Digital Commons Network^™

Genomic Selection For Dwarf Bunt Resistance In Winter Wheat, William Krause

All Graduate Theses and Dissertations, Fall 2023 to Present

Dwarf bunt (DB), caused by the pathogen Tilletia controversa J.G. Kühn [as 'contraversa'], is a fungal disease that poses yield and grain quality risks to winter wheat (Triticum aestivum) production in the Intermountain West and abroad. The infection replaces the grain with a collection of spores that are spread by wind during the following harvest. In addition to wheat, DB also infects other cereal grains and wild grasses. Genomic selection (GS) is a plant breeding method that can determine percent infection of related varieties by using phenotypic data and genetic data within a prediction model. A panel …

Designing Technology-Enriched Learning Environments: The Effects Of An Agent-Based Computer Model On Biology Students' Understanding Of The Covid-19 Pandemic And The Nature Of Models In Science, April Sullivan

All Graduate Theses and Dissertations, Fall 2023 to Present

Science education researchers have called for increased attention to the science practice of modeling to engage students in authentic scientific inquiry. A major challenge to integrating the modeling practice into science instruction is that students tend to conceptualize models as static end-products of research rather than generative tools for theory-building. Engaging students in using computer models, specifically agent-based computer models (ABMs), to explain and predict scientific phenomena could improve students' understanding of models in science. In this design-based research project I investigate the effects of an ABM-supported learning environment on high-school biology students' understanding of the COVID-19 pandemic and the …

Adolescent Mental Health And Social Media: The Roles Of Psychosocial Development And Online Interaction, Mark L. Ferguson

All Graduate Theses and Dissertations, Fall 2023 to Present

Social media has become an integral part of adolescent life, and its effects on adolescents’ mental health has been studied for over twenty years. However, the research approaches used to discover connections between adolescent social media use and their mental health have been diverse, and findings have varied over time. This study sought to explore the potential relationships between adolescent social media use and mental health by including several different variables that aren’t typically accounted for in the same study, such as attachment to parents and peers, internal psychological development, emotional intensity towards social media use, and how adolescents feel …

Mathematical And Statistical Methods To Harness Limited Data In Models For Ecological Space Use Under Global Change, Sarah C. Bogen

All Graduate Theses and Dissertations, Fall 2023 to Present

The dynamics of how plants and animals use space in their habitats has important implications for the fields of ecology and conservation. However, understanding and responding to these spatial and temporal dynamics is often limited by data availability, financial resources and biases. As average global temperatures increase, suitable habitats shift poleward and require local populations to move with suitable habitat, adapt to the changing environment, or risk extinction. Capacity to persist without movement may be estimated by considering changes to a combination of habitat characteristics. Capacity to track suitable habitat may be modeled through synthesizing information on species demographic mechanisms …

Tumor Expression Of Cd83 Reduces Glioma Progression And Is Associated With Reduced Immunosuppression, Malcolm F Mcdonald, Rachel Naomi Curry, Isabella O'Reilly, Brittney Lozzi, Alexis Cervantes, Zhung-Fu Lee, Anna Rosenbaum, Peihao He, Carrie Mohila, Arif O Harmanci, Akdes Serin Harmanci, Benjamin Deneen, Ganesh Rao

Faculty, Staff and Student Publications

Immunosuppression in malignant glioma remains a barrier to therapeutic development. CD83 overexpression in human and mouse glioma increases survival. CD83+ tumor cells promote signatures related to cytotoxic T cells, enhanced activation of CD8+ T cells, and increased proinflammatory cytokines. These findings suggest that tumor-expressed CD83 could mediate tumor-immune communications.

Steering Research On Mrna Splicing In Cancer Towards Clinical Translation, Olga Anczukow, Frédéric H-T Allain, Brittany L Angarola, Douglas L Black, Angela N Brooks, Chonghui Cheng, Ana Conesa, Edie I Crosse, Eduardo Eyras, Ernesto Guccione, Sydney X Lu, Karla M Neugebauer, Priyanka Sehgal, Xiao Song, Zuzana Tothova, Juan Valcárcel, Kevin M Weeks, Gene W Yeo, Andrei Thomas-Tikhonenko

Faculty, Staff and Students Publications

Splicing factors are affected by recurrent somatic mutations and copy number variations in several types of haematologic and solid malignancies, which is often seen as prima facie evidence that splicing aberrations can drive cancer initiation and progression. However, numerous spliceosome components also 'moonlight' in DNA repair and other cellular processes, making their precise role in cancer difficult to pinpoint. Still, few would deny that dysregulated mRNA splicing is a pervasive feature of most cancers. Correctly interpreting these molecular fingerprints can reveal novel tumour vulnerabilities and untapped therapeutic opportunities. Yet multiple technological challenges, lingering misconceptions, and outstanding questions hinder clinical translation. …

Foster Youth Experiencing Homelessness In Texas: An Analysis Of Risk And Protective Factors That Impact Housing Stability, Monique Willoughby

Electronic Theses and Dissertations

While research on youth homelessness continues to grow, not much is known about the differences that exist between states. To address specific concerns effectively, a more nuanced and granular approach to assessment is needed. Specifically, Texas youth who are transitioning from foster and other systems of care into young adulthood and more independent living will need tailored support to adequately address their needs. This study is a step in that direction. Through identification of risks factors that predict homelessness for these youth, social workers, counselors, case managers, and other human services providers and advocates can better assess, plan, and intervene …

Dual-Channel Side Channel Attack: Improved Aes Key Decryption By Combining Power And Electromagnetic Side Channels With Convolutional Neural Networks, Sean P. O'Neill

Theses and Dissertations

This research introduces a novel DL approach for SCA that combines power consumption and EM signals to enhance encryption key deduction by leveraging a dual-channel CNN architecture. A new dataset, consisting of simultaneous power and EM signal collections during 128-bitAES encryption, was developed to train and evaluate the model’s effectiveness. The combined approach achieved an 88% reduction in traces needed, from 50 traces to 6, for encryption key classification, outperforming traditional methods such as random forest, DPA, DEMA,and individual side channel CNN models. These findings highlight the potential of integrating multiple side channels in SCA to improve performance without the …

Retinal Ganglion Cell Circuits And Glial Interactions In Humans And Mice, Kang-Chieh Huang, Mohamed Tawfik, Melanie A Samuel

Faculty, Staff and Students Publications

Retinal ganglion cells (RGCs) are the brain's gateway for vision, and their degeneration underlies several blinding diseases. RGCs interact with other neuronal cell types, microglia, and astrocytes in the retina and in the brain. Much knowledge has been gained about RGCs and glia from mice and other model organisms, often with the assumption that certain aspects of their biology may be conserved in humans. However, RGCs vary considerably between species, which could affect how they interact with their neuronal and glial partners. This review details which RGC and glial features are conserved between mice, humans, and primates, and which differ. …

Health Implications Of Racial Differences In Serum Growth Differentiation Factor Levels Among Men With Obesity, Siresha Bathina, Virginia Fuenmayor Lopez, Mia Prado, Elliot Ballato, Georgia Colleluori, Maryam Tetlay, Dennis Tan Villareal, Sanjay Mediwala, Rui Chen, Clifford Qualls, Reina Armamento-Villareal

Faculty, Staff and Students Publications

Growth differentiation factor (GDF15) has been considered a biomarker and recently a hormonal driver for diseases in different populations. However, the role of GDF15 as a biomarker of health outcomes in obese men from different racial/ethnic background has not been evaluated. The objective of this study was to investigate the racial/ethnic differences on the relationship between GDF15 and markers of glucometabolic status, hormonal profile, body composition and bone mineral density (BMD) in obese men. One hundred ninety-three obese men from diverse racial/ethnic backgrounds were enrolled. BMD and body composition were measured by dual energy X-ray absorptiometry. Serum GDF15, osteocalcin, C-terminal …

An Adaptive And Parallel Direct Solver For Elliptic Partial Differential Equations, Damyn Chipman

Boise State University Theses and Dissertations

We introduce the quadtree-adaptive Hierarchical Poincaré-Steklov (QAHPS) method, an adaptive direct method for solving elliptic partial differential equations on a hierarchy of adaptively refined finite volume meshes. The QAHPS method builds up a solution operator set with O(N^3/2) complexity that acts as the factorization of the system matrix, with linear O(N) complexity for the application of the solution operator set to any number of right-hand side vectors. As the solution operator set is built up by merging local subdomains, it can be adapted as the mesh is refined and coarsened. The method is an …

Pathophysiology And Treatment Of Prediabetes And Type 2 Diabetes In Youth, Fida Bacha, Tamara S Hannon, Mustafa Tosur, Julie M Pike, Ashley Butler, Kalie L Tommerdahl, Philip S Zeitler

Faculty, Staff and Students Publications

Youth-onset type 2 diabetes is a heterogeneous disease with increasing prevalence in relation to increased rates of obesity in children. It has genetic, epigenetic, social, and environmental determinants. Youth-onset type 2 diabetes is alarming given a rapidly progressive course compared with the course of adult-onset disease, early-onset vascular complications, and long-term exposure to hyperglycemia and associated complications. It is often preceded by prediabetes, a disease phase where defects in β-cell function relative to insulin sensitivity emerge. Herein, we review the current understanding of the pathophysiology of prediabetes and type 2 diabetes in youth. We describe the mechanisms underlying insulin resistance, …

The Long Road Of Drug Development For Endometriosis – Pains, Gains, And Hopes, Zian Liao, Diana Monsivais, Martin M Matzuk

Faculty, Staff and Students Publications

Endometriosis, defined by the growth of endometrial tissues outside of the uterine cavity, is a global health burden for ∼200 million women. Patients with endometriosis usually present with chronic pain and are often diagnosed with infertility. The pathogenesis of endometriosis is still an open question; however, tissue stemness and immunological and genetic factors have been extensively discussed in the establishment of endometriotic lesions. Current treatments for endometriosis can be categorized into pharmacological management of hormone levels and surgical removal of the lesions. Both approaches have limited efficacy, with recurrences often encountered; thus, there is no complete cure for the disease …

Deep Subseafloor Sediments In Guaymas Basin Harbor Cosmopolitan Microbiota And Traces Of Hydrothermal Populations, Paraskevi Mara, David Beaudoin, Ivano Aiello, Yuki Morono, David Geller-Mcgrath, Virginia P. Edgcomb, Andreas Teske

Faculty Research, Scholarly, and Creative Activity

Environmental factors shape subsurface microbial ecosystems, and well-characterized sites are ideal for determining how environmental parameters shape sediment communities. Sediments from eight geologically and thermally distinct sites were drilled during International Ocean Discovery Program Expedition 385 in Guaymas Basin, an expedition focused on the hydrothermal deep biosphere. Using high-throughput 16S ribosomal nucleic acid sequencing, cell counts, phylogenetics, metatranscriptomics, and mineralogical/elemental X-ray spectroscopy, we examine linkages and feedbacks between mineral composition, temperature, geochemistry, and microbial populations. We show subsurface life is dominated by heterotrophic, cosmopolitan prokaryotes that thrive within a range of sediments and temperature conditions across Guaymas Basin. Hydrothermally-affiliated lineages …

Private Landowner Interest In Prescribed Fire In California: Findings From Workshops In The Sierra Nevada, Kate M. Wilkin, Amanda M. Stasiewicz, Susan D. Kocher

Faculty Research, Scholarly, and Creative Activity

Background: Globally, prescribed fire political interest and practice has been rekindled following recent devastating wildfire seasons. This phenomenon was especially acute in areas with dual wildfire and forest health crises, like California. Previous research has investigated prescribed fire on public lands or on private lands in other regions, but little is known about prescribed fire practice or interest on private lands in California. Therefore, we sought to understand private land managers’ perceptions of prescribed fire compared to other land management techniques, treatment pathways, motivations, and barriers to complete these treatments in California. Results: Before workshops on prescribed fire for private …

Beyond Boundaries: Governance Considerations For Climate-Driven Habitat Shifts Of Highly Migratory Marine Species Across Jurisdictions, Bianca S. Santos, Elliott L. Hazen, Heather Welch, Nerea Lezama-Ochoa, Barbara A. Block, Daniel P. Costa, Scott A. Shaffer, Larry B. Crowder

Faculty Research, Scholarly, and Creative Activity

The mobile nature of migratory marine animals across jurisdictional boundaries can challenge the management of biodiversity, particularly under global environmental change. While projections of climate-driven habitat change can reveal whether marine species are predicted to gain or lose habitat in the future, geopolitical boundaries and differing governance regimes may influence animals’ abilities to thrive in new areas. Broad geographic movements and diverse governance approaches elicit the need for strong international collaboration to holistically manage and conserve these shared migratory species. In this study, we use data from the Tagging of Pacific Predators program to demonstrate the feasibility of using climate-driven …

Food Insecurity Knowledge And Training Among College Students In Health Majors, Virginia B. Gray, Cara Cuite, Megan Patton-López, Rickelle Richards, Mateja Savoie-Roskos, Stephanie Machado, Emily Heying, Matthew Landry, Susan Chen, Rebecca L. Hagedorn-Hatfield, Georgianna Mann, Zubaida Qamar, Kendra Oonorasak, Victoria A. Zigmont

Faculty Research, Scholarly, and Creative Activity

Objective: To describe current food insecurity (FI)-related training among nutrition/dietetics, public health, and social work students. Methods: A cross-sectional online survey was used among students (n = 306) enrolled in health-related programs at 12 US universities. Participants reported FI-related course-based and extracurricular experiences and rated confidence to address FI on a scale of 1–3. Open-ended questions investigated perceived definitions of FI and impactful course activities. Descriptive statistics and thematic analysis were used for data analysis. Results: Participants’ FI definitions were multifaceted. Most (80.6%) reported FI being covered in at least 1 course. The overall mean confidence to address FI was …

Drivers Of Variability In Surf Zone Habitat Use By Sandy Beach Fish: Unwitting Citizen Scientists Reveal Detailed Spatiotemporal Patterns, Ryan Hepburn, Tim Scott, Sam Prodger, Benjamin J. Ciotti

School of Biological and Marine Sciences

Surf zones of sandy beaches are among the most heavily impacted aquatic ecosystems, yet are of criticalecological importance for inshore fish and fisheries. Knowledge of the drivers of fish habitat use in surf zones isneeded across broad scales to advise conservation and fisheries management, but sampling capabilities can belimited in spatio-temporal extent and resolution. The lesser weever Echiichthys vipera is a small, benthic,venomous fish that dominates surf zone fish assemblages in Northwest Europe and inflicts painful stings onbeachgoers. This study capitalises on an extensive record of E. vipera sting incidents to characterise variations insurf zone habitat use in relation to …

Interpreting The Spatial Distribution Of Soil Properties With A Physically-Based Distributed Hydrological Model, Zamir Libohova, Marcelo Mancini, Hans Edwin Winzeler, Quentin D. Read, Ning Sun, Dylan Beaudette, Candiss Williams, Joshua Michael Blackstock, Sergio H.G. Silva, Nilton Curi, Kabindra Adhikari, Amanda Ashworth, Joshua O. Minai, Phillip R. Owens

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Digital soil maps are commonly data-driven as the development of physically-based models for soil mapping is difficult due to the complexity of soils. However, physically-based hydrologic models have been successful in simulating water dynamics. Since water movement is a major driver of pedogenesis, the physical rules that govern water movement might help explain and predict the spatial variation of soil properties. Here, we demonstrate the novel use of a physically-based, distributed hydrologic model to inform the spatial distribution of soil properties. The Distributed Hydrology Soil Vegetation Model (DHSVM) was utilized to simulate soil moisture content (SM) and water table …

Pathogenicity And Virulence Of Human Respiratory Syncytial Virus: Multifunctional Nonstructural Proteins Ns1 And Ns2, Trudy N Merritt, Jingjing Pei, Daisy W Leung

2020-Current year OA Pubs

Human respiratory syncytial virus (hRSV) is a major cause of lower respiratory tract infections in young children, the elderly, and immunocompromised. Despite its discovery over 60 years ago and the global impact on human health, limited effective prophylactic or therapeutic options have been available for hRSV infections. This has largely been attributed to the legacy of vaccine failure in the 1960s using a formalin-inactivated RSV , which led to enhancement of disease post exposure to hRSV infection and hampered subsequent development of vaccine candidates. Recent FDA approval of vaccines for older adults and pregnant individuals are major advancements but leaves …

Unravelling Large-Scale Patterns And Drivers Of Biodiversity In Dry Rivers, Arnaud Foulquier, Thibault Datry, Roland Corti, Daniel Von Schiller, Klement Tockner, Rachel Stubbington, Mark O. Gessner, Frédéric Boyer, Marc Ohlmann, Wilfried Thuiller, Delphine Rioux, Christian Miquel, Ricardo Albariño, Daniel C. Allen, Florian Altermatt, Maria Isabel Arce, Shai Arnon, Damien Banas, Andy Banegas-Medina, Erin Beller, Melanie L. Blanchette, Joanna Blessing, Iola Gonçalves Boëchat, Kate Boersma, Michael Bogan, Núria Bonada

Research outputs 2022 to 2026

More than half of the world’s rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries …

Higher Habitual Intakes Of Flavonoids And Flavonoid-Rich Foods Are Associated With A Lower Incidence Of Type 2 Diabetes In The Uk Biobank Cohort, Alysha S. Thompson, Amy Jennings, Nicola P. Bondonno, Anna Tresserra-Rimbau, Benjamin H. Parmenter, Claire Hill, Aurora Perez-Cornago, Tilman Kühn, Aedín Cassidy

Research outputs 2022 to 2026

Aim: To examine the associations of a diet high in flavonoid-rich foods, as reflected by a “Flavodiet Score” (FDS), the major individual food contributors to flavonoid intake, and flavonoid subclasses with type 2 diabetes (T2D) risk in the UK Biobank cohort. Materials and methods: Flavonoid intakes were estimated from ≥2 dietary assessments among 113,097 study participants [age at enrolment: 56 ± 8 years; 57% female] using the U.S Department of Agriculture (USDA) databases. Multivariable Cox proportional hazards models were used to investigate associations between dietary exposures and T2D. Results: During 12 years of follow-up, 2628 incident cases of T2D were …

Infant-Derived Human Nasal Organoids Exhibit Relatively Increased Susceptibility, Epithelial Responses, And Cytotoxicity During Rsv Infection, Gina M Aloisio, Divya Nagaraj, Ashley M Murray, Emily M Schultz, Trevor Mcbride, Letisha Aideyan, Erin G Nicholson, David Henke, Laura Ferlic-Stark, Anubama Rajan, Amal Kambal, Hannah L Johnson, Elina Mosa, Fabio Stossi, Sarah E Blutt, Pedro A Piedra, Vasanthi Avadhanula

Faculty, Staff and Students Publications

Background: Respiratory syncytial virus (RSV) causes significant morbidity and mortality, especially in young children. Why RSV infection in children is more severe compared to healthy adults is not fully understood.

Methods: We used ex-vivo human nasal organoid platforms from infants and adults to investigate the underlying mechanism of this disease disparity at the initial site of RSV replication, the nasal epithelium.

Results: Infant-derived human nasal organoid-air liquid interface (HNO-ALIs) lines were more susceptible to early RSV replication. Moreover, infant-derived HNO-ALIs elicited a statistically significant greater overall cytokine response, enhanced mucous production, and greater cellular damage compared to their adult counterparts. …

Genomic Insights Into Key Mechanisms For Carbon, Nitrogen, And Phosphate Assimilation By The Acidophilic, Halotolerant Genus Acidihalobacter Members, Himel Nahreen Khaleque, Homayoun Fathollahzadeh, Anna H. Kaksonen, Jorge Valdés, Eva Vergara, David S. Holmes, Elizabeth L.J. Watkin

Research outputs 2022 to 2026

In-depth comparative genomic analysis was conducted to predict carbon, nitrogen, and phosphate assimilation pathways in the halotolerant, acidophilic genus Acidihalobacter. The study primarily aimed to understand how the metabolic capabilities of each species can determine their roles and effects on the microbial ecology of their unique saline and acidic environments, as well as in their potential application to saline water bioleaching systems. All four genomes encoded the genes for the complete tricarboxylic acid cycle, including 2-oxoglutarate dehydrogenase, a key enzyme absent in obligate chemolithotrophic acidophiles. Genes for a unique carboxysome shell protein, csoS1D, typically found in halotolerant bacteria but not …

Organ Pedalboard As A Rehabilitation Tool: A Qualitative Exploratory Study Of Healthcare Providers’ Perceptions And Recommendations, Mandy M.P. Kan, Wai Hang Kwok, Eric C. Fan, Fadi M. Al Zoubi

Research outputs 2022 to 2026

Objective This qualitative study explored healthcare providers’ perceptions and attitudes regarding the use of organ pedalboards as a rehabilitation tool, particularly for lower extremity conditions. The study also sought to identify the perceived barriers and facilitators to adopting organ pedalboards within rehabilitation settings, as well as gather healthcare providers’ recommendations for integrating this tool into clinical practice. Method Healthcare providers, including physiotherapists, occupational therapists, music therapists, and sports therapists, were recruited for focus group interviews using purposive and snowball sampling. At the outset of the interview, participants watched an organist playing musical notes on a pedalboard and had the opportunity …

What Journalism Feels Like: Considering The Body Of The Journalist, Mark Deuze, Laura Glitsos

Research outputs 2022 to 2026

All journalists have bodies. This commonsensical fact acquires more currency every day as the work of reporters and editors becomes automated, robotized, and taken over by (generative) artificial intelligence. The embodied nature of news work matters, not in the least because of the personal attachment practitioners have to what journalism is, or should be. However, in the rich history of journalism studies, bodily perspectives are remarkably absent—beyond descriptions of journalists as sociodemographic profiles. In this essay, we explore various theoretical frameworks to bring the body back into the study and practice of journalism. In our argument, we apply the insights …

Global Patterns And Drivers Of Fish Reproductive Potential On Coral Reefs, Jeneen Hadj-Hammou, Joshua E. Cinner, Diego R. Barneche, Iain R. Caldwell, David Mouillot, James P.W. Robinson, Nina M.D. Schiettekatte, Alexandre C. Siqueira, Brett M. Taylor, Nicholas A.J. Graham

Research outputs 2022 to 2026

Fish fecundity scales hyperallometrically with body mass, meaning larger females produce disproportionately more eggs than smaller ones. We explore this relationship beyond the species-level to estimate the “reproductive potential” of 1633 coral reef sites distributed globally. We find that, at the site-level, reproductive potential scales hyperallometrically with assemblage biomass, but with a smaller median exponent than at the species-level. Across all families, modelled reproductive potential is greater in fully protected sites versus fished sites. This difference is most pronounced for the important fisheries family, Serranidae. When comparing a scenario where 30% of sites are randomly fully protected to a current …

Π-Hub: The Proteomic Navigator Of The Human Body, Fuchu He, Ruedi Aebersold, Mark S Baker, Xiuwu Bian, Xiaochen Bo, Daniel W Chan, Cheng Chang, Luonan Chen, Xiangmei Chen, Yu-Ju Chen, Heping Cheng, Ben C Collins, Fernando Corrales, Jürgen Cox, Weinan E, Jennifer E Van Eyk, Jia Fan, Pouya Faridi, Daniel Figeys, George Fu Gao, Wen Gao, Zu-Hua Gao, Keisuke Goda, Wilson Wen Bin Goh, Dongfeng Gu, Changjiang Guo, Tiannan Guo, Yuezhong He, Albert J R Heck, Henning Hermjakob, Tony Hunter, Narayanan Gopalakrishna Iyer, Ying Jiang, Connie R Jimenez, Lokesh Joshi, Neil L Kelleher, Ming Li, Yang Li, Qingsong Lin, Cui Hua Liu, Fan Liu, Guang-Hui Liu, Yansheng Liu, Zhihua Liu, Teck Yew Low, Ben Lu, Matthias Mann, Anming Meng, Robert L Moritz, Edouard Nice, Guang Ning, Gilbert S Omenn, Christopher M Overall, Giuseppe Palmisano, Yaojin Peng, Charles Pineau, Terence Chuen Wai Poon, Anthony W Purcell, Jie Qiao, Roger R Reddel, Phillip J Robinson, Paola Roncada, Chris Sander, Jiahao Sha, Erwei Song, Sanjeeva Srivastava, Aihua Sun, Siu Kwan Sze, Chao Tang, Liujun Tang, Ruijun Tian, Juan Antonio Vizcaíno, Chanjuan Wang, Chen Wang, Xiaowen Wang, Xinxing Wang, Yan Wang, Tobias Weiss, Mathias Wilhelm, Robert Winkler, Bernd Wollscheid, Limsoon Wong, Linhai Xie, Wei Xie, Tao Xu, Tianhao Xu, Liying Yan, Jing Yang, Xiao Yang, John Yates, Tao Yun, Qiwei Zhai, Bing Zhang, Hui Zhang, Lihua Zhang, Lingqiang Zhang, Pingwen Zhang, Yukui Zhang, Yu Zi Zheng, Qing Zhong, Yunping Zhu, Π-Hub Consortium

Faculty, Staff and Students Publications

The human body contains trillions of cells, classified into specific cell types, with diverse morphologies and functions. In addition, cells of the same type can assume different states within an individual's body during their lifetime. Understanding the complexities of the proteome in the context of a human organism and its many potential states is a necessary requirement to understanding human biology, but these complexities can neither be predicted from the genome, nor have they been systematically measurable with available technologies. Recent advances in proteomic technology and computational sciences now provide opportunities to investigate the intricate biology of the human body …

Genome-Wide Cross-Disease Analyses Highlight Causality And Shared Biological Pathways Of Type 2 Diabetes With Gastrointestinal Disorders, Emmanuel O. Adewuyi, Tenielle Porter, Eleanor K. O’Brien, Oladapo Olaniru, Giuseppe Verdile, Simon M. Laws

Research outputs 2022 to 2026

Studies suggest links between diabetes and gastrointestinal (GI) traits; however, their underlying biological mechanisms remain unclear. Here, we comprehensively assess the genetic relationship between type 2 diabetes (T2D) and GI disorders. Our study demonstrates a significant positive global genetic correlation of T2D with peptic ulcer disease (PUD), irritable bowel syndrome (IBS), gastritis-duodenitis, gastroesophageal reflux disease (GERD), and diverticular disease, but not inflammatory bowel disease (IBD). We identify several positive local genetic correlations (negative for T2D – IBD) contributing to T2D’s relationship with GI disorders. Univariable and multivariable Mendelian randomisation analyses suggest causal effects of T2D on PUD and gastritis-duodenitis and …

Metabolomic-Derived Endotypes Of Age-Related Macular Degeneration (Amd): A Step Towards Identification Of Disease Subgroups, Kevin Mendez, Ines Lains, Rachel S. Kelly, João Gil, Rufino Silva, John Miller, Demetrios G. Vavvas, Ivana Kim, Joan Miller, Liming Liang, Jessica A. Lasky-Su, Deeba Husain

Research outputs 2022 to 2026

Age-related macular degeneration (AMD) is a leading cause of blindness worldwide, with a complex pathophysiology and phenotypic diversity. Here, we apply Similarity Network Fusion (SNF) to cluster AMD patients into putative metabolomics-derived endotypes. Using a discovery cohort of 163 AMD patients from Boston, US, and a validation cohort of 214 patients from Coimbra, Portugal, we identified four distinct metabolomics-derived endotypes with varying retinal structural and functional characteristics, confirmed across both cohorts. Patients clustered into Endotype 1 exhibited a milder form of AMD and were characterized by low levels of amino acids in specific metabolic pathways. Meanwhile, patients clustered into both …