , '24, Taixi Gong , '24, H. Satake, A. M. Klein, Y. Sasakura, Bradley Justin Davidson

Biology Faculty Works

Neurons contribute to the complex interplay of signals that mediate heart development and homeostasis. Although a limited set of studies suggest that neuronal peptides impact vertebrate heart growth, the specific contributions of these peptides to cardiomyocyte progenitor differentiation or proliferation have not been elucidated. Here, we show that the neuropeptide tachykinin along with canonical Wnt signaling regulate cardiomyocyte progenitor proliferation in the chordate model Ciona robusta. In C. robusta, the heart continues to grow throughout adulthood and classic histological studies indicate that a line of undifferentiated cells may serve as a reserve progenitor lineage. We found that this line of …

Semiochemicals And Odorant Receptors Underlying Potato Cultivar Susceptibility And Resistance To Potato Tuber Moth, Ruipeng Chen, Wangtao Hu, Qin Hu, Junjie Yan, Jiao Yin, Fathiya M. Khamis, Yulin Gao, Walter S. Leal

All Peer-Reviewed Publications

Infestation of potato by the potato tuber moth (Phthorimaea operculella) varies markedly among cultivars, yet the chemical and molecular mechanisms underlying this variation remain poorly understood. Here, we combine field surveys, chemical ecology, functional genomics, and structural modeling to reveal how cultivar-specific volatile profiles shape moth oviposition behavior and pest outcomes. Field and laboratory assays identified marked differences in adult attraction, oviposition, and larval damage among potato cultivars, which correlated with distinct blends of emitted volatile organic compounds (VOCs). Behavioral analyses revealed that among other VOCs, trans-nerolidol and β-ionone act as attractants, whereas 3-carene and benzyl tiglate function as oviposition …

Predictive Analytics In Oncology And Ophthalmology: Machine Learning Applications For Diabetic Retinopathy And Breast Cancer, Ali Abidalkareem

Electronic Theses and Dissertations 2020 - Present

The convergence of artificial intelligence and healthcare represents one of the most transformative developments in modern medicine, with deep learning technologies emerging as powerful tools for addressing complex diagnostic challenges. This dissertation develops and validates machine learning frameworks that address critical challenges in medical diagnosis through innovative approaches to data augmentation, feature learning, and classification, focusing on two fundamental problems: Diabetic Retinopathy (DR) severity classification using multi-model convolutional neural networks (CNNs), and breast cancer stage identification using microRNA (miRNA) gene expression biomarkers. For diabetic retinopathy classification, this work proposes an ensemble deep learning framework that integrates Diffusion-based data augmentation for …

Safety And Efficacy Of Ciltacabtagene Autoleucel For Relapsed/Refractory Multiple Myeloma: A Cibmtr Study., Doris K Hansen, Danai Dima, Hira Mian, Jakob Devos, Ruta Brazauskas, Temitope Oloyede, Aimaz Afrough, Nausheen Ahmed, Larry Anderson, Rahul Banerjee, Jesus G Berdeja, Aram Bidikian, Binod Dhakal, Ajoy Dias, Yvonne Efebera, Muhammad Salman Faisal, Lohith Gowda, Hamza Hashmi, Abu-Sayeef Mirza, Meera Mohan, Ravi Narra, Ashley E Rosko, Mark Schroeder, Taiga Nishihori, Heather Landau, Saad Usmani, Marcelo C Pasquini, Othman S Akhtar, Surbhi Sidana, Krina K Patel

Oncology Articles

Ciltacabtagene autoleucel (cilta-cel), an anti-B-cell maturation antigen (BCMA) chimeric antigen receptor T-cell (CAR-T) therapy, was approved in 2022 for heavily pretreated relapsed/refractory multiple myeloma (RRMM). This study evaluates the safety and efficacy of cilta-cel in RRMM patients reported to the Center for International Blood and Marrow Transplant Research registry between March 2022 and December 2023 who met commercial release specifications. Among 595 patients, median age was 64 years, 57% were male, and 70% had ≥1 comorbidity. Extramedullary disease and marrow plasma cell burden ≥ 50% were present in 13% and 14% of patients, respectively. The median number of prior lines …

Artificial Intelligence In Low-Dose Computed Tomography Lung Cancer Screening: Clinical Integration, Validation, And Translational Challenges, Valeria Vanessa Varela Betancourt, Archana Acharya, Nusrat Jahan, Udit Kapahi, Insharah Khalid, Syed Maaz Shah, Hassan Ibrahim, Bushra Nawaz, Shazma Shayan, Maia Valls Palacios Reese, Sheeza Nadeem, Manju Rai

Student Publications

Lung cancer remains the leading cause of cancer-related mortality worldwide, largely due to late-stage diagnosis. Low-dose computed tomography (LDCT) screening has demonstrated significant mortality reduction in high-risk populations; however, its widespread implementation is limited by high false-positive rates, inter-reader variability, and substantial workflow burden. Artificial intelligence (AI) has emerged as a promising adjunct to address these challenges by enhancing diagnostic consistency, efficiency, and risk stratification in LDCT-based screening. This narrative review aims to synthesize current evidence on AI methodologies, clinical applications, validation studies, and translational challenges in LDCT-based lung cancer screening. A structured literature search was conducted across PubMed, Scopus, …

Electroenzymatic Cascades For Nitrogen Upgrading: Beyond Ammonia Towards Value-Added Nitrogen Chemicals, Rohit G. Jadhav, Vamshi Krishna Kamaja, Wassim El Housseini, Monica Brachi, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

The global transition toward sustainable chemical manufacturing demands technologies that leverage natural carbon and nitrogen cycles while minimizing reliance on sacrificial reagents and fossil resources. These biogeochemical cycles are fundamental to life, and enzymes catalyze many of their key transformations. Bio electrochemical, specifically electroenzymatic, systems offer a promising route to sustainable synthesis by enabling selective redox transformations powered by electricity. However, whereas carbon-cycle enzymes are now well established in bio electrochemical synthesis, enzymes from the nitrogen cycle remain comparatively underexplored. Moreover, the nitrogen cycle alone does not access many value-added nitrogen-containing products, which require additional C-N bond formation and organic …

Dapk2 Regulates Pkm2 Phosphorylation At Threonine 45 To Facilitate Disturbed Flow-Induced Atherosclerosis, Shuai Guo, Long Xu, Yixin Chen, Yuan Zhao, Yuting Zhang, Runfa Yu, Kaixiang Cao, Litao Wang, Wenjia Ai, Jiang-Yun Luo, Lu Lu, Jun He, Yuan Zhou, Li Wang, Andrew H Baker, Yuqing Huo, Yiming Xu

Faculty, Staff and Students Publications

Background: Oscillatory shear stress (OSS), resulting from disturbed blood flow, is implicated in atherosclerotic plaque formation by incompletely understood mechanisms. This study aims to elucidate the involvement of death-associated protein kinase (DAPK) 2 in OSS-induced endothelial cell (EC) activation and atherosclerosis.

Methods: Publicly available resources, including genome-wide microarray, RNA sequencing, and single-cell RNA sequencing, were utilized to identify key OSS-sensitive regulatory factors. Techniques such as mass spectrometry, immunoprecipitation, proximity ligation assay, and RNA sequencing were employed to identify pyruvate kinase M2 (PKM2) as the binding protein of DAPK2 and determine the specific site of PKM2 phosphorylation by DAPK2. To assess …

Global Impact Of Germline Structural Variation On The Cancer Proteome, Fengju Chen, Yiqun Zhang, Luis F Paulin, Darshan S Chandrashekar, Sooryanarayana Varambally, Fritz J Sedlazeck, Chad J Creighton

Faculty, Staff and Students Publications

Proteome and transcriptome data combined can help assess the relevance of non-coding germline variants. Here, we combine germline Structural Variants (SVs) with mass spectrometry-based proteomics on tumors from 1637 cancer patients spanning various tumor tissues of origin to determine the extent SV breakpoint patterns involve differential protein expression of nearby genes. Rare and singleton SVs disrupting protein expression of known cancer susceptibility genes collectively involve 6% of patients. About 24% of the hundreds of genes with SV-associated non-coding cis-regulatory alterations at the mRNA level are similarly associated at the protein level. Both rare and common SVs may associate with differential …

The Effects Of Dietary Protein Manipulation On Operant Demand, Brianna R. Lilly

LSU Master's Theses

Previous work with dietary protein restriction in rodents has demonstrated that rodents fed a low protein diet exhibit physiological effects such as lower rates of weight gain and increased levels of circulating fibroblast growth factor 21 (FGF21). Dietary protein restriction also produces behavioral effects. Compared to rodents that are not protein-restricted, rodents that are protein-restricted exhibit increased food intake and higher preference for a protein vs. carbohydrate solution. Additionally, protein-restricted rodents will respond at higher levels for a protein reinforcer than non-restricted rodents. The current study assessed the effect of dietary protein restriction on operant protein demand during and after …

The "Quiet Professionals": Oral Histories Of The United States Special Forces Veterans Of The Global War On Terror, Chase Rumbley

Electronic Theses and Dissertations 2020 - Present

This thesis examines how United States Army Special Forces veterans of the Global War on Terror narrate the identity of the "Quiet Professional" across training, deployment, and post-service life. Drawing on oral history interviews with four retired Green Berets, as well as archival and material culture analysis, the study approaches Special Forces as a distinctive military institution shaped by narrative, institutional formation, and war. It argues that Special Forces ethos is not a fixed warrior identity, but a lived and contested achievement produced through rites of passage, embodied hardship, informal legitimacy, and collective memory. Participants describe becoming Special Forces as …

Enhanced Dietary Monitoring Using Fecal Genomics For Childhood Malnutrition Interventions, Ammara Aqeel, Najeeha T Iqbal, Sanam Iram Soomro, Sheraz Ahmed, Teresa K Mcdonald, Olivia Osborne, Sharon Jiang, Nolan Ives, Kazi Ahsan, Fayaz Umrani, Michael J Barratt, Jeffrey I Gordon, Syed Asad Ali, Lawrence A David

2020-Current year OA Pubs

Ready-to-use therapeutic and supplementary foods (RUTF/RUSF) are a primary treatment for childhood malnutrition in Community Management of Acute Malnutrition (CMAM) programs. However, measuring intervention compliance is labor intensive and unreliable. We applied FoodSeq, a fecal genomic dietary assessment biomarker, in malnourished infants (3-15 months) from Matiari, Pakistan. FoodSeq identified a significant increase in the abundance of DNA from chickpea, a primary RUSF ingredient, during RUSF administration and captured region-specific complementary feeding practices, including age-inappropriate feeding practices such as wide-spread tea consumption. Our findings highlight the potential of dietary genomics as an empirical and scalable tool for compliance monitoring and dietary …

Herpes Simplex Virus Type 1 R-Loops Are Targets For Apobec-Mediated Mutagenesis, Márton Miskei, Dóra Varga, Lilla Hornyák, Éva Sipos, Éva Nagy, Qiuzhen Li, Zsolt Karányi, Zoltán Szabó, Rachel Deweerd, Abby M Green, Dávid Szüts, Eszter Csoma, Lóránt Székvölgyi

2020-Current year OA Pubs

APOBEC3 enzymes are key effectors of antiviral immunity that introduce mutations into viral genomes. We show that viral R-loops serve as preferred substrates for APOBEC3-mediated mutagenesis during herpes simplex virus type 1 (HSV-1) infection. APOBEC3 enzymes are recruited to viral R-loops, generating clustered C-to-T mutations in genes critical for viral assembly. Importantly, R-loops alone are not mutagenic, and APOBEC3 enzymes do not edit HSV-1 without an R-loop; mutagenesis occurs when R-loops and APOBEC3 enzymes interact. These findings identify endogenous R-loops formed during the HSV-1 life cycle as focal vulnerabilities and highlight R-loop-APOBEC3 coupling as a mechanism for antiviral mutagenesis.

Drawing-Based Story Telling Influence On Children Language Development And Social Aspect, Hariddha Yuni Sulistyaningrum, Imanuel Hitipeuw, Triyono Triyono

Jurnal Pendidikan Humaniora

Language and social development of children plays an important role in influencing further development. The objectives of this research are to determine the effect of drawing based on story- telling toward language development and social development of children age 5–6 years. Single subject research with reversal design ABAB was used in this experimental research. Four kindergarten children identified having language and social problems became the subjects. The observation was used to col- lect data. In addition, the data were put into graphs to be analyzed by using visual inspection. The results showed that drawing activities based on story telling could …

Blended Learning Method Within Indonesian Higher Education Institutions, Zamzami Zainuddin, Cut Muftia Keumala

Jurnal Pendidikan Humaniora

This article aims to explore the potential development of a Blended learning model in Indonesian higher education institutions. The paper attempts to explain the concept of the Blended learning in terms of theory and practice, based on the literature discussed in several reputable international jour- nals. Initially, this method proposes to improve the deficiencies of a traditional learning model which is lack of technological resources and at the same time to improve the gap of e-learning practice which is lack of a face-to-face learning experience. In the blended instruction, students will learn through a face- to-face interaction in the classroom …