Digital Commons Network^™

Predicting Radiotherapy Patient Outcomes With Real-Time Clinical Data Using Mathematical Modelling, Alexander P Browning, Thomas D Lewin, Ruth E Baker, Philip K Maini, Eduardo G Moros, Jimmy Caudell, Helen M Byrne, Heiko Enderling

Faculty, Staff and Student Publications

Longitudinal tumour volume data from head-and-neck cancer patients show that tumours of comparable pre-treatment size and stage may respond very differently to the same radiotherapy fractionation protocol. Mathematical models are often proposed to predict treatment outcome in this context, and have the potential to guide clinical decision-making and inform personalised fractionation protocols. Hindering effective use of models in this context is the sparsity of clinical measurements juxtaposed with the model complexity required to produce the full range of possible patient responses. In this work, we present a compartment model of tumour volume and tumour composition, which, despite relative simplicity, is …

Carbon Cycle–Climate Feedbacks In The Post-Paris World, David S. Schimel, Dustin Carroll

Faculty Research, Scholarly, and Creative Activity

The Paris Agreement calls for emissions reductions to limit climate change, but how will the carbon cycle change if it is successful? The land and oceans currently absorb roughly half of anthropogenic emissions, but this fraction will decline in the future. The amount of carbon that can be released before climate is mitigated depends on the amount of carbon the ocean and terrestrial ecosystems can absorb. Policy is based on model projections, but observations and theory suggest that climate effects emerging in today’s climate will increase and carbon cycle tipping points may be crossed. Warming temperatures, drought, and a slowing …

Short Peripheral Blood Leukocyte Telomere Length In Rheumatoid Arthritis-Interstitial Lung Disease, Tracy J Doyle, Pierre-Antoine Juge, Anna L Peljto, Seoyeon Lee, Avram D Walts, Anthony Joseph Esposito, Sergio Poli, Ritu Gill, Hiroto Hatabu, Mizuki Nishino, Paul F Dellaripa, Michael E Weinblatt, Nancy A Shadick, M Kristen Demoruelle, Jeffrey A Sparks, Ivan O Rosas, Benjamin Granger, Kevin D Deane, Bruno Crestani, Paul J Wolters, Philippe Dieudé, Joyce S Lee

Faculty, Staff and Students Publications

Shortened telomere lengths (TLs) can be caused by single nucleotide polymorphisms and loss-of-function mutations in telomere-related genes (TRG), as well as ageing and lifestyle factors such as smoking. Our objective was to determine if shortened TL is associated with interstitial lung disease (ILD) in individuals with rheumatoid arthritis (RA). This is the largest study to demonstrate and replicate that shortened peripheral blood leukocytes-TL is associated with ILD in patients with RA compared with RA without ILD in a multinational cohort, and short PBL-TL was associated with baseline disease severity in RA-ILD as measured by forced vital capacity percent predicted.

Revealing Chronic Disease Progression Patterns Using Gaussian Process For Stage Inference, Yanfei Wang, Weiling Zhao, Angela Ross, Lei You, Hongyu Wang, Xiaobo Zhou

Faculty, Staff and Student Publications

OBJECTIVE: The early stages of chronic disease typically progress slowly, so symptoms are usually only noticed until the disease is advanced. Slow progression and heterogeneous manifestations make it challenging to model the transition from normal to disease status. As patient conditions are only observed at discrete timestamps with varying intervals, an incomplete understanding of disease progression and heterogeneity affects clinical practice and drug development.

MATERIALS AND METHODS: We developed the Gaussian Process for Stage Inference (GPSI) approach to uncover chronic disease progression patterns and assess the dynamic contribution of clinical features. We tested the ability of the GPSI to reliably …

Spectator 2024-01-18, Editors Of The Spectator

The Spectator

No abstract provided.

Translating The Potential Of The Urine Steroid Metabolome To Stage Nafld (Trust-Nafld): Study Protocol For A Multicentre, Prospective Validation Study, Hamish Miller, David Harman, Guruprasad Padur Aithal, Pinelopi Manousou, Jeremy F. Cobbold, Richard Parker, David Sheridan, Philip N. Newsome, Fredrik Karpe, Matthew Neville, Wiebke Arlt, Alice J. Sitch, Marta Korbonits, Michael Biehl, William Alazawi, Jeremy W. Tomlinson

Peninsula Medical School

Introduction Non-alcoholic fatty liver disease (NAFLD) affects approximately one in four individuals and its prevalence continues to rise. The advanced stages of NAFLD with significant liver fibrosis are associated with adverse morbidity and mortality outcomes. Currently, liver biopsy remains the 'gold-standard' approach to stage NAFLD severity. Although generally well tolerated, liver biopsies are associated with significant complications, are resource intensive, costly, and sample only a very small area of the liver as well as requiring day case admission to a secondary care setting. As a result, there is a significant unmet need to develop non-invasive biomarkers that can accurately stage …

The Global Impact Of Offshore Wind Farms On Ecosystem Services, Stephen C.L. Watson, Paul J. Somerfield, Anaëlle J. Lemasson, Antony M. Knights, Andrew Edwards-Jones, Joana Nunes, Christine Pascoe, Caroline Louise Mcneill, Michaela Schratzberger, Murray S.A. Thompson, Elena Couce, Claire L. Szostek, Heather Baxter, Nicola J. Beaumont

School of Biological and Marine Sciences

Understanding the global impact of offshore wind farms (OWF) on biodiversity and ecosystem services (ES) is crucial in developing sustainable energy transition pathways. This study takes a holistic approach, coupling a semi-systematic review with a novel analytical methodology, to consider the consequences of construction & operation of OWF deployment on biodiversity and ES. 314 pieces of evidence taken from 132 peer-reviewed studies provide the basis to determine the ecological and ES impacts. The process showed that construction impacts were predominantly negative across the ecological subject groups (52%), compared with positive impacts (8%) with several species of fish (e.g. brill, cod, …

Causes, Functions, And Therapeutic Possibilities Of Rna Secondary Structure Ensembles And Alternative States, Ritwika Bose, Irfana Saleem, Anthony M Mustoe

Faculty, Staff and Students Publications

RNA secondary structure plays essential roles in encoding RNA regulatory fate and function. Most RNAs populate ensembles of alternatively paired states and are continually unfolded and refolded by cellular processes. Measuring these structural ensembles and their contributions to cellular function has traditionally posed major challenges, but new methods and conceptual frameworks are beginning to fill this void. In this review, we provide a mechanism- and function-centric compendium of the roles of RNA secondary structural ensembles and minority states in regulating the RNA life cycle, from transcription to degradation. We further explore how dysregulation of RNA structural ensembles contributes to human …

Effects Of Supramaximal Anderson Quarter-Squats As A Potentiating Stimulus On Discus Performance In Division I Throwers: A Pilot Study, Ogochukwu I. Nwachukwu, Mark Debeliso Phd, Marcus M. Lawrence Phd

International Journal of Exercise Science

International Journal of Exercise Science 17(6): 99-114, 2024. No study has assessed supramaximal (over 100% 1RM) back squat variations as a potentiating stimulus in collegiate throwers. The purpose of this study was to test the hypothesis that a supramaximal Anderson (bottom-up) quarter squat potentiating stimulus would improve discus throw performance in Division I throwers compared to a dynamic warm-up alone. Nine NCAA division I thrower athletes (age: 20.1±1.4 years; 1RM back squat/body weight: 2.5±0.4 kg) randomly completed two sessions separated by at least 72 hours. One session involved a standardized dynamic warm-up alone (DyWU) followed by three trials of maximal …

Heavy Metals Contamination Alters Soil Microbes, Ali Cass

Posters-at-the-Capitol

Urban green spaces can improve food security, enhance biodiversity, and provide recreational and educational opportunities in cities. Converting abandoned or vacant lots to functional urban green spaces such as parks or gardens is a promising way to increase urban canopy cover, make use of available land, and mitigate food insecurity. However, research has shown that heavy metal soil contamination is a major concern in urban vacant lots, not just for human health, but also for the plants, wildlife, and soil organisms that play crucial roles in providing beneficial ecosystem services. In our study, we asked whether heavy metals impacted soil …

Avaren-Fc, A Novel Immunotherapeutic, Recruits Nk Cells In B16f10 Melanoma Tumor Tissue, Sreevatsa Vemuri, Katarina Mayer, Nobuyuki Matoba

Posters-at-the-Capitol

Melanoma is the fifth most common cancer in the US, with limited effective immunotherapeutic options available for patients. Avaren-Fc (AvFc) is a novel experimental immunotherapeutic agent with a unique “lectibody” property. It is capable of targeting cancer cells through the selective recognition of high mannose glycans, which are aberrantly overrepresented on the surface of malignant cells. AvFc can interact with circulating effector immune cells equipped with Fc receptors, such as natural killer (NK) cells to induce antibody-dependent cell-mediated cytotoxicity (ADCC) and kill cancer cells. Previous work has shown that AvFc effectively induces ADCC activity against B16F10 cancer cells in vitro …

Predicting The Reactions Of Cs2, Ocs, And Co2 With Group Iv And Group Vi Transition Metal Oxides, Marissa Shea Blair, Zachary Ryan Lee Phd, David A. Dixon Phd

Posters-at-the-Capitol

Building on a recent serious of high level electronic structure studies of Lewis acid gas reactions with metal oxide sorbents, DFT (B3LYP and ωB97X-D) and CCSD(T) methods are being used to predict the Lewis acid-base addition (physisorption) and formation of metal oxide carbonate/thiocarbonate formation (chemisorption) reactions of CS2, OCS, and CO2 of CS2, OCS, and CO2 with Group IV (MO2)n and Group VI (MO3)n (n = 1 - 3) nanoclusters. For the Group IV oxides, chemisorption to form terminal carbonates and thiocarbonates is predicted to be the most favored, with thiocarbonate ligand binding energies slightly more exothermic than their carbonate …

Attitudes Of South-Central Kentucky Residents Towards Coyotes And Their Management, Andrew T. Mcqueen, Stephen Sumithran Phd

Posters-at-the-Capitol

The existence of the coyote in the eastern U.S. is a recent development and the public’s perception of coyotes has been widely studied in urban areas. However, perceptions in rural areas, especially rural Appalachia, have been largely unstudied. It is necessary for wildlife managers to understand the public’s perceptions of coyotes and coyote management when creating management plans. We conducted a public survey in South-central Kentucky to determine perceptions toward coyotes and coyote management methods. The survey contained questions about demographics (age, gender, county of residence, landownership, etc.), perceptions (fears, opinions), knowledge (true/false questions), and preferred management practices (hunting, trapping, …

Triterpenoid Cddo-Ea Protects From Obesity And Insulin Resistance In An Animal Model Of Type 2 Diabetes, A. Cantu, Denae Cantu, Cordelia Rasa, Shizue Mito, Juan C. Lopez-Alvarenga, Sara M. Reyna

Research Symposium

Background: Type 2 diabetes (T2D) is characterized by insulin resistance, an impaired response to insulin by cells. Although several medications target insulin sensitivity, they fail to prevent progression to T2D in most high-risk individuals. Oleanolic acid (OA) is a pentacyclic triterpenoid found in plants with unique cardioprotective and anti-diabetic properties. OA can serve as a scaffold to produce synthetic molecules, known as synthetic oleanane triterpenoids (SOs), with enhanced biological activity. Our published findings show that the SO CDDO-EA (2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid-ethyl amide) facilitates translocation of the glucose transporter protein, GLUT4, as a new mechanism of CDDO-EA in regulating glucose metabolism. Thus, …

Nurturing The Environment: Enhancing Pet-Plastic Degradation By A Slow-Growing Miracle Microbe, Felipe-Andrés Piedra, Anthony Maresso

Research Symposium

Background: Plastic pollution is a global problem of enormous (5.5 billion tons) and growing proportion (1). A promising solution involves fermentation of plastic waste to produce microbial biomass that can be used in a range of applications including compost production. However, few microbial species able to consume plastic waste have been identified, and those that have been, including the recently discovered gram-negative bacterial species Ideonella sakaiensis (I. sakaiensis) which consumes polyethylene terephthalate (PET) (2) – a common throwaway plastic – do so exceedingly slowly (2). Here we report results from a screen of 190 carbon sources to identify small molecule …

Rational Design Of An Antimicrobial Peptide, Elvira Alanis, Miguel Alanis, Frank B. Dean, Yonghong Zhang

Research Symposium

Background: Clostridioides difficile is a gram-positive, spore-forming anaerobic bacterium that is the leading cause of nosocomial infections. Due to its detergent-resistant spores and antibiotic resistance, C. difficile infection is an urgent threat since it is difficult to eliminate, allowing it to persist in healthcare institutions. Inadequate treatments available for this infection lead to the problem that C. difficile infection rates may rise in coming years due to an increase in hospital-acquired infections following the COVID-19 pandemic, and therefore the discovery of new antimicrobial compounds is of utmost importance. Antimicrobial peptides (AMPs) have become a promising alternative due to their …

Pentachlorophenol Degradation In The Heterogeneous Catalytic Ozonation Process Using Al2o3 As A Catalyst Agent, Tariq J. Al-Musawi

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

In this study, an investigation of the catalytic ozonation of pentachlorophenol (PCP) in the presence of aluminum oxide (Al2O3) and the formation of byproducts during the ozonation has been done. From the results, it is clear that catalytic ozonation in the presence of Al2O3 can substantially enhance the efficiency of the PCP degradation to a higher degree than when the ozonation process alone is used. Several environmental parameters, including the pH of the solution, initial PCP concentration, Al2O3 dosage and dissolved ozone concentration were also investigated in terms of their influence. The highest efficiency of PCP degradation (100% degradation) was …

Sustainable Development Via Blockchain Technology, Salar Essa, Eslam Mohamed Husein Al-Khateeb

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

The use of blockchain technology provides a reliable system for digital services, promoting trust and decentralization. It offers a range of benefits such as automation, resilience, immutability, and trust, making it an excellent enabler for sustainable development. This article aims to highlight the potential of blockchain technology in supporting the transition to a sustainable society by explaining its fundamental properties and available options. It also outlines the challenges that hinder blockchain technology's full potential. Therefore, the article encourages professionals, enthusiasts, and researchers from various sectors to continue exploring blockchain technology while raising awareness of its thoughtful and prudent usage.

Artificial Intelligence And Sustainable Development, Riyam K. Marjan, Ali Mohammed Hasan Zubaidi

Al-Mustaqbal Journal of Sustainability in Engineering Sciences

The use of artificial intelligence (AI) is rapidly transforming various areas such as business, corporate practices, and governmental policy. With its deep learning capabilities, machines and robotics equipped with AI have brought significant disruptions and opportunities to these fields, as well as larger trends in global sustainability. The AI revolution could lead to a positive future where machines and humans coexist in harmony, or a negative one filled with conflict, poverty, and suffering. The impact of AI on the United Nations Sustainable Development Goals (SDGs) is still uncertain, as it could either accelerate progress or hinder it. This article examines …

Wnt Signaling In Cell Adhesion, Development, And Colon Cancer, Nydia Tejeda-Muñoz, Kuo-Ching Mei

Pharmacy Faculty Scholarship

Wnt signaling is essential for embryonic development, influencing processes such as axis formation, cell proliferation and differentiation, cell fate decisions, and axon guidance. It also plays a role in maintaining tissue homeostasis in adult organisms. The loss of normal cell polarity and adhesion caused by Wnt signaling activation is a fundamental step for tumor progression and metastasis. Activating the canonical Wnt pathway is a driving force in many human cancers, especially colorectal, hepatocellular, and mammary carcinomas. Wnt causes the stabilization and nuclear transport of newly synthesized transcriptional regulator β-catenin. The generally accepted view is that the canonical effects of Wnt …

Development And Evaluation Of A Mitochondrial Dna Marker For The Detection Of Rattus Rattus And Rattus Norvegicus Fecal Contamination, A'Aden Redhead

Graduate Research Showcase

No abstract provided.

Electron Trajectories And Critical Current In A Two-Dimensional Planar Magnetically Insulated Crossed-Field Gap, Xiaojun Zhu, Jack K. Wright, N. R. Sree Harsha, Jim Browning, Allen L. Garner

Electrical and Computer Engineering Faculty Publications and Presentations

The critical current in a one-dimensional (1D) crossed-field gap is defined by the transition from a cycloidal flow to a near-Brillouin (nB) state characterized by electron flow orthogonal to both the electric and magnetic fields and uniform virtual cathode formation. Motivated by recent studies on space-charge-limited current in non-magnetic diodes, we assess the meaning of critical current in a magentically insulated two-dimensional (2D) planar crossed-field geometry. Particle-in-cell (PIC) simulations demonstrate that binary behavior between a laminar and turbulent state does not occur in 2D because the virtual cathode is nonuniform. Rather than a distinct nB state above the critical current …

Disruption Of The Arabidopsis Acyl-Activating Enzyme 3 Impairs Seed Coat Mucilage Accumulation And Seed Germination, Ninghui Cheng, Paul A Nakata

Faculty, Staff and Students Publications

The Acyl-activating enzyme (AAE) 3 gene encodes an oxalyl-CoA synthetase that catalyzes the conversion of oxalate to oxalyl-CoA as the first step in the CoA-dependent pathway of oxalate catabolism. Although the role of this enzyme in oxalate catabolism has been established, its biological roles in plant growth and development are less understood. As a step toward gaining a better understanding of these biological roles, we report here a characterization of the Arabidopsis thaliana aae3 (Ataae3) seed mucilage phenotype. Ruthidium red (RR) staining of Ataae3 and wild type (WT) seeds suggested that the observed reduction in Ataae3 …

Sod1 Is A Synthetic Lethal Target In Ppm1d-Mutant Leukemia Cells, Linda Zhang, Joanne I Hsu, Etienne D Braekeleer, Chun-Wei Chen, Tajhal D Patel, Alejandra G Martell, Anna G Guzman, Katharina Wohlan, Sarah M Waldvogel, Hidetaka Urya, Ayala Tovy, Elsa Callen, Rebecca Murdaugh, Rosemary Richard, Sandra Jansen, Lisenka Vissers, Bert B A De Vries, Andre Nussenzweig, Shixia Huang, Cristian Coarfa, Jamie N Anastas, Koichi Takahashi, George Vassiliou, Margaret A Goodell

Faculty, Staff and Students Publications

The DNA damage response is critical for maintaining genome integrity and is commonly disrupted in the development of cancer. PPM1D (protein phosphatase, Mg2+/Mn2+ dependent 1D) is a master negative regulator of the response; gain-of-function mutations and amplifications of PPM1D are found across several human cancers making it a relevant pharmacologic target. Here, we used CRISPR/Cas9 screening to identify synthetic-lethal dependencies of PPM1D, uncovering superoxide dismutase-1 (SOD1) as a potential target for PPM1D-mutant cells. We revealed a dysregulated redox landscape characterized by elevated levels of reactive oxygen species and a compromised response to oxidative stress in PPM1D-mutant cells. Altogether, our …

Conserved Chromatin And Repetitive Patterns Reveal Slow Genome Evolution In Frogs, Jessen V. Bredeson, Austin B. Mudd, Sofia Medina-Ruiz, Therese Mitros, Owen Kabnick Smith, Kelly E. Miller, Jessica B. Lyons, Sanjit S. Batra, Joseph Park, Kodiak C. Berkoff, Christopher Plott, Jane Grimwood, Jeremy Schmutz, Guadalupe Aguirre-Figueroa, Mustafa K. Khokha, Maura Lane, Isabelle Philipp, Mara Laslo, James Hanken, Gwenneg Kerdivel, Nicolas Buisine

Pacific Faculty Work

Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a …

Ecological Diversification In An Adaptive Radiation Of Plants: The Role Of De Novo Mutation And Introgression, Benjamin Stone, Carolyn A. Wessinger

Faculty Publications

Adaptive radiations are characterized by rapid ecological diversification and speciation events, leading to fuzzy species boundaries between ecologically differentiated species. Adaptive radiations are therefore key systems for understanding how species are formed and maintained, including the role of de novo mutations versus preexisting variation in ecological adaptation and the genome-wide consequences of hybridization events. For example, adaptive introgression, where beneficial alleles are transferred between lineages through hybridization, may fuel diversification in adaptive radiations and facilitate adaptation to new environments. In this study, we employed whole-genome resequencing data to investigate the evolutionary origin of hummingbird-pollinated flowers and to characterize genome-wide patterns …

The Lumberjack, January 17, 2024

Cal Poly Humboldt's Student Newspaper

The student newspaper of Humboldt State University.

Cholinergic Activation Of Corticofugal Circuits In The Adult Mouse Prefrontal Cortex, Allan Gulledge

Dartmouth Scholarship

Acetylcholine (ACh) promotes neocortical output to the thalamus and brainstem by preferentially enhancing the postsynaptic excitability of layer 5 pyramidal tract (PT) neurons relative to neighboring intratelencephalic (IT) neurons. Less is known about how ACh regulates the excitatory synaptic drive of IT and PT neurons. To address this question, spontaneous excitatory postsynaptic potentials (sEPSPs) were recorded in dual recordings of IT and PT neurons in slices of prelimbic cortex from adult female and male mice. ACh (20 µM) enhanced sEPSP amplitudes, frequencies, rise-times, and half-widths preferentially in PT neurons. These effects were blocked by the muscarinic receptor antagonist atropine (1 …

Standardized Pre-Clinical Surgical Animal Model Protocol To Investigate The Cellular And Molecular Mechanisms Of Ischemic Flap Healing, Edita Aksamitiene, Ryan Heffelfinger, Jan Hoek, Edmund Pribitkin

Department of Otolaryngology - Head and Neck Surgery Faculty Papers

BACKGROUND: Some of the most complex surgical interventions to treat trauma and cancer include the use of locoregional pedicled and free autologous tissue transfer flaps. While the techniques used for these reconstructive surgery procedures have improved over time, flap complications and even failure remain a significant clinical challenge. Animal models are useful in studying the pathophysiology of ischemic flaps, but when repeatability is a primary focus of a study, conventional in-vivo designs, where one randomized subset of animals serves as a treatment group while a second subset serves as a control, are at a disadvantage instigated by greater subject-to-subject variability. …

2024-01-17 The Shutdown Of Murphy Elevators, Jocelyn Garcia

The Spectator Online

No abstract provided.