Medical Specialties Commons^™

Implementation, Enrollment, And Engagement In An Opt-Out Telehealth Pharmacist-Assisted Tobacco Treatment Program For Patients Seen In Oncology Outpatient Clinics, K. Michael Cummings, Benjamin A. Toll, Vincent Talbot, Avery Roberson, Dianne Wilson, Martha Dunlap, Emily C. Ware, Amanda M. Palmer, Asia A. Bliss, Vincent S. Anokye, Graham Warren

Markey Cancer Center Faculty Publications

OBJECTIVE: To describe the workflow, reach, cost, and self-reported quit rates for an opt-out tobacco treatment program (TTP) for patients seen in 43 oncology outpatient clinics.

METHODS: Between May 25, 2021, and December 31, 2022, adult patients (≥18 years) visiting clinics affiliated with the Medical University of South Carolina Hollings Cancer Center were screened for smoking status. Those currently smoking were referred to a telehealth pharmacy-assisted TTP. An attempt was made to contact referred patients by phone. Patients reached were offered free smoking cessation counseling and a 2-week starter kit of nicotine replacement medication. A random sample of 420 patients …

Iron Oxide Nanozymes Enhanced By Ascorbic Acid For Macrophage-Based Cancer Therapy, Zhongchao Yi, Xiaoyue Yang, Ying Liang, Sheng Tong

Markey Cancer Center Faculty Publications

In recent years, using pharmacological ascorbic acid has emerged as a promising therapeutic approach in cancer treatment, owing to its capacity to induce extracellular hydrogen peroxide (H2O 2) production in solid tumors. The H2 O 2 is then converted into cytotoxic hydroxyl free radicals (HO•) by redox-active Fe2+ inside cells. However, the high dosage of ascorbic acid required for efficacy is hampered by adverse effects such as kidney stone formation. In a recent study, we demonstrated the efficient catalytic conver- sion of H2 O2 to HO• by wüstite (Fe 1−xO) nanoparticles (WNPs) through a heterogenous Fenton reaction. Here, we explore …

Challenges Of Spatially Resolved Metabolism In Cancer Research, Andrew N. Lane, Richard M. Higashi, Teresa W-M Fan

Markey Cancer Center Faculty Publications

Stable isotope-resolved metabolomics comprises a critical set of technologies that can be applied to a wide variety of systems, from isolated cells to whole organisms, to define metabolic pathway usage and responses to perturbations such as drugs or mutations, as well as providing the basis for flux analysis. As the diversity of stable isotope-enriched compounds is very high, and with newer approaches to multiplexing, the coverage of metabolism is now very extensive. However, as the complexity of the model increases, including more kinds of interacting cell types and interorgan communication, the analytical complexity also increases. Further, as studies move further …

Decentralized Clinical Trials For Medications To Reduce The Risk Of Dementia: Consensus Report And Guidance, Leanne Howard, Carla Abdelnour, Erin Abner, Ricardo F. Allegri, Hiroko H. Dodge, Serge Gauthier, Camilla M. Hoyos, Gregory Jicha, Patrick G. Kehoe, Catherine J. Mummery, Adesola Ogunniyi, Nikolaos Scarmeas, Xiaoying Chen, Jodie R. Titiner, Christopher R. Weber, Ruth Peters

Neurology Faculty Publications

INTRODUCTION: Recent growth in the functionality and use of technology has prompted an increased interest in the potential for remote or decentralized clinical trials in dementia. There are many potential benefits associated with decentralized medication trials, but we currently lack specific recommendations for their delivery in the dementia field.

METHODS: A modified Delphi method engaged an expert panel to develop recommendations for the conduct of decentralized medication trials in dementia prevention. A working group of researchers and clinicians with expertise in dementia trials further refined the recommendations.

RESULTS: Overall, the recommendations support the delivery of decentralized trials in dementia prevention …

Type-2 Diabetes, Pancreatic Amylin, And Neuronal Metabolic Remodeling In Alzheimer's Disease, Noah Leibold, James R. Bain, Florin Despa

Neurology Faculty Publications

Type-2 diabetes raises the risk for Alzheimer’s disease (AD)-type dementia and the conversion from mild cognitive impairment to dementia, yet mechanisms connecting type-2 diabetes to AD remain largely unknown. Amylin, a pancreatic 𝜷-cell hormone co-secreted with insulin, participates in the central regulation of satiation, but also forms pancreatic amyloid in persons with type-2 diabetes and synergistically interacts with brain amyloid 𝜷 (A𝜷) pathology, in both sporadic and familial Alzheimer’s disease (AD). Growing evidence from studies of tumor growth, together with early observations in skeletal muscle, indicates amylin as a potential trigger of cellular metabolic reprogramming. Because the blood, cerebrospinal fluid, …

A Pathologic Study Of Perivascular Ptdp-43 Lin Bodies In Late-Nc, Ryan K. Shahidehpour, Peter T. Nelson, Adam D. Bachstetter

Neurology Faculty Publications

Background TAR DNA-Binding Protein 43 (TDP-43) pathological inclusions are a distinctive feature in dozens of neurodegenerative pathologies, including limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC). Prior investigations identified vascular-associated TDP-43-positive micro-lesions, known as “Lin bodies,” located on or near the brain capillaries of some individuals with LATE-NC. This study aimed to investigate the relationship between the accumulation of Lin bodies and glial cells in LATE-NC and the potential co-localization with ferritin, a protein associated with iron storage. Using multiplexed immunohistochemistry and digital pathology tools, we conducted pathological analyses to investigate the relationship between Lin bodies and glial markers (GFAP for …

Ceramide-Mediated Orchestration Of Oxidative Stress Response Through Filopodia-Derived Small Extracellular Vesicles, Zainuddin Quadri, Ahmed Elsherbini, Simone M. Crivelli, Salim S. El-Amouri, Priyanka Tripathi, Zhihui Zhu, Xiaojia Ren, Liping Zhang, Stefka D. Spassieva, Mariana N. Nikolova‑Karakashian, Erhard Bieberich

Markey Cancer Center Faculty Publications

Extracellular vesicles (EVs) are shed from the plasma membrane, but the regulation and function of these EVs remain unclear. We found that oxidative stress induced by H 2 O 2 in Hela cells stimulated filopodia formation and the secretion of EVs. EVs were small (150 nm) and labeled for CD44, indicating that they were derived from filopodia. Filopodia-derived small EVs (sEVs) were enriched with the sphingolipid ceramide, consistent with increased ceramide in the plasma membrane of filopo- dia. Ceramide was colocalized with neutral sphingomyelinase 2 (nSMase2) and acid sphingomyelinase (ASM), two sphingomyelinases generating ceramide at the plasma membrane. Inhibition of …

Soxb1 Transcription Factors Are Essential For Initiating And Maintaining Neural Plate Border Gene Expression, Elizabeth Schock, Joshua R. York, Austin P. Li, Ashlyn Y. Tu, Carole Labonne

Markey Cancer Center Faculty Publications

SoxB1 transcription factors (Sox2/3) are well known for their role in early neural fate specification in the embryo, but little is known about functional roles for SoxB1 factors in non-neural ectodermal cell types, such as the neural plate border (NPB). Using Xenopus laevis, we set out to determine whether SoxB1 transcription factors have a regulatory function in NPB formation. Here, we show that SoxB1 factors are necessary for NPB formation, and that prolonged SoxB1 factor activity blocks the transition from a NPB to a neural crest state. Using ChIP-seq, we demonstrate that Sox3 is enriched upstream of NPB genes in …

14-3-3Ζ Suppresses Rankl Signaling By Destabilizing Traf6, R. Ayyasamy, S. Fan, P. Czernik, B. Lecka-Czernik, Somsubhra Chattopadhyay, R. Chakravarti

Markey Cancer Center Faculty Publications

Macrophages are essential regulators of inflammation and bone loss. Receptor activator of nuclear factor-κβ ligand (RANKL), a pro-inflammatory cytokine, is responsible for macrophage differentiation to osteoclasts and bone loss. We recently showed that 14-3-3ζ-knockout (Ywhaz^KO) rats exhibit increased bone loss in the inflammatory arthritis model. 14-3-3ζ is a cytosolic adaptor protein that actively participates in many signaling transductions. However, the role of 14-3-3ζ in RANKL signaling or bone remodeling is unknown. We investigated how 14-3-3ζ affects osteoclast activity by evaluating its role in RANKL signaling. We utilized 14-3-3ζ-deficient primary bone marrow–derived macrophages obtained from wildtype and Ywhaz^{KO …}

Discussions Of Cancer Survivorship Care Needs: Are There Rural Versus Urban Inequities?, Tyrone F. Borders, Lindsey R. Hammerslag

Markey Cancer Center Faculty Publications

Background: Rural cancer survivors may face greater challenges receiving survivorship care than urban cancer survivors.

Purpose: To test for rural versus urban inequities and identify other correlates of discussions about cancer survivorship care with healthcare professionals.

Methods: Data are from the 2017 Medical Expenditure Panel Survey (MEPS), which included a cancer survivorship supplement. Adult survivors were asked if they discussed with a healthcare professional 5 components of survivorship care: need for follow-up services, lifestyle/health recommendations, emotional/social needs, long-term side effects, and a summary of treatments received. The Behavioral Model of Health Services guided the inclusion of predisposing, enabling, and need …

Diffuse Reflectance Spectroscopy For Optical Characterizations Of Orthotopic Head And Neck Cancer Models In Vivo, Pranto Soumik Saha, Jing Yan, Caigang Zhu

Markey Cancer Center Faculty Publications

We demonstrated an easy-to-build, portable diffuse reflectance spectroscopy device along with a Monte Carlo inverse model to quantify tissue absorption and scattering-based parameters of orthotopic head and neck cancer models in vivo. Both tissue-mimicking phantom studies and animal studies were conducted to verify the optical spectroscopy system and Monte Carlo inverse model for the accurate extraction of tissue optical properties. For the first time, we reported the tissue absorption and scattering coefficients of mouse normal tongue tissues and tongue tumor tissues. Our in vivo animal studies showed reduced total hemoglobin concentration, lower tissue vascular oxygen saturation, and increased tissue scattering …

A Probabilistic Approach To Estimate The Temporal Order Of Pathway Mutations Accounting For Intra-Tumor Heterogeneity, Menghan Wang, Yanqi Xie, Jinpeng Liu, Austin Li, Li Chen, Arnold Stromberg, Susanne Arnold, Chunming Liu, Chi Wang

Markey Cancer Center Faculty Publications

The development of cancer involves the accumulation of somatic mutations in several essential biological pathways. Delineating the temporal order of pathway mutations during tumori- genesis is crucial for comprehending the biological mechanisms underlying cancer development and identifying potential targets for therapeutic intervention. Several computational and statistical methods have been introduced for estimating the order of somatic mutations based on mutation profile data from a cohort of patients. However, one major issue of current methods is that they do not take into account intra-tumor heterogeneity (ITH), which limits their ability to accurately discern the order of pathway mutations. To address this …

Response To Replication Stress And Maintenance Of Genome Stability By Wrn, The Werner Syndrome Protein, David K. Orren, Amrita Machwe

Markey Cancer Center Faculty Publications

Werner syndrome (WS) is an autosomal recessive disease caused by loss of function of WRN. WS is a segmental progeroid disease and shows early onset or increased frequency of many characteristics of normal aging. WRN possesses helicase, annealing, strand exchange, and exonuclease activities and acts on a variety of DNA substrates, even complex replication and re- combination intermediates. Here, we review the genetics, biochemistry, and probably physiological functions of the WRN protein. Although its precise role is unclear, evidence suggests WRN plays a role in pathways that respond to replication stress and maintain genome stability particularly in telomeric regions.

Discussions Of Cancer Survivorship Care Needs: Are There Rural Versus Urban Inequities?, Tyrone F. Borders, Lindsey R. Hammerslag

Nursing Faculty Publications

Background: Rural cancer survivors may face greater challenges receiving survivorship care than urban cancer survivors.

Purpose: To test for rural versus urban inequities and identify other correlates of discussions about cancer survivorship care with healthcare professionals.

Methods: Data are from the 2017 Medical Expenditure Panel Survey (MEPS), which included a cancer survivorship supplement. Adult survivors were asked if they discussed with a healthcare professional 5 components of survivorship care: need for follow-up services, lifestyle/health recommendations, emotional/social needs, long-term side effects, and a summary of treatments received. The Behavioral Model of Health Services guided the inclusion of predisposing, enabling, and need …

Bet Inhibition Decreases Hmgcs2 And Sensitizes Resistant Pancreatic Tumors To Gemcitabine., Aubrey L. Miller, Samuel C. Fehling, Rebecca B. Vance, Dongquan Chen, Eric Josh Brown, M. Iqbal Hossain, Eric O. Heard, Shaida A. Andrabi, Hengbin Wang, Eddy S. Yang, Donald J. Buchsbaum, Robert C. A. M. Van Waardenburg, Susan L. Bellis, Karina J. Yoon

Markey Cancer Center Faculty Publications

Efforts to develop targetable molecular bases for drug resistance for pancreatic ductal adenocarcinoma (PDAC) have been equivocally successful. Using RNA-seq and ingenuity pathway analysis we identified that the superpathway of cholesterol biosynthesis is upregulated in gemcitabine resistant (gemR) tumors using a unique PDAC PDX model with resistance to gemcitabine acquired in vivo. Analysis of additional in vitro and in vivo gemR PDAC models showed that HMG-CoA synthase 2 (HMGCS2), an enzyme involved in cholesterol biosynthesis and rate limiting in ketogenesis, is overexpressed in these models. Mechanistic data demonstrate the novel findings that HMGCS2 contributes to gemR and confers metastatic properties …

Long-Term Outcomes In Patients Using Protocol-Directed Active Surveillance For Prostate Cancer, Lisa F. Newcomb, Jeannette M. Schenk, Yingye Zheng, Menghan Liu, Kehao Zhu, James D. Brooks, Peter R. Carroll, Atreya Dash, Claire M. De La Calle, William J. Ellis, Christopher P. Filson, Martin E. Gleave, Michael A. Liss, Frances Martin, Jesse K. Mckenney, Todd M. Morgan, Maria S. Tretiakova, Andrew A. Wagner, Peter S. Nelson, Daniel W. Lin

Markey Cancer Center Faculty Publications

IMPORTANCE: Outcomes from protocol-directed active surveillance for favorable-risk prostate cancers are needed to support decision-making.

OBJECTIVE: To characterize the long-term oncological outcomes of patients receiving active surveillance in a multicenter, protocol-directed cohort.

DESIGN, SETTING, AND PARTICIPANTS: The Canary Prostate Active Surveillance Study (PASS) is a prospective cohort study initiated in 2008. A cohort of 2155 men with favorable-risk prostate cancer and no prior treatment were enrolled at 10 North American centers through August 2022.

EXPOSURE: Active surveillance for prostate cancer.

MAIN OUTCOMES AND MEASURES: Cumulative incidence of biopsy grade reclassification, treatment, metastasis, prostate cancer mortality, overall mortality, and recurrence after …

Assessing The Feasibility Of A Multimodal Liquid Biopsy For The Diagnosis Of Hpv-Associated Oropharyngeal Squamous Cell Carcinoma., James S. Lewis, Saskia Naegele, Vasileios Efthymiou, Mitra Mehrad, Kim A. Ely, Tim Waterboer, Krystle A. Lang Kuhs, Seth J. Davis, Kelsey Richard, Dipon Das, Daniel L. Faden

Markey Cancer Center Faculty Publications

OBJECTIVES: In this feasibility study, we explored the combined use of circulating tumor human papillomavirus (HPV) DNA (ctHPVDNA) and HPV serology as diagnostic tests for HPV-associated oropharyngeal squamous cell carcinoma (OPSCC).

METHODS: Among patients with research-banked serum or plasma at diagnosis, IgG antibodies to oncoproteins from HPV types 16, 18, 31, 33, 35, 45, 52, and 58 were detected with multiplex serology. Positivity for HPV 16 was defined based on detection of combinations of anti-E6, E1, E2, and E7 and for other high-risk types on detection of anti-E6 and anti-E7. Circulating tumor HPV DNA was detected by custom digital droplet …

Insights Into The Influence Of Income Variability On Cardiovascular Risk In Non-Elderly Adults With Type 2 Diabetes, Ketrell Mcwhorter

UK CARES Faculty Publications

No abstract provided.

Neural Mechanisms Of Respiratory Interoception, Pei-Ying Sarah Chan, Lu-Yuan Lee, Paul W. Davenport

UK CARES Faculty Publications

Respiratory interoception is one of the internal bodily systems that is comprised of different types of somatic and visceral sensations elicited by different patterns of afferent input and respiratory motor drive mediating multiple respiratory modalities. Respiratory interoception is a complex system, having multiple afferents grouped into afferent clusters and projecting into both discriminative and affective centers that are directly related to the behavioral assessment of breathing. The multi-afferent system provides a spectrum of input that result in the ability to interpret the different types of respiratory interceptive sensations. This can result in a response, commonly reported as breathlessness or dyspnea. …

Limbic-Predominant Age-Related Tdp-43 Encephalopathy (Late-Nc): Co-Pathologies And Genetic Risk Factors Provide Clues About Pathogenesis, Peter T. Nelson, David Fardo, Xian Wu, Khine Zin Aung, Matthew D. Cykowski, Yuriko Katsumata

Neurology Faculty Publications

Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is detectable at autopsy in more than one- third of people beyond age 85 years and is robustly associated with dementia independent of other pathologies. Although LATE-NC has a large impact on public health, there remain uncertainties about the underlying biologic mechanisms. Here, we review the literature from human studies that may shed light on pathogenetic mechanisms. It is increasingly clear that certain combinations of pathologic changes tend to coexist in aging brains. Although “pure” LATE-NC is not rare, LATE-NC often coexists in the same brains with Alzheimer disease neuropathologic change, brain arteriolosclerosis, …

Comprehensive Assessment Of Tdp‑43 Neuropathology Data In The National Alzheimer’S Coordinating Center Database, Davis C. Woodworth, Katelynn M. Nguyen, Lorena Sordo, Kiana A. Scambray, Elizabeth Head, Claudia H. Kawas, María M. Corrada, Peter T. Nelson, S. Ahmad Sajjadi

Neurology Faculty Publications

TDP-43 proteinopathy is a salient neuropathologic feature in a subset of frontotemporal lobar degeneration (FTLD-TDP), in amyotrophic lateral sclerosis (ALS-TDP), and in limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC), and is associated with hippocampal sclerosis of aging (HS-A). We examined TDP-43-related pathology data in the National Alzheimer’s Coordinating Center (NACC) in two parts: (I) availability of assessments, and (II) associations with clinical diagnoses and other neuropathologies in those with all TDP-43 measures available. Part I: Of 4326 participants with neuropathology data collected using forms that included TDP-43 assessments, data availability was highest for HS-A (97%) and ALS (94%), followed by …

Single-Cell Analysis Identifies Plk1 As A Driver Of Immunosuppressive Tumor Microenvironment In Luad, Yifan Kong, Chaohao Li, Jinpeng Liu, Sai Wu

Markey Cancer Center Faculty Publications

PLK1 (Polo-like kinase 1) plays a critical role in the progression of lung adenocarcinoma (LUAD). Recent studies have unveiled that targeting PLK1 improves the efficacy of immuno- therapy, highlighting its important role in the regulation of tumor immunity. Nevertheless, our understanding of the intricate interplay between PLK1 and the tumor microenvironment (TME) remains incomplete. Here, using genetically engineered mouse model and single- cell RNA-seq analysis, we report that PLK1 promotes an immunosuppressive TME in LUAD, characterized with enhanced M2 polarization of tumor associated macrophages (TAM) and dampened antigen presentation process. Mechanistically, elevated PLK1 coin- cides with increased secretion of CXCL2 …

Androgen Aggravates Aortic Aneurysms Via Suppression Of Pd-1 In Mice, Xufang Mu, Shu Liu, Zhuoran Wang, Kai Jiang, Timothy S. Mcclintock, Arnold Stromberg, Alejandro V. Tezanos, Eugene S. Lee, John A. Curci, Ming C. Gong, Zhenheng Guo

Markey Cancer Center Faculty Publications

Androgen has long been recognized for its pivotal role in the sexual dimorphism of cardiovascular diseases, including aortic aneurysms (AAs), a devastating vascular disease with a higher prevalence and fatality rate in men than in women. However, the mechanism by which androgen mediates AAs is largely unknown. Here, we found that male, not female, mice developed AAs when exposed to aldosterone and high salt (Aldo-salt). We revealed that androgen and androgen receptors (ARs) were crucial for this sexually dimorphic response to Aldo-salt. We identified programmed cell death protein 1 (PD-1), an immune checkpoint, as a key link between androgen and …

Smoking Cessation By Cancer Treatment Status Among Cervical Cancer Survivors, Cherell Cottrell-Daniels, Charles E. Hoogland, Bethany Shorey Fennell, Vani N. Simmons, Damon J. Vidrine, Jennifer I. Vidrine

Markey Cancer Center Faculty Publications

Introduction: Continued smoking following a cancer diagnosis is associated with poorer cancer treatment outcomes and survival times. Little is known about how cancer treatment status at the time of tobacco treatment enrollment impacts long-term smoking cessation outcomes. Using data from a smoking cessation RCT, this study compared long-term cessation outcomes of women undergoing active treatment for cervical cancer at trial enrollment (n=40) to outcomes of women with a history of cervical cancer or cervical intraepithelial neoplasia (CIN) who were not undergo- ing active cancer treatment at enrollment (n=154)

Methods: Participants (n=194) were randomized to Standard Treatment (ST) or ST plus …

A Framework And Process For Community‑Engaged, Mixed‑Methods Cancer Needs Assessments, Todd Burus, Jessica R. Thompson, Caree R. Mcafee, Lovoria B. Williams, Jennifer R. Knight, Bin Huang, Sarojini Kanotra, Natalie P. Wilhite, Elaine Russell, Melinda Rogers, Connie L. Sorrell, Christine Stroebel, Rachael King, Pamela C. Hull

Markey Cancer Center Faculty Publications

Purpose

Community health needs assessments are required for most state and local public health agencies and non-profit hospitals. Typically based on community health improvement planning models, these assessments encompass overall com- munity health and multiple diseases to inform program planning. National Cancer Institute (NCI)-designated Cancer Centers and community-based cancer-focused programs share the goal of reducing cancer burden in the catchment areas they serve. However, to date, no published models exist to guide cancer-specific needs assessments for a determined geographic area that can inform both public health and research initiatives. The purpose of this article is to outline a cancer needs …

Clinical And Genomic Features Of Patients With Renal Cell Carcinoma And Advanced Chronic Kidney Disease: Analysis Of A Multi-Institutional Database., Corbin J. Eule, Junxiao Hu, Dale Hedges, Alkesh Jani, Thomas Pshak, Brandon J. Manley, Alejandro Sanchez, Robert Dreicer, Zin W. Myint, Yousef Zakharia, Elaine T. Lam

Markey Cancer Center Faculty Publications

BACKGROUND: Patients with advanced chronic kidney disease (ACKD) are at an increased risk of developing renal cell carcinoma (RCC), but molecular alterations in RCC specimens arising from ACKD and overall survival (OS) in affected patients are not well defined.

PATIENTS AND METHODS: Using the Oncology Research Information Exchange Network (ORIEN) Total Cancer Care

RESULTS: Of 296 patients with RCC, 61 met the criteria for ACKD. The most common somatic mutations in the overall cohort were in

CONCLUSIONS: Using the clinicogenomic ORIEN database, our study found lower rates of

Travel-Time Disparities In Access To Proton Beam Therapy For Cancer Treatment, Todd Burus, Alexander D. Vanhelene, Michael K. Rooney, Krystle A. Lang Kuhs, W. Jay Christian, Christopher Mcnair, Sanjay Mishra, Arnold C. Paulino, Grace L. Smith, Steven J. Frank, Jeremy L. Warner

Markey Cancer Center Faculty Publications

IMPORTANCE Proton beam therapy is an emerging radiotherapy treatment for patients with cancer that may produce similar outcomes as traditional photon-based therapy for many cancers while delivering lower amounts of toxic radiation to surrounding tissue. Geographic proximity to a proton facility is a critical component of ensuring equitable access both for indicated diagnoses and ongoing clinical trials.

OBJECTIVE To characterize the distribution of proton facilities in the US, quantify drive-time access for the population, and investigate the likelihood of long commutes for certain population subgroups.

DESIGN, SETTING, AND PARTICIPANTS This population-based cross-sectional study analyzed travel times to proton facilities in …

Inchi Isotopologue And Isotopomer Specifications, Hunter N. B. Moseley, Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Emma L. Schymanski

Markey Cancer Center Faculty Publications

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically‑resolved chemi‑ cal entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically‑ resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry.

Scientific contribution

This new extension to the InChI standard …

Protein Oxidation In Aging And Alzheimer’S Disease Brain, Rukhsana Sultana, D. Allan Butterfield

Markey Cancer Center Faculty Publications

Proteins are essential molecules that play crucial roles in maintaining cellular homeostasis and carrying out biological functions such as catalyzing biochemical reactions, structural proteins, immune response, etc. However, proteins also are highly susceptible to damage by reactive oxygen species (ROS) and reactive nitrogen species (RNS). In this review, we summarize the role of protein oxidation in normal aging and Alzheimer’s disease (AD). The major emphasis of this review article is on the carbonylation and nitration of proteins in AD and mild cognitive impairment (MCI). The oxidatively modified proteins showed a strong correlation with the reported changes in brain structure, carbohydrate …

Predicting The Pathway Involvement Of Metabolites Based On Combined Metabolite And Pathway Features, Erik D. Huckvale, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

A major limitation of most metabolomics datasets is the sparsity of pathway annotations for detected metabolites. It is common for less than half of the identified metabolites in these datasets to have a known metabolic pathway involvement. Trying to address this limitation, machine learning models have been developed to predict the association of a metabolite with a “pathway category”, as defined by a metabolic knowledge base like KEGG. Past models were implemented as a single binary classifier specific to a single pathway category, requiring a set of binary classifiers for generating the predictions for multiple pathway categories. This past approach …