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Hernia Recurrence Risk Matters More Than Mesh Type To Patients Undergoing Ventral Hernia Repair, Stephanie Martinez Ugarte, Mokunfayo O Fajemisin, Chelsea J Guy-Frank, Dalya M Ferguson, Jonah J Stulberg, Lillian S Kao, Julie L Holihan Jul 2025

Hernia Recurrence Risk Matters More Than Mesh Type To Patients Undergoing Ventral Hernia Repair, Stephanie Martinez Ugarte, Mokunfayo O Fajemisin, Chelsea J Guy-Frank, Dalya M Ferguson, Jonah J Stulberg, Lillian S Kao, Julie L Holihan

Faculty, Staff and Student Publications

Introduction: Patients' perceptions about synthetic mesh for ventral hernia repair (VHR) may stem from a lack of knowledge of risks. We assessed patients' threshold for accepting the risk of hernia recurrence to avoid synthetic mesh.

Methods: Patients ≥18 y old with prior or upcoming VHR viewed a one-time video decision aid describing recurrence risk with biologic versus synthetic mesh. Patients chose between these options using a probability trade-off (PTO) technique, varying hernia recurrence rate with biologic mesh. Based on randomized trials, the recurrence rate using synthetic mesh was 9%. The PTO score was the recurrence rate (0%-100%) at which patients …


Outcomes And Toxicity Following 3 Or More Definitive Courses Of Thoracic Radiation Therapy For Non-Small Cell Lung Cancer, Abigael Odwuor, Percy Lee, Joe Y Chang, Saumil Gandhi, Zhongxing Liao, Steven H Lin, Aileen Chen, Quynh-Nhu Nguyen, Michael S O'Reilly, Stephen G Chun, Julianna Bronk, David Qian, Matthew S Ning Jul 2025

Outcomes And Toxicity Following 3 Or More Definitive Courses Of Thoracic Radiation Therapy For Non-Small Cell Lung Cancer, Abigael Odwuor, Percy Lee, Joe Y Chang, Saumil Gandhi, Zhongxing Liao, Steven H Lin, Aileen Chen, Quynh-Nhu Nguyen, Michael S O'Reilly, Stephen G Chun, Julianna Bronk, David Qian, Matthew S Ning

Faculty, Staff and Student Publications

Purpose: Salvage re-irradiation is increasingly utilized to manage non-small cell lung cancer (NSCLC) locoregional recurrence or new lung primaries in previously treated areas. There is sparse information on efficacy and toxicity profile. We report a large experience of patients treated with multiple courses of definitive radiation for new and recurrent NSCLC.

Methods and materials: Medical records of patients who underwent ≥ 3 definitive thoracic radiation therapy (RT) courses for new or recurrent NSCLC at our cancer center from 2012 through 2021 were retrospectively reviewed following institutional review board approval. Toxicity was graded per Common Terminology Criteria for Adverse Events (CTCAE) …


Histone Lysine Methyltransferases Mll3 And Mll4 Direct Gene Expression To Produce Platelets Efficiently, Guozhen Gao, Josimar Dornelas Moreira, Prosun Das, Kevin Lin, Kai Ge, Taiping Chen, Yue Lu, Margarida A Santos Jul 2025

Histone Lysine Methyltransferases Mll3 And Mll4 Direct Gene Expression To Produce Platelets Efficiently, Guozhen Gao, Josimar Dornelas Moreira, Prosun Das, Kevin Lin, Kai Ge, Taiping Chen, Yue Lu, Margarida A Santos

Faculty, Staff and Student Publications

Circulating blood platelets are responsible for maintaining hemostasis. They are released into blood vessels from mature megakaryocytes. Although several transcription factors have been reported to orchestrate the transcriptional programs required for platelet production, how chromatin regulators control these processes is still poorly understood. MLL3 and MLL4 are the main lysine methyltransferases responsible for the deposition of H3K4me1 histone marks at enhancers. MLL3 and MLL4 typically form complexes with other co-factors, such as PTIP. Recently, we showed that loss of PTIP leads to decreased platelet numbers in mice. Here, we find that, although MLL3/4 double deficiency does not alter megakaryopoiesis and …


Crem Is A Regulatory Checkpoint Of Car And Il-15 Signalling In Nk Cells, Hind Rafei, Rafet Basar, Sunil Acharya, Yu-Sung Hsu, Pinghua Liu, Deqiang Zhang, Toszka Bohn, Qingnan Liang, Vakul Mohanty, Ranjan Upadhyay, Ping Li, Pravin Phadatare, Merve Dede, Donghai Xiong, Huihui Fan, Corry Mathew Jones, Sebastian Kunz, May Daher, Ana Karen Nunez Cortes, Mayra Shanley, Bin Liu, Sadie Mae Moseley, Chenyu Zhang, Dexing Fang, Pinaki Banerjee, Nadima Uprety, Ye Li, Rejeena Shrestha, Xinhai Wan, Hong Shen, Vernikka Woods, April Lamour Gilbert, Seema Rawal, Jinzhuang Dou, Yukun Tan, Jeong-Min Park, Francia Reyes Silva, Alexander Biederstädt, Mecit Kaplan, Xin Ru Jiang, Inci Biederstädt, Bijender Kumar, Silvia Tiberti, Madison Moore, Jingling Jin, Ryan Z Yang, Luis Muniz-Feliciano, Samuel Rosemore, Paul Lin, Gary M Deyter, Natalie Wall Fowlkes, Abhinav K Jain, David Marin, Anirban Maitra, Ken Chen, Tobias Bopp, Elizabeth J Shpall, Katayoun Rezvani Jul 2025

Crem Is A Regulatory Checkpoint Of Car And Il-15 Signalling In Nk Cells, Hind Rafei, Rafet Basar, Sunil Acharya, Yu-Sung Hsu, Pinghua Liu, Deqiang Zhang, Toszka Bohn, Qingnan Liang, Vakul Mohanty, Ranjan Upadhyay, Ping Li, Pravin Phadatare, Merve Dede, Donghai Xiong, Huihui Fan, Corry Mathew Jones, Sebastian Kunz, May Daher, Ana Karen Nunez Cortes, Mayra Shanley, Bin Liu, Sadie Mae Moseley, Chenyu Zhang, Dexing Fang, Pinaki Banerjee, Nadima Uprety, Ye Li, Rejeena Shrestha, Xinhai Wan, Hong Shen, Vernikka Woods, April Lamour Gilbert, Seema Rawal, Jinzhuang Dou, Yukun Tan, Jeong-Min Park, Francia Reyes Silva, Alexander Biederstädt, Mecit Kaplan, Xin Ru Jiang, Inci Biederstädt, Bijender Kumar, Silvia Tiberti, Madison Moore, Jingling Jin, Ryan Z Yang, Luis Muniz-Feliciano, Samuel Rosemore, Paul Lin, Gary M Deyter, Natalie Wall Fowlkes, Abhinav K Jain, David Marin, Anirban Maitra, Ken Chen, Tobias Bopp, Elizabeth J Shpall, Katayoun Rezvani

Faculty, Staff and Student Publications

Chimeric antigen receptor (CAR) natural killer (NK) cell immunotherapy offers a promising approach against cancer1-3. However, the molecular mechanisms that regulate CAR-NK cell activity remain unclear. Here we identify the transcription factor cyclic AMP response element modulator (CREM) as a crucial regulator of NK cell function. Transcriptomic analysis revealed a significant induction of CREM in CAR-NK cells during the peak of effector function after adoptive transfer in a tumour mouse model, and this peak coincided with signatures of both activation and dysfunction. We demonstrate that both CAR activation and interleukin-15 signalling rapidly induce CREM upregulation in NK cells. Functionally, CREM …


Coordinated Regulation By Lncrnas Results In Tight Lncrna-Target Couplings, Hua-Sheng Chiu, Sonal Somvanshi, Chung-Te Chang, Eric James De Bony De Lavergne, Zhaowen Wei, Chih-Hung Hsieh, Wim Trypsteen, Kathleen A Scorsone, Ektaben Patel, Tien T Tang, David B Flint, Mohammad Javad Najaf Panah, Hyunjae Ryan Kim, Purva Rathi, Yan-Hwa Wu Lee, Sarah E Woodfield, Sanjeev A Vasudevan, Andras Attila Heczey, M Waleed Gaber, Gabriel O Sawakuchi, Ting-Wen Chen, Pieter Mestdagh, Xuerui Yang, Pavel Sumazin Jul 2025

Coordinated Regulation By Lncrnas Results In Tight Lncrna-Target Couplings, Hua-Sheng Chiu, Sonal Somvanshi, Chung-Te Chang, Eric James De Bony De Lavergne, Zhaowen Wei, Chih-Hung Hsieh, Wim Trypsteen, Kathleen A Scorsone, Ektaben Patel, Tien T Tang, David B Flint, Mohammad Javad Najaf Panah, Hyunjae Ryan Kim, Purva Rathi, Yan-Hwa Wu Lee, Sarah E Woodfield, Sanjeev A Vasudevan, Andras Attila Heczey, M Waleed Gaber, Gabriel O Sawakuchi, Ting-Wen Chen, Pieter Mestdagh, Xuerui Yang, Pavel Sumazin

Faculty, Staff and Student Publications

The determination of long non-coding RNA (lncRNA) function is a major challenge in RNA biology with applications to basic, translational, and medical research. We developed BigHorn to computationally infer lncRNA-DNA interactions that mediate transcription and chromatin-remodeling factor activity. Its accurate inference enabled the identification of lncRNAs that coordinately regulate both the transcriptional and post-transcriptional processing of their targets. These lncRNAs may act as molecular chaperones, regulating the stability and translation of mRNAs they helped transcribe, leading to tightly coupled expression profiles. Our analysis suggests that lncRNAs regulate cancer genes across tumor contexts, thus propagating the effects of non-coding alterations to …


Protocol To Detect M22g Modification On Single Trna Iso-Decoders By Immuno-Northern Blotting, Sseu-Pei Hwang, Katherine Barondeau, Catherine Denicourt Jul 2025

Protocol To Detect M22g Modification On Single Trna Iso-Decoders By Immuno-Northern Blotting, Sseu-Pei Hwang, Katherine Barondeau, Catherine Denicourt

Faculty, Staff and Student Publications

tRNA modifications are highly dynamic and play crucial roles in regulating gene expression. Here, we present an assay for analyzing N2, N2-dimethylguanosine (m22G) modifications on tRNAs using an antibody-based detection approach. We describe steps for isolating tRNAs from human cells via ion-exchange chromatography, capturing specific tRNA iso-decoders on streptavidin magnetic beads, and detecting modifications through immuno-northern blotting. This approach enables researchers to investigate other tRNA modifications using specific antibodies or downstream approaches such as mass spectrometry.


Mitigating Regression Faults Induced By Feature Evolution In Deep Learning Systems, Hanmo Yu, Zan Wang, Xuyang Chen, Junjie Chen, Jun Sun, Shuang Liu, Zishuo Dong Jul 2025

Mitigating Regression Faults Induced By Feature Evolution In Deep Learning Systems, Hanmo Yu, Zan Wang, Xuyang Chen, Junjie Chen, Jun Sun, Shuang Liu, Zishuo Dong

Research Collection School Of Computing and Information Systems

Deep learning (DL) systems have been widely utilized across various domains. However, the evolution of DL systems can result in regression faults. In addition to the evolution of DL systems through the incorporation of new data, feature evolution, such as the addition of new features, is also common and can introduce regression faults. In this work, we first investigate the underlying factors that are correlated with regression faults in feature evolution scenarios, i.e., redundancy and contribution shift. Based on our investigation, we propose a novel mitigation approach called FeaProtect, which aims to minimize the impact of these two factors. To …


End Matter, Vol. 16 Jul 2025

End Matter, Vol. 16

Monographs of the Western North American Naturalist

No abstract provided.


Front Matter, Vol. 16 Jul 2025

Front Matter, Vol. 16

Monographs of the Western North American Naturalist

No abstract provided.


Mammals Of Malheur National Wildlife Refuge And Surrounding Harney County, Oregon, John E. Cornely, Leslie N. Carraway Jul 2025

Mammals Of Malheur National Wildlife Refuge And Surrounding Harney County, Oregon, John E. Cornely, Leslie N. Carraway

Monographs of the Western North American Naturalist

Malheur National Wildlife Refuge (NWR), located in southeastern Oregon, is part of the National Wildlife Refuge System (NWRS) of the United States. Currently, NWRS includes more than 568 NWRs, 38 Wetland Management Districts, and 5 Marine National Monuments. Malheur NWR, like a majority of the refuges in the NWRS, was established for the conservation of migratory birds. Many of these NWRs also provide significant habitat for mammals. Malheur NWR, one of the oldest (established 1908) and largest refuges in the system, is one of those with significant habitat for mammals. In addition to the refuge, we have included Harney County, …


Teacher Identification Of Learned Helplessness And Supportive Strategies, Kathleen A. De Jong Jul 2025

Teacher Identification Of Learned Helplessness And Supportive Strategies, Kathleen A. De Jong

Master's Theses & Capstone Projects

Learned helplessness is a common problem in the upper grades of compulsory education. It creates frustration and has a significant negative impact on academic achievement. Teachers need to accurately identify learned helplessness behaviors before they can promote effective strategies for student autonomy, resilience, and academic success. Research has shown that appropriate strategies successfully mitigate or prevent learned helplessness, but misguided strategies will exacerbate the problem. This study aims to examine the behaviors that teachers currently associate with learned helplessness and the strategies they have found to be successful in mitigating its effects in their classrooms. After reviewing literature on learned …


Trauma-Informed Training For Early Childhood Educators, Tarah Bryant Jul 2025

Trauma-Informed Training For Early Childhood Educators, Tarah Bryant

Master's Theses & Capstone Projects

More students are arriving in the early childhood classroom with trauma. This trauma can lead to PTSD (post-traumatic stress disorder), ADHD and reactive attachment disorder. This leads to early childhood teachers feeling burned out and experiencing secondary trauma. Despite this, early childhood educators are not getting additional training that would help support children who have exposure to trauma. In addition, the training they have received doesn't include classroom strategies or social-emotional materials that would address the uptick in trauma-impacted children. The purpose of this study was to look at the perspectives of early childhood educators when it comes to their …


Instructional Design: An Overview Of Critical Sources, Robyn Hartman Jul 2025

Instructional Design: An Overview Of Critical Sources, Robyn Hartman

Library Faculty Publications

Instructional design serves as the backbone of effective education and training across diverse learning environments. From traditional classrooms to corporate training programs and online learning platforms, thoughtfully designed instruction creates the foundation for meaningful learning experiences. This essay provides a comprehensive overview of key resources in instructional design in higher education, offering both historical context and contemporary applications for professionals in the field. This essay is intended for novice higher education instructional designers seeking to build their foundational knowledge and experienced subject-matter educators looking to deepen their understanding of design principles and practices for their courses.


Grokformer: Graph Fourier Kolmogorov‑Arnold Transformers, Guoguo Ai, Guansong Pang, Hezhe Qiao, Yuan Gao, Hui Yan Jul 2025

Grokformer: Graph Fourier Kolmogorov‑Arnold Transformers, Guoguo Ai, Guansong Pang, Hezhe Qiao, Yuan Gao, Hui Yan

Research Collection School Of Computing and Information Systems

Graph Transformers (GTs) have demonstrated remarkable performance in graph representation learning over popular graph neural networks (GNNs). However, self-attention, the core module of GTs, preserves only low-frequency signals in graph features, leading to ineffectiveness in capturing other important signals like high-frequency ones. Some recent GT models help alleviate this issue, but their flexibility and expressiveness are still limited since the filters they learn are fixed on predefined graph spectrum or spectral order. To tackle this challenge, we propose a Graph Fourier Kolmogorov-Arnold Transformer (GrokFormer), a novel GT model that learns highly expressive spectral filters with adaptive graph spectrum and spectral …


Cracking Aegis: An Adversarial Llm-Based Game For Raising Awareness Of Vulnerabilities In Privacy Protection, Jiaying Fu, Yiyang Lu, Zehua Yang, Fiona Fui-Hoon Nah, Ray Lc Jul 2025

Cracking Aegis: An Adversarial Llm-Based Game For Raising Awareness Of Vulnerabilities In Privacy Protection, Jiaying Fu, Yiyang Lu, Zehua Yang, Fiona Fui-Hoon Nah, Ray Lc

Research Collection School Of Computing and Information Systems

Traditional methods for raising awareness of privacy protection often fail to engage users or provide hands-on insights into how privacy vulnerabilities are exploited. To address this, we incorporate an adversarial mechanic in the design of the dialogue-based serious game Cracking Aegis. Leveraging LLMs to simulate natural interactions, the game challenges players to impersonate characters and extract sensitive information from an AI agent, Aegis. A user study (n=22) revealed that players employed diverse deceptive linguistic strategies, including storytelling and emotional rapport, to manipulate Aegis. After playing, players reported connecting in-game scenarios with real-world privacy vulnerabilities, such as phishing and impersonation, and …


The Miseducation Of Model Minorities: The Gospel Of ‘Schoolvation’ And The Myth Of The Schooled Society, Justin Kh Tse Jul 2025

The Miseducation Of Model Minorities: The Gospel Of ‘Schoolvation’ And The Myth Of The Schooled Society, Justin Kh Tse

Research Collection College of Integrative Studies

The ‘model minority’, the phenomenon of some ‘minority’ communities (or some members within them) achieving social and economic advancement despite encountering the difficulties of assimilating into a mainstream society, is often described as a myth, especially as one of the central problematics in Asian American studies. Usually, the modern use of the word myth is pejorative: the model minority in this sense refers to a false empirical description of some minorities and should be quantitatively disaggregated and qualitatively debunked. In this article, I want to explore the model minority as another kind of myth, in the classical sense of mythos, …


Renal G Protein-Coupled Estrogen Receptor 1 Regulates The Epithelial Sodium Channel Promoting Natriuresis To A Greater Extent In Females, Victoria L Nasci, Jean C Bopassa, Elena Mironova, Megan Rhoads, Ravneet Singh, Dennis P Buehler, David M Pollock, Oleh M Pochynyuk, James D Stockand, Eman Y Gohar Jul 2025

Renal G Protein-Coupled Estrogen Receptor 1 Regulates The Epithelial Sodium Channel Promoting Natriuresis To A Greater Extent In Females, Victoria L Nasci, Jean C Bopassa, Elena Mironova, Megan Rhoads, Ravneet Singh, Dennis P Buehler, David M Pollock, Oleh M Pochynyuk, James D Stockand, Eman Y Gohar

Faculty, Staff and Student Publications

Hypertension prevalence is lower in women than men. Enhanced renal sodium (Na+) handling in females has been implicated in sex-differences in hypertension. Epithelial Na+ channel (ENaC) is a key contributor to Na+ homeostasis and is regulated by estrogen. Recent evidence suggests G protein-coupled estrogen receptor 1 (GPER1) evokes a female-specific natriuresis that involves endothelin-1 (ET-1). ET-1 has been shown to downregulate ENaC activity, but whether GPER1 regulates ENaC to modulate natriuresis is unknown. We tested the hypothesis that renal GPER1 functionally interacts with ENaC to promote natriuresis in a sex-specific manner. RNAscope confirmed co-expression of GPER1 and ENaC in rat …


Religious Beliefs, Cooperation, And Evolutionary Mechanisms, Nicole Fellice Ko, Norman P. Li Jul 2025

Religious Beliefs, Cooperation, And Evolutionary Mechanisms, Nicole Fellice Ko, Norman P. Li

Research Collection School of Social Sciences

Religion is an organized system of spiritual beliefs, practices, and rituals that often involve a sense of the divine (Schilbrack, 2022). An evolutionary mechanism is an evolved set of traits that interpret environmental inputs and generate behavioral responses that enhance survival or reproductive success (Li et al., 2018). Cooperation refers to the act of individuals or groups working together to achieve a shared goal or mutual benefit (Alós-Ferrer & Garagnani, 2020).


Basic Rabbit Selection And Breeding Considerations, Joseph Okoh, Jessie Hadfield Jul 2025

Basic Rabbit Selection And Breeding Considerations, Joseph Okoh, Jessie Hadfield

All Current Publications

This fact sheet is designed to assist rabbit producers in understanding breed selection for a profitable enterprise. It can also serve as a training tool for new producers, aiding them in breed selection and breeding practices.


Expanding Equity And Innovation In Pharmaceutical Law And Drug Development: Paying Clinical Trial Participants For Their Data, Steve Calandrillo, Bernadette Tosti, Jefferson Smith, Jamison Koeman Jul 2025

Expanding Equity And Innovation In Pharmaceutical Law And Drug Development: Paying Clinical Trial Participants For Their Data, Steve Calandrillo, Bernadette Tosti, Jefferson Smith, Jamison Koeman

Articles

Bringing a drug to market is exceedingly expensive and exposes pharmaceutical manufacturers to significant legal risk. But when companies are successful, their profits make the PowerBall jackpot look like petty cash. Staggering rewards measure in the billions or millions for the firms, CEOs, pharmacies, drug benefit managers, data brokers, and many more actors in the pharmaceutical-to-patient pipeline. The only individuals who don’t get paid handsomely are the clinical trial participants, whose voluntary participation and data helped make those successes possible. It is long past time that we reform the legal and regulatory roadblocks to paying clinical trial participants in the …


Clinical Evaluation Of The Healgen Rapid Covid-19 Antigen Test As A Point-Of-Care Diagnostic Tool, Stephen A Young, Hua Zhang, Jose Rodriguez, David Mishkin, Ward Paine, Li Seyfried, Latisha Hargrove, Dennis L Broyles, Chermaen Lindberg, Anurag Purushothaman, Stacey House Jul 2025

Clinical Evaluation Of The Healgen Rapid Covid-19 Antigen Test As A Point-Of-Care Diagnostic Tool, Stephen A Young, Hua Zhang, Jose Rodriguez, David Mishkin, Ward Paine, Li Seyfried, Latisha Hargrove, Dennis L Broyles, Chermaen Lindberg, Anurag Purushothaman, Stacey House

2020-Current year OA Pubs

BACKGROUND: Development of readily available Rapid COVID-19 Antigen tests essential for promptly identifying SARS-CoV2 infection and preventing its spread.

METHODS: This study evaluated the clinical performance of the Healgen Rapid COVID-19 antigen test as a point-of-care diagnostic tool with 806 evaluable subjects who were within 6 days post-symptom onset. The results from the Healgen test were compared to the results from Emergency Use Authorization (EUA) approved SARS-CoV-2 RT-PCR tests.

RESULTS: Out of the 806 evaluable subjects, 140 tested positive and 640 tested negative for SARS-CoV-2 with the Healgen COVID-19 test, showing good agreement with the EUA RT-PCR results. There were …


Dna Methylation Epitypes Of Burkitt Lymphoma With Distinct Molecular And Clinical Features, Nicole Thomas, Nancy L Bartlett, Et Al. Jul 2025

Dna Methylation Epitypes Of Burkitt Lymphoma With Distinct Molecular And Clinical Features, Nicole Thomas, Nancy L Bartlett, Et Al.

2020-Current year OA Pubs

UNLABELLED: The genetic subtypes of Burkitt lymphoma have been defined, but the role of epigenetics remains to be comprehensively characterized. We searched genomic DNA from 218 patients across four continents for recurrent DNA methylation patterns and their associations with clinical and molecular features. We identified DNA methylation patterns that were not fully explained by the Epstein-Barr virus status or mutation status, leading to two epitypes described here as HypoBL and HyperBL. Each is characterized by distinct genomic and clinical features including global methylation, mutation burden, aberrant somatic hypermutation, and survival outcomes. Methylation, gene expression, and mutational differences between the epitypes …


Utility Of The Us Preventive Services Task Force For Preeclampsia Risk Assessment And Aspirin Prophylaxis, Thomas F Mcelrath, Antonina I Frolova, Et Al. Jul 2025

Utility Of The Us Preventive Services Task Force For Preeclampsia Risk Assessment And Aspirin Prophylaxis, Thomas F Mcelrath, Antonina I Frolova, Et Al.

2020-Current year OA Pubs

IMPORTANCE: The US Preventive Services Task Force (USPSTF) guidelines on preeclampsia risk assessment and aspirin prophylaxis (AP) have not been evaluated for clinical utility.

OBJECTIVE: To evaluate which characteristics in the USPSTF guidelines identify risk status and the association of preeclampsia risk with AP recommendations.

DESIGN, SETTING, AND PARTICIPANTS: This observational cohort study enrolled from July 2020 to March 2023 with data analysis performed from October to December 2024. Enrollment occurred at 11 centers throughout the US or via direct-to-participant recruitment. Pregnant participants aged 18 years or older with a singleton pregnancy less than 22 weeks' gestation were selected via …


Genetic Structuring And Estimation Of Reproductive Adults In Onchocerca Volvulus: A Genome-Wide Analysis Across Hosts And Regions, Pawan Kumar, Young-Jun Choi, Kerstin Fischer, Shannon M. Hedtke, Anusha Kode, Nicholas Opoku, Lincoln Gankpala, Tony O. Ukety, Jöel Lonema Mande, Timothy J. C. Anderson, Warwick N. Grant, Peter U. Fischer, Makedonka Mitreva Jul 2025

Genetic Structuring And Estimation Of Reproductive Adults In Onchocerca Volvulus: A Genome-Wide Analysis Across Hosts And Regions, Pawan Kumar, Young-Jun Choi, Kerstin Fischer, Shannon M. Hedtke, Anusha Kode, Nicholas Opoku, Lincoln Gankpala, Tony O. Ukety, Jöel Lonema Mande, Timothy J. C. Anderson, Warwick N. Grant, Peter U. Fischer, Makedonka Mitreva

2020-Current year OA Pubs

Genomic analysis of parasites can deepen our understanding of their transmission, population structure, and important biological characteristics. Onchocerciasis (river blindness), caused by the parasitic nematode Onchocerca volvulus, involves adult worms residing in subcutaneous nodules that produce larval-stage microfilariae (mf), which are routinely detected in the skin for diagnosis. Whole-genome studies of mf are limited; most analyses have focused on the mitochondrial genome. We conducted a genome-wide analysis with 94% median nuclear genome coverage, analyzing 171, 37, and 98 mf from 16, 3, and 5 individuals from Ghana, Liberia, and the Democratic Republic of Congo, respectively. These data were used to …


Robust Photogrammetric Scalp Morphology Estimation For Functional Optical Neuroimaging, Abigail L Magee, Calamity Svoboda, Tessa G George, Alvin A Agato, Edward J Richter, Joseph P Culver, Adam T Eggebrecht Jul 2025

Robust Photogrammetric Scalp Morphology Estimation For Functional Optical Neuroimaging, Abigail L Magee, Calamity Svoboda, Tessa G George, Alvin A Agato, Edward J Richter, Joseph P Culver, Adam T Eggebrecht

2020-Current year OA Pubs

SIGNIFICANCE: Optical functional neuroimaging relies upon accurate anatomical models to provide optimal data registration and image reconstruction.

AIM: We establish and validate a robust photogrammetric algorithm for scalp morphology that utilizes 3-dimensional (3D) imaging with a photogrammetric cap to provide individualized scalp morphology estimation through hair in the absence of magnetic resonance imaging (MRI).

APPROACH: The scalp morphology estimation uses a flexible, neoprene cap and 3D-printed photogrammetric modules with fiducials. We create a sparse scalp sampling and align the MNI152 atlas to generate the scalp morphology estimation. We used the international 10 to 20 electroencephalogram positions for alignment and calculated …


Projection-Tags Enable Multiplex Projection Tracing And Multi-Modal Profiling Of Projection Neurons, Lite Yang, Fang Liu, Hannah Hahm, Takao Okuda, Xiaoyue Li, Yufen Zhang, Vani Kalyanaraman, Monique R Heitmeier, Vijay K Samineni Jul 2025

Projection-Tags Enable Multiplex Projection Tracing And Multi-Modal Profiling Of Projection Neurons, Lite Yang, Fang Liu, Hannah Hahm, Takao Okuda, Xiaoyue Li, Yufen Zhang, Vani Kalyanaraman, Monique R Heitmeier, Vijay K Samineni

2020-Current year OA Pubs

Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain-wide projections. However, investigating the complex wiring diagram, spatial organization, transcriptional, and epigenetic landscapes of brain-wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons in female mice. Projection-TAGs can be leveraged …


Molecular Profile Of Adult Primary Leptomeningeal Gliomatosis Aligns With Glioblastoma, Idh-Wildtype, Yi Zhu, Darin D Carabenciov, Derek R Johnson, Jorge A Trejo-Lopez, Aivi T Nguyen, Aditya Raghunathan, Giuseppe Lanzino, Cristiane M Ida, Cinthya J Zepeda-Mendoza, Surendra Dasari, Emilie Russler-Germain, Sonika Dahiya, Martha Quezado, Kenneth Aldape, Caterina Giannini Jul 2025

Molecular Profile Of Adult Primary Leptomeningeal Gliomatosis Aligns With Glioblastoma, Idh-Wildtype, Yi Zhu, Darin D Carabenciov, Derek R Johnson, Jorge A Trejo-Lopez, Aivi T Nguyen, Aditya Raghunathan, Giuseppe Lanzino, Cristiane M Ida, Cinthya J Zepeda-Mendoza, Surendra Dasari, Emilie Russler-Germain, Sonika Dahiya, Martha Quezado, Kenneth Aldape, Caterina Giannini

2020-Current year OA Pubs

Adult primary leptomeningeal gliomatosis (PLG) is a rare, rapidly progressive and fatal disease characterized by prominent leptomeningeal infiltration by a glial tumor without an identifiable parenchymal mass. The molecular profile of adult PLG has not been well-characterized. We report the clinical, pathological, and molecular findings of six adult PLG patients (five males and one female), median age 58 years. All cases exhibited pathological leptomeningeal enhancement at presentation. Leptomeningeal biopsy was diagnostic in five (of six) cases, revealing infiltration by an astrocytic glioma with mitotic activity, lacking microvascular proliferation or necrosis. One case was diagnosed at autopsy. All tumors were IDH-wildtype, …


Automated Assignment Grading With Large Language Models: Insights From A Bioinformatics Course, Pavlin G Poličar, Martin Špendl, Tomaž Curk, Blaž Zupan Jul 2025

Automated Assignment Grading With Large Language Models: Insights From A Bioinformatics Course, Pavlin G Poličar, Martin Špendl, Tomaž Curk, Blaž Zupan

Faculty, Staff and Students Publications

Motivation: Providing students with individualized feedback through assignments is a cornerstone of education that supports their learning and development. Studies have shown that timely, high-quality feedback plays a critical role in improving learning outcomes. However, providing personalized feedback on a large scale in classes with large numbers of students is often impractical due to the significant time and effort required. Recent advances in natural language processing and large language models (LLMs) offer a promising solution by enabling the efficient delivery of personalized feedback. These technologies can reduce the workload of course staff while improving student satisfaction and learning outcomes. Their …


Glioblastoma-Instructed Astrocytes Suppress Tumour-Specific T Cell Immunity, Camilo Faust Akl, Brian M Andersen, Zhaorong Li, Federico Giovannoni, Martin Diebold, Liliana M Sanmarco, Michael Kilian, Luca Fehrenbacher, Florian Pernin, Joseph M Rone, Hong-Gyun Lee, Gavin Piester, Jessica E Kenison, Joon-Hyuk Lee, Tomer Illouz, Carolina M Polonio, Léna Srun, Jazmin Martinez, Elizabeth N Chung, Anton Schüle, Agustin Plasencia, Lucinda Li, Kylynne Ferrara, Mercedes Lewandrowski, Craig A Strathdee, Lorena Lerner, Christophe Quéva, Iain C Clark, Benjamin Deneen, Judy Lieberman, David H Sherr, Jack P Antel, Michael A Wheeler, Keith L Ligon, E Antonio Chiocca, Marco Prinz, David A Reardon, Francisco J Quintana Jul 2025

Glioblastoma-Instructed Astrocytes Suppress Tumour-Specific T Cell Immunity, Camilo Faust Akl, Brian M Andersen, Zhaorong Li, Federico Giovannoni, Martin Diebold, Liliana M Sanmarco, Michael Kilian, Luca Fehrenbacher, Florian Pernin, Joseph M Rone, Hong-Gyun Lee, Gavin Piester, Jessica E Kenison, Joon-Hyuk Lee, Tomer Illouz, Carolina M Polonio, Léna Srun, Jazmin Martinez, Elizabeth N Chung, Anton Schüle, Agustin Plasencia, Lucinda Li, Kylynne Ferrara, Mercedes Lewandrowski, Craig A Strathdee, Lorena Lerner, Christophe Quéva, Iain C Clark, Benjamin Deneen, Judy Lieberman, David H Sherr, Jack P Antel, Michael A Wheeler, Keith L Ligon, E Antonio Chiocca, Marco Prinz, David A Reardon, Francisco J Quintana

Faculty, Staff and Students Publications

Glioblastoma is the most common and aggressive primary brain cancer and shows minimal response to therapies. The immunosuppressive tumour microenvironment in glioblastoma contributes to the limited therapeutic response. Astrocytes are abundant in the central nervous system and have important immunoregulatory roles. However, little is known about their role in the immune response to glioblastoma1. Here we used single-cell and bulk RNA sequencing of clinical glioblastoma samples and samples from preclinical models, multiplexed immunofluorescence, in vivo CRISPR-based cell-specific genetic perturbations and in vitro mouse and human experimental systems to address this gap in knowledge. We identified an astrocyte subset …


No One Acts Alone-Unravelling The Compositional Influences Of Organic Compounds In Offshore Produced Water On Zebrafish Embryotoxicity, Lisbet Sørensen, Paul Mccormack, Paul Sutton, Julia Farkas, Sonnich Meier, Steven J. Rowland, Trond Nordtug, Bjørn Henrik Hansen Jul 2025

No One Acts Alone-Unravelling The Compositional Influences Of Organic Compounds In Offshore Produced Water On Zebrafish Embryotoxicity, Lisbet Sørensen, Paul Mccormack, Paul Sutton, Julia Farkas, Sonnich Meier, Steven J. Rowland, Trond Nordtug, Bjørn Henrik Hansen

School of Geography, Earth and Environmental Sciences

Offshore produced water (PW) is one of the largest and most chemically complex effluents of waste directly and intentionally discharged into the marine environment. Although it is well known that PW can be severely toxic to marine organisms, the mechanisms of toxicity remain poorly understood, contributed by the lack of comprehensive chemical characterization of the PW. In this study, we applied elements of effects-directed analysis with the aim to identify organic chemical drivers of toxicity in PW towards fish early life stages. A solvent extract of a PW was fractioned based on compound functionality and chemically characterized by a concert …