Digital Commons Network^™

Host Dna Depletion On Frozen Human Respiratory Samples Enables Successful Metagenomic Sequencing For Microbiome Studies, Minsik Kim, Raymond C Parrish, Michael J Tisza, Viral S Shah, Thi Tran, Matthew Ross, Juwan Cormier, Aribah Baig, Ching-Ying Huang, Laura Brenner, Isabel Neuringer, Katrine Whiteson, J Kirk Harris, Amy D Willis, Peggy S Lai

Faculty, Staff and Students Publications

Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed …

An Annotated Biobank Of Triple Negative Breast Cancer Patient-Derived Xenografts Featuring Treatment-Naïve And Longitudinal Samples Throughout Neoadjuvant Chemotherapy, Amanda L Rinkenbaugh, Yuan Qi, Shirong Cai, Jiansu Shao, Faiza Hancock, Sabrina Jeter-Jones, Xiaomei Zhang, Emily Powell, Lei Huo, Rosanna Lau, Chunxiao Fu, Rebekah Gould, Petra Den Hollander, Elizabeth E Ravenberg, Jason B White, Gaiane M Rauch, Banu Arun, Clinton Yam, Alastair M Thompson, Gloria V Echeverria, Stacy L Moulder, W Fraser Symmans, Jeffrey T Chang, Helen Piwnica-Worms

Faculty, Staff and Students Publications

Triple negative breast cancer (TNBC) that fails to respond to neoadjuvant chemotherapy (NACT) can be lethal. Developing effective strategies to eradicate chemoresistant disease requires experimental models that recapitulate the heterogeneity characteristic of TNBC. To that end, we established a biobank of 92 orthotopic patient-derived xenograft (PDX) models of TNBC from the tumors of 75 patients enrolled in the ARTEMIS clinical trial ( NCT02276443 ) at MD Anderson Cancer Center, including 12 longitudinal sets generated from serial patient biopsies collected throughout NACT and from metastatic disease. Models were established from both chemosensitive and chemoresistant tumors, and nearly 30% of PDX models …

Breast Cancer Screening In Transgender Women With High-Risk Family History, John F. Lloyd

Clinical Research in Practice: The Journal of Team Hippocrates

A clinical decision report using:

de Blok CJM, Wiepjes CM, Nota NM, et al. Breast cancer risk in transgender people receiving hormone treatment: nationwide cohort study in the Netherlands. BMJ. 2019;365:l1652. https://doi.org/10.1136/bmj.l1652

for a transgender woman with family history of breast cancer.

The Use Of Chewing Gum To Alleviate Thirst In Chf Patients Requiring Fluid Restrictions And Oral Diuretics, Madeline B. Simone

Clinical Research in Practice: The Journal of Team Hippocrates

A clinical decision report using:

Allida SM, Shehab S, Inglis SC, Davidson PM, Hayward CS, Newton PJ. A RandomisEd ControLled TrIal of ChEwing Gum to RelieVE Thirst in Chronic Heart Failure (RELIEVE-CHF). Heart Lung Circ. 2021;30(4):516-524. https://doi.org/10.1016/j.hlc.2020.09.004

for a woman with heart failure and under fluid restriction.

Etanercept, Methotrexate, Or Combined Therapy For Improving Rheumatoid Arthritis Symptoms, Ajith Dupati

Clinical Research in Practice: The Journal of Team Hippocrates

A clinical decision report using:

van der Heijde D, Klareskog L, Rodriguez-Valverde V, et al. Comparison of etanercept and methotrexate, alone and combined, in the treatment of rheumatoid arthritis: two-year clinical and radiographic results from the TEMPO study, a double-blind, randomized trial. Arthritis Rheum. 2006;54(4):1063-1074. https://doi.org/10.1002/art.21655

for a patient with rheumatoid arthritis.

Comparison Of Toxic Element Cadmium Levels In Female Patients With ‎Benign And ‎‎‎Malignant Uterine Tumors‎ By Flame Atomic Absorption ‎Spectrometry ., Hiba Ghmeedh Adhab, Liwaa Hussein Mahdi, Eman M. Al-Hilo

Maaen Journal for Medical Sciences

Cadmium is a toxic heavy metal known to be associated with various health issues, including cancer. Elevated blood cadmium levels can be a concern and may require medical evaluation and intervention. Some studies describing the etiology of cancer have focused on heavy metals, however, there is little information available for uterine cancer. This study assessed the levels of cadmium in the serum of 60 women with benign and malignant uterine tumors. Blood samples were obtained and analyzed using FAAS spectrometry in Najaf City, Iraq. Serum cadmium levels exhibited higher concentration in patients with malignant uterine tumors than those with benign …

Japanese Philosophy Of Moral Education: From Watsuji Tetsurô To Mori Akira, Anton Sevilla-Liu

Budhi: A Journal of Ideas and Culture

This article builds on the ethics of Watsuji Tetsurô (1889 1960) through a comparison with Mori Akira’s (1915–1976) the philosophy of education to show how Watsuji’s “ethics of emptiness” can be concretely manifested in human formation. While keeping Watsuji’s ethics in view, this article examines Mori Akira’s early philosophy of moral education in the 1950s, which can be found in his philosophy book, his teacher’s manual, and his moral education student textbooks. This article begins with Watsuji’s idea of “human existence” and its similarities with Mori Akira’s idea of “human becoming,” which adds a developmental angle to Watsuji’s tensional view …

The Filipino Primitive: Accumulation And Resistance In The American Museum, Sarita Echavez See, Jpaul S. Manzanilla

Budhi: A Journal of Ideas and Culture

The Filipino Primitive: Accumulation and Resistance in the American Museum, Sarita Echavez See

A Tale Of Two Walls: A Comparison Of The Green Wall Projects In Inner Mongolia And The Sahelo-Saharan Regions, Daniel Chen Ratilla

Budhi: A Journal of Ideas and Culture

Desertification as a bio-physical stressor threatens food and water security, and is exacerbated by climate change. Other issues such as peace, gender equity, and livelihood are some examples of socio-economic issues also connected to desertification. This is apparent in the cases of Inner Mongolia and the Sahelo-Saharan region, where desertification has spurred the creation of afforestation projects, colloquially known as “Green Walls”: these are the Three-North Shelterbelt Project, and the Great Green Wall of the Sahara and the Sahel Initiative, respectively. This paper explores the principles of environmental ethics (such as vulnerability, common goods, biological and cultural diversity, and environmental …

Indigenous Liberation Theology And Spirituality: Looking To The Past For Answers In The Present, Kathleen Nadeau, Jojo M. Fung

Budhi: A Journal of Ideas and Culture

Pope Francis’s Laudato si’: On the Care of Our Common Home offers a framework for dealing with poverty, ecological degradation, and climate change in the Philippines. His interconnected and holistic ecological spirituality shares some commonalities with indigenous spirituality where the earth is a gift from God to be taken care of—not taken advantage of or taken for granted. In this paper, we explore how this integrated approach of indigenous spirituality and liberation theology offers some long-term solutions to the problems of poverty and climate-change. Taking the position of being politically engaged in the world accords well with indigenous spirituality, this …

Sustaining Temporal Peace: A Worldview For Sustainable Living Inspired By Saint Augustine's Philosophy, Joseph Emmanuel D. Sta. Maria

Budhi: A Journal of Ideas and Culture

My paper aims to use the philosophical resources of Saint Augustine’s thought, particularly as found in the City of God, in order to sketch a basic worldview which can educate and lead people towards living lives that promote sustainable development. Specifically, I wish to show how Saint Augustine’s concepts of order, rightly ordered love, and temporal peace can serve as material to create a rough metaphysical framework in which human beings are understood to be an integrated part of a greater whole which is the earth. The ethical corollary of this framework is that human beings should act in such …

Penny, Pollard, Sarah Winn

Querying the Past: LGBTQ Maine Oral History Project Collection

Penny Pollard is a 71-year-old lesbian, who grew up in a middle-class Catholic family in Massachusetts and is the youngest of three children. She discusses her coming out process, her experiences in the LGBTQ community in San Francisco during the HIV/AIDS epidemic, and her career path which included various jobs such as furniture making, and speech-language pathology. Penny describes facing some discrimination and backlash when coming out, particularly from old friends and coworkers but also finding acceptance and community, especially after moving to Portland, Maine. She shares the story of how she met her now-wife when moving to Portland Maine. …

Quality Assurance Report For Year 2023 Estuarine Water Quality Datasonde Monitoring, Lara M. Martin

PREP Reports & Publications

No abstract provided.

Red Snapper (Lutjanus Campechanus) Neurocranium, Michelle Bassali, Anthony D'Auria, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Changes In Marital Sorting: Theory And Evidence From The Us, Pierre-André Chiappori, Monica Costa Dias, Costas Meghir, Hanzhe Zhang

Cowles Foundation Discussion Papers

Positive assortative matching refers to the tendency of individuals with similar characteristics to form partnerships. Measuring the extent to which assortative matching differs between two economies is challenging when the marginal distributions of the characteristic along which sorting takes place (e.g., education) change for either or both sexes. We show how the use of different measures can generate different conclusions. We provide axiomatic characterization for measures such as the odds ratio, normalized trace, and likelihood ratio, and provide a structural economic interpretation of the odds ratio. We then use our approach to consider how marital sorting by education changed between …

Enhancing Muscle Health And Modulating Immune Response With Galectin-1 In Lgmd2b/R2 Models, Stefannia Esparza Pulido

Theses and Dissertations

Limb-Girdle Muscular Dystrophy Type 2B/R2 (LGMD2B/R2) is a type of dysferlinopathy, a progressive muscle-wasting disorder caused by mutations in the dysferlin gene. Hallmarks of the disease include chronic inflammation, impaired muscle regeneration, and eventual muscle degeneration. Currently, no FDA-approved therapies are available for dysferlinopathies. Recombinant human Galectin-1 (rHsGal-1) has shown multiple roles in maintaining skeletal muscle homeostasis, promoting muscle repair, enhancing myogenesis, and modulating inflammation by downregulating the NF-κB pathway. The ability of rHsGal-1 to modulate the immune response is particularly promising for therapeutic applications in patients with LGMD2B/R2. In this study, we evaluated the effects of rHsGal-1 in a …

Nutrition Recommendations For Patients On Weight Loss Drugs, Crystal M. Duque Rdn-Ldn, Toye Jackman

Department of Nutrition Student Projects

This paper provides a comprehensive, evidence-based framework for dietitians counseling patients who are using GLP-1 receptor agonists, such as Ozempic and Wegovy, for weight management. These medications are rapidly gaining popularity for their effectiveness in supporting weight loss; however, they come with unique nutritional considerations that require tailored guidance. This review outlines key aspects of GLP-1 mechanisms of action, emphasizing how these medications alter digestive processes, specifically impacting the absorption and metabolism of essential macronutrients, including proteins and dietary fibers. The paper also highlights hydration needs to support optimal health and weight loss outcomes in patients on GLP-1 therapies. Additionally, …

Functions Of Tam Receptors And Ligands Protein S And Gas6 In Atherosclerosis And Cardiovascular Disease, Teagan Prouse, Samarpan Majumder, Rinku Majumder

School of Medicine Faculty Publications

Atherosclerosis and cardiovascular disease are associated with high morbidity and mortality in industrialized nations. The Tyro3, Axl, and Mer (TAM) family of receptor tyrosine kinases is involved in the amplification or resolution of atherosclerosis pathology and other cardiovascular pathology. The ligands of these receptors, Protein S (PS) and growth arrest specific protein 6 (Gas6), are essential for TAM receptor functions in the amplification and resolution of atherosclerosis. The Axl-Gas6 interaction has various effects on cardiovascular disease. Mer and PS dampen inflammation, thereby protecting against atherosclerosis progression. Tyro3, the least studied TAM receptor in cardiovascular disease, appears to protect against fibrosis …

The Climate Impact Of Tropical Peatland Degradation, René Dommain, Steve Frolking, Aurich Jeltsch-Thömmes, Fortunat Joos, John Couwenberg, Paul Glaser, Alexander Cobb, Charles Harvey

Faculty Publications

Southeast Asia is a global hotspot of peatland degradation and related greenhouse gas emissions. Anthropogenic impacts, mainly associated with agricultural conversion, shift Southeast Asian peatlands from carbon sinks to significant carbon sources. Here we first describe the impacts of anthropogenic drainage on landscape-scale carbon dynamics of individual peatlands and then use an impulse‐response model of radiative forcing to quantify the climate impacts of peat-carbon losses. Whereas water-table elevation (i.e. drainage depth) determines the magnitude of CO2 emissions at the site-scale, the geometric arrangement of artificial drainage networks determines carbon losses on the landscape-scale. Among all peatland greenhouse gas fluxes, the …

Implications Of Energetic Neutral Atoms Observed With Ibex-Lo For The Pressure Balance In The Heliosphere, André Galli, Peter Wurz, Nathan A. Schwadron, Eberhard Möbius, Stephen A. Fuselier, Justyna M. Sokół, Maciej Bzowski, Paweł Swaczyna, Kostas Dialynas, David J. Mccomas

Faculty Publications

Energetic Neutral Atoms (ENAs) from the heliosphere are a unique means to remotely image the boundary regions of our heliosphere. NASA's Interstellar Boundary Explorer (IBEX) has been very successful in measuring these ENAs since 2008 at energies from tens of eV to 6 keV.The ENA low energy range from tens of eV to solar wind energy (roughly 1 keV) has been sampled throughout an entire solar cycle with the IBEX-Lo ENA imager. This enables us to study the physical implications for the structure of the heliosphere and for the parent proton populations in the heliosheath and other plasma regions that …

Variation In Diet And Leafy Browse Offerings Amongcolobus Monkeys (Colobus Spp.) And Langurs(Trachypithecus Spp.) In Aza Facilities, Maura R. Plocek, Noah T. Dunham

Student Scholarship

Providing nutritionally balanced diets is a key aspect of successful husbandry and can help support sustainable ex situ populations. This study focuses on the diets of zoo‐housed colobus monkeys (Colobus angolensis and C. guereza) and langurs (Trachypithecus cristatus and T. francoisi) across AZA institutions. We utilized survey responses from 34 institutions to (1)document the extent of dietary variation with regard to food categories and macronutrients offered, (2) assess interspecific variation in diets offered, and (3) identify important aspects of browse provisioning among institutions. A total of 95 different food items and 229 common‐name browse types were …

Invited Perspective: Climate Change And Maternal Mental Health-Looking Beyond High-Income Countries, Andrea G Buchwald, Sarah Boudova

Department of Obstetrics and Gynecology Faculty Papers

No abstract provided.

Immuno-Informatics Insight Into The Relationship Between Cholesterol And Cytokines In Cutaneous Leishmaniasis: From Clinics To Computation, Evan H. Sulaiman, Layth J. Mohammad, Allaa H. Thanoon, Isaac Karimi

Sultan Qaboos University Medical Journal

Objectives: The role of serum cholesterol and its interactions with cytokines in human cutaneous leishmaniasis (CL) pathophysiology is unknown. This study aimed to evaluate the correlation among serum total cholesterol (TC), very-low-density lipoprotein cholesterol (VLDL-C), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG) and cytokines (including interleukin [IL] 10), IL-12 and tumour necrosis factor-alpha [TNF-α]) in CL. The cholesterol–cytokine network was analysed to illuminate the pathogenesis of CL. Methods: This case-control study was conducted from December 2022 to March 2023 in hospitals within Baghdad and Wasit provinces, Iraq, and included CL and CL-free subjects ranging between 20–30 years …

The Impact Of The Fruit And Seed Of Date On Childbirth Stages And Pregnancy Complications, Fatemeh A. Rahnemaei, Zahra A. Kashani, Mohammadamin Jandaghian-Bidgoli, Farinaz Rahimi, Farzaneh Zaheri, Fatemeh Abdi

Sultan Qaboos University Medical Journal

This review aimed to investigate the effects of date fruit products on childbirth and pregnancy-related complications. MeSH keywords were systematically searched in scientific databases, and 16 articles were reviewed. It was found that consuming 7 date fruits (average of 80 g) per day for 2–4 weeks before the estimated date of delivery leads to a better cervical dilatation at admission or improvement of Bishop score, a decrease in the need for induction or stimulation of labour and an increase in effective uterine contractions, which, in turn, decreases the duration of pregnancy and the different stages of labour. Additionally, date fruit …

A Prospective Cohort Study On The Effect Of Antiseizure Medications On Thyroid Function In Children Aged 6 Months To 12 Years With Epilepsy, Shivaprasad Mohankumar, Ramachandran Rameshkumar, Tamil Selvan, Hanumanthappa Nandeesha, Delhikumar Cg

Sultan Qaboos University Medical Journal

Objectives: This study aimed to explore the effect of antiseizure medications (ASM) on thyroid function in children with epilepsy. Methods: A prospective study involving children between 6 months and 12 years of age with new-onset seizures who took ASM within 2 months was conducted in the Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India, between August 2019 to March 2022. Thyroid function tests—free T3, free T4 and thyroid stimulating hormone (TSH)—were done at baseline and after completing 3 months by competitive immunoassay using direct chemiluminescent technology. The primary outcome was the proportion of patients diagnosed with thyroid …

Spatial Pattern And Differential Expression Analysis With Spatial Transcriptomic Data, Fei Qin, Xizhi Luo, Bo Cai Ph.D., Feifei Xiao, Guoshuai Cai

Faculty Publications

The emergence of spatial transcriptomic technologies has opened new avenues for investigating gene activities while preserving the spatial context of tissues. Utilizing data generated by such technologies, the identification of spatially variable (SV) genes is an essential step in exploring tissue landscapes and biological processes. Particularly in typical experimental designs, such as case-control or longitudinal studies, identifying SV genes between groups is crucial for discovering significant biomarkers or developing targeted therapies for diseases. However, current methods available for analyzing spatial transcriptomic data are still in their infancy, and none of the existing methods are capable of identifying SV genes between …

The Climate Impact Of Tropical Peatland Degradation, René Dommain, Steve Frolking, Aurich Jeltsch-Thömmes, Fortunat Joos, John Couwenberg, Paul Glaser, Alexander Cobb, Charles Harvey

Faculty Publications

Southeast Asia is a global hotspot of peatland degradation and related greenhouse gas emissions. Anthropogenic impacts, mainly associated with agricultural conversion, shift Southeast Asian peatlands from carbon sinks to significant carbon sources. Here we first describe the impacts of anthropogenic drainage on landscape-scale carbon dynamics of individual peatlands and then use an impulse‐response model of radiative forcing to quantify the climate impacts of peat-carbon losses. Whereas water-table elevation (i.e. drainage depth) determines the magnitude of CO2 emissions at the site-scale, the geometric arrangement of artificial drainage networks determines carbon losses on the landscape-scale. Among all peatland greenhouse gas fluxes, the …

Implications Of Energetic Neutral Atoms Observed With Ibex-Lo For The Pressure Balance In The Heliosphere, André Galli, Peter Wurz, Nathan A. Schwadron, Eberhard Möbius, Stephen A. Fuselier, Justyna M. Sokół, Maciej Bzowski, Paweł Swaczyna, Kostas Dialynas, David J. Mccomas

Faculty Publications

Energetic Neutral Atoms (ENAs) from the heliosphere are a unique means to remotely image the boundary regions of our heliosphere. NASA's Interstellar Boundary Explorer (IBEX) has been very successful in measuring these ENAs since 2008 at energies from tens of eV to 6 keV.The ENA low energy range from tens of eV to solar wind energy (roughly 1 keV) has been sampled throughout an entire solar cycle with the IBEX-Lo ENA imager. This enables us to study the physical implications for the structure of the heliosphere and for the parent proton populations in the heliosheath and other plasma regions that …

A New Synthesis Of Arctic-Boreal Carbon Fluxes For Improved Carbon Budget Estimates, Anna Virkkala, Isabel Wargowsky, Judith Vogt, Mckenzie Kuhn, Susan Natali, Brendan Rogers, Mathias Goeckede, Kyle Arndt, Jennifer Watts, Tiffany Windholz, Simran Madaan

Faculty Publications

The Arctic-boreal zone and its permafrost regions have historically been sparsely measured for carbon dioxide and methane fluxes. This data sparsity has created significant uncertainties in Arctic-boreal carbon budget estimates. However, over the past decade, the availability of Arctic-boreal carbon flux data has increased substantially. Yet, it remains scattered across different repositories, papers, and unpublished sources, making it hard to estimate more accurate Arctic-boreal carbon budgets. To address this research gap, we have compiled a database of Arctic-boreal carbon fluxes (ABCFlux v2) from flux repositories, literature, and site principal investigators, which will be openly distributed. The database includes carbon dioxide …

Novel Cuprotosis-Related Gene Signature: A Prognostic Indicator And Regulator Of The Glioma Immune Microenvironment, Dongming Gao, Youyuan Bao, Wenyin Shi, Lei Li, Liang Gao

Department of Radiation Oncology Faculty Papers

Background: Glioma is a primary malignant brain tumor with a poor prognosis. Glioma-related biomarkers need to be identified to enable the personalized treatment of and predict the prognosis of glioma patients. Cuproptosis is an unusual mechanism of cell death, and is closely associated with disease progression and the immune-microenvironment of the tumor. However, the function of cuproptosis in glioma is still unclear, therefore the aim of this study was to investigate the role of cuproptosis-related genes in gliomas.

Methods: We examined the relationship between cuproptosis and glioma using the clinical and expression data of glioma tumors from The Cancer Genome …