Digital Commons Network^™

History Of Incarceration And Dental Care Use Among Older Adults In The United States, Alexander Testa, Dylan B Jackson, Carmen Gutierrez, Chantal Fahmy, Vahed Maroufy, Rafael Samper-Ternent, Ana C Neumann

Faculty, Staff and Student Publications

INTRODUCTION: Dental care is a critical component of healthy aging; however, emerging evidence suggests that having been previously incarcerated is a risk factor for not using dental care services. This study investigates the relationship between prior incarceration and dental care among older adults and assesses whether wealth and dental insurance explain this relationship.

METHODS: Data are from the Health and Retirement Study, a nationally representative sample of community-dwelling older adults in the United States, collected in 2012 and 2014. Multivariable logistic regression is used to assess the relationship between a history of incarceration and dental care. Mediation analyses were conducted …

Personhood, Politics, Assisted Reproduction, And The Law Post-Dobbs, Myrisha S. Lewis

Faculty Publications

With the end of the federal constitutional right to abortion, state legislatures and state courts have become far more important in the sphere of reproductive rights. Before Dobbs, anti-abortion advocates had significant (albeit increasingly porous) ceilings on what they could prohibit in relation to reproductive health care. A significant check on those actions is now gone.

In the wake of Dobbs, societal debates about personhood have increased and expanded in terms of their practical implications. Before Dobbs, anti-abortion advocates admitted that Roe and subsequent cases limited the scope of their arguments, especially in relation to the legality …

Review: White Before Whiteness In The Late Middle Ages, Alani Hicks-Bartlett

Quidditas

No abstract provided.

Access To Science And Scholarship: Building An Evidence Base To Support The Future Of Open Research Policy, Clarke & Esposito

Copyright, Fair Use, Scholarly Communication, etc.

Today, the MIT Press is releasing a comprehensive report that addresses how open access policies shape research and what is needed to maximize their positive impact on the research ecosystem.

The report, entitled “Access to Science & Scholarship 2024: Building an Evidence Base to Support the Future of Open Research Policy,” is the outcome of a National Science Foundation-funded workshop held at the D.C. headquarters of the American Association for the Advancement of Science on September 20, 2024.

While open access aims to democratize knowledge, its implementation has been a factor in the consolidation of the academic publishing industry, an …

Rights And Redress For Transgender Survivors Of Prison Rape: The Failures Of The Prison Rape Elimination Act, Natalie Hatton

William & Mary Law Review

This Note will argue that PREA [Prison Rape Elimination Act] provides meager protection and insufficient relief to transgender individuals who have been victims of sexual violence while incarcerated and that the existing mechanisms for relief are insufficient. Because PREA contains no private cause of action to allow survivors of rape to sue for violations of PREA, transgender rape survivors’ pain remains unredressed. To address this problem, this Note puts forth a combination of solutions to remove barriers to redress for transgender survivors of prison rape, including amending PREA to include a private cause of action and repealing provisions of the …

The Ltar Grazing Land Common Experiment At Walnut Gulch Experimental Watershed, Phil Heilman, Steven R. Archer, C Jason Williams, Russell L. Scott, David C. Goodrich, Chandra Holifield Collins, Adam Naito, Guillermo Ponce-Campos

Journal Articles

The Walnut Gulch Experimental Watershed (WGEW) Long-Term Agroecosystem Research (LTAR) network common experiment addresses the aspirational practice of brush management (BM) to reverse the prevailing condition of woody plant encroachment (WPE) and increase perennial native grass production. Across the western United States, the decision to implement BM includes consideration of management objectives, cost, and the expected impact on a diverse suite of ecosystem services.Maintaining or restoring grass cover will help meet the LTAR sustainable production, economic, and social goals, and averting degradation will meet environmental goals. This common experiment, focused on hydrologic and erosion impacts of BM, aims to inform …

A Phase I Dose Escalation Study Of The Lrp5 Antagonist Bi 905681 In Patients With Advanced And Metastatic Solid Tumors, D. R. Spigel, J. S. Wang, L. Pronk, B. Muskens, M. Teufel, Babar Bashir, H. Burris

Department of Medical Oncology Faculty Papers

BACKGROUND: The Wnt pathway is involved in proliferation and tissue homeostasis. Aberrant activation promotes cancer cell proliferation and survival. Inhibition of the low-density lipoprotein receptor-related protein 5/6 (LRP5/6) coreceptors that regulate Wnt signaling could prevent cancer cell proliferation. BI 905681 is a novel LRP5 antagonist that has demonstrated potent in vivo antitumor activity.

PATIENTS AND METHODS: This was a phase I, dose escalation study (NCT04147247) evaluating BI 905681 in patients with advanced solid tumors over two dosing schedules (schedule A: every 3 weeks, 3-week cycles and schedule B: every 2 weeks, 4-week cycles). The primary endpoint was the maximum tolerated …

Alfred Russel Wallace Notes 32. Wallace On The Tigers Of Singapore, Charles H. Smith

Faculty/Staff Personal Papers

Historian John van Wyhe has written a good deal on Alfred Russel Wallace’s travels in the Malay Archipelago in the 1850s and 1860s, in so doing coming to a number of generally derogative surmises on Wallace’s thoughts and collecting efforts that disagree with the conclusions made by other scholars. In this work one example of such treatment is given, concerning Wallace’s estimation of the number of persons in Singapore attacked by tigers over the middle years of that century.

Genomic Analysis Of Intracranial And Subcortical Brain Volumes Yields Polygenic Scores Accounting For Variation Across Ancestries, Luis M García-Marín, Adrian I Campos, Santiago Diaz-Torres, Jill A Rabinowitz, Zuriel Ceja, Brittany L Mitchell, Katrina L Grasby, Jackson G Thorp, Ingrid Agartz, Saud Alhusaini, David Ames, Philippe Amouyel, Ole A Andreassen, Konstantinos Arfanakis, Alejandro Arias-Vasquez, Nicola J Armstrong, Lavinia Athanasiu, Mark E Bastin, Alexa S Beiser, David A Bennett, Joshua C Bis, Marco P M Boks, Dorret I Boomsma, Henry Brodaty, Rachel M Brouwer, Jan K Buitelaar, Ralph Burkhardt, Wiepke Cahn, Vince D Calhoun, Owen T Carmichael, Mallar Chakravarty, Qiang Chen, Christopher R K Ching, Sven Cichon, Benedicto Crespo-Facorro, Fabrice Crivello, Anders M Dale, George Davey Smith, Eco J C De Geus, Philip L De Jager, Greig I De Zubicaray, Stéphanie Debette, Charles Decarli, Chantal Depondt, Sylvane Desrivières, Srdjan Djurovic, Stefan Ehrlich, Susanne Erk, Thomas Espeseth, Guillén Fernández, Irina Filippi, Simon E Fisher, Debra A Fleischman, Evan Fletcher, Myriam Fornage, Andreas J Forstner, Clyde Francks, Barbara Franke, Tian Ge, Aaron L Goldman, Hans J Grabe, Robert C Green, Oliver Grimm, Nynke A Groenewold, Oliver Gruber, Vilmundur Gudnason, Asta K Håberg, Unn K Haukvik, Andreas Heinz, Derrek P Hibar, Saima Hilal, Jayandra J Himali, Beng-Choon Ho, David F Hoehn, Pieter J Hoekstra, Edith Hofer, Wolfgang Hoffmann, Avram J Holmes, Georg Homuth, Norbert Hosten, M Kamran Ikram, Jonathan C Ipser, Clifford R Jack, Neda Jahanshad, Erik G Jönsson, Rene S Kahn, Ryota Kanai, Marieke Klein, Maria J Knol, Lenore J Launer, Stephen M Lawrie, Stephanie Le Hellard, Phil H Lee, Hervé Lemaître, Shuo Li, David C M Liewald, Honghuang Lin, W T Longstreth, Oscar L Lopez, Michelle Luciano, Pauline Maillard, Andre F Marquand, Nicholas G Martin, Jean-Luc Martinot, Karen A Mather, Venkata S Mattay, Katie L Mcmahon, Patrizia Mecocci, Ingrid Melle, Andreas Meyer-Lindenberg, Nazanin Mirza-Schreiber, Yuri Milaneschi, Thomas H Mosley, Thomas W Mühleisen, Bertram Müller-Myhsok, Susana Muñoz Maniega, Matthias Nauck, Kwangsik Nho, Wiro J Niessen, Markus M Nöthen, Paul A Nyquist, Jaap Oosterlaan, Massimo Pandolfo, Tomas Paus, Zdenka Pausova, Brenda W J H Penninx, G Bruce Pike, Bruce M Psaty, Benno Pütz, Simone Reppermund, Marcella D Rietschel, Shannon L Risacher, Nina Romanczuk-Seiferth, Rafael Romero-Garcia, Gennady V Roshchupkin, Jerome I Rotter, Perminder S Sachdev, Philipp G Sämann, Arvin Saremi, Muralidharan Sargurupremraj, Andrew J Saykin, Lianne Schmaal, Helena Schmidt, Reinhold Schmidt, Peter R Schofield, Markus Scholz, Gunter Schumann, Emanuel Schwarz, Li Shen, Jean Shin, Sanjay M Sisodiya, Albert V Smith, Jordan W Smoller, Hilkka S Soininen, Vidar M Steen, Dan J Stein, Jason L Stein, Sophia I Thomopoulos, Arthur W Toga, Diana Tordesillas-Gutiérrez, Julian N Trollor, Maria C Valdes-Hernandez, Dennis Van T Ent, Hans Van Bokhoven, Dennis Van Der Meer, Nic J A Van Der Wee, Javier Vázquez-Bourgon, Dick J Veltman, Meike W Vernooij, Arno Villringer, Louis N Vinke, Henry Völzke, Henrik Walter, Joanna M Wardlaw, Daniel R Weinberger, Michael W Weiner, Wei Wen, Lars T Westlye, Eric Westman, Tonya White, A Veronica Witte, Christiane Wolf, Jingyun Yang, Marcel P Zwiers, M Arfan Ikram, Sudha Seshadri, Paul M Thompson, Claudia L Satizabal, Sarah E Medland, Miguel E Rentería

Faculty, Staff and Student Publications

Subcortical brain structures are involved in developmental, psychiatric and neurological disorders. Here we performed genome-wide association studies meta-analyses of intracranial and nine subcortical brain volumes (brainstem, caudate nucleus, putamen, hippocampus, globus pallidus, thalamus, nucleus accumbens, amygdala and the ventral diencephalon) in 74,898 participants of European ancestry. We identified 254 independent loci associated with these brain volumes, explaining up to 35% of phenotypic variance. We observed gene expression in specific neural cell types across differentiation time points, including genes involved in intracellular signaling and brain aging-related processes. Polygenic scores for brain volumes showed predictive ability when applied to individuals of diverse …

Sex Differences In Hypertension And Its Management Throughout Life, Wan-Jin Yeo, Rahul Abraham, Aditya L Surapaneni, Pascal Schlosser, Shoshana H Ballew, Bige Ozkan, Carina M Flaherty, Bing Yu, Joseph V Bonventre, Chirag R Parikh, Paul L Kimmel, Ramachandran S Vasan, Josef Coresh, Morgan E Grams

Faculty, Staff and Student Publications

Background: The prevalence of hypertension and uncontrolled hypertension may differ by age and sex.

Methods: We included participants in the Atherosclerosis Risk in Communities study at seven study visits over 33 years (visit 1: 15 636 participants; mean age, 54 years; 55% women), estimating sex differences in prevalence of hypertension (systolic blood pressure ≥130 mm Hg; diastolic blood pressure ≥80 mm Hg; or self-reported antihypertension medication use) and uncontrolled hypertension (systolic blood pressure ≥140 mm Hg or diastolic blood pressure ≥90 mm Hg) using unadjusted and comorbidity-adjusted models.

Results: The prevalence of hypertension increased with age from 40% (ages, 43-46 …

Loss Of Sc5d Results In Micrognathia Due To A Failure In Osteoblast Differentiation, Chihiro Iwaya, Akiko Suzuki, Junichi Iwata

Faculty, Staff and Student Publications

INTRODUCTION: Mutations in genes related to cholesterol metabolism, or maternal diet and health status, affect craniofacial bone formation. However, the precise role of intracellular cholesterol metabolism in craniofacial bone development remains unclear.

OBJECTIVE: The aim of this study is to determine how cholesterol metabolism aberrations affect craniofacial bone development.

METHODS: Mice with a deficiency in Sc5d, which encodes an enzyme involved in cholesterol synthesis, were analyzed with histology, micro computed tomography (microCT), and cellular and molecular biological methods.

RESULTS: Sc5d null mice exhibited mandible hypoplasia resulting from defects in osteoblast differentiation. The activation of the hedgehog and WNT/β-catenin signaling pathways, …

Survival In Patients With Rheumatoid Arthritis And Early Breast Cancer Treated With Tumor Necrosis Factor Inhibitors, Juan I Ruiz, Xiudong Lei, Wu Chi-Fang, Sharon H Giordano, Hui Zhao, Suja S Rajan, Heather Lin, Maria E Suarez-Almazor

Faculty, Staff and Student Publications

Background: There have been concerns about the use of tumor necrosis factor inhibitors (TNFi) for autoimmune disease in patients with recently diagnosed cancer. We assessed the survival of patients with rheumatoid arthritis (RA) and newly diagnosed early breast cancer (BC) treated with TNFi in the first two years after BC diagnosis.

Methods: We identified patients in two datasets: (1) Optum's de-identified Clinformatics® Data Mart Database (CDM), (2) Surveillance, Epidemiology, and End Results program (SEER) and Texas Cancer Registry (TCR) Medicare-linked cohort. We grouped patients according to whether they received TNFi, conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) only, or no DMARDs …

Impact Of Racial, Ethnic, And Socioeconomic Disparities On Presentation And Survival Of Hcc: A Multicenter Study, Nicole E Rich, Patricia D Jones, Hong Zhu, Tanushree Prasad, Amy Hughes, Sandi Pruitt, Caitlin C Murphy, Karim Seif-El-Dahan, Darine Daher, Gloria Figueroa, Stephanie Castaneda, Lisa Quirk, Michael Gonzales, Osiris Carranza, Samantha Bourque, Nargis Baset, Adam C Yopp, Amit G Singal

Faculty, Staff and Student Publications

BACKGROUND: Racial and ethnic disparities have been reported for HCC prognosis, although few studies fully account for clinically important factors and social determinants of health, including neighborhood socioeconomic status.

METHODS: We conducted a retrospective multicenter cohort study of patients newly diagnosed with HCC from January 2010 through August 2018 at 4 large health systems in the United States. We used multivariable logistic regression and cause-specific Cox proportional hazard models to identify factors associated with early-stage HCC presentation and overall survival.

RESULTS: Of 2263 patients with HCC (37.6% non-Hispanic White, 23.5% non-Hispanic Black, 32.6% Hispanic, and 6.4% Asian/other), 42.0% of patients …

Verifying Models Of The Underwater Soundscape From Wind And Ships With Benchmark Scenariosa), S Bruce Martin, Martin Siderius, Michael A. Ainslie, Michele B. Halvorsen, Leila Hatch, Mark K. Prior, Daniel Brooker, James Caplinger, Christine Erbe, John Gebbie, Multiple Additional Authors

Electrical and Computer Engineering Faculty Publications and Presentations

Models of the underwater acoustic soundscape are important for evaluating the effects of human generated sounds on marine life. The performance of models can be validated against measurements or verified against each other for consistency. A verification workshop was held to compare models that predict the soundscape from wind and vessels and estimate detection ranges for a submerged target. Eight modeling groups participated in the workshop which predicted sound levels with observation windows of 1 min and 1 km2. Substantial differences were found in how modelers computed the propagation losses for decidecade bands and estimated the source level of wind. …

Microrna-1307-3p Contributes To Breast Cancer Progression Through Prm2, José Roberto Estupiñan-Jiménez, Valeria Villarreal-García, Vianey Gonzalez-Villasana, Pablo E Vivas-Mejia, Jose Manuel Vazquez-Guillen, Patricio Adrián Zapata-Morin, Marienid Flores-Colón, Claudia Altamirano-Torres, Ezequiel Viveros-Valdez, Cristina Ivan, Mohammed H Rashed, Recep Bayraktar, Cristina Rodríguez-Padilla, Gabriel Lopez-Berestein, Diana Resendez-Perez

Faculty, Staff and Student Publications

Background: Despite advances in screening and therapy, breast cancer (BC) remains the predominant cancer in women globally. Dysregulation of microRNAs (miRNAs) is pivotal in carcinogenesis across various cancers, including BC. Evidence indicates that miR-1307-3p is upregulated in BC tumors, yet its target genes are not fully elucidated. This study aimed to explore how miR-1307-3p regulates BC proliferation, migration, invasion, and angiogenesis and to identify potential target genes.

Methods: Basal miR-1307-3p levels were quantified in BC cell lines MDA-MB-231 and MCF-7, as well as MCF-10A using quantitative real-time reverse transcription-PCR (RT-qPCR). The impact of miR-1307-3p inhibition on BC cell proliferation, migration, …

3d Printed Microfluidic Fabrication Methodology, Characterization, Mechanical Design, And Applications In Electrostatic Artificial Muscles And Benthic Microbial Fuel Cells, Terak B. Hornik

Master's Theses

The fabrication of microfluidic devices often requires specialized methods. The development of these methods requires careful characterization and understanding of the processes involved. Using primarily PolyJet 3D printing technology, microfluidics offers a wide scope of applications such as microfluidic benthic microbial fuel cells (MBMFCs) and electrostatic artificial muscles. MBMFCs benefit from the confinement of the microbes resulting in close proximity between the electrode and the organisms. Using a modular design called the Sponge, assembly and upscaling is possible. Electrostatic artificial muscles benefit from a microfluidic approach due to the non-linearity of electrostatic attraction creating disproportionate benefits when miniaturized. When designed …

Impact Of Participation In Cardiac Rehabilitation Post Myocardial-Infarction: An Integrative Review, Zoie Maynard, Mallory Stinson

Master's Projects

As one of the most common causes of hospitalization, the prevalence of myocardial infarction is indisputable Since this condition is so ubiquitous, a treatment protocol is initiated with methods to help patients modify their lifestyle, treat their underlying disease process, educate them to prevent reoccurrence, and improve their healthcare outcomes. This protocol relies heavily on the use of cardiac rehabilitation. Despite the implementation of this treatment protocol, the concern for recurrence and rehospitalization remains. The goal of this integrative review is to determine how participation in cardiac rehabilitation post-myocardial infarction impacts healthcare outcomes including rates of rehospitalization and depression. The …

A Randomized Controlled Trial Of Tickoff® (Metarhizium Anisopliae Icipe 7) For Control Of Tick Infestations And Transmission Of Tick-Borne Infections In Extensively Grazed Zebu Cattle In Coastal Kenya, Joseph Wang Ang’A Oundo, Shewit Kalayou, Gerrit Gort, Gebbiena M. Bron, Constantianus J.M. Koenraadt, Quirine Ten Bosch, Daniel Masiga

All Peer-Reviewed Publications

The entomopathogenic fungus Metarhizium anisopliae isolate ICIPE 7 is being developed as an eco-friendly alternative to chemical acaricides in managing natural tick infestation on livestock. Its impact on tick infestation and tick-borne infections in cattle under natural conditions are yet unclear. We conducted a randomized controlled field trial to assess the safety and effects of Tickoff® (a formulation of M. anisopliae isolate ICIPE 7) and the chemical acaricide Triatix® on tick infestation and incidence of Anaplasma marginale and Theileria parva in extensively grazed zebu cattle in coastal Kenya. A total of 217 eligible herds comprising 1459 intent-to-treat zebu cattle were …

A Survey Of Jamaica Constabulary Force Officers’ Opinions About Juveniles, The Causes Of Delinquency And Self-Legitimacy, Sh -Shanna Ellington

All Dissertations

This study explored the perceptions of Jamaica Constabulary Force (JCF) officers regarding juveniles, the causes of juvenile delinquency, and their self-legitimacy. It examined whether these perceptions were influenced by demographic factors such as police officers’ age, gender, rank, years of service, age at entry into the police force, educational level, and divisional classification. Additionally, it investigated the relationship between officers' perceptions of juveniles, causes of juvenile delinquency and their sense of self-legitimacy.

Previous research had extensively studied juvenile delinquency, causes of juvenile delinquency and police legitimacy, but there remained a significant gap in understanding how Jamaica police officers’ demographics influenced …

Deciphering Rodent Behavior: Unraveling Complex Decision-Making Through High-Throughput Data Analysis In Behavioral Neuroscience, Atanu Giri

Open Access Theses & Dissertations

Understanding the effects of substance use on decision-making is critical for both clinical andtranslational research. In this thesis, I present two complementary studies that explore decision- making behavior in rodents with a focus on alcohol consumption and novel experimental frame- works. The first study examines the impact of acute alcohol consumption on decision-making in a behavioral approach-avoidance task. Rats were presented with a concurrent choice of consuming alcohol and sucrose mixtures across four distinct concentrations, allowing for the analysis of ap- proach or avoidance behavior. Sex-dependent differences emerged, with male rats demonstrating a significantly higher tendency to approach higher alcohol …

The Association Of Migration-Related Stress With Poor Mental Health Among Recently Resettled Afghan Refugees, Munjireen Sifat, Sarah Kenney, Venera Bekteshi, Shawn Chiang, Motolani Ogunsanya, Laili Boozary, Adam Alexander, Darla Kendzor

Department of Medical Oncology Faculty Papers

BACKGROUND: The resettlement of Afghan refugees in Oklahoma City, OK, provides a critical context for examining the mental health challenges faced by this population due to post-migration stressors.

METHODS: This study utilized online surveys to recently resettled Afghan refugees in Oklahoma City, with support provided by bilingual research assistants to accommodate low literacy rates. Surveys, initially in English, were professionally translated into Dari and Pashto and validated through back-translation.

RESULTS: Participants (N = 348) were majority of Pashtun ethnicity. High rates of mental health issues were evident, with 62.1 % of participants screening positive for depression and 20.1 % …

Georgia Library Spotlight: Anthropology Day At Reese Library, Augusta University, Aspasia Luster, Angela Bratton, Thomas Weeks

Georgia Library Quarterly

No abstract provided.

The Association Between Food Production, Food Security, Household Consumer Behaviour And Waist-Hip Ratio Amongst Women In Smallholder Farming Households In Kilifi County, Kenya, Rosebella Iseme, Eunice Muthoni, Roselyter Riang’A, Felix Agoi, Noveline Khatievi, James Orwa, Beatrice Karembo Karisa, Bibi Abdallah Bakari, Morris Ogero, Mwanamaka Mabruki, Cyprian Mostert, Anthony Ngugi

Population Health, East Africa

Food insecurity disproportionately affects smallholder farming households and within them women, who bear primary caregiving responsibilities and contend with time and resource constraints that heighten their vulnerability to adverse nutrition-related health outcomes. This study cross-sectionally investigates the association between food production practices, household consumer behaviour, and the experience of food insecurity with women's waist-hip ratio (WHR), a key indicator of abdominal obesity, in a coastal community in Kenya. In total, 394 households were randomly selected from a list of farming households in Kaloleni and Rabai sub-counties of Kilifi. Trained enumerators administered questionnaires to adult female family members who play a …

Integration Across Biophysical Scales Identifies Molecular And Cellular Correlates Of Person-To-Person Variability In Human Brain Connectivity, Bernard Ng, Shinya Tasaki, Kelsey M Greathouse, Courtney K Walker, Ada Zhang, Sydney Covitz, Matt Cieslak, Audrey J Weber, Ashley B Adamson, Julia P Andrade, Emily H Poovey, Kendall A Curtis, Hamad M Muhammad, Jakob Seidlitz, Ted Satterthwaite, David A Bennett, Nicholas T Seyfried, Jacob Vogel, Chris Gaiteri, Jeremy H Herskowitz

Faculty, Staff and Student Publications

Brain connectivity arises from interactions across biophysical scales, ranging from molecular to cellular to anatomical to network level. To date, there has been little progress toward integrated analysis across these scales. To bridge this gap, from a unique cohort of 98 individuals, we collected antemortem neuroimaging and genetic data, as well as postmortem dendritic spine morphometric, proteomic and gene expression data from the superior frontal and inferior temporal gyri. Through the integration of the molecular and dendritic spine morphology data, we identified hundreds of proteins that explain interindividual differences in functional connectivity and structural covariation. These proteins are enriched for …

A Site-Wise Reliability Analysis Of The Abcd Diffusion Fractional Anisotropy And Cortical Thickness: Impact Of Scanner Platforms, Yezhi Pan, L Elliot Hong, Ashley Acheson, Paul M Thompson, Neda Jahanshad, Alyssa H Zhu, Jiaao Yu, Chixiang Chen, Tianzhou Ma, Ho-Ling Liu, Jelle Veraart, Els Fieremans, Nicole R Karcher, Peter Kochunov, Shuo Chen

Faculty, Staff and Student Publications

The Adolescent Brain and Cognitive Development (ABCD) project is the largest study of adolescent brain development. ABCD longitudinally tracks 11,868 participants aged 9-10 years from 21 sites using standardized protocols for multi-site MRI data collection and analysis. While the multi-site and multi-scanner study design enhances the robustness and generalizability of analysis results, it may also introduce nonbiological variances including scanner-related variations, subject motion, and deviations from protocols. ABCD imaging data were collected biennially within a period of ongoing maturation in cortical thickness and integrity of cerebral white matter. These changes can bias the classical test-retest methodologies, such as intraclass correlation …

Single-Cell Integration Reveals Metaplasia In Inflammatory Gut Diseases, Amanda J Oliver, Ni Huang, Raquel Bartolome-Casado, Ruoyan Li, Simon Koplev, Hogne R Nilsen, Madelyn Moy, Batuhan Cakir, Krzysztof Polanski, Victoria Gudiño, Elisa Melón-Ardanaz, Dinithi Sumanaweera, Daniel Dimitrov, Lisa Marie Milchsack, Michael E B Fitzpatrick, Nicholas M Provine, Jacqueline M Boccacino, Emma Dann, Alexander V Predeus, Ken To, Martin Prete, Jonathan A Chapman, Andrea C Masi, Emily Stephenson, Justin Engelbert, Sebastian Lobentanzer, Shani Perera, Laura Richardson, Rakeshlal Kapuge, Anna Wilbrey-Clark, Claudia I Semprich, Sophie Ellams, Catherine Tudor, Philomeena Joseph, Alba Garrido-Trigo, Ana M Corraliza, Thomas R W Oliver, C Elizabeth Hook, Kylie R James, Krishnaa T Mahbubani, Kourosh Saeb-Parsy, Matthias Zilbauer, Julio Saez-Rodriguez, Marte Lie Høivik, Espen S Bækkevold, Christopher J Stewart, Janet E Berrington, Kerstin B Meyer, Paul Klenerman, Azucena Salas, Muzlifah Haniffa, Frode L Jahnsen, Rasa Elmentaite, Sarah A Teichmann

Faculty, Staff and Student Publications

The gastrointestinal tract is a multi-organ system crucial for efficient nutrient uptake and barrier immunity. Advances in genomics and a surge in gastrointestinal diseases1,2 has fuelled efforts to catalogue cells constituting gastrointestinal tissues in health and disease3. Here we present systematic integration of 25 single-cell RNA sequencing datasets spanning the entire healthy gastrointestinal tract in development and in adulthood. We uniformly processed 385 samples from 189 healthy controls using a newly developed automated quality control approach (scAutoQC), leading to a healthy reference atlas with approximately 1.1 million cells and 136 fine-grained cell states. We anchor 12 gastrointestinal disease datasets spanning …

A Rigorous Multi-Laboratory Study Of Known Pdac Biomarkers Identifies Increased Sensitivity And Specificity Over Ca19-9 Alone, Brian Haab, Lu Qian, Ben Staal, Maneesh Jain, Johannes Fahrmann, Christine Worthington, Denise Prosser, Liudmila Velokokhatnaya, Camden Lopez, Runlong Tang, Mark W Hurd, Gopalakrishnan Natarajan, Sushil Kumar, Lynette Smith, Sam Hanash, Surinder K Batra, Anirban Maitra, Anna Lokshin, Ying Huang, Randall E Brand

Faculty, Staff and Student Publications

A blood test that enables surveillance for early-stage pancreatic ductal adenocarcinoma (PDAC) is an urgent need. Independent laboratories have reported PDAC biomarkers that could improve biomarker performance over CA19-9 alone, but the performance of the previously reported biomarkers in combination is not known. Therefore, we conducted a coordinated case/control study across multiple laboratories using common sets of blinded training and validation samples (132 and 295 plasma samples, respectively) from PDAC patients and non-PDAC control subjects representing conditions under which surveillance occurs. We analyzed the training set to identify candidate biomarker combination panels using biomarkers across laboratories, and we applied the …

Epigenomic And Transcriptomic Profiling Of Solitary Fibrous Tumors Identifies Site-Specific Patterns And Candidate Genes Regulated By Dna Methylation, Hannah C Beird, Jeffrey M Cloutier, Nalan Gokgoz, Christopher Eeles, Anthony M Griffin, Davis R Ingram, Khalida M Wani, Rossana Lazcano Segura, Luca Cohen, Carl Ho, Jay S Wunder, Irene L Andrulis, P Andrew Futreal, Benjamin Haibe-Kains, Alexander J Lazar, Wei-Lien Wang, Joanna Przybyl, Elizabeth G Demicco

Faculty, Staff and Student Publications

A solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm that can arise at any anatomical site and is characterized by recurrent NAB2::STAT6 fusions and metastatic progression in 10% to 30%. The cell of origin has not been identified. Despite some progress in understanding the contribution of heterogeneous fusion types and secondary mutations to SFT biology, epigenetic alterations in extrameningeal SFT remain largely unexplored, and most sarcoma research to date has focused on the use of methylation profiling for tumor classification. We interrogated genome-wide DNA methylation in 79 SFTs to identify informative epigenetic changes. RNA-seq data from targeted panels and …

Intra-Tumoral And Peripheral Blood Tigit And Pd-1 As Immune Biomarkers In Nodular Lymphocyte Predominant Hodgkin Lymphoma, Jay Gunawardana, Soi C Law, Muhammed B Sabdia, Éanna Fennell, Aoife Hennessy, Ciara I Leahy, Paul G Murray, Karolina Bednarska, Sandra Brosda, Judith Trotman, Leanne Berkahn, Andreea Zaharia, Simone Birch, Melinda Burgess, Dipti Talaulikar, Justina N Lee, Emily Jude, Eliza A Hawkes, Sanjiv Jain, Karthik Nath, Cameron Snell, Fiona Swain, Joshua W D Tobin, Colm Keane, Mohamed Shanavas, Emily Blyth, Christian Steidl, Kerry Savage, Pedro Farinha, Merrill Boyle, Barbara Meissner, Michael R Green, Francisco Vega, Maher K Gandhi

Faculty, Staff and Student Publications

In classical Hodgkin lymphoma (cHL), responsiveness to immune-checkpoint blockade (ICB) is associated with specific tumor microenvironment (TME) and peripheral blood features. The role of ICB in nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is not established. To gain insights into its potential in NLPHL, we compared TME and peripheral blood signatures between HLs using an integrative multiomic analysis. A discovery/validation approach in 121 NLPHL and 114 cHL patients highlighted >2-fold enrichment in programmed cell death-1 (PD-1) and T-cell Ig and ITIM domain (TIGIT) gene expression for NLPHL versus cHL. Multiplex imaging showed marked increase in intra-tumoral protein expression of PD-1+ (and/or …

A Complementary Metaproteomic Approach To Interrogate Microbiome Cultivated From Clinical Colon Biopsies, Van-An Duong, Altai Enkhbayar, Nobel Bhasin, Lakmini Senavirathna, Eva C Preisner, Kristi L Hoffman, Richa Shukla, Robert R Jenq, Kai Cheng, Mary P Bronner, Daniel Figeys, Robert A Britton, Sheng Pan, Ru Chen

Faculty, Staff and Student Publications

The human gut microbiome plays a vital role in preserving individual health and is intricately involved in essential functions. Imbalances or dysbiosis within the microbiome can significantly impact human health and are associated with many diseases. Several metaproteomics platforms are currently available to study microbial proteins within complex microbial communities. In this study, we attempted to develop an integrated pipeline to provide deeper insights into both the taxonomic and functional aspects of the cultivated human gut microbiomes derived from clinical colon biopsies. We combined a rapid peptide search by MSFragger against the Unified Human Gastrointestinal Protein database and the taxonomic …