Digital Commons Network^™

Riparian Restoration Increases Soil Microbial Biomass In Marin County Rangelands, But Soil Carbon Stock Is Less Responsive, Sherilyn Kathryn Reinhart

Master's Theses

Land use change has caused the degradation of 70% of the Earth’s soils, directly altering soil microbial communities and carbon cycling. Interest in carbon farming practices is growing, but studies that document the nuances of soil carbon flux in specific bioregions are still too few. In this study, I examined how one practice, riparian restoration, alters soil carbon stock and microbial community structure over time. Using a paired sampling time series design, I collected soil samples from twelve riparian forests and adjacent rangelands near Marin County, California. Young and mature sites ranged from five to 29 years since restoration, and …

Examining The Relationship Between Artificial Intelligence And Disability, Luke Abell, Ben Anderson, Andres Arbulu, Cailyn Bowerman, Ethan Brown, Logan Busch, Eliana Chinitz, Shaan Choksi, Charles Clark, Alexander Claure, Meaghan Crites, Amalia Daniell, Stephen Dombrowski, Clara Dotterer, Jordyn Fink, Jake Fox, Akanksha Garg, Ishaan Ghosh, Cristian Gorayeb, Lia Gosselin, Simon Hasik, Alexis Hawkins, Charles Dickerson Iv, Chistopher Johnson, Cj Kulprathipanja, Claire Lindborg, Josh Lorenz, Luke Mcdonald, Daniella Nahnsen, Arwa Neemuchwala, Sage Nichols, Henrique Ortega, Krish Patel, Daniel Paul, Andres Ravelo, Daniel Reyes, Francesca Rovetto, Santiago Sacchini, Juan Santos, Mauricio Saturno, Carter Schaffer, Joey Schlosser, Anna Scroggings, Dylan Smith, Daniel Tejeira, Kenny Teng, Diya Tibrewala, Max Young, Robert Zeltsman, Bradley S. Duerstock, Maxwell Mensah

Undergraduate Coursework

No abstract provided.

Re: Butte Priority Soils Operable Unit (Bpsou) Draft Final Bres No. 94 – Rialto Dump Reclamation Improvement (Ri) Field Sampling Plan (Fsp)., Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Optimizing Workflow And Patient Outcomes: The Impact Of The Modified Adult Difficult Intravenous Access (A-Diva) Scale On Peripheral Iv Access: A Quality Improvement Project, Dakota S. Weaver, Ryan O'Sullivan

Doctor of Nurse Anesthesia Practice (DNAP) Manuscripts

Peripheral intravenous cannulation (PIVC) is one of the most performed invasive procedures in hospital settings, yet it is frequently associated with multiple attempts in patients with difficult intravenous access (DIVA). In obstetric (OB) triage settings, where time-sensitive care is critical, failed PIVC attempts can delay treatment and negatively affect patient experience. The Modified Adult Difficult Intravenous Access (A-DIVA) scale is a validated tool designed to identify patients at risk for DIVA and guide early use of advanced techniques such as ultrasound (US) guidance.

A QI initiative was implemented in the OB triage unit of a large academic hospital. The tool …

Covid-19-Associated Mucormycosis Mimicking Odontogenic Pain: A Report Of Three Cases, Pegah Sarraf, Mahboube Hasheminasab, Mehrfam Khoshkhounejad, Seyed A. Abaee, Pardis Akbari, Mohammad H. Nekoofar, Paul M.H. Dummer

Pacific Faculty Work

Aim: The aim of this study was to present three cases of COVID-19-related mucormycosis mimicking endodontic pain and to discuss the relevant dental and medical literature for this potential life-threatening disease. Summary: Mucormycosis (previously called zygomycosis) is a rare but serious infection caused by a group of fungi called mucormycetes. Mucormycosis mainly affects people who are medically compromised and have systemic health conditions or take drugs that lower their immune response. There has been an increase in case reports/series of mucormycosis in individuals diagnosed with COVID-19. This is likely attributable to the high doses and prolonged use of corticosteroids in …

Decomposing Trends In The Gender Gap For Highly Educated Workers, Joseph G. Altonji, John Eric Humphries, Yagmur Yuksel, Ling Zhong

Cowles Foundation Discussion Papers

This paper examines the gender gap in log earnings among full-time, college-educated workers born between 1931 and 1984. Using data from the National Survey of College Graduates and other sources, we decompose the gender earnings gap across birth cohorts into three components: (i) gender differences in the relative returns to undergraduate and graduate fields, (ii) gender-specific trends in undergraduate field, graduate degree attainment, and graduate field, and (iii) a cohortspecific “residual component” that shifts the gender gap uniformly across all college graduates. We have three main findings. First, when holding the relative returns to fields constant, changes in fields of …

Covid-19 Crisis: Contemporary Trauma Theory And Clinical Social Workers’ Perspectives Of Work-Related Secondary Trauma Post-Pandemic, Dr. Veronica Y. Griffin

Walden Dissertations and Doctoral Studies

The COVID-19 pandemic was an unprecedented global crisis that challenged clinical social workers’ traditional client-centered strategies and exposed some to secondary trauma. The purpose of this qualitative study was to explore clinical social workers’ perspectives on work-related secondary trauma post-COVID-19 pandemic using the contemporary trauma theory as the theoretical framework. The research question involved exploring their perspectives of how this trauma affected their biopsychosocial functioning. Semi-structured interviews were conducted with eight participants who were clinical social workers between 28 and 36. Using thematic analysis, themes were identified and grouped into the three functioning groups: personal, relationships, and career. Twelve themes …

Staff Education On Suicidal Screening In Young African American Male Adults With Bipolar Disorders, Tokunbo Ndidi Allen

Walden Dissertations and Doctoral Studies

This Doctor of Nursing Practice education project aimed to enhance mental health providers’ preparedness in culturally competent suicide screening, specifically for African American males with bipolar disorder in a behavioral health department. The practice issue identified was a lack of documented training, leading to underdiagnosis, missed interventions, and health disparities driven by cultural stigma, provider discomfort, and the absence of standardized guidelines. This represents a serious patient safety concern for African American males with mood disorders, such as bipolar, who are significantly underserved in mental health care. The guiding question was: Does a suicide screening education program improve the knowledge …

Unh Study Finds Walkable Neighborhoods Eased Pandemic Mental Health Declines, Aaron Sanborn

UNH Today Archive

No abstract provided.

Re: Butte Priority Soils Operable Unit (Bpsou) Draft Final Insufficiently Reclaimed Sites Field Sampling And Investigation Plan (Fsp): Bres No. 91 – Robert Emmett Dumps, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Statistical Analysis Of Multi-Endpoint Phenotypic Screening Increases Sensitivity Of Planarian Neurotoxicity Testing, Danielle Ireland, L. J. Word, Eva-Maria S. Collins

Biology Faculty Works

There is an urgent need for high-throughput screening (HTS) models to replace, refine, and/or reduce (“3Rs”) vertebrate toxicity testing. Replacing in vivo animal studies is challenging for neurotoxicity and developmental neurotoxicity (DNT), where the functional relevancy of adverse outcomes needs to be assessed on the whole organism. We previously screened the NTP 87-compound library (NTP87), consisting of known and suspected developmental neurotoxicants, and showed that planarian HTS can identify known (developmental) neurotoxicants. Because analysis methods can impact screening results, and our original analysis used the lowest-observed-effect-level (LOEL) only, we hypothesized that the use of state-of-the-art statistical analysis would increase the …

Objective Performance Status: Enhancing Cancer Patient Fitness Assessment With Wearable Technology., Joseph Mccollom Do, Mazie Tsang

PCI Publications and Projects

Research output: Contribution to journal › Editorial › peer-review

August 21, 2025, James Madison University

The Breeze, 2020-

The Breeze is the student newspaper of James Madison University in Harrisonburg, Virginia.

Implementation Of Patient-Centered Approaches To Enhance Engagement And Satisfaction In Psychiatric Care Within A Family Mental Health Service, Nnenna Attah

Walden Dissertations and Doctoral Studies

Summary I conducted this evaluation of a quality improvement initiative at a family mental health service center aimed to enhance patient engagement and satisfaction in psychiatric care through patient-centered approaches. The practice problem addressed in this project was the lack of patient engagement and satisfaction. This issue is critical to address within the context of nursing practice because patient-centered care is fundamental to improving clinical outcomes, patient satisfaction, and overall quality of care. The practice-focused question was: How can patient-centered approaches enhance patient engagement and satisfaction in psychiatric care? In the project, I focused on evaluating the impact of patient-centered …

Change For The Use Of Phenobarbital In Severe Alcohol Withdrawal Syndrome, Rylee J. Studiner

Walden Dissertations and Doctoral Studies

Alcohol withdrawal syndrome (AWS) is a critical condition commonly encountered in hospital settings. If not properly treated, AWS can progress to seizures, delirium tremens, and death. Traditionally, benzodiazepines guided by the Clinical Institute Withdrawal Assessment for Alcohol Scale, Revised (CIWA-Ar), have served as a mainstay of treatment. However, emerging evidence supports the use of phenobarbital as a pharmacologic alternative and the Severity of Ethanol Withdrawal Scale (SEWS) as a more objective and clinically practical assessment tool. This doctor of nursing practice (DNP) project aimed to develop an evidence-based clinical practice guideline (CPG) for the use of phenobarbital in managing severe …

Association Of Glucagon-Like Peptide-1 Receptor Agonists With Cancer Risk In Older Adults With Type 2 Diabetes, Ying Lu, Hao Dai, Huilin Tang, William T Donahoo, Thomas J George, Ramon C Sun, Sizun Jiang, Aik Choon Tan, Yi Guo, Jonathan D Licht, John M Allen, Kelvin P Lee, Jingchuan Guo, Jiang Bian

Faculty, Staff and Student Publications

Objective: The real-world evidence on the association between glucagon-like peptide-1 receptor agonists (GLP-1RAs) and cancer risk remains limited and mixed.

Methods: In 2013-2020 national Medicare claims data, we included cancer-naïve patients with type 2 diabetes (T2D). We identified those who initiated GLP-1 RA, sodium-glucose cotransporter 2 inhibitor (SGLT2i), or dipeptidyl peptidase 4 inhibitor (DPP4i) and conducted 1:1 propensity score matching for confounding adjustment. Cox proportional hazards models were used to estimate hazard ratios (HR) of nine obesity-associated cancers (thyroid, pancreatic, bladder, colorectal, lung, kidney, breast, endometrial, and prostate cancer).

Results: In the matched GLP-1RA versus SGLT2i cohort (n = 21,362 …

Dclk1 Isoform (Dclk1-S) As A Critical Player In Promoting Inflammation, Tissue Remodeling, And Emt In Mouse Models Of Colitis., Kafayat Yusuf, Badal C. Roy, William L. Hauser, Mazin Al-Kasspooles, Sierra Sanchez, Thomas M. Attard, Dong Pei, Venkatesh Sampath, Shrikant Anant, Shahid Umar

Manuscripts, Articles, Book Chapters and Other Papers

BACKGROUND AND AIMS: The Doublecortin-like kinase-1 (DCLK1) plays a chemosensory role in the gut. It's role in the context of inflammatory diseases including inflammatory bowel disease (IBD), has not been thoroughly investigated. This study explored the role of the DCLK1 isoform (DCLK1-S) in promoting infectious/chemical colitis by utilizing high-throughput imaging mass cytometry (IMC).

METHODS: Transgenic mice were either infected with Citrobacter rodentium (CR) or received DSS and tissues/cells were processed via standard techniques. IMC workflow was adapted by Fluidigm (renamed Standard BioTools). Raw data was fed to Multiplexed Cell Dataset (MCD) Viewer for image generation and analyzed via histoCAT. Promoters …

Prefrontal Cortex Astrocytes Modulate Distinct Neuronal Populations To Control Anxiety-Like Behavior, Eunyoung Kim, Hairuo Du, Yanqi Tan, Brandon L Brown, Yaowen Chang, Blanca Díaz-Castro, Jonathan V Sweedler, Xinzhu Yu

Faculty, Staff and Student Publications

Accumulating evidence has supported diverse regulatory functions of astrocytes in different neural circuits as well as various aspects of complex behaviors. However, little is known about how astrocytes regulate different neuronal subpopulations that are linked to specific behavioral aspects within a single brain region. Here, we show that astrocytes in the medial prefrontal cortex (mPFC) encode anxiogenic environmental cues in freely behaving mice. Silencing mPFC astrocyte Ca

Phase 1/2 Trial Of Encorafenib, Cetuximab, And Nivolumab In Microsatellite Stable Brafv600e Metastatic Colorectal Cancer, Van K Morris, Christine M Parseghian, Vahid Bahrambeigi, Nourhan Abdelfattah, Lianchun Xiao, Anjali Agrawal, Kangyu Lin, Kanwal P S Raghav, Robert A Wolff, Arvind Dasari, Ryan W Huey, Bryan K Kee, Michael J Overman, Jason A Willis, Phat H Le, Michelle Escano, Yunyu C Baig, Kelsey Pan, David Menter, Alda L Tam, Wai C Foo, Li Shen, Hey Min Lee, Thomas D Gallup, Cori Margain, Dave Gallup, Kimal I Rajapakshe, Paola A Guerrero, Jing Wang, Ryan B Corcoran, Anirban Maitra, Kyuson Yun, Scott Kopetz

Faculty, Staff and Student Publications

The BRAF inhibitor encorafenib and anti-epidermal growth factor receptor (EGFR) antibody cetuximab modestly improve survival for patients with microsatellite stable (MSS) BRAFV600E metastatic colorectal cancer (mCRC), characterized by higher immune activation than MSS BRAFwild-type colorectal cancer (CRC). In this phase 1/2 study (NCT04017650) of 26 participants with MSS BRAFV600E mCRC who received encorafenib, cetuximab, and anti-PD-1 antibody nivolumab, we report an overall response rate of 50% (95% confidence interval [CI] 29–71) and median progression-free survival of 7.4 months (95% CI, 5.6–9.6). Transcriptomic profiling of pretreatment biopsies and extracellular vesicle RNA (evRNA) isolated from plasma show …

Molecular Identification Of Acinetobacter Baumannii Isolated From Clinical Samples In Iraq By Using Multiplex Pcr, Yaseen Ismael Mamoori, Ibrahim Abdulla Ahmed, May Ridha Jaafer, Ayat Muneam Ali, Sabreen Ali Hadi

Baghdad Science Journal

Acinetobacter baumannii is one of the most clinically significant pathogens that cause severe nosocomial infections. Rapid identification of this bacterial species is essential so that proper treatment can be provided and outbreaks can be controlled. In this study, a multiplex PCR was used to identify A. baumannii. Twenty clinical isolates of A. baumannii and three each of Gram+ve (Staphylococcus aureus, Bacillus licheniformis, Micrococcus yunnanensis) and Gram−ve (Proteus mirabilis, Pseudomonas aeruginosa, Klebsiella pneumoniae) bacterial isolates were subjected to singleplex and multiplex PCR reactions using three sets of species-specific primers (P-Ab-ITS-F, P-Ab-ITS-R; …

Determination Of Microplastic Compounds In Some Species Of Freshwater Snails In Brantas River, East Java, Indonesia, R Adharyan Islamy, Yuni Kilawati, Veryl Hasan, Fitri Sil Valen, Noorhidayah Mamat, Ahmad Syazni Kamarudin, Yunita Maimunah

Baghdad Science Journal

This research examines microplastic contamination patterns in three ecologically significant freshwater gastropods—Pomacea canaliculata, Filopaludina javanica, and Sulcospira testudinaria—in Indonesia's Brantas River system. Through systematic sampling at three downstream locations, we quantified and characterized microplastics within the digestive tracts of these molluscan species. The results demonstrate universal microplastic ingestion across all taxa, though with notable interspecific variation. The invasive P. canaliculata showed the highest contamination levels (4.5 microplastic particles per individual, average weight 15.2g), predominantly comprising textile fibers and plastic fragments. In contrast, F. javanica specimens (average 10.8g) contained primarily cosmetic microbeads and packaging films (2.7 particles/individual), …

Enhancing Interprofessional Competence Among Speech Pathology, Nursing, Social Work, And Psychology Students Using Simulated Case Presentations, Elizabeth Oommen, Emily Helder, Kayla Johnson, Stacia L. Hoeksema, Laura Schipper

University Faculty Publications and Creative Works

Background: This study assesses the impact of an Interprofessional Education (IPE) program (which included simulated case presentations), on the perceived competence and quality of interprofessional (IP) work products of undergraduate social work, nursing, psychology students, and graduate students in speech-language pathology.

Methods: Participants included 123 students who participated in IP colloquiums through reviewing clinical cases, developing IP assessment and treatment goals, and presenting these to fellow students and faculty. Pre- and post-testing using IPEC Competency Self-Assessment Tool was used for assessment. For each colloquium, the students from all disciplines also submitted a single worksheet for their assigned case, …

Re: Butte Priority Soils Operable Unit (Bpsou) Draft Final Insufficiently Reclaimed Sites Field Sampling Plan (Fsp): Bres No. 26 – Cripple Dump, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Re: Butte Priority Soils Operable Unit (Bpsou) Draft Final Insufficiently Reclaimed Sites Field Sampling And Investigation Plan (Fsp): Bres No. 177 – North Alice Culvert, Mike Mcanulty

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Comparative Modeling Of Nuclear Energy Consumption In The United States And France: An Optimized Structure-Adaptive Grey Model, Alae Chahid '25, Naima Shifa

Student Research

This study investigates nuclear energy consumption trends in the United States, and France by applying advanced time-series modeling and computational optimization techniques. Using annual consumption data from 2005 to 2023, the research compares the predictive accuracy under data scarcity of the AutoRegressive Integrated Moving Average (ARIMA), Grey Model (1,1,t), Grey Model(1,1,t²), and an Optimized Structure-Adaptive Grey Model (OSGM). This OSGM (1,1,_) the traditional Grey Model (1,1) by introducing time-dependent terms and parameter tuning through particle swarm optimization and Monte Carlo simulations. Models are trained and tested using an in-sample and out-of-sample period framework. Then, forecast accuracies are compared using Mean …

Evaluating Snapshotnir For Tissue Oxygenation Measurement Across Skin Types After Mastectomy, Saif Badran, Sara Saffari, William R Moritz, Gary B Skolnick, Amanda M Westman, Mitchell A Pet, Justin M Sacks

2020-Current year OA Pubs

Accurate monitoring of mastectomy skin flap (MSF) perfusion is critical, especially in patients with darker skin pigmentation at higher risk of misdiagnosed tissue ischemia. Near-infrared spectroscopy (NIRS) devices, such as SnapshotNIR, offer real-time tissue oxygen saturation measurements (StO

Circzfr/Ythdf3 Axis Drives Lymph Node Metastasis In Cervical Cancer Via Fasn Translation, Mingyi Zhou, Yan Gao, Yong Zhang, Lian He, Bo Gao, Yue Zhang, Francois X Claret, George A Calin, Danbo Wang

Faculty, Staff and Student Publications

Background: Lymph node metastasis is a key driver of poor outcomes in cervical cancer. However, the molecular mechanisms of circular RNAs (circRNAs) driving cervical cancer lymph node metastasis remain unclear.

Methods: We identified circZFR, fatty acid synthase (FASN) and YTH N6-methyladenosine RNA binding protein F3 (YTHDF3) protein expression in the cervical cancer patients with long and short disease-free survival (DFS). Functional experiments were performed to investigate the function of circZFR, FASN and YTHDF3 on cell migration and invasion. MeRIP-qPCR, RNA pulldown, RNA Immunoprecipitation (RIP), and Co-Immunoprecipitation (Co-IP) assays were executed to investigate the mechanism of circZFR regulating FASN protein expression. …

Human Interpretable Grammar Encodes Multicellular Systems Biology Models To Democratize Virtual Cell Laboratories, Jeanette A I Johnson, Daniel R Bergman, Heber L Rocha, David L Zhou, Eric Cramer, Ian C Mclean, Yoseph W Dance, Max Booth, Zachary Nicholas, Tamara Lopez-Vidal, Atul Deshpande, Randy Heiland, Elmar Bucher, Fatemeh Shojaeian, Matthew Dunworth, André Forjaz, Michael Getz, Inês Godet, Furkan Kurtoglu, Melissa Lyman, John Metzcar, Jacob T Mitchell, Andrew Raddatz, Jacobo Solorzano, Aneequa Sundus, Yafei Wang, David G Denardo, Andrew J Ewald, Daniele M Gilkes, Luciane T Kagohara, Ashley L Kiemen, Elizabeth D Thompson, Denis Wirtz, Laura D Wood, Pei-Hsun Wu, Neeha Zaidi, Lei Zheng, Jacquelyn W Zimmerman, Jude M Phillip, Elizabeth M Jaffee, Joe W Gray, Lisa M Coussens, Young Hwan Chang, Laura M Heiser, Genevieve L Stein-O'Brien, Elana J Fertig, Paul Macklin

Faculty, Staff and Student Publications

Cells interact as dynamically evolving ecosystems. While recent single-cell and spatial multi-omics technologies quantify individual cell characteristics, predicting their evolution requires mathematical modeling. We propose a conceptual framework-a cell behavior hypothesis grammar-that uses natural language statements (cell rules) to create mathematical models. This enables systematic integration of biological knowledge and multi-omics data to generate in silico models, enabling virtual "thought experiments" that test and expand our understanding of multicellular systems and generate new testable hypotheses. This paper motivates and describes the grammar, offers a reference implementation, and demonstrates its use in developing both de novo mechanistic models and those informed …

Leveraging Sequences Missing From The Human Genome To Diagnose Cancer, Ilias Georgakopoulos-Soares, Christopher A Maher, Et Al.

2020-Current year OA Pubs

BACKGROUND: Cancer diagnosis using cell-free DNA (cfDNA) has the potential to improve treatment and survival but has several technical limitations.

METHODS: In this study, we developed a prediction model based on neomers, DNA sequences 13-17 nucleotides in length that are predominantly absent from the genomes of healthy individuals and are created by tumor-associated mutations.

RESULTS: We show that neomer-based classifiers can accurately detect cancer, including early stages, and distinguish subtypes and features. Analysis of 2577 cancer genomes from 21 cancer types shows that neomers can distinguish tumor types with higher accuracy than state-of-the-art methods. Generation and analysis of 465 cfDNA …

Tort Liability For Failure To Age Gate: A Promising Regulatory Response To Digital Public Health Hazards, Matthew B. Lawrence, Brett Frischmann, Avi Sholkoff

Faculty Publications

Tort liability for failure to “age gate” is a promising legal response to the public health hazards of AI, social media, sports gambling, and other digital spaces. Tort liability for failure to “age gate” hinges liability for harms to minors on an app’s failure to take reasonable steps to prevent minors from gaining access or otherwise to apply appropriate governance rules, such as privacy-protective default settings or ensuring genuine parental consent. While no one legal response is a panacea, tort liability for failure to age gate carries several distinctive advantages that make it a particularly promising option at this stage …